ORCID Profile
0000-0002-6380-7421
Current Organisation
Ludwig-Maximilians-Universität München
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Genetics | Molecular Evolution | Marine and Estuarine Ecology (incl. Marine Ichthyology) | Sensory Systems | Gene Expression | Protein Targeting And Signal Transduction | Animal Systematics, Taxonomy And Phylogeny | Invasive Species Ecology | Biotechnology Not Elsewhere Classified | Neurosciences | Invertebrate Biology | Conservation And Biodiversity | Population, Ecological and Evolutionary Genetics |
ANZSRC Socio-Economic Objective (SEO)
Aquaculture | Primary animal products not elsewhere classified | Control of Pests, Diseases and Exotic Species in Marine Environments | Ceramics, glass and industrial mineral products not elsewhere classified | Integrated (ecosystem) assessment and management | Tourism not elsewhere classified | Marine Flora, Fauna and Biodiversity | Biological sciences | Other
Related Links
Publications
DNA-Barcoding — Schlüssel zu den Geheimnissen der Schwämme
Publisher: Springer Science and Business Media LLC
Date: 02-2012
Phylogenetic Diversity and Community Structure of the Symbionts Associated with the Coralline Sponge Astrosclera willeyana of the Great Barrier Reef
Publisher: Springer Science and Business Media LLC
Date: 24-03-2013
DOI: 10.1007/S00248-013-0212-5
Abstract: The coralline sponge Astrosclera willeyana, considered to be a living representative of the reef-building stromatoporoids of the Mesozoic and the Paleozoic periods, occurs widely throughout the Indo-Pacific oceans. We aimed to examine, for the first time, the phylogenetic ersity of the microbial symbionts associated with A. willeyana using molecular methods and to investigate the spatial variability in the sponge-derived microbial communities of A. willeyana from erse sites along the Great Barrier Reef (GBR). Both denaturing gradient gel electrophoresis (DGGE) analyses of 12 Astrosclera specimens and sequencing of a 16S rRNA gene clone library, constructed using a specimen of A. willeyana from the Yonge Reef (380 clones), revealed the presence of a complex microbial community with high ersity. An assessment of the 16S rRNA gene sequences to the particular phylogenetic groups showed domination of the Chloroflexi (42 %), followed by the Gammaproteobacteria (14 %), Actinobacteria (11 %), Acidobacteria (8 %), and the Deferribacteres (7 %). Of the microbes that were identified, a further 15 % belonged to the Deltaproteobacteria, Alphaproteobacteria, and Nitrospirae genera. The minor phylogenetic groups Gemmatimonadetes, Spirochaetes, Cyanobacteria, Poribacteria, and the Archaea composed 3 % of the community. Over 94 % of the sequences obtained from A. willeyana grouped together with other sponge- or coral-derived sequences, and of these, 72 % formed, with nearest relatives, 46 sponge-specific or sponge-coral clusters, highlighting the uniqueness of the microbial consortia in sponges. The DGGE results showed clear isions according to the geographical origin of the s les, indicating closer relationships between the microbial communities with respect to their geographic origin (northern vs. southern GBR).
The systematics of Raspailiidae (Demospongiae: Poecilosclerida: Microcionina) re-analysed with a ribosomal marker
Publisher: Cambridge University Press (CUP)
Date: 12-2007
DOI: 10.1017/S0025315407058201
Abstract: We present a 28S rDNA gene tree of selected Raspailiidae, Axinellidae and other demosponges to obtain insight into raspailiid phylogeny and character evolution. The Raspailiidae in our data set cluster in a well-supported clade, distinguished from Axinellidae, Agelasida and Hadromerida. Raspailia ( s . s .), Eurypon , Sollasella , Aulospongus and Ectyoplasia form a Raspailiidae clade. Some Raspailia subgenera, in particular R . ( Parasyringella ), are not retrieved monophyletically. Trikentrion falls into the Thrinacophorinae, and not the Cyamoninae as earlier hypothesized. The axinellid genera Ptilocaulis and Reniochalina also cluster with Raspailiidae, distant from the other Axinellidae. The suitability of particular morphological characters for raspailiid phylogeny is discussed.
Historical biogeography and mitogenomics of two endemic Mediterranean gorgonians (Holaxonia, Plexauridae)
Publisher: Springer Science and Business Media LLC
Date: 18-01-2017
Octocoral sclerite ultrastructures and experimental approach to underlying biomineralisation principles
Publisher: Royal Society of Chemistry (RSC)
Date: 2007
DOI: 10.1039/B711068E
A mitochondrial intron in a verongid sponge.
Publisher: Springer Science and Business Media LLC
Date: 13-11-2015
DOI: 10.1007/S00239-014-9653-9
Abstract: We discovered for the first time a mitochondrial intron in a non-tetillid demosponge, which sheds new light on the interpretation of mitochondrial intron evolution among non-bilaterian animals and has consequences for phylogenetic and DNA barcoding studies. The newly discovered class 1 intron of Aplysinella rhax (Verongida) CO1 has an ORF for a putative LAGLIDADG-type and resembles other sponge and cnidarian mitochondrial introns. Our analysis of the Aplysinella rhax intron underlines that the patchy distribution of introns in sponges is caused by a combination of horizontal and vertical transmission. Further implications for CO1 phylogenetic and barcoding projects are discussed.
A morphometric and genetic framework for the genusGazellade Blainville, 1816 (Ruminantia: Bovidae) with special focus on Arabian and Levantine mountain gazelles
Publisher: Oxford University Press (OUP)
Date: 11-10-2013
DOI: 10.1111/ZOJ.12066
The reef cave dwelling ultraconservative coralline demospongeAstrosclera willeyana Lister 1900 from the Indo-Pacific
Publisher: Springer Science and Business Media LLC
Date: 12-1998
DOI: 10.1007/BF02537358
The Magellania venosa Biomineralizing Proteome: A Window into Brachiopod Shell Evolution
Publisher: Oxford University Press (OUP)
Date: 24-04-2015
DOI: 10.1093/GBE/EVV074
Phylogeny of Tetillidae (Porifera, Demospongiae, Spirophorida) based on three molecular markers
Publisher: Elsevier BV
Date: 05-2013
DOI: 10.1016/J.YMPEV.2013.02.018
Abstract: Tetillidae are spherical to elliptical cosmopolitan demosponges. The family comprises eight genera: namely, Acanthotetilla Burton, 1959, Amphitethya Lendenfeld, 1907, CinachyraSollas, 1886, CinachyrellaWilson, 1925, Craniella Schmidt, 1870, Fangophilina Schmidt, 1880, Paratetilla Dendy, 1905, and Tetilla Schmidt, 1868. These genera are characterized by few conflicting morphological characters, resulting in an ambiguity of phylogenetic relationships. The phylogeny of tetillid genera was investigated using the cox1, 18S rRNA and 28S rRNA (C1-D2 domains) genes in 88 specimens (8 genera, 28 species). Five clades were identified: (i) Cinachyrella, Paratetilla and Amphitethya species, (ii) Cinachyrella levantinensis, (iii) Tetilla, (iv) Craniella, Cinachyra and Fangophilina and (v) Acanthotetilla. Consequently, the phylogenetic analysis supports the monophyly of Tetilla, a genus lacking any known morphological synapomorphy. Acanthotetilla is also recovered. In contrast, within the first clade, species of the genera Paratetilla and Amphitethya were nested within Cinachyrella. Similarly, within the fourth clade, species of the genera Cinachyra and Fangophilina were nested within Craniella. As previously postulated by taxonomists, the loss of ectodermal specialization (i.e., a cortex) has occurred several times independently. Nevertheless, the presence or absence of a cortex and its features carry a phylogenetic signal. Surprisingly, the common view that assumes close relationships among sponges with porocalices (i.e., surface depressions) is refuted.
TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly
Publisher: Cold Spring Harbor Laboratory
Date: 18-02-2021
DOI: 10.1101/2021.02.18.431773
Abstract: The use of RNA-Seq data and the generation of de novo transcriptome assemblies have been pivotal for studies in ecology and evolution. This is distinctly true for non-model organisms, where no genome information is available. Nevertheless, studies of differential gene expression, DNA enrichment baits design, and phylogenetics can all be accomplished with the data gathered at the transcriptomic level. Multiple tools are available for transcriptome assembly, however, no single tool can provide the best assembly for all datasets. Therefore, a multi assembler approach, followed by a reduction step, is often sought to generate an improved representation of the assembly. To reduce errors in these complex analyses while at the same time attaining reproducibility and scalability, automated workflows have been essential in the analysis of RNA-Seq data. However, most of these tools are designed for species where genome data is used as reference for the assembly process, limiting their use in non-model organisms. We present TransPi, a comprehensive pipeline for de novo transcriptome assembly, with minimum user input but without losing the ability of a thorough analysis. A combination of different model organisms, k-mer sets, read lengths, and read quantities were used for assessing the tool. Furthermore, a total of 49 non-model organisms, spanning different phyla, were also analyzed. Compared to approaches using single assemblers only, TransPi produces higher BUSCO completeness percentages, and a concurrent significant reduction in duplication rates. TransPi is easy to configure and can be deployed seamlessly using Conda, Docker and Singularity.
A revised phylogeny of Antilopini (Bovidae, Artiodactyla) using combined mitochondrial and nuclear genes
Publisher: Elsevier BV
Date: 05-2013
DOI: 10.1016/J.YMPEV.2013.02.015
Abstract: Antilopini (gazelles and their allies) are one of the most erse but phylogenetically controversial groups of bovids. Here we provide a molecular phylogeny of this poorly understood taxon using combined analyses of mitochondrial (CYTB, COIII, 12S, 16S) and nuclear (KCAS, SPTBN1, PRKCI, MC1R, THYR) genes. We explore the influence of data partitioning and different analytical methods, including Bayesian inference, maximum likelihood and maximum parsimony, on the inferred relationships within Antilopini. We achieve increased resolution and support compared to previous analyses especially in the two most problematic parts of their tree. First, taxa commonly referred to as "gazelles" are recovered as paraphyletic, as the genus Gazella appears more closely related to the Indian blackbuck (Antilope cervicapra) than to the other two gazelle genera (Nanger and Eudorcas). Second, we recovered a strongly supported sister relationship between one of the dwarf antelopes (Ourebia) and the Antilopini subgroup Antilopina (Saiga, Gerenuk, Springbok, Blackbuck and gazelles). The assessment of the influence of taxon s ling, outgroup rooting, and data partitioning in Bayesian analyses helps explain the contradictory results of previous studies.
Spatial patterns in the distribution of benthic assemblages across a large depth gradient in the Coral Sea, Australia
Publisher: Springer Science and Business Media LLC
Date: 06-01-2016
A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform
Publisher: Wiley
Date: 25-03-2018
DOI: 10.1002/MBO3.611
Novel Scenarios of Early Animal Evolution--Is It Time to Rewrite Textbooks?
Publisher: Oxford University Press (OUP)
Date: 28-03-2013
DOI: 10.1093/ICB/ICT008
Abstract: Understanding how important phenotypic, developmental, and genomic features of animals originated and evolved is essential for many fields of biological research, but such understanding depends on robust hypotheses about the phylogenetic interrelationships of the higher taxa to which the studied species belong. Molecular approaches to phylogenetics have proven able to revolutionize our knowledge of organismal evolution. However, with respect to the deepest splits in the metazoan Tree of Life-the relationships between Bilateria and the four non-bilaterian phyla (Porifera, Placozoa, Ctenophora, and Cnidaria)-no consensus has been reached yet, since a number of different, often contradictory, hypotheses with sometimes spectacular implications have been proposed in recent years. Here, we review the recent literature on the topic and contrast it with more classical perceptions based on analyses of morphological characters. We conclude that the time is not yet ripe to rewrite zoological textbooks and advocate a conservative approach when it comes to developing scenarios of the early evolution of animals.
The last common ancestor of animals lacked the HIF pathway and respired in low-oxygen environments
Publisher: eLife Sciences Publications, Ltd
Date: 06-02-2018
DOI: 10.7554/ELIFE.31176
Abstract: Animals have a carefully orchestrated relationship with oxygen. When exposed to low environmental oxygen concentrations, and during periods of increased energy expenditure, animals maintain cellular oxygen homeostasis by enhancing internal oxygen delivery, and by enabling the anaerobic production of ATP. These low-oxygen responses are thought to be controlled universally across animals by the hypoxia-inducible factor (HIF). We find, however, that sponge and ctenophore genomes lack key components of the HIF pathway. Since sponges and ctenophores are likely sister to all remaining animal phyla, the last common ancestor of extant animals likely lacked the HIF pathway as well. Laboratory experiments show that the marine sponge Tethya wilhelma maintains normal transcription under oxygen levels down to 0.25% of modern atmospheric saturation, the lowest levels we investigated, consistent with the predicted absence of HIF or any other HIF-like pathway. Thus, the last common ancestor of all living animals could have metabolized aerobically under very low environmental oxygen concentrations.
Nano-cluster composite structure of calcitic sponge spicules—A case study of basic characteristics of biominerals
Publisher: Elsevier BV
Date: 2006
DOI: 10.1016/J.JINORGBIO.2005.10.005
Abstract: Spicules of calcareous sponges are elaborately shaped skeletal elements that nonetheless show characteristics of calcite single-crystals. Our atomic force microscopic and transmission electron microscopic investigation of the triradiate spicules of the sponge Pericharax heteroraphis reveals a nano-cluster structure with mostly well-aligned small crystal domains and pockets with accumulated domain misalignments. Combined high-resolution and energy-filtering transmission electron microscopy revealed carbon enrichments located in between crystal domain boundaries, which strongly suggests an intercalated network-like proteinaceous organic matrix. This matrix is proposed to be involved in the nano-clustered calcite precipitation via a transient phase that may enable a 'brick-by-brick' formation of composite and yet single-crystalline spicules with elaborate morphologies. This composite cluster structure reduces the brittleness of the material by dissipating strain energy and deflecting crack propagation from the calcite cleavage planes, but the lattice symmetry and anisotropic growth properties of calcite still play a major role in the morphogenesis of these unusual calcite single-crystals. Our structural, crystallographic, textural, and chemical analysis of sponge spicules corroborates the view that nano-clustered crystal growth, induced by organic matrices, is a basic characteristic of biomineralisation that enables the production of composite materials with elaborate morphologies.
Profiling cellular diversity in sponges informs animal cell type and nervous system evolution
Publisher: Cold Spring Harbor Laboratory
Date: 05-09-2019
DOI: 10.1101/758276
Abstract: The evolutionary origin of metazoan cell types such as neurons, muscles, digestive, and immune cells, remains unsolved. Using whole-body single-cell RNA sequencing in a sponge, an animal without nervous system and musculature, we identify 18 distinct cell types comprising four major families. This includes nitric-oxide sensitive contractile cells, digestive cells active in macropinocytosis, and a family of amoeboid-neuroid cells involved in innate immunity. We uncover ‘presynaptic’ genes in an amoeboid-neuroid cell type, and ‘postsynaptic’ genes in digestive choanocytes, suggesting asymmetric and targeted communication. Corroborating this, long neurite-like extensions from neuroid cells directly contact and enwrap choanocyte microvillar collars. Our data indicate a link between neuroid and immune functions in sponges, and suggest that a primordial neuro-immune system cleared intruders and controlled ciliary beating for feeding.
Phylogeography of the crown-of-thorns starfish: genetic structure within the Pacific species
Publisher: Springer Science and Business Media LLC
Date: 17-01-2013
Mid-chain branched alkanoic acids from 'living fossil' demosponges: A link to ancient sedimentary lipids?
Publisher: Elsevier BV
Date: 1999
The fatty acids of calcareous sponges (Calcarea, Porifera)
Publisher: Elsevier BV
Date: 09-2006
DOI: 10.1016/J.CHEMPHYSLIP.2006.06.001
Abstract: Twenty-nine specimens of calcareous sponges (Class Calcarea, Phylum Porifera), covering thirteen representative species of the families Soleneiscidae, Leucaltidae, Levinellidae, Leucettidae, Clathrinidae, Sycettidae, Grantiidae, Jenkinidae, and Heteropiidae were analysed for their fatty acids. The fatty acids of Calcarea generally comprise saturated and monounsaturated linear (n-), and terminally methylated (iso-, anteiso-) C(14)-C(20) homologues. Furthermore, polyunsaturated C(22) fatty acids and the isoprenoic 4,8,12-trimethyltridecanoic acid were found. The most prominent compounds are n-C(16), iso-C(17), iso-C(18), n-C(18), n-C(20). In addition, a high abundance of the exotic 16-methyloctadecanoic acid (anteiso-C(19)) appears to be a characteristic trait of Calcarea. Long-chain 'demospongic acids', typically found in Demospongiae and Hexactinellida, are absent in Calcarea. The completely different strategy of calcarean fatty acid synthesis supports their phylogenetic distinctiveness from a common Demospongiae/Hexactinellida taxon. Both intraspecific and intraclass patterns of Calcarea showed great similarity, suggesting a conserved fatty acid composition that already existed in the last common ancestor of Calcinea and Calcaronea, i.e. before subclasses erged.
The era of reference genomes in conservation genomics
Publisher: Elsevier BV
Date: 03-2022
DOI: 10.1016/J.TREE.2021.11.008
Abstract: Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global bio ersity. These genomes provide unique insights into genomic ersity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.
Transcriptomic response of Cinachyrella cf. cavernosa sponges to spatial competition
Publisher: Cold Spring Harbor Laboratory
Date: 05-07-2021
DOI: 10.1101/2021.07.05.451097
Abstract: Spatial competition in the intertidal zones drives the community structure in marine benthic habitats. Organisms inhabiting these areas not only need to withstand fluctuations of temperature, water level, pH, and salinity, but also need to compete for the best available space. Sponges are key members of the intertidal zones, and their life history processes (e.g. growth, reproduction, and regeneration) are affected by competition. Here we used transcriptomics to investigate the effects of interspecific competition between the tetillid sponge Cinachyrella cf. cavernosa , the zoantharid Zoanthus sansibaricus , and the macroalgae Dictyota ciliolata . The analysis of differentially expressed genes showed that Z. sansibaricus was the most stressful competitor to C . cf. cavernosa , which showed an increased rate of cellular respiration under stress of competition. Similarly, an up-regulation of energy metabolism, lipid metabolism, and the heat-shock protein (HSP) 70 was also observed along with an indication of a viral infection and decreased ability to synthesise protein. A down-regulation of purine and pyrimidine metabolism indicated reduction in physiological activities of the competing sponges. Moreover, a putative case of possible kleptocnidism, not previously reported in Cinachyrella cf. cavernosa was also observed. This study opens the door for more detailed investigations of marine organisms competing for spatial resources using transcriptome data.
Molecular evolution of rDNA in early diverging Metazoa: First comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera
Publisher: Springer Science and Business Media LLC
Date: 27-02-2008
Abstract: The cytoplasmic ribosomal small subunit (SSU, 18S) ribosomal RNA (rRNA) is the most frequently-used gene for molecular phylogenetic studies. However, information regarding its secondary structure is neglected in most phylogenetic analyses. Incorporation of this information is essential in order to apply specific rRNA evolutionary models to overcome the problem of co-evolution of paired sites, which violates the basic assumption of the independent evolution of sites made by most phylogenetic methods. Information about secondary structure also supports the process of aligning rRNA sequences across taxa. Both aspects have been shown to increase the accuracy of phylogenetic reconstructions within various taxa. Here, we explore SSU rRNA secondary structures from the three extant classes of Phylum Porifera (Grant, 1836), a pivotal, but largely unresolved taxon of early branching Metazoa. This is the first phylogenetic study of poriferan SSU rRNA data to date that includes detailed comparative secondary structure information for all three sponge classes. We found base compositional and structural differences in SSU rRNA among Demospongiae, Hexactinellida (glass sponges) and Calcarea (calcareous sponges). We showed that analyses of primary rRNA sequences, including secondary structure-specific evolutionary models, in combination with reconstruction of the evolution of unusual structural features, reveal a substantial amount of additional information. Of special note was the finding that the gene tree topologies of marine haplosclerid demosponges, which are inconsistent with the current morphology-based classification, are supported by our reconstructed evolution of secondary structure features. Therefore, these features can provide alternative support for sequence-based topologies and give insights into the evolution of the molecule itself. To encourage and facilitate the application of rRNA models in phylogenetics of early metazoans, we present 52 SSU rRNA secondary structures over the taxonomic range of Porifera in a database, along with some basic tools for relevant format-conversion. We demonstrated that sophisticated secondary structure analyses can increase the potential phylogenetic information of already available rDNA sequences currently accessible in databases and conclude that the importance of SSU rRNA secondary structure information for phylogenetic reconstruction is still generally underestimated, at least among certain early branching metazoans.
Managing and sharing the escalating number of sponge unknowns: The spongemaps project
Publisher: Oxford University Press (OUP)
Date: 07-05-2013
DOI: 10.1093/ICB/ICT038
Abstract: Contemporary collections of sponges in the Indo-west Pacific have escalated substantially due to pharmaceutical discovery, national bioregional planning, and compliance with international conventions on the seabed and its marine genetic resources beyond national jurisdictions. These partially processed operational taxonomic unit (OTU) collections now vastly outweigh the expertise available to make them better "known" via complete taxonomy, yet for many bioregions they represent the most significant body of currently available knowledge. Increasing numbers of cryptic species, previously undetected morphologically, are now being discovered by molecular and chemical analyses. The uncoordinated and fragmented nature of many previous collections, however, means that knowledge and expertise gained from a particular project are often lost to future projects without a bio ersity informatics legacy. Integrating these erse data (GIS OTUs images molecular, chemical, and other datasets) required a two-way iterative process so far unavailable for sponges with existing bio ersity informatics tools. SpongeMaps arose from the initial need for online collaboration to integrate morphometric data with molecular barcodes, including the Porifera Tree of Life (PorTol) project. It provides interrogation of existing data to better process new collections capacity to create new OTUs publication of online pages for in idual species, so as to interpret GIS and other data for online bio ersity databases and services and automatic links to external datasets for taxonomic hierarchy, specimen GIS and mapping, DNA sequence data, chemical structures, and images.
Body-plan reorganization in a sponge correlates with microbiome change
Publisher: Cold Spring Harbor Laboratory
Date: 23-07-2022
DOI: 10.1101/2022.07.22.501172
Abstract: Mounting evidence suggests that animals and their associated bacteria interact via intricate molecular mechanisms, and it is hypothesized that disturbances to the microbiome can influence animal development. Sponges erged from other animals more than 750 MYA and represent one of the earliest branching animal phyla that exhibit symbiotic relationships with erse bacteria. Over 41 microbial phyla have been found in association with sponges, forming a holobiont that is integral to aquatic ecosystems worldwide. Sponge-associated microbes contain an enriched set of proteins bearing eukaryotic-like domains, and their metabolism supports the host with nutrients. This indicates strong physiological interconnections in the holobiont, which are thought to be modulated by sponge immunity and pattern-recognition proteins. Despite the hypothesized tight physiological integration and ancient origin of the sponge holobiont, the effect of changes in the symbiotic community on the sponge metabolism and morphogenesis remains poorly understood. Here, we show that the loss of a key microbial sponge symbiont correlates with a stark body plan reorganization of the sponge host. This reorganization is coupled with broad transcriptomic changes and includes the modulation of signaling pathways known to be involved in morphogenesis and innate immune response in sponges and other animals. This study provides a combined genetic, physiological, and morphological assessment of the effect of changes in the microbiome on sponge post-embryonic development and homeostasis. The drastic microbiome reorganization and the correlated response observed in the sponge host provide evidence for a coupling between sponge transcriptomic state and the state of its microbiome. Our results suggest that sponges use molecular mechanisms to respond to changes in their microbiome and that the ability to sense and respond to microbiome perturbations has deep evolutionary origins among animals.
Molecular Phylogenetic Evaluation of Classification and Scenarios of Character Evolution in Calcareous Sponges (Porifera, Class Calcarea)
Publisher: Public Library of Science (PLoS)
Date: 27-03-2012
Genetic structure of the crown-of-thorns seastar in the Pacific Ocean, with focus on Guam
Publisher: PeerJ
Date: 05-05-2016
DOI: 10.7717/PEERJ.1970
Abstract: Population outbreaks of the corallivorous crown-of-thorns seastar (COTS), Acanthaster ‘planci’ L. , are among the most important biological disturbances of tropical coral reefs. Over the past 50 years, several devastating outbreaks have been documented around Guam, an island in the western Pacific Ocean. Previous analyses have shown that in the Pacific Ocean, COTS larval dispersal may be geographically restricted to certain regions. Here, we assess the genetic structure of Pacific COTS populations and compared s les from around Guam with a number of distant localities in the Pacific Ocean, and focused on determining the degree of genetic structure among populations previously considered to be isolated. Using microsatellites, we document substantial genetic structure between 14 localities from different geographical regions in the Pacific Ocean. Populations from the 14 locations s led were found to be structured in three significantly differentiated groups: (1) all locations immediately around Guam, as well as Kingman Reef and Swains Island (2) Japan, Philippines, GBR and Vanuatu and (3) Johnston Atoll, which was significantly different from all other localities. The lack of genetic differentiation between Guam and extremely distant populations from Kingman Reef and Swains Island suggests potential long-distance dispersal of COTS in the Pacific.
NUMTs in the Sponge Genome Reveal Conserved Transposition Mechanisms in Metazoans
Publisher: Oxford University Press (OUP)
Date: 18-08-2010
Abstract: The transposition of parts of the mitochondrial (mt) genetic material into the nuclear genome (NUMTs) occurs in a wide range of eukaryotes. Here, we show that NUMTs exist for nearly all regions of the mt genome in the demosponge Amphimedon queenslandica, a representative of the oldest phyletic lineage of animals. Because the sponge NUMTs are small and noncoding, and transposed via a DNA intermediate, as in eumetazoans, we infer that the transpositonal processes underlying NUMT formation in contemporary animals existed in their most recent common ancestor. In contrast to most bilaterians, Amphimedon NUMTs are inserted into regions of high gene density. Given the common features of metazoan NUMTs, the reduction in animal mt genome sizes relative to other eukaryotes may be the product of the mt DNA transposition mechanisms that evolved along the metazoan stem.
Calcite Formation in Soft Coral Sclerites Is Determined by a Single Reactive Extracellular Protein
Publisher: Elsevier BV
Date: 09-2011
Animal Biocalcification, Evolution
Publisher: Springer Netherlands
Date: 2011
<strong>Revision of the brachiopod genus <em>Amphithyris</em> (Rhynchonelliformea: Platidiidae) with descriptions of two new species</strong>
Publisher: Magnolia Press
Date: 07-08-2014
DOI: 10.11646/ZOOTAXA.3847.2.3
Abstract: The recent brachiopod genus Amphithyris Thomson belongs to the family Platidiidae and to date comprises five species, A. seminula (Philippi, 1836), A. buckmani Thomson, 1918, A. hallettensis Foster, 1974, A. richardsonae C bell & Fleming, 1981 and A. parva MacKinnon, Hiller, Long & Marshall, 2008. Like other platidiid genera, Amphithyris has a worldwide distribution, but is mainly found in the southern hemisphere, with the exception of A. seminula which occurs in the Mediterranean Sea. This study is the first revision of the genus Amphithyris. We describe two new species, A. cavernicola n. sp. from the Queensland Plateau, Coral Sea, Australia and A. comitodentis n. sp. from deep waters east of the South Island, New Zealand. A. cavernicola n. sp. represents the first record of the genus from Australian waters, whereas A. comitodentis n. sp. is the first species in the genus recorded from the deep sea. Additionally, we identified the type material of A. seminula in the brachiopod collection of the Museum für Naturkunde, Berlin and designated a lectotype for this species. Despite their simple shell morphology and few diagnostic features, we were able to clearly discriminate the (now) seven species by morphological (shell) characters such as absence resence of a median septum, absence resence of capillae, shell convexity and/or combinations of these. On the basis of all known records, the present distribution of Amphithyris spp. and a Cretaceous origin of the genus is discussed.
Oxygen isotope fractionation in marine aragonite of coralline sponges
Publisher: Elsevier BV
Date: 05-2000
Short-Term Exposure to High-Temperature Water Causes a Shift in the Microbiome of the Common Aquarium Sponge Lendenfeldia chondrodes
Publisher: Springer Science and Business Media LLC
Date: 07-08-2020
DOI: 10.1007/S00248-020-01556-Z
Abstract: Marine sponges harbor erse microbiomes that contribute to their energetic and metabolic needs. Although numerous studies on sponge microbial ersity exist, relatively few focused on sponge microbial community changes under different sources of environmental stress. In this study, we assess the impact of elevated seawater temperature on the microbiome of cultured Lendenfeldia chondrodes , a coral reef sponge commonly found in marine aquaria. Lendenfeldia chondrodes exhibits high thermal tolerance showing no evidence of tissue damage or bleaching at 5 °C above control water temperature (26 °C). High-throughput sequencing of the bacterial 16S rRNA V4 region revealed a response of the microbiome of L. chondrodes to short-term exposure to elevated seawater temperature. Shifts in abundance and richness of the dominant bacterial phyla found in the microbiome of this species, namely Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes, characterized this response. The observed resilience of L. chondrodes and the responsiveness of its microbiome to short-term increases in seawater temperature suggest that this holobiont may be capable of acclimating to anthropogenic-driven sublethal environmental stress via a re-accommodation of its associated bacterial community. This sheds a new light on the potential for resilience of some sponges to increasing surface seawater temperatures and associated projected regime shifts in coral reefs.
Molecular and mineral responses of corals grown under artificial Calcite Sea conditions
Publisher: Cold Spring Harbor Laboratory
Date: 28-02-2022
DOI: 10.1101/2022.02.25.481970
Abstract: The formation of skeletal structures composed of different calcium carbonate polymorphs (aragonite and calcite) appears to be regulated both biologically and environmentally. Among environmental factors influencing aragonite and calcite precipitation, changes in seawater conditions – primarily in the molar ratio of magnesium and calcium during so-called “Calcite” ( m Mg: m Ca below 2) or “Aragonite” seas ( m Mg: m Ca above 2) – have had profound impacts on the distribution and performance of marine calcifiers throughout the Earth’s history. Nonetheless, the fossil record shows that some species appear to have counteracted such changes and kept their skeleton polymorph unaltered. Here, the aragonitic octocoral Heliopora coerulea and the aragonitic scleractinian Montipora digitata were exposed to Calcite Sea-like m Mg: m Ca with various levels of changes in magnesium and calcium concentration, and both mineralogical (i.e., CaCO 3 polymorph) and gene expression changes were monitored. Both species maintained aragonite deposition at lower m Mg: m Ca ratios, while concurrent calcite presence was only detected in M. digitata . Despite a strong variability between independent experimental replicates for both species, the expression for a set of putative calcification-related genes, including known components of scleractinian skeleton organic matrix, was found to consistently change at lower m Mg: m Ca. These results support previously proposed involvements of the skeleton organic matrix in counteracting decreases in seawater m Mg: m Ca. Although no consistent changes in expression for calcium and magnesium transporters were observed, down-regulation calcium channels in H. coerulea in one experimental replicate and at an m Mg: m Ca of 2.5 might indicate the possibility of active calcium uptake regulation by the corals under altered m Mg: m Ca.
New insights into the phylogeny of glass sponges (Porifera, Hexactinellida): Monophyly of Lyssacinosida and Euplectellinae, and the phylogenetic position of Euretidae
Publisher: Elsevier BV
Date: 07-2009
Correction: Comparative genomics and the nature of placozoan species
Publisher: Public Library of Science (PLoS)
Date: 19-09-2018
New and Biologically Active Imidazole Alkaloids from Two Sponges of the Genus Leucetta
Publisher: American Chemical Society (ACS)
Date: 09-07-2002
DOI: 10.1021/NP020050C
Abstract: Chemical investigation of two sponges, Leucetta chagosensis and Leucetta cf chagosensis, collected from the Great Barrier Reef and the Fiji Islands, respectively, has led to the isolation of three new imidazole alkaloids (1-3), along with the known compounds isonaamine B (4) and naamine A (5). The structures of the new compounds (1-3) were elucidated by employing spectroscopic techniques (NMR, MS, UV, and IR). The structures of the known compounds 4 and 5 were determined by comparison of their (1)H and (13)C NMR spectroscopic data with published values. Compounds 1 and 2 were found to be cytotoxic toward several tumor cell lines (GI(50) values ranged from 1.3 to 7.0 microg/mL).
OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences
Publisher: Oxford University Press (OUP)
Date: 02-06-2009
DOI: 10.1093/NAR/GKP434
Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model
Publisher: Cold Spring Harbor Laboratory
Date: 07-07-2017
DOI: 10.1101/159806
Abstract: Approximately 80% of all recent sponge species belong to the class Demospongiae. Yet, despite their ersity and importance, accurate ergence times are still unknown for most demosponge clades. The estimation of demosponge ergence time is key to answering fundamental questions like e.g. the origin of Demospongiae, their ersification and historical biogeography. Molecular sequence data alone is not informative on an absolute time scale, and therefore needs to be “calibrated” with additional data such as fossils. Here, we apply the fossilized birth-death model (FBD), which has the advantage, compared to strict node dating with the oldest fossil occurrences, that it allows for the inclusion of young and old fossils in the analysis of ergence time. We use desma-bearing sponges, a erse group of demosponges that form rigid skeletons and have a rich and continuous fossil record dating back to the Cambrian (∼500 Ma), aiming to date the demosponge radiation and constrain the timing of key evolutionary events, like the transition from marine to freshwater habitats. To do so, we assembled mitochondrial genomes of six desma-bearing demosponges from size-selected reduced-representation genomic libraries and apply a fossilized birth-death model including 30 fossils and 33 complete demosponge mitochondrial genomes to infer a dated phylogeny of Demospongiae. Our study supports a Neoproterozoic origin of Demospongiae. Novel age estimates for the split of freshwater and marine sponges dating back to the Carboniferous and the previously assumed Recent (∼18 Ma) ersification of freshwater sponges is supported. Moreover, we provide detailed age estimates for a possible ersification of Tetractinellidae (∼315 Ma), the Astrophorina (∼240 Ma), the Spirophorina (∼120 Ma) and the family Corallistidae (∼188 Ma) all of which are considered as key groups for dating the Demospongiae, due to their extraordinary rich and continuous fossil history.
Challenges for biodiversity research in Europe
Publisher: Elsevier BV
Date: 2011
The role of homology and orthology in the phylogenomic analysis of metazoan gene content
Publisher: Cold Spring Harbor Laboratory
Date: 08-06-2018
DOI: 10.1101/341115
Abstract: Resolving animal (Metazoa) relationships is crucial to our understanding of, for ex le, the origin of their key traits such as muscles, guts and nerves. However, a broadly accepted metazoan consensus phylogeny has yet to emerge. In part this is because the genomes of deeply- erging and fast-evolving lineages may undergo significant gene turnover, reducing the number of orthologs shared with related phyla. This can limit the usefulness of traditional phylogenetic methods that rely on alignments of orthologous sequences. Phylogenetic analysis of gene content has the potential to circumvent this orthology requirement, with binary presence/absence of homologous gene families representing a source of phylogenetically informative characters. Applying binary substitution models to the gene content of 26 complete animal genomes, we demonstrate that patterns of gene conservation differ markedly depending on whether gene families are defined by orthology or homology, i.e., whether paralogs are excluded or included. We conclude that the placement of deeply- erging lineages, like ctenophores, may exceed the limit of resolution afforded by methods based on comparisons of orthologous protein supermatrices, and novel approaches are required to fully capture the evolutionary signal from genes within genomes.
Evaluation and validation of reference genes for qPCR analysis to study climate change-induced stresses in Sinularia cf. cruciata (Octocorallia: Alcyonidae)
Publisher: Elsevier BV
Date: 10-2016
A short LSU rRNA fragment as a standard marker for integrative taxonomy in calcareous sponges (Porifera: Calcarea)
Publisher: Springer Science and Business Media LLC
Date: 25-11-2015
Erratum to: Precious coral and rock sponge gardens on the deep aphotic fore-reef of Osprey Reef (Coral Sea, Australia)
Publisher: Springer Science and Business Media LLC
Date: 18-10-2011
Calcium isotope fractionation in calcite and aragonite
Publisher: Elsevier BV
Date: 09-2005
Similar Ratios of Introns to Intergenic Sequence across Animal Genomes
Publisher: Oxford University Press (OUP)
Date: 06-2017
DOI: 10.1093/GBE/EVX103
Bearing the wrong identity: A case study of an Indo-Pacific common shallow water sponge of the genus Neopetrosia (Haplosclerida; Petrosiidae)
Publisher: Magnolia Press
Date: 15-10-2018
DOI: 10.11646/ZOOTAXA.4500.1.2
Abstract: Sponges of the order Haplosclerida are often abundant and characteristic components of Indo-Pacific reefs, but are often misidentified, because of the lack of clear distinctive morphological characters. Neopetrosia exigua is an ex le of a haplosclerid sponge that is very common in Indonesian shallow coral reef environments but bears several different names. In the present study we investigated type material of several Indo-Pacific Neopetrosia species with a similar morphology and examined freshly collected specimen materials including specimens that are deposited at several institutions. In addition, we used molecular phylogenetic methods for assisting the morphological examinations. We conclude that the true identity of Neopetrosia exigua should be Neopetrosia chaliniformis. Likewise, N. exigua and N. pacifica should be considered as junior synonyms of N. chaliniformis. In conclusion, we advocate that molecular barcoding could significantly aid on sponge species’ delimitation that possess limited morphological characters.
A new sponge genus from the Chengjiang biota with an intriguing combination of skeletal characters
Publisher: Springer Science and Business Media LLC
Date: 09-06-2023
DOI: 10.1007/S12542-023-00652-Y
Abstract: The development of fossil sponge systematics is hindered by factors such as their low anatomical complexity and the low preservation potential of many characters used in the definition of extant sponge clades. Here we describe Calliospongia chunchengia gen. et sp. nov., a new sponge from the Lower Cambrian Chengjiang biota, which possesses a unique combination of characters. The skeleton of C. chunchengia is similar to those of leptomitid protomonaxonids in being composed of large spicules arranged longitudinally. However, it is distinct enough to belong in its own genus and even question a leptomitid affinity, because, unlike the members of this group, which usually have two categories of diactine spicules, its skeleton is entirely composed of triactines. The new taxon shares the presence of large megascleres with demosponges, hexactinellids and the ascosponges, suggesting an affinity to the total group of Silicea. It is also reminiscent of the hexactinellid-like reticulosans, showing a potential connection between two major types of Early Palaeozoic sponge body plans. A more accurate definition of the Cambro-Ordovician groups and the creation of a total evidence framework that integrates extinct and extant sponge morphology into the phylogenetic scenario derived from phylogenomics seem to be essential steps for the improvement of our understanding of early sponge evolution.
Two Pione species (Hadromerida, Clionaidae) from the Red Sea: a taxonomical challenge
Publisher: Springer Science and Business Media LLC
Date: 24-06-2010
First evaluation of mitochondrial DNA as a marker for phylogeographic studies of Calcarea: a case study from Leucetta chagosensis
Publisher: Springer Science and Business Media LLC
Date: 07-07-2011
The lysidyl aminoacyl transfer RNA synthetase intron, a new marker for demosponge phylogeographics – case study on Neopetrosia
Publisher: Cambridge University Press (CUP)
Date: 12-11-2016
DOI: 10.1017/S0025315415001721
Abstract: Suitable genetic markers for population studies in sponges are necessary to further our understanding of bio ersity and dispersal patterns, and contribute to conservation efforts. Due to the slow mitochondrial substitution rates in demosponges, nuclear introns are among the preferable markers for phylogeographic studies, but so far only the second intron of the ATP synthetase beta subunit-gene (ATPSβ) has been successfully established. In the present study, we analyse the intron of the Lysidyl Aminoacyl Transfer RNA Synthetase (LTRS), another potential marker to study demosponge intraspecific relationships, on s les of Neopetrosia chaliniformis from various locations in the Indo-Pacific and compare its variation with a mitochondrial marker (CO2). LTRS recovers several reciprocal monophyletic groups among the Indo-Pacific N. chaliniformis and provides a potential alternative to ATPSβ.
Sponge Paleogenomics Reveals an Ancient Role for Carbonic Anhydrase in Skeletogenesis
Publisher: American Association for the Advancement of Science (AAAS)
Date: 29-06-2007
Abstract: Sponges (phylum Porifera) were prolific reef-building organisms during the Paleozoic and Mesozoic ∼542 to 65 million years ago. These ancient animals inherited components of the first multicellular skeletogenic toolkit from the last common ancestor of the Metazoa. Using a paleogenomics approach, including gene- and protein-expression techniques and phylogenetic reconstruction, we show that a molecular component of this toolkit was the precursor to the α-carbonic anhydrases (α-CAs), a gene family used by extant animals in a variety of fundamental physiological processes. We used the coralline demosponge Astrosclera willeyana , a “living fossil” that has survived from the Mesozoic, to provide insight into the evolution of the ability to biocalcify, and show that the α-CA family expanded from a single ancestral gene through several independent gene-duplication events in sponges and eumetazoans.
The phylogeny of halichondrid demosponges: past and present re-visited with DNA-barcoding data
Publisher: Springer Science and Business Media LLC
Date: 03-2012
Symbiophagy and biomineralization in the “living fossil”Astrosclera willeyana
Publisher: Informa UK Limited
Date: 12-12-2013
DOI: 10.4161/AUTO.27319
Development of microsatellite loci in the common reef starfish Linckia laevigata and Linckia multifora
Publisher: Wiley
Date: 25-09-2012
Anaerobic metabolism of Foraminifera thriving below the seafloor
Publisher: Springer Science and Business Media LLC
Date: 08-07-2020
DOI: 10.1038/S41396-020-0708-1
Abstract: Foraminifera are single-celled eukaryotes (protists) of large ecological importance, as well as environmental and paleoenvironmental indicators and biostratigraphic tools. In addition, they are capable of surviving in anoxic marine environments where they represent a major component of the benthic community. However, the cellular adaptations of Foraminifera to the anoxic environment remain poorly constrained. We s led an oxic-anoxic transition zone in marine sediments from the Namibian shelf, where the genera Bolivina and Stainforthia dominated the Foraminifera community, and use metatranscriptomics to characterize Foraminifera metabolism across the different geochemical conditions. Relative Foraminifera gene expression in anoxic sediment increased an order of magnitude, which was confirmed in a 10-day incubation experiment where the development of anoxia coincided with a 20–40-fold increase in the relative abundance of Foraminifera protein encoding transcripts, attributed primarily to those involved in protein synthesis, intracellular protein trafficking, and modification of the cytoskeleton. This indicated that many Foraminifera were not only surviving but thriving, under the anoxic conditions. The anaerobic energy metabolism of these active Foraminifera was characterized by fermentation of sugars and amino acids, fumarate reduction, and potentially dissimilatory nitrate reduction. Moreover, the gene expression data indicate that under anoxia Foraminifera use the phosphogen creatine phosphate as an ATP store, allowing reserves of high-energy phosphate pool to be maintained for sudden demands of increased energy during anaerobic metabolism. This was co-expressed alongside genes involved in phagocytosis and clathrin-mediated endocytosis (CME). Foraminifera may use CME to utilize dissolved organic matter as a carbon and energy source, in addition to ingestion of prey cells via phagocytosis. These anaerobic metabolic mechanisms help to explain the ecological success of Foraminifera documented in the fossil record since the Cambrian period more than 500 million years ago.
Towards a DNA taxonomy of Caribbean demosponges: A gene tree reconstructed from partial mitochondrial CO1 gene sequences supports previous rDNA phylogenies and provides a new perspective on the systematics of Demospongiae
Publisher: Cambridge University Press (CUP)
Date: 12-2007
DOI: 10.1017/S0025315407058195
Abstract: We present the most comprehensive cytochrome oxidase subunit 1 gene tree published to date for demosponges based on new sequences. The CO1 barcoding fragment is sequenced for 65 species from the Caribbean Sea, and its gene tree reconstructed. Although its deeper nodes are not particularly well-supported, the gene tree provides a variety of information for new phylogenetic patterns, as well as support for previously published 28S rDNA gene trees. In our analysis Halichondriidae cluster with Suberitidae, supporting previous 28S rDNA data. Chelae-bearing Poecilosclerida are monophyletic but most taxa lacking chelae in this dataset cluster more distantly. Haplosclerida are not resolved monophyletically under this fragment. While some species exhibit distinct barcodes, some genera contain species that share CO1 haplotypes.
Body-Plan Reorganization in a Sponge Correlates with Microbiome Change
Publisher: Oxford University Press (OUP)
Date: 06-2023
Abstract: Mounting evidence suggests that animals and their associated bacteria interact via intricate molecular mechanisms, and it is hypothesized that disturbances to the microbiome influence animal development. Here, we show that the loss of a key photosymbiont (i.e., bleaching) upon shading correlates with a stark body-plan reorganization in the common aquarium cyanosponge Lendenfeldia chondrodes. The morphological changes observed in shaded sponges include the development of a thread-like morphology that contrasts with the flattened, foliose morphology of control specimens. The microanatomy of shaded sponges markedly differed from that of control sponges, with shaded specimens lacking a well-developed cortex and choanosome. Also, the palisade of polyvacuolar gland-like cells typical in control specimens was absent in shaded sponges. The morphological changes observed in shaded specimens are coupled with broad transcriptomic changes and include the modulation of signaling pathways involved in animal morphogenesis and immune response, such as the Wnt, transforming growth factor β (TGF-β), and TLR–ILR pathways. This study provides a genetic, physiological, and morphological assessment of the effect of microbiome changes on sponge postembryonic development and homeostasis. The correlated response of the sponge host to the collapse of the population of symbiotic cyanobacteria provides evidence for a coupling between the sponge transcriptomic state and the state of its microbiome. This coupling suggests that the ability of animals to interact with their microbiomes and respond to microbiome perturbations has deep evolutionary origins in this group.
Nothing in (sponge) biology makes sense – except when based on holotypes
Publisher: Cambridge University Press (CUP)
Date: 04-05-2015
DOI: 10.1017/S0025315415000521
Abstract: Sponge species are infamously difficult to identify for non-experts due to their high morphological plasticity and the paucity of informative morphological characters. The use of molecular techniques certainly helps with species identification, but unfortunately it requires prior reference sequences. Holotypes constitute the best reference material for species identification, however their usage in molecular systematics and taxonomy is scarce and frequently not even attempted, mostly due to their antiquity and preservation history. Here we provide case studies in which we demonstrate the importance of using holotype material to answer phylogenetic and taxonomic questions. We also demonstrate the possibility of sequencing DNA fragments out of century-old holotypes. Furthermore we propose the deposition of DNA sequences in conjunction with new species descriptions.
A rapidly evolving secretome builds and patterns a sea shell
Publisher: Springer Science and Business Media LLC
Date: 22-11-2006
Abstract: Instructions to fabricate mineralized structures with distinct nanoscale architectures, such as seashells and coral and vertebrate skeletons, are encoded in the genomes of a wide variety of animals. In mollusks, the mantle is responsible for the extracellular production of the shell, directing the ordered biomineralization of CaCO 3 and the deposition of architectural and color patterns. The evolutionary origins of the ability to synthesize calcified structures across various metazoan taxa remain obscure, with only a small number of protein families identified from molluskan shells. The recent sequencing of a wide range of metazoan genomes coupled with the analysis of gene expression in non-model animals has allowed us to investigate the evolution and process of biomineralization in gastropod mollusks. Here we show that over 25% of the genes expressed in the mantle of the vetigastropod Haliotis asinina encode secreted proteins, indicating that hundreds of proteins are likely to be contributing to shell fabrication and patterning. Almost 85% of the secretome encodes novel proteins remarkably, only 19% of these have identifiable homologues in the full genome of the patellogastropod Lottia scutum . The spatial expression profiles of mantle genes that belong to the secretome is restricted to discrete mantle zones, with each zone responsible for the fabrication of one of the structural layers of the shell. Patterned expression of a subset of genes along the length of the mantle is indicative of roles in shell ornamentation. For ex le, Has-sometsuke maps precisely to pigmentation patterns in the shell, providing the first case of a gene product to be involved in molluskan shell pigmentation. We also describe the expression of two novel genes involved in nacre (mother of pearl) deposition. The unexpected complexity and evolvability of this secretome and the modular design of the molluskan mantle enables ersification of shell strength and design, and as such must contribute to the variety of adaptive architectures and colors found in mollusk shells. The composition of this novel mantle-specific secretome suggests that there are significant molecular differences in the ways in which gastropods synthesize their shells.
Mitochondrial RNA processing in absence of tRNA punctuations in octocorals
Publisher: Springer Science and Business Media LLC
Date: 17-06-2017
New Non-Bilaterian Transcriptomes Provide Novel Insights into the Evolution of Coral Skeletomes
Publisher: Oxford University Press (OUP)
Date: 13-09-2019
DOI: 10.1093/GBE/EVZ199
Abstract: A general trend observed in animal skeletomes—the proteins occluded in animal skeletons—is the copresence of taxonomically widespread and lineage-specific proteins that actively regulate the biomineralization process. Among cnidarians, the skeletomes of scleractinian corals have been shown to follow this trend. However, distributions and phylogenetic analyses of biomineralization-related genes are often based on only a few species, with other anthozoan calcifiers such as octocorals (soft corals), not being fully considered. We de novo assembled the transcriptomes of four soft-coral species characterized by different calcification strategies (aragonite skeleton vs. calcitic sclerites) and data-mined published nonbilaterian transcriptome resources to construct a taxonomically comprehensive sequence database to map the distribution of scleractinian and octocoral skeletome components. Cnidaria shared no skeletome proteins with Placozoa or Ctenophora, but did share some skeletome proteins with Porifera, such as galaxin-related proteins. Within Scleractinia and Octocorallia, we expanded the distribution for several taxonomically restricted genes such as secreted acidic proteins, scleritin, and carbonic anhydrases, and propose an early, single biomineralization-recruitment event for galaxin sensu stricto. Additionally, we show that the enrichment of acidic residues within skeletogenic proteins did not occur at the Corallimorpharia–Scleractinia transition, but appears to be associated with protein secretion into the organic matrix. Finally, the distribution of octocoral calcification-related proteins appears independent of skeleton mineralogy (i.e., aragonite/calcite) with no differences in the proportion of shared skeletogenic proteins between scleractinians and aragonitic or calcitic octocorals. This points to skeletome homogeneity within but not between groups of calcifying cnidarians, although some proteins such as galaxins and SCRiP-3a could represent instances of commonality.
Structure and composition of calcareous sponge spicules: A review and comparison to structurally related biominerals
Publisher: Elsevier BV
Date: 04-2008
DOI: 10.1016/J.MICRON.2007.01.006
Abstract: Since the early 19th century, the skeletons of calcareous sponges (Porifera: Calcarea) with their mineralized spicules have been investigated for their morphologies, structures, and mineralogical and organic compositions. These biomineral spicules, up to about 10mm in size, with one to four rays called actines, have various specific shapes and consist mainly of magnesium-calcite: in only one case has an additional phase of stabilized amorphous CaCO3 (ACC) been discovered. The spicules are invariably covered by a thin organic sheath and display a number of intriguing properties. Despite their complex morphologies and rounded surfaces without flat crystal faces they behave largely as single crystal in iduals of calcite, and to some degree crystallographic orientation is related to morphology. Despite their single-crystalline nature, most spicules show nearly isotropic fracture behaviour, not typical for calcite crystals, indicating enhanced fracture resistance. These unusual morphological and mechanical properties are the result of their mechanism of growth. Each spicule is formed by specialized cells (sclerocytes) that supply mineral ions or particles associated by organic macromolecules to extracellular cavities, where assembly and crystallization in alignment with an initial seed crystal (nucleus) takes place. As a result of discontinuous mineral deposition, cross-sections of larger spicules display concentric layering that mantles a central calcitic rod. On a smaller scale, the entire spicule displays a 'nano-cluster' structure with crystallographically aligned and putatively semicoherent crystal domains as well as a dispersed organic matrix intercalated between domain boundaries. This ultrastructure dissipates mechanical stress and deflects propagating fractures. Additionally, this nano-cluster construction, probably induced by intercalated organic substances, enables the formation of complex crystal morphologies independent of crystal faces. In this review, the current knowledge about the structure, composition, and formation of calcareous sponge spicules is summarised and discussed. Comparisons of calcareous sponge spicules with the amorphous silica spicules of sponges of the classes Hexactinellida and Demospongiae, as well as with calcitic skeletal elements of echinoderms are drawn. Despite the variety of poriferan spicule mineralogy and the distant phylogenetic relationship between sponges and echinoderms, all of these biominerals share similarities regarding their nano-scale construction. Furthermore, echinoderm skeletal elements resemble calcareous sponge spicules in that they represent magnesium-bearing calcite single-crystals with extremely complex morphologies.
A fragmented metazoan organellar genome: the two mitochondrial chromosomes of Hydra magnipapillata
Publisher: Springer Science and Business Media LLC
Date: 26-07-2008
Abstract: Animal mitochondrial (mt) genomes are characteristically circular molecules of ~16–20 kb. Medusozoa (Cnidaria excluding Anthozoa) are exceptional in that their mt genomes are linear and sometimes sub ided into two to presumably four different molecules. In the genus Hydra , the mt genome comprises one or two mt chromosomes. Here, we present the whole mt genome sequence from the hydrozoan Hydra magnipapillata , comprising the first sequence of a fragmented metazoan mt genome encoded on two linear mt chromosomes (mt1 and mt2). The H. magnipapillata mt chromosomes contain the typical metazoan set of 13 genes for respiratory proteins, the two rRNA genes and two tRNA genes. All genes are unidirectionally oriented on mt1 and mt2, and several genes overlap. The gene arrangement suggests that the two mt chromosomes originated from one linear molecule that separated between nd5 and rns . Strong correlations between the AT content of rRNA genes ( rns and rnl ) and the AT content of protein-coding genes among 24 cnidarian genomes imply that base composition is mainly determined by mt genome-wide constraints. We show that identical inverted terminal repeats (ITR) occur on both chromosomes these ITR contain a partial copy or part of the 3' end of cox1 (54 bp). Additionally, both mt chromosomes possess identical oriented sequences (IOS) at the 5' and 3' ends (5' and 3' IOS) adjacent to the ITR. The 5' IOS contains trnM and non-coding sequences (119 bp), whereas the 3' IOS comprises a larger part (mt2) with a larger partial copy of cox1 (243 bp). ITR are also documented in the two other available medusozoan mt genomes ( Aurelia aurita and Hydra oligactis ). In H. magnipapillata , the arrangement of ITR and 5' IOS and 3' IOS suggest that these regions are crucial for mt DNA replication and/or transcription initiation. An analogous organization occurs in a highly fragmented ichthyosporean mt genome. With our data, we can reject a model of mt replication that has previously been proposed for Hydra . This raises new questions regarding replication mechanisms probably employed by all medusozoans, and also has general implications for the expected organization of fragmented linear mt chromosomes of other taxa.
Return of the ghosts of dispersal past: historical spread and contemporary gene flow in the blue sea star <I>Linckia laevigata</I>
Publisher: Bulletin of Marine Science
Date: 2014
Barcoding Sponges: An Overview Based on Comprehensive Sampling
Publisher: Public Library of Science (PLoS)
Date: 03-07-2012
Soft sponges with tricky tree: On the phylogeny of dictyoceratid sponges
Publisher: Hindawi Limited
Date: 28-01-2020
DOI: 10.1111/JZS.12351
Correction: Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp.
Publisher: Springer Science and Business Media LLC
Date: 24-09-2019
Transcriptomic Resilience of a Coral Holobiont to Low pH
Publisher: Cold Spring Harbor Laboratory
Date: 29-06-2017
DOI: 10.1101/157008
Abstract: Ocean acidification is considered as one of the major threats for coral reefs at a global scale. Marine calcifying organisms, including stony corals, are expected to be the most affected by the predicted decrease of the surface water pH at the end of the century. The severity of the impacts on coral reefs remains as matter of controversy. Although previous studies have explored the physiological response of stony corals to changes in pH, the response of the holobiont (i.e. the coral itself plus its symbionts) remains largely unexplored. In the present study, we assessed the changes in overall gene expression of the coral Montipora digitata and its microalgal symbionts after a short (three days) and a longer (42 days) exposure to low pH (7.6). The short-term exposure to low pH caused small differences in the expression level of the host, impacting mostly genes associated with stress response in other scleractinians. Resilience to Acidification of a Coral Holobiont Longer exposure to low pH resulted in no significant changes in gene expression of the coral host. Gene expression in the eukaryotic symbionts remained unaltered at both exposure times. Our findings suggest resilience, in terms of gene expression, of the Montipora digitata holobiont to pH decrease, as well as capability to acclimatize to extended periods of exposure to low pH.
Low genetic structuring among Pericharax heteroraphis (Porifera: Calcarea) populations from the Great Barrier Reef (Australia), revealed by analysis of nrDNA and nuclear intron sequences
Publisher: Springer Science and Business Media LLC
Date: 10-07-2007
Private collections of fossils are a plus
Publisher: Springer Science and Business Media LLC
Date: 08-2014
DOI: 10.1038/512371C
Analysis of evolutionary, biogeographical and taxonomic patterns of nucleotide composition in demosponge rRNA
Publisher: Cambridge University Press (CUP)
Date: 12-2007
DOI: 10.1017/S0025315407058183
Abstract: The ribosome is the location of protein translation and therefore a pivotal macromolecular complex for all organisms. The RNA molecules involved in the formation and functioning of the ribosome (rRNA) are partially single-stranded (loops) and partially double-stranded (helices or stems) as a result of pairing of complementary regions in either their own or other rRNA subunits. This pattern provides the rRNA with a secondary structure crucial for its functionality. The stability of these secondary structures is mediated by their base compositions: a helix rich in G-C pairs possesses a higher thermodynamic stability than an A-T rich counterpart. However, the base composition of these structures is neither homogeneous throughout the molecule nor throughout the demosponge taxa. Here, we present patterns of biased nucleotide composition in demosponge 28S rDNA. We analyse their correlation in respect to environment and taxonomy. We find significantly higher G+C contents in haplosclerid demosponges compared to other orders and investigate evidence for an association between water temperature and rRNA base composition in demosponges.
A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals
Publisher: Elsevier BV
Date: 04-2017
DOI: 10.1016/J.CUB.2017.02.031
Abstract: Resolving the early ersification of animal lineages has proven difficult, even using genome-scale datasets. Several phylogenomic studies have supported the classical scenario in which sponges (Porifera) are the sister group to all other animals ("Porifera-sister" hypothesis), consistent with a single origin of the gut, nerve cells, and muscle cells in the stem lineage of eumetazoans (bilaterians + ctenophores + cnidarians). In contrast, several other studies have recovered an alternative topology in which ctenophores are the sister group to all other animals (including sponges). The "Ctenophora-sister" hypothesis implies that eumetazoan-specific traits, such as neurons and muscle cells, either evolved once along the metazoan stem lineage and were then lost in sponges and placozoans or evolved at least twice independently in Ctenophora and in Cnidaria + Bilateria. Here, we report on our reconstruction of deep metazoan relationships using a 1,719-gene dataset with dense taxonomic s ling of non-bilaterian animals that was assembled using a semi-automated procedure, designed to reduce known error sources. Our dataset outperforms previous metazoan gene superalignments in terms of data quality and quantity. Analyses with a best-fitting site-heterogeneous evolutionary model provide strong statistical support for placing sponges as the sister-group to all other metazoans, with ctenophores emerging as the second-earliest branching animal lineage. Only those methodological settings that exacerbated long-branch attraction artifacts yielded Ctenophora-sister. These results show that methodological issues must be carefully addressed to tackle difficult phylogenetic questions and pave the road to a better understanding of how fundamental features of animal body plans have emerged.
Diversity in a Cold Hot-Spot: DNA-Barcoding Reveals Patterns of Evolution among Antarctic Demosponges (Class Demospongiae, Phylum Porifera)
Publisher: Public Library of Science (PLoS)
Date: 19-06-2015
MtDNA diversity of the Indonesian giant barrel sponge Xestospongia testudinaria (Porifera: Haplosclerida) – implications from partial cytochrome oxidase 1 sequences
Publisher: Cambridge University Press (CUP)
Date: 09-09-2016
DOI: 10.1017/S0025315415001149
Abstract: The Indonesian archipelago is a ‘hotspot’ for invertebrate bio ersity (‘Coral Triangle’). In this area of ‘peak’ bio ersity, the origins of this high species ersity have often been debated. Xestospongia testudinaria is one of the sponge species that dominates coral reef sponge communities in this region. The role of the so-called ‘giant barrel sponge’ for the reef ecosystem has been studied repeatedly, as have its various bioactive compounds. However, the genetic variation of this iconic sponge in the region remains unknown. We investigate over 200 barrel sponge s les from Indonesia, and neighbouring as well as more distant localities (Saudi Arabia, Tanzania, Thailand, Taiwan, Java, Sulawesi and the Great Barrier Reef, Australia) using the mitochondrial cytochrome oxidase subunit 1. We compare our results with those from the studies on the congeneric barrel sponges Xestospongia muta from the Caribbean, and Xestospongia bergquistia from the Indo-Pacific, and observe a high degree of overlapping haplotypes between the three barrel sponge species, likely indicating the presence of ancestral polymorphisms. We discuss the implications of these findings to better interpret the phylogeography of barrel sponge taxa in the Indo-Pacific.
Characterization of the proteinaceous skeletal organic matrix from the precious coralCorallium konojoi
Publisher: Wiley
Date: 03-10-2014
Abstract: The Japanese red and pink corals are known to be precious because of their commercial value resulting from their use in ornaments, jewelry, and medicine. Precious corals are very interesting models for biomineralization studies and possess two different skeletal structures: an axial skeleton and an endoskeleton (sclerites). Although it has long been known that the organic matrix proteins existing in coral skeletons are critical for the oriented precipitation of CaCO3 crystals, these proteins in moderate deep-sea Japanese precious corals remain uncharacterized. Therefore, in this study, we performed skeletal whole proteome analyses using 1D and 2D electrophoresis, nano-LC, and MALDI-TOF-TOF MS. We identified a total of 147 functional coral skeletal organic matrix proteins (120 from the sclerites and 36 from the axial skeleton), including two calcium-binding calmodulin. Among the organic matrix proteins identified, nine key proteins are highly typical and common in both skeletons. Strong glycosylation activity, which is essential for skeletal formation in calcifying organisms, was detected in both skeletons. This work demonstrates unique biomineralization-related proteins in precious corals and provides the first description of the major proteinaceous components of CaCO3 minerals in precious corals, enabling the comparative investigation of biocalcification in other octocorals.
OrthoSelect: a protocol for selecting orthologous groups in phylogenomics
Publisher: Springer Science and Business Media LLC
Date: 16-07-2009
Transcriptional response of the calcification and stress response toolkits in an octocoral under heat and pH stress
Publisher: Cold Spring Harbor Laboratory
Date: 15-07-2020
DOI: 10.1101/2020.07.15.202069
Abstract: Up to one-third of all described marine species inhabit coral reefs, but the future of these hyper erse ecosystems is insecure due to local and global threats, such as overfishing, eutrophication, ocean warming, and acidification. Although these impacts are expected to have a net detrimental effect on reefs, it has been shown that some organisms like octocorals may remain unaffected, or benefit from, anthropogenically induced environmental change, and may replace stony corals in future reefs. Despite their potential importance in future shallow-water coastal environments, the molecular mechanisms leading to the resilience to anthropogenic-induced stress observed in octocorals remain unknown. Here, we use manipulative experiments, proteomics, and transcriptomics to show that the molecular toolkit used by Pinnigorgia flava, a common Indo-Pacific gorgonian octocoral, to deposit its calcium-carbonate skeleton is resilient to heat and seawater acidification stress. Sublethal heat stress triggered a stress response in P. flava but did not affect the expression of 27 transcripts encoding Skeletal Organic Matrix (SOM) proteins. Exposure to seawater acidification did not cause a stress response but triggered the downregulation of many transcripts, including an osteonidogen homolog present in the SOM. The observed transcriptional decoupling of the skeletogenic and stress-response toolkits provides insights into the mechanisms of resilience to anthropogenically-driven environmental change observed in octocorals.
Molecular phylogeny of glass sponges (Porifera, Hexactinellida): increased taxon sampling and inclusion of the mitochondrial protein-coding gene, cytochrome oxidase subunit I
Publisher: Springer Science and Business Media LLC
Date: 15-06-2011
First evaluation of mitochondrial DNA as a marker for phylogeographic studies of Calcarea: a case study from Leucetta chagosensis
Publisher: Springer Netherlands
Date: 07-07-2011
Genetic data confirms the enigmatic demosponge Janulum as haplosclerid
Publisher: Magnolia Press
Date: 09-03-2023
DOI: 10.11646/ZOOTAXA.5254.1.10
Abstract: Historically, sponge classification is based on the interpretation of morphological characters, whose phylogenetic information content is frequently limited, subject to homoplasies, or prone to environmental plasticity (e.g., Chombard et al. 1998). Therefore, the currently accepted order-level classification of its largest class, Demospongiae, has been largely revised with molecular phylogenetic data (Morrow & Cárdenas 2015). Nevertheless, numerous sponge genera with ambiguous or provisoric phylogenetic placement still await definite classification.
Phylogeography of the crown-of-thorns starfish in the Indian Ocean.
Publisher: Public Library of Science (PLoS)
Date: 21-08-2012
Molecular paleobiology — Progress and perspectives
Publisher: Elsevier BV
Date: 06-2016
New non-bilaterian transcriptomes provide novel insights into the evolution of coral skeletomes
Publisher: Cold Spring Harbor Laboratory
Date: 31-03-2019
DOI: 10.1101/594242
Abstract: A general feature of animal skeletomes is the co-presence of taxonomically widespread and lineage-specific proteins that actively regulate the biomineralization process. Among cnidarians, the skeletomes of scleractinian corals have been shown to follow this trend, however in this group distribution and phylogenetic analyses of biomineralization-related genes have been often based on limited numbers of species, with other anthozoan calcifiers such as octocorals, being overlooked. We de-novo sequenced the transcriptomes of four soft-coral species characterized by different calcification strategies (aragonite skeleton vs . calcitic sclerites) and data-mined published non-bilaterian transcriptomic resources to construct a taxonomically comprehensive sequence database to map the distribution of scleractinian and octocoral skeletome components. At the large scale, no protein showed a ‘Cnidaria+Placozoa’ or ‘Cnidaria+Ctenophora’ distribution, while some were found in cnidarians and Porifera. Within Scleractinia and Octocorallia, we expanded the distribution for several taxonomically restricted genes (TRGs) and propose an alternative evolutionary scenario, involving an early single biomineralization-recruitment event, for galaxin sensu stricto . Additionally, we show that the enrichment of acidic residues within skeletogenic proteins did not occur at the Corallimorpharia-Scleractinia transition, but appears to be associated with protein secretion in the organic matrix. Finally, the distribution of octocoral calcification-related proteins appears independent of skeleton mineralogy ( i . e . aragonite/calcite) with no differences on the proportion of shared skeletogenic proteins between scleractinians and aragonitic or calcitic octocorals. This points to skeletome homogeneity within but not between groups of calcifying cnidarians, although some proteins like galaxins and SCRiP-3a could represent instances of commonality.
Similar ratios of introns to intergenic sequence across animal genomes
Publisher: Cold Spring Harbor Laboratory
Date: 09-08-2016
DOI: 10.1101/068627
Abstract: One central goal of genome biology is to understand how the usage of the genome differs between organisms. Our knowledge of genome composition, needed for downstream inferences, is critically dependent on gene annotations, yet problems associated with gene annotation and assembly errors are usually ignored in comparative genomics. Here we analyze the genomes of 68 species across 12 animal phyla and some single-cell eukaryotes for general trends in genome composition and transcription, taking into account problems of gene annotation. We show that, regardless of genome size, the ratio of introns to intergenic sequence is comparable across essentially all animals, with nearly all deviations dominated by increased intergenic sequence. Genomes of model organisms have ratios much closer to 1:1, suggesting that the majority of published genomes of non-model organisms are underannotated and consequently omit substantial numbers of genes, with likely negative impact on evolutionary interpretations. Finally, our results also indicate that most animals transcribe half or more of their genomes arguing against differences in genome usage between animal groups, and also suggesting that the transcribed portion is more dependent on genome size than previously thought.
Evolution, radiation and chemotaxonomy of Lamellodysidea, a demosponge genus with anti-plasmodial metabolites
Publisher: Springer Science and Business Media LLC
Date: 05-02-2012
Non-monophyly of most supraspecific taxa of calcareous sponges (Porifera, Calcarea) revealed by increased taxon sampling and partitioned Bayesian analysis of ribosomal DNA
Publisher: Elsevier BV
Date: 09-2006
DOI: 10.1016/J.YMPEV.2006.04.016
Abstract: Calcareous sponges (Porifera, Calcarea) play an important role for our understanding of early metazoan evolution, since several molecular studies suggested their closer relationship to Eumetazoa than to the other two sponge 'classes,' Demospongiae and Hexactinellida. The ision of Calcarea into the subtaxa Calcinea and Calcaronea is well established by now, but their internal relationships remain largely unresolved. Here, we estimate phylogenetic relationships within Calcarea in a Bayesian framework, using full-length 18S and partial 28S ribosomal DNA sequences. Both genes were analyzed separately and in combination and were further partitioned by stem and loop regions, the former being modelled to take non-independence of paired sites into account. By substantially increasing taxon s ling, we show that most of the traditionally recognized supraspecific taxa within Calcinea and Calcaronea are not monophyletic, challenging the existing classification system, while monophyly of Calcinea and Calcaronea is again highly supported.
Homoplasious colony morphology and mito-nuclear phylogenetic discordance among Eastern Pacific octocorals
Publisher: Elsevier BV
Date: 05-2016
DOI: 10.1016/J.YMPEV.2016.02.023
Abstract: Octocorals are a erse and ecologically important group of cnidarians. However, the phylogenetic relationships of many octocoral groups are not well understood and are based mostly on mitochondrial sequence data. In addition, the discovery and description of new gorgonian species displaying unusual or intermediate morphologies and uncertain phylogenetic affinities further complicates the study of octocoral systematics and raises questions about the role played by processes such as plasticity, crypsis, and convergence in the evolution of this group of organisms. Here, we use nuclear (i.e. 28S rDNA) and mitochondrial (mtMutS) markers and a s le of Eastern Pacific gorgonians thought to be remarkable from a morphological point of view to shed light on the morphological ersification among these organisms. Our study reveals the loss of the anastomosed colony morphology in two unrelated lineages of the seafan genus Pacifigorgia and offers strong evidence for the independent evolution of a whip-like morphology in two lineages of Eastern Pacific Leptogorgia. Additionally, our data revealed one instance of mito-nuclear discordance in the genera Leptogorgia and Eugorgia, which may be the results of incomplete lineage sorting or ancient hybridization-introgression events. Our study stresses the importance of comprehensive taxonomic s ling and the use of independent sources of evidence to address the phylogenetic relationships and clarifying the evolution of octocorals.
A threat to coral reefs multiplied? Four species of crown-of-thorns starfish.
Publisher: The Royal Society
Date: 30-09-2008
Abstract: In the face of ever-increasing threats to coral reef ecosystems, it is essential to understand the impact of natural predators in order to devise appropriate management strategies. Destructive population explosions of the crown-of-thorns starfish Acanthaster planci have devastated coral reefs throughout the Indo-Pacific for decades. But despite extensive research, the causes of outbreaks are still unclear. An important consideration in this research is that A. planci has been regarded as a single taxonomic entity. Using molecular data from its entire distribution, we find that A. planci is in fact a species complex. This discovery has important consequences for future coral reef research, and might prove critical for successful reef conservation management.
Reply to Halanych et al.: Ctenophore misplacement is corroborated by independent datasets
Publisher: Proceedings of the National Academy of Sciences
Date: 09-02-2016
Unsuspected diversity of Niphargus amphipods in the chemoautotrophic cave ecosystem of Frasassi, central Italy
Publisher: Springer Science and Business Media LLC
Date: 09-06-2010
Abstract: The sulfide-rich Frasassi caves in central Italy contain a rare ex le of a freshwater ecosystem supported entirely by chemoautotrophy. Niphargus ictus , the sole hipod species previously reported from this locality, was recently shown to host the first known case of a freshwater chemoautotrophic symbiosis. Since the habitat of N. ictus is highly fragmented and is comprised of streams and lakes with various sulfide concentrations, we conducted a detailed study to examine the potential genetic ersity of this species within Frasassi. By sequencing one nuclear (ITS) and two mitochondrial (COI and 12S) regions, we show that four partially sympatric Niphargus clades are present in Frasassi. Morphological and behavioral data obtained for three of these clades are perfectly congruent with this molecular delineation and make it possible to distinguish them in the field. Phylogenetic analyses of 28S ribosomal DNA sequences reveal that, among the four clades, only two are closely related to each other. Moreover, these four clades occupy distinct niches that seem to be related to the chemical properties and flow regimes of the various water bodies within Frasassi. Our results suggest that four distinct Niphargus species are present in Frasassi and that they originated from three or four independent invasions of the cave system. At least two among the four species harbor Thiothrix epibionts, which paves the way for further studies of the specificity and evolutionary history of this symbiosis.
First evidence of miniature transposable elements in sponges (Porifera)
Publisher: Springer Science and Business Media LLC
Date: 08-06-2011
Manzacidin D: An unprecedented secondary metabolite from the 'living fossil' sponge Astrosclera willeyana
Publisher: Elsevier BV
Date: 06-1997
Comparative mitogenomics, phylogeny and evolutionary history of Leptogorgia (Gorgoniidae)
Publisher: Elsevier BV
Date: 10-2017
DOI: 10.1016/J.YMPEV.2017.08.001
Abstract: Molecular analyses of the ecologically important gorgonian octocoral genus Leptogorgia are scant and mostly deal with few species from restricted geographical regions. Here we explore the phylogenetic relationships and the evolutionary history of Leptogorgia using the complete mitochondrial genomes of six Leptogorgia species from different localities in the Atlantic, Mediterranean and eastern Pacific as well as four other genera of Gorgoniidae and Plexauridae. Our mitogenomic analyses showed high inter-specific ersity, variable nucleotide substitution rates and, for some species, novel genomic features such as ORFs of unknown function. The phylogenetic analyses using complete mitogenomes and an extended mtMutS dataset recovered Leptogorgia as polyphyletic, and the species considered in the analyses were split into two defined groups corresponding to different geographic regions, namely the eastern Pacific and the Atlantic-Mediterranean. Our phylogenetic analysis based on mtMutS also showed a clear separation between the eastern Atlantic and South African Leptogorgia, suggesting the need of a taxonomic revision for these forms. A time-calibrated phylogeny showed that the separation of eastern Pacific and western Atlantic species started ca. 20Mya and suggested a recent ergence for eastern Pacific species and for L. sarmentosa-L. capverdensis. Our results also revealed high inter-specific ersity among eastern Atlantic and South African species, highlighting a potential role of the geographical ersification processes and geological events occurring during the last 30Ma in the Atlantic on the evolutionary history of these organisms.
The curious case of Gazella arabica
Publisher: Springer Science and Business Media LLC
Date: 04-2012
Systematics of ‘lithistid’ tetractinellid demosponges from the Tropical Western Atlantic – implications for phylodiversity and bathymetric distribution
Publisher: PeerJ
Date: 22-04-2019
DOI: 10.7287/PEERJ.PREPRINTS.27673V1
Abstract: Background: Among all present demosponges, lithistids represent a polyphyletic group with exceptionally well preserved fossils dating back to the Cambrian. Knowledge of their recent ersity, particularly in the Tropical Western Atlantic Ocean (TWA) where they are common in deep waters, is scarce making any comparison between present and past major ‘lithistid’ faunas difficult. In addition, the lack of sufficient molecular and morphological data h er any predictions on phylogenetic relationships or phylo ersity from this region. The Harbor Branch Oceanographic Institute (HBOI, Fort Pierce, Florida) holds the largest collection of TWA lithistid sponges worldwide, however, the majority remain to be taxonomically identified and revised. Methods/Principal Findings: In this study we provide sequences of 249 lithistid demosponges using two independent molecular markers (28S rDNA (C1-D2) and cox1 mtDNA). In addition, a morphological documentation of 70 lithistid specimens is provided in the database of the Sponge Barcoding Project (SBP). This integrated dataset represents the largest and most comprehensive of the TWA lithistids to date. The phylogenetic ersity of ‘lithistid’ demosponges in the Bahamas and Jamaica are high in comparison to other TWA regions Theonellidae and Corallistidae dominate the fauna, while Neopeltidae and Macandrewiidae are rare. A new tetractinellid suborder, one new genus and several new species are recognized and the Pacific ‘lithistid’ genera, Herengeria and Awhiowhio , are reported from the TWA for the first time. The higher-taxa relationships of desma-bearing tetractinellids are discussed and topics for revision suggested. Conclusion: This first integrative approach of TWA ‘lithistid’ demosponges contributes to a better understanding of their phylogenetic affinities, ersity and bathymetric distribution patterns within the TWA. As in the Pacific, the TWA ‘lithistid’ demosponges dominate deep-water habitats. Deeper taxonomic investigations will undoubtedly contribute to a better comparison between present major ‘lithistid’ faunas and their fossil record in the Mesozoic.
Comparative proteomics of octocoral and scleractinian skeletomes and the evolution of coral calcification
Publisher: Cold Spring Harbor Laboratory
Date: 30-12-2019
DOI: 10.1101/2019.12.30.891028
Abstract: Corals are ecosystem engineers of the coral reefs, one of the most bio erse but severely threatened marine ecosystems. The ability of corals to form the three dimensional structure of reefs depends on the precipitation of calcium carbonate under biologically control. However, the exact mechanisms underlying this biologically controlled biomineralization remain to be fully unelucidated, for ex le whether corals employ a different molecular machinery for the deposition of different calcium carbonate (CaCO 3 ) polymorphs (i.e., aragonite or calcite). Here we used tandem mass spectrometry (MS/MS) to compare skeletogenic proteins, i.e., the proteins occluded in the skeleton of three octocoral and one scleractinian species: Tubipora musica and Sinularia cf. cruciata , both forming calcite sclerites, the blue coral Heliopora coerulea with an aragonitic rigid skeleton, and the scleractinian aragonitic Montipora digitata . We observed extremely low overlap between aragonitic and calcitic species, while a core set of proteins is shared between octocorals producing calcite sclerites. However, the same carbonic anhydrase (CruCA4) is employed for the formation of skeletons of both polymorphs. Similarities could also be observed between octocorals and scleractinians, including the presence of a galaxin-like protein. Additionally, as in scleractinians, some octocoral skeletogenic proteins, such as acidic proteins and scleritin, appear to have been secondarily co-opted for calcification and likely derive from proteins playing different extracellular functions. In H. coerulea , co-option was characterized by aspartic acid-enrichment of proteins. This work represents the first attempt to identify the molecular basis underlying coral skeleton polymorph ersity, providing several new research targets and enabling both future functional and evolutionary studies aimed at elucidating the origin and evolution of biomineralization in corals.
Mineralization of the metre-long biosilica structures of glass sponges is templated on hydroxylated collagen
Publisher: Springer Science and Business Media LLC
Date: 23-11-2010
DOI: 10.1038/NCHEM.899
Abstract: The minerals involved in the formation of metazoan skeletons principally comprise glassy silica, calcium phosphate or carbonate. Because of their ancient heritage, glass sponges (Hexactinellida) may shed light on fundamental questions such as molecular evolution, the unique chemistry and formation of the first skeletal silica-based structures, and the origin of multicellular animals. We have studied anchoring spicules from the metre-long stalk of the glass rope sponge (Hyalonema sieboldi Porifera, Class Hexactinellida), which are remarkable for their size, durability, flexibility and optical properties. Using slow-alkali etching of biosilica, we isolated the organic fraction, which was revealed to be dominated by a hydroxylated fibrillar collagen that contains an unusual [Gly-3Hyp-4Hyp] motif. We speculate that this motif is predisposed for silica precipitation, and provides a novel template for biosilicification in nature.
Mitochondrial genomes of the freshwater sponges Spongilla lacustris and Ephydatia cf. muelleri
Publisher: Informa UK Limited
Date: 2016
Molecular phylogeny of glass sponges (Porifera, Hexactinellida): increased taxon sampling and inclusion of the mitochondrial protein-coding gene, cytochrome oxidase subunit I
Publisher: Springer Netherlands
Date: 2011
Staying well connected-Lithistid sponges on seamounts
Publisher: Cambridge University Press (CUP)
Date: 22-06-2016
DOI: 10.1017/S0025315415000831
Abstract: Three species of lithistid sponges, Neoaulaxinia zingiberadix, Isabella mirabilis and Neoschrammeniella fulvodesmus were collected from deep seamounts off New Caledonia to address questions about their population structure, gene flow and the relative contribution of sexual and asexual reproductive strategies to their populations. The sponges were tested by sequencing the ITS (internal transcribed spacer) and CO1 regions of their genomes. These rare and presumably ancient sponges have a distribution restricted to seamounts in the south-western Pacific. Deep seamounts represent geographically separated islands. Although the sponges could be expected to have sexual reproduction restricted to near neighbours due to low sexual dispersal opportunities via larvae, this study found surprisingly high levels of gene flow between the seamounts. Amongst the specimens of N. zingiberadix taken from two seamounts there was no population structure CO1 resulted in identical genotypes. For the population structure within N. fulvodesmus , as revealed by ITS, most of the variation was within each in idual from the six seamounts on which it occurred and CO1 revealed no difference between in iduals or seamounts. The third species I. mirabilis showed four genotypes based on CO1, which were distributed across all the seamounts. Indirect measures of different species showed a range of reproductive strategies from asexual to sexual, but with much higher connection between seamounts than previously thought. In idual seamounts did not show a separate population structure as one might expect from ‘islands’. The conclusion must be that these sponges have mechanisms to attain greater dispersal than previously thought.
First evidence of miniature transposable elements in sponges (Porifera)
Publisher: Springer Netherlands
Date: 2011
A hypercalcified sponge with soft relatives: Vaceletia is a keratose demosponge
Publisher: Elsevier BV
Date: 04-2008
A new species of crown-of-thorns sea star, Acanthaster benziei sp. nov. (Valvatida: Acanthasteridae), from the Red Sea
Publisher: Magnolia Press
Date: 17-11-2022
DOI: 10.11646/ZOOTAXA.5209.3.7
Abstract: A new species of crown-of-thorns sea star (CoTS), Acanthaster benziei sp. nov., is described based on four specimens collected from Saudi Arabia’s Red Sea coast where it inhabits coral reefs. Species delimitation from congeners in the species complex, i.e., Acanthaster planci, Acanthaster mauritiensis and Acanthaster cf. solaris, is primarily based on distinct and diagnostic mitochondrial DNA sequence regions. Species separation of Acanthaster benziei is additionally justified due to diagnostic morphological characters: fewer arms narrower and thinner spines fanned spine tips in primary and latero-oral spines a wider tip or tapering shape in circumoral spines and rhombus-shaped oral pedicellariae.
CO1 phylogenies in diploblasts and the 'Barcoding of Life' - Are we sequencing a suboptimal partition?
Publisher: Wiley
Date: 06-2006
Transcriptomic response of Cinachyrella cf. cavernosa sponges to spatial competition
Publisher: Wiley
Date: 16-09-2023
DOI: 10.1111/MEC.17122
Bottomless barrel-sponge species in the Indo-Pacific?
Publisher: Magnolia Press
Date: 06-07-2016
DOI: 10.11646/ZOOTAXA.4136.2.11
Abstract: The use of nuclear markers, in addition to traditional mitochondrial markers, helps to clarify hidden patterns of genetic structure in natural populations (Palumbi & Baker, 1994). This is particularly evident among demosponges that possess slow mitochondrial evolutionary rates compared to Bilateria, where nuclear intron markers can aid in the understanding of shallow level phylogenetic relationships (Shearer et al., 2002). Ideally, these nuclear markers (i) are evolutionary well-conserved across different lineages, (ii) produce licons holding a number of sites with sufficient variability to answer the relevant phylogenetic question, (iii) derive from single copy genes (see review in Zhang & Hewitt, 2003). A popular method to lify intron markers uses EPIC (Exon-Primed, Intron-Crossing) primers that anneal to the more conserved flanking exon regions and subsequently bridge the intron during lification (Palumbi & Baker, 1994).
Rossellid glass sponges (Porifera, Hexactinellida) from New Zealand waters, with description of one new genus and six new species
Publisher: Pensoft Publishers
Date: 17-09-2021
DOI: 10.3897/ZOOKEYS.1060.63307
Abstract: New Zealand’s surrounding deep waters have become known as a ersity hotspot for glass sponges (Porifera: Hexactinellida) in recent years, and description and collection efforts are continuing. Here we report on eight rossellids (Hexasterophora: Lyssacinosida: Rossellidae) collected during the 2017 RV Sonne cruise SO254 by ROV Kiel 6000 as part of Project PoribacNewZ of the University of Oldenburg, Germany. The material includes six species new to science, two of which are assigned to a so far undescribed genus we further re-describe two previously known species. The known extant rossellid ersity from the New Zealand region is thus almost doubled, from nine species in five genera to 17 species in eight genera. The specimens described here are only a small fraction of hexactinellids collected on cruise SO254. Unfortunately, the first author passed away while working on this collection, only being able to complete the nine descriptions reported here. The paper concludes with an obituary to him, the world-leading expert on glass sponge taxonomy who will be greatly missed.
CO I Barcoding Reveals New Clades and Radiation Patterns of Indo-Pacific Sponges of the Family Irciniidae (Demospongiae: Dictyoceratida)
Publisher: Public Library of Science (PLoS)
Date: 04-2010
ALG11 – A new variable DNA marker for sponge phylogeny: Comparison of phylogenetic performances with the 18S rDNA and the COI gene
Publisher: Elsevier BV
Date: 06-2012
DOI: 10.1016/J.YMPEV.2012.02.008
Abstract: Phylogenetic relationships within sponge classes are highly debated. The low phylogenetic signal observed with some current molecular data can be attributed to the use of few markers, usually slowly-evolving, such as the nuclear rDNA genes and the mitochondrial COI gene. In this study, we conducted a bioinformatics search for a new molecular marker. We sought a marker that (1) is likely to have no paralogs (2) evolves under a fast evolutionary rate (3) is part of a continuous exonic region and (4) is flanked by conserved regions. Our search suggested the nuclear ALG11 as a potential suitable marker. We next demonstrated that this marker can indeed be used for solving phylogenetic relationships within sponges. Specifically, we successfully lified the ALG11 gene from DNA s les of representatives from all four sponge classes as well as from several cnidarian classes. We also lified the 18S rDNA and the COI gene for these species. Finally, we analyzed the phylogenetic performance of ALG11 to solve sponge relationships compared to and in combination with the nuclear 18S rDNA and the COI mtDNA genes. Interestingly, the ALG11 marker seems to be superior to the widely-used COI marker. Our work thus indicates that the ALG11 marker is a relevant marker which can complement and corroborate the phylogenetic inferences observed with nuclear ribosomal genes. This marker is also expected to contribute to resolving evolutionary relationships of other apparently slow-evolving animal phyla, such as cnidarians.
Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny
Publisher: Cold Spring Harbor Laboratory
Date: 19-11-2021
DOI: 10.1101/2021.11.19.469253
Abstract: An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although datasets of several hundred thousand amino acids are nowadays routinely used to test phylogenetic hypotheses, key deep nodes in the metazoan tree remain unresolved: the root of animals, the root of Bilateria, and the monophyly of Deuterostomia. Instead of using the standard approach of amino acid datasets, we performed analyses of newly assembled genome gene content and morphological datasets to investigate these recalcitrant nodes in the phylogeny of animals. We explored extensively the choices for assembling the genome gene content dataset and model choices of morphological analyses. Our results are robust to these choices and provide additional insights into the early evolution of animals, they are consistent with sponges as the sister group of all the other animals, the worm-like bilaterian lineage Xenacoelomorpha as the sister group of the other Bilateria, and tentatively support monophyletic Deuterostomia.
A Soft Spot for Chemistry–Current Taxonomic and Evolutionary Implications of Sponge Secondary Metabolite Distribution
Publisher: MDPI AG
Date: 04-08-2021
DOI: 10.3390/MD19080448
Abstract: Marine sponges are the most prolific marine sources for discovery of novel bioactive compounds. Sponge secondary metabolites are sought-after for their potential in pharmaceutical applications, and in the past, they were also used as taxonomic markers alongside the difficult and homoplasy-prone sponge morphology for species delineation (chemotaxonomy). The understanding of phylogenetic distribution and distinctiveness of metabolites to sponge lineages is pivotal to reveal pathways and evolution of compound production in sponges. This benefits the discovery rate and yield of bioprospecting for novel marine natural products by identifying lineages with high potential of being new sources of valuable sponge compounds. In this review, we summarize the current biochemical data on sponges and compare the metabolite distribution against a sponge phylogeny. We assess compound specificity to lineages, potential convergences, and suitability as diagnostic phylogenetic markers. Our study finds compound distribution corroborating current (molecular) phylogenetic hypotheses, which include yet unaccepted polyphyly of several demosponge orders and families. Likewise, several compounds and compound groups display a high degree of lineage specificity, which suggests homologous biosynthetic pathways among their taxa, which identifies yet unstudied species of this lineage as promising bioprospecting targets.
A new thecideid genus and species (Brachiopoda, Recent) from submarine caves of Osprey Reef (Queensland Plateau, Coral Sea, Australia)
Publisher: Informa UK Limited
Date: 06-2003
DNA taxonomy of sponges - Progress and perspectives
Publisher: Cambridge University Press (CUP)
Date: 12-2007
DOI: 10.1017/S0025315407058274
Abstract: Sponges (Phylum Porifera) are among the most ancestral metazoans and are frequently difficult to identify, even by taxonomic experts, due to their lack of complex morphological characters. However, poriferans are highly erse, ecologically important and of significant importance to pharmaceutical and biomaterials industries. Therefore, means of unambiguous identification are urgently needed. A DNA taxonomic system, and in particular sponge DNA barcodes, will provide a set of indispensable tools to aid taxonomists and ecologists in the rapid identification of sponge species, which will enhance the discovery of drug-producing species. Here, we will argue for the implementation of a DNA supported taxonomic system and introduce the Sponge Barcoding Project.
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
Publisher: Public Library of Science (PLoS)
Date: 15-03-2011
Leucamide A: A New Cytotoxic Heptapeptide from the Australian Sponge Leucetta microraphis
Publisher: American Chemical Society (ACS)
Date: 17-06-2002
DOI: 10.1021/JO020058R
Abstract: Leucamide A (1), a bioactive cyclic heptapeptide containing a unique mixed 4,2-bisheterocycle tandem pair consisting of a methyloxazole and thiazole subunit was isolated together with the known compound BRS1 (2), from the dichloromethane extract of the Australian marine sponge Leucetta microraphis. The planar structure of leucamide A (1) was elucidated by employing spectroscopic techniques (NMR, MS, UV, and IR). Its absolute stereochemistry was established by chemical degradation, derivatization, and chiral GC[bond]MS analysis. A conformational analysis of 1 was made using MMFF. Leucamide A (1) was found to be moderately cytotoxic toward several tumor cell lines.
Phylogeography of western Pacific Leucetta 'chagosensis' (Porifera: Calcarea) from ribosomal DNA sequences: implications for population history and conservation of the Great Barrier Reef World Heritag
Publisher: Wiley
Date: 09-2002
DOI: 10.1046/J.1365-294X.2002.01570.X
Abstract: Leucetta 'chagosensis' is a widespread calcareous sponge, occurring in shaded habitats of Indo-Pacific coral reefs. In this study we explore relationships among 19 ribosomal DNA sequence types (the ITS1-5.8S-ITS2 region plus flanking gene sequences) found among 54 in iduals from 28 locations throughout the western Pacific, with focus on the Great Barrier Reef (GBR). Maximum parsimony analysis revealed phylogeographical structuring into four major clades (although not highly supported by bootstrap analysis) corresponding to the northern/central GBR with Guam and Taiwan, the southern GBR and subtropical regions south to Brisbane, Vanuatu and Indonesia. Subsequent nested clade analysis (NCA) confirmed this structure with a probability of > 95%. After NCA of geographical distances, a pattern of range expansion from the internal Indonesian clade was inferred at the total cladogram level, as the Indonesian clade was found to be the internal and therefore oldest clade. Two distinct clades were found on the GBR, which narrowly overlap geographically in a line approximately from the Whitsunday Islands to the northern Swain Reefs. At various clade levels, NCA inferred that the northern GBR clade was influenced by past fragmentation and contiguous range expansion events, presumably during/after sea level low stands in the Pleistocene, after which the northern GBR might have been recolonized from the Queensland Plateau in the Coral Sea. The southern GBR clade is most closely related to subtropical L. 'chagosensis', and we infer that the southern GBR probably was recolonized from there after sea level low stands, based on our NCA results and supported by oceanographic data. Our results have important implications for conservation and management of the GBR, as they highlight the importance of marginal transition zones in the generation and maintenance of species rich zones, such as the Great Barrier Reef World Heritage Area.
Transcriptional response of the calcification and stress response toolkits in an octocoral under heat and pH stress.
Publisher: Wiley
Date: 25-11-2022
DOI: 10.1111/MEC.16266
Abstract: Up to one-third of all described marine species inhabit coral reefs, but the future of these hyper erse ecosystems is insecure due to local and global threats, such as overfishing, eutrophication, ocean warming and acidification. Although these impacts are expected to have a net detrimental effect on reefs, it has been shown that some organisms such as octocorals may remain unaffected, or benefit from, anthropogenically induced environmental change, and may replace stony corals in future reefs. Despite their potential importance in future shallow-water coastal environments, the molecular mechanisms leading to the resilience to anthropogenically induced stress observed in octocorals remain unknown. Here, we use manipulative experiments, proteomics and transcriptomics to show that the molecular toolkit used by Pinnigorgia flava, a common Indo-Pacific gorgonian octocoral, to deposit its calcium carbonate skeleton is resilient to heat and seawater acidification stress. Sublethal heat stress triggered a stress response in P. flava but did not affect the expression of 27 transcripts encoding skeletal organic matrix (SOM) proteins. Exposure to seawater acidification did not cause a stress response but triggered the downregulation of many transcripts, including an osteonidogen homologue present in the SOM. The observed transcriptional decoupling of the skeletogenic and stress-response toolkits provides insights into the mechanisms of resilience to anthropogenically driven environmental change observed in octocorals.
Systematics and spicule evolution in dictyonal sponges (Hexactinellida: Sceptrulophora) with description of two new species
Publisher: Oxford University Press (OUP)
Date: 25-11-2011
Molecular phylogeny of Abyssocladia (Cladorhizidae: Poecilosclerida) and Phelloderma (Phellodermidae: Poecilosclerida) suggests a diversification of chelae microscleres in cladorhizid sp
Publisher: Wiley
Date: 17-08-2012
Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny
Publisher: Public Library of Science (PLoS)
Date: 23-03-2023
DOI: 10.1371/JOURNAL.PONE.0282444
Abstract: An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although datasets of several hundred thousand amino acids are nowadays routinely used to test phylogenetic hypotheses, key deep nodes in the metazoan tree remain unresolved: the root of animals, the root of Bilateria, and the monophyly of Deuterostomia. Instead of using the standard approach of amino acid datasets, we performed analyses of newly assembled genome gene content and morphological datasets to investigate these recalcitrant nodes in the phylogeny of animals. We explored extensively the choices for assembling the genome gene content dataset and model choices of morphological analyses. Our results are robust to these choices and provide additional insights into the early evolution of animals, they are consistent with sponges as the sister group of all the other animals, the worm-like bilaterian lineage Xenacoelomorpha as the sister group of the other Bilateria, and tentatively support monophyletic Deuterostomia.
Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals
Publisher: Elsevier BV
Date: 12-2017
DOI: 10.1016/J.CUB.2017.11.008
Abstract: The relationships at the root of the animal tree have proven difficult to resolve, with the current debate focusing on whether sponges (phylum Porifera) or comb jellies (phylum Ctenophora) are the sister group of all other animals [1-5]. The choice of evolutionary models seems to be at the core of the problem because Porifera tends to emerge as the sister group of all other animals ("Porifera-sister") when site-specific amino acid differences are modeled (e.g., [6, 7]), whereas Ctenophora emerges as the sister group of all other animals ("Ctenophora-sister") when they are ignored (e.g., [8-11]). We show that two key phylogenomic datasets that previously supported Ctenophora-sister [10, 12] display strong heterogeneity in amino acid composition across sites and taxa and that no routinely used evolutionary model can adequately describe both forms of heterogeneity. We show that data-recoding methods [13-15] reduce compositional heterogeneity in these datasets and that models accommodating site-specific amino acid preferences can better describe the recoded datasets. Increased model adequacy is associated with significant topological changes in support of Porifera-sister. Because adequate modeling of the evolutionary process that generated the data is fundamental to recovering an accurate phylogeny [16-20], our results strongly support sponges as the sister group of all other animals and provide further evidence that Ctenophora-sister represents a tree reconstruction artifact. VIDEO ABSTRACT.
High germline mutation rates but not extreme population size outbreaks influence genetic diversity in crown-of-thorns sea stars
Publisher: Cold Spring Harbor Laboratory
Date: 30-06-2023
DOI: 10.1101/2023.06.28.546961
Abstract: Lewontin’s paradox, the observation that levels of genetic ersity (π) among animals do not scale linearly with variation in census population sizes ( N c ), is an evolutionary conundrum, where the most extreme mismatches between π and N c are found for highly abundant marine invertebrates. Yet, whether new mutations influence π relative to extrinsic processes remains unknown for most taxa. Here, we provide the first direct germline mutation rate ( μ ) estimate for a marine invertebrate, using high-coverage (60x) whole-genome sequencing of wild-caught Acanthaster cf. solaris crown-of-thorns sea stars (Echinodermata). We also provide empirical estimates of adult N c in Australia’s Great Barrier Reef to jointly examine the determinants of π. Based on direct observations of 63 de novo mutations across 14 parent-offspring trios, the A. cf. solaris mean μ was 9.13 x 10 -09 mutations per-site per-generation (95% CI: 6.51 x 10 -09 to 1.18 x 10 -08 ). This value exceeds estimates for other invertebrates, showing greater concordance with reported vertebrate germline mutation rates. Lower-than-expected N e (∼70,000-180,000) and low N e / N c values (0.0047-0.048) indicated significant genetic drift and weak influences of contemporary population outbreaks on long-term π. Our findings of elevated μ and low N e in A. cf. solaris may help explain high mutational loads and extreme polymorphism levels observed in some marine invertebrate taxa and are consistent with μ evolving in response to N e (drift-barrier hypothesis). This study advances our understanding of the processes controlling levels of natural genetic variation and provides new data valuable for further testing hypotheses about mutation rate evolution across animal phyla.
Keratose sponge MuseOMICS: setting reference points in dictyoceratid demosponge phylogeny
Publisher: Magnolia Press
Date: 12-10-2022
Poriferan survivin exhibits a conserved regulatory role in the interconnected pathways of cell cycle and apoptosis
Publisher: Springer Science and Business Media LLC
Date: 23-07-2010
DOI: 10.1038/CDD.2010.87
A taxogenomics approach uncovers a new genus in the phylum Placozoa
Publisher: Cold Spring Harbor Laboratory
Date: 12-10-2017
DOI: 10.1101/202119
Abstract: The Placozoa [1] is a monotypic phylum of non-bilaterian marine animals. Its only species, Trichoplax adhaerens , was described in 1883 [2], Despite the worldwide distribution of placozoans [3–6], morphological differences are lacking among isolates from different geographic areas and, consequently, no other species in this phylum has been described and accepted for more than 130 years. However, recent single-gene studies on the genetic ersity of this “species” have revealed deeply ergent lineages of, as yet, undefined taxonomic ranks [3,5,6], Since single genes are not considered sufficient to define species [7], a whole nuclear genome comparison appears the most appropriate approach to determine relationships between placozoan lineages. Such a “taxogenomics” approach can help discover and diagnose potential additional species and, therefore, develop a much-needed, more robust, taxonomic framework for this phylum. To achieve this we sequenced the genome of a placozoan lineage isolated from Hong Kong (lineage H13), which is distantly related to T. adhaerens [6]. The 87 megabase genome assembly contains 12,010 genes. Comparison to the T. adhaerens genome [8] identified an average protein distance of 24.4% in more than 2,700 screened one-to-one orthologs, similar to levels observed between the chordate classes mammals and birds. Genome rearrangements are commonplace and % of genes are not collinear (i.e. they are not in the same order in the two genomes). Finally, a multi-gene distance comparison with other non-bilaterian phyla indicate genus level differences to T. adhaerens . These data highlight the large genomic ersity within the Placozoa and justifies the designation of lineage HI3 as a new species, Xxxxxxxxx yyyyyyyyyyyyy 1 gen. et spaec. nov., now the second described placozoan species and the first in a new genus. Phylogenomic analyses furthermore supports a robust placement of the Placozoa as sister to a cnidarian-bilaterian clade.
The sterols of calcareous sponges (Calcarea, Porifera)
Publisher: Elsevier BV
Date: 11-2008
DOI: 10.1016/J.CHEMPHYSLIP.2008.07.001
Abstract: Sponges are sessile suspension-feeding organisms whose internal phylogenetic relationships are still the subject of intense debate. Sterols may have the potential to be used as independent markers to test phylogenetic hypotheses. Twenty representative specimens of calcareous sponges (class Calcarea, phylum Porifera) with a broad coverage within both subclasses Calcinea and Calcaronea were analysed for their sterol content. Two major pseudohomologous series were found, accompanied by some additional sterols. The first series encompassing conventional C(27) to C(29)Delta(5,7,22) sterols represented the major sterols, with ergosterol (ergosta-5,7,22-trien-3beta-ol, C(28)Delta(5,7,22)) being most prominent in many species. The second series consisted of unusual C(27) to C(29)Delta(5,7,9(11),22) sterols. Cholesterol occurred sporadically, mostly in trace amounts. The sterol patterns did not resolve intraclass phylogenetic relationships, namely the distinction between the subclasses, Calcinea and Calcaronea. This pointed towards major calcarean lipid traits being established prior to the separation of subclasses. Furthermore, calcarean sterol patterns clearly differ from those found in Hexactinellida, whereas partial overlap occurred with some Demospongiae. Hence, sterols only partly reflect the phylogenetic separation of Calcarea from both of the other poriferan classes that was proposed by recent molecular work and fatty acid analyses.
Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding
Publisher: Springer Science and Business Media LLC
Date: 20-03-2017
Phylogenomics Revives Traditional Views on Deep Animal Relationships
Publisher: Elsevier BV
Date: 04-2009
DOI: 10.1016/J.CUB.2009.02.052
Abstract: The origin of many of the defining features of animal body plans, such as symmetry, nervous system, and the mesoderm, remains shrouded in mystery because of major uncertainty regarding the emergence order of the early branching taxa: the sponge groups, ctenophores, placozoans, cnidarians, and bilaterians. The "phylogenomic" approach [1] has recently provided a robust picture for intrabilaterian relationships [2, 3] but not yet for more early branching metazoan clades. We have assembled a comprehensive 128 gene data set including newly generated sequence data from ctenophores, cnidarians, and all four main sponge groups. The resulting phylogeny yields two significant conclusions reviving old views that have been challenged in the molecular era: (1) that the sponges (Porifera) are monophyletic and not paraphyletic as repeatedly proposed [4-9], thus undermining the idea that ancestral metazoans had a sponge-like body plan (2) that the most likely position for the ctenophores is together with the cnidarians in a "coelenterate" clade. The Porifera and the Placozoa branch basally with respect to a moderately supported "eumetazoan" clade containing the three taxa with nervous system and muscle cells (Cnidaria, Ctenophora, and Bilateria). This new phylogeny provides a stimulating framework for exploring the important changes that shaped the body plans of the early erging phyla.
Microbial diversity in the coralline sponge Vaceletia crypta
Publisher: Springer Science and Business Media LLC
Date: 30-01-2013
DOI: 10.1007/S10482-013-9884-6
Abstract: Coralline sponges of the genus Vaceletia are regarded as 'living fossils', the only recent members of the so-called 'sphinctozoan-type' sponges that contributed to reef-building during the Palaeozoic and Mesozoic eras. Vaceletia species were thought to be extinct until the discovery of Vaceletia crypta in the 1970s. Here, we used molecular methods to provide first insights into the microbial ersity of these coralline sponges. Both denaturing gradient gel electrophoresis (DGGE) analyses of 19 Vaceletia specimens and the analysis of 427 clones from a bacterial 16S rRNA gene clone library of a specimen of V. crypta from the Great Barrier Reef (Australia) revealed high ersity and a complex composition with a relatively uniform phylogenetic distribution. Only a single archaeal 16S rRNA phylotype was recovered. The most abundant bacteria were the Chloroflexi (35 %). Of the microbial community, 58 % consisted of the Gammaproteobacteria, Gemmatimonadetes, Actinobacteria, Nitrospira, Deltaproteobacteria, Deferribacteres and Acidobacteria, with nearly equal representation. Less abundant members of the microbial community belonged to the Alphaproteobacteria (3 %), as well as to the Poribacteria, Betaproteobacteria, Cyanobacteria, Spirochaetes, Bacteroidetes, Deinococcus-Thermus and Archaea (all together 4 %). Of the established 96 OTUs, 88 % were closely related to other sponge-derived sequences and thereof 71 OTUs fell into sponge- or sponge-coral specific clusters, which underscores that the "living fossil" coralline sponge Vaceletia shares features of its microbial community with other sponges. The DGGE cluster analysis indicated distinct microbial communities in the different growth forms (solitary and colonial) of Vaceletia species.
Analysis of the Proteinaceous Components of the Organic Matrix of Calcitic Sclerites from the Soft Coral Sinularia sp.
Publisher: Public Library of Science (PLoS)
Date: 14-03-2013
Systematic relationships of five newly sequenced cervid species
Publisher: PeerJ
Date: 04-08-2016
DOI: 10.7717/PEERJ.2307
Abstract: Cervid phylogenetics has been puzzling researchers for over 150 years. In recent decades, molecular systematics has provided new input for both the support and revision of the previous results from comparative anatomy but has led to only partial consensus. Despite all of the efforts to reach taxon-wide species s ling over the last two decades, a number of cervid species still lack molecular data because they are difficult to access in the wild. By extracting ancient DNA from museum specimens, in this study, we obtained partial mitochondrial cytochrome b gene sequences for Mazama bricenii , Mazama chunyi , Muntiacus atherodes , Pudu mephistophiles , and Rusa marianna , including three holotypes. These new sequences were used to enrich the existing mitochondrial DNA alignments and yielded the most taxonomically complete data set for cervids to date. Phylogenetic analyses provide new insights into the evolutionary history of these five species. However, systematic uncertainties within Muntiacus persist and resolving phylogenetic relationships within Pudu and Mazama remain challenging.
Correction: Diversity in a Cold Hot-Spot: DNA-Barcoding Reveals Patterns of Evolution among Antarctic Demosponges (Class Demospongiae, Phylum Porifera)
Publisher: Public Library of Science (PLoS)
Date: 14-07-2015
Molecular paleobiology of early-branching animals: integrating DNA and fossils elucidates the evolutionary history of hexactinellid sponges
Publisher: No publisher found
Date: 2013
DOI: 10.5061/DRYAD.SM01B
Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri
Publisher: Springer Science and Business Media LLC
Date: 27-07-2020
DOI: 10.1038/S41467-020-17397-W
Abstract: The genomes of non-bilaterian metazoans are key to understanding the molecular basis of early animal evolution. However, a full comprehension of how animal-specific traits, such as nervous systems, arose is hindered by the scarcity and fragmented nature of genomes from key taxa, such as Porifera. Ephydatia muelleri is a freshwater sponge found across the northern hemisphere. Here, we present its 326 Mb genome, assembled to high contiguity (N50: 9.88 Mb) with 23 chromosomes on 24 scaffolds. Our analyses reveal a metazoan-typical genome architecture, with highly shared synteny across Metazoa, and suggest that adaptation to the extreme temperatures and conditions found in freshwater often involves gene duplication. The pancontinental distribution and ready laboratory culture of E. muelleri make this a highly practical model system which, with RNAseq, DNA methylation and bacterial licon data spanning its development and range, allows exploration of genomic changes both within sponges and in early animal evolution.
Spicule formation in calcareous sponges: Coordinated expression of biomineralization genes and spicule-type specific genes
Publisher: Springer Science and Business Media LLC
Date: 13-04-2017
DOI: 10.1038/SREP45658
Abstract: The ability to form mineral structures under biological control is widespread among animals. In several species, specific proteins have been shown to be involved in biomineralization, but it is uncertain how they influence the shape of the growing biomineral and the resulting skeleton. Calcareous sponges are the only sponges that form calcitic spicules, which, based on the number of rays (actines) are distinguished in diactines, triactines and tetractines. Each actine is formed by only two cells, called sclerocytes. Little is known about biomineralization proteins in calcareous sponges, other than that specific carbonic anhydrases (CAs) have been identified, and that uncharacterized Asx-rich proteins have been isolated from calcitic spicules. By RNA-Seq and RNA in situ hybridization (ISH), we identified five additional biomineralization genes in Sycon ciliatum: two bicarbonate transporters (BCTs) and three Asx-rich extracellular matrix proteins (ARPs). We show that these biomineralization genes are expressed in a coordinated pattern during spicule formation. Furthermore, two of the ARPs are spicule-type specific for triactines and tetractines (ARP1 or SciTriactinin ) or diactines (ARP2 or SciDiactinin ). Our results suggest that spicule formation is controlled by defined temporal and spatial expression of spicule-type specific sets of biomineralization genes.
Short-term exposure to high-water temperature causes a shift in the microbiome of the common aquarium sponge Lendenfeldia chondrodes
Publisher: Cold Spring Harbor Laboratory
Date: 10-01-2020
DOI: 10.1101/2020.01.10.901363
Abstract: Marine sponges harbor erse microbiomes that contribute to their energetic and metabolic needs. Although numerous studies on sponge microbial ersity exist, relatively few focused on sponge microbial community changes under different sources of environmental stress. In this study, we assess the impact of elevated seawater temperature on the microbiome of cultured Lendenfeldia chondrodes , a coral reef sponge commonly found in marine aquaria. Lendenfeldia chondrodes exhibits high thermal tolerance showing no evidence of tissue damage or bleaching at 5 °C above control water temperature (26 °C). High-throughput sequencing of the bacterial 16S rRNA V4 region revealed a response of the microbiome of L. chondrodes to short-term exposure to elevated seawater temperature. Shifts in abundance and richness of the dominant bacterial phyla found in the microbiome of this species, namely Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes, characterized this response. The observed resilience of L. chondrodes and the responsiveness of its microbiome to short-term increases in seawater temperature suggest that this holobiont may be capable of acclimating to anthropogenic-driven sublethal environmental stress via a re-accommodation of its associated bacterial community. This sheds a new light on the potential for resilience of some sponges to increasing surface seawater temperatures and associated projected regime shifts in coral reefs.
Molecular biodiversity of Red Sea demosponges
Publisher: Elsevier BV
Date: 04-2016
DOI: 10.1016/J.MARPOLBUL.2015.12.004
Abstract: Sponges are important constituents of coral reef ecosystems, including those around the Arabian Peninsula. Despite their importance, our knowledge on demosponge ersity in this area is insufficient to recognize, for ex le, faunal changes caused by anthropogenic disturbances. We here report the first assessment of demosponge molecular bio ersity from Arabia, with focus on the Saudi Arabian Red Sea, based on mitochondrial and nuclear ribosomal molecular markers gathered in the framework of the Sponge Barcoding Project. We use a rapid molecular screening approach on Arabian demosponge collections and analyze results in comparison against published material in terms of bio ersity. We use a variable region of 28S rDNA, applied for the first time in the assessment of demosponge molecular ersity. Our data constitutes a solid foundation for a future more comprehensive understanding of sponge bio ersity of the Red Sea and adjacent waters.
New insights into the vertebral Hox code of archosaurs
Publisher: Wiley
Date: 09-2015
DOI: 10.1111/EDE.12136
Abstract: Variation in axial formulae (i.e., number and identity of vertebrae) is an important feature in the evolution of vertebrates. Vertebrae at different axial positions exhibit a region-specific morphology. Key determinants for the establishment of particular vertebral shapes are the highly conserved Hox genes. Here, we analyzed Hox gene expression in the presacral vertebral column in the Nile crocodile in order to complement and extend a previous examination in the alligator and thus establish a Hox code for the axial skeleton of crocodilians in general. The newly determined expression of HoxA-4, C-5, B-7, and B-8 all revealed a crocodilian-specific pattern. HoxA-4 and HoxC-5 characterize cervical morphologies and the latter furthermore is associated with the position of the forelimb relative to the axial skeleton. HoxB-7 and HoxB-8 map exclusively to the dorsal vertebral region. The resulting expression patterns of these two Hox genes is the first description of their exact expression in the archosaurian embryo. Our comparative analyses of the Hox code in several amniote taxa provide new evidence that evolutionary differences in the axial skeleton correspond to changes in Hox gene expression domains. We detect two general processes: (i) expansion of a Hox gene's expression domain as well as (ii) a shift of gene expression. We infer that the ancestral archosaur Hox code may have resembled that of the crocodile. In association with the evolution of morphological traits, it may have been modified to patterns that can be observed in birds.
Anion inhibition studies of an α-carbonic anhydrase from the living fossil Astrosclera willeyana
Publisher: Elsevier BV
Date: 02-2012
DOI: 10.1016/J.BMCL.2011.12.085
Abstract: An α-carbonic anhydrase (CA, EC 4.2.1.1) isolated from the living fossil sponge Astrosclera willeyana, Astrosclerin, was investigated for its inhibition profile with simple inorganic anions, complex anions and other small molecules known to interact with these zinc enzymes. Astrosclerin is a catalytically highly efficient enzyme, and is inhibited in the low micromolar range by sulfamide, sulfamic acid, phenylboronic acid and phenylarsonic acid, and in the submillimolar range by a variety of anions including fluoride, chloride, cyanate, thiocyanate, cyanide, hydrogen sulfide, bisulfate, stannate, perosmate, anadate, perrhenate, perruthenate, selenocyanide, trithiocarbonate, diethyldithiocarbamate and iminodisulfonate. Less efficient Astrosclerin inhibitors were sulfate, bromide, iodide, azide, bicarbonate, carbonate, tetraborate and perchlorate (K(I)s of 5.11-30.6mM) whereas tetrafluoroborate was not at all inhibitory. Because Astrosclerin is involved in calcification processes in vivo, its anion inhibition profile may be important for future studies designed to shed light on the physiologic functions of α-CAs in marine organisms.
Slime away: a simple CTAB-based high molecular weight DNA and RNA extraction protocol for "difficult" invertebrates (rev20200518) v1
Publisher: ZappyLab, Inc.
Date: 06-07-2021
DOI: 10.17504/PROTOCOLS.IO.BWCWPAXE
Abstract: Protocols for the extraction of nucleic acids of recalcitrant non-model invertebrates are lacking. Here we present an extraction protocol for the extraction of DNA and RNA from mucus-rich invertebrate species. We have successfully used the protocol for the extraction of high-molecular-weight DNA from cnidarians and poriferans and to recover high-quality RNA from s les impossible to extract with commercial methods.
Revision of the genus Fascaplysinopsis, the type species Fascaplysinopsis reticulata (Hentschel, 1912) (Porifera, Dictyoceratida, Thorectidae) and descriptions of two new genera and seven new species
Publisher: Magnolia Press
Date: 19-09-2023
Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA)
Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/IS16059
Abstract: The Global Invertebrate Genomics Alliance (GIGA), a collaborative network of erse scientists, marked its second anniversary with a workshop in Munich, Germany in 2015, where international attendees focused on discussing current progress, milestones and bioinformatics resources. The community determined the recruitment and training of talented researchers as one of the most pressing future needs and identified opportunities for network funding. GIGA also promotes future research efforts to prioritise taxonomic ersity and create new synergies. Here, we announce the generation of a central and simple data repository portal with a wide coverage of available sequence data, via the compagen platform, in parallel with more focused and specialised organism databases to globally advance invertebrate genomics. This article serves the objectives of GIGA by disseminating current progress and future prospects in the science of invertebrate genomics with the aim of promotion and facilitation of interdisciplinary and international research.
Phylogenetic Analyses Under Secondary Structure-Specific Substitution Models Outperform Traditional Approaches: Case Studies with Diploblast LSU
Publisher: Springer Science and Business Media LLC
Date: 24-04-2007
DOI: 10.1007/S00239-006-0146-3
Abstract: Many rDNA molecular phylogenetic studies result in trees that are incongruent to either alternative gene tree reconstructions and/or morphological assumptions. One reason for this outcome might be the application of suboptimal phylogenetic substitution models. While the most commonly implemented models describe the evolution of independently evolving characters fairly well, they do not account for character dependencies such as rRNA strands that form a helix in the ribosome. Such nonindependent sites require the use of models that take into account the coevolution of the complete nucleotide pair (doublet). We analyzed 28S rDNA (LSU) demosponge phylogenies using a "doublet" model for pairing sites (rRNA-helices) and compared our findings with the results of "standard" approaches using Bayes factors. We demonstrate that paired and unpaired sites of the same gene result in different reconstructions and that usage of a doublet model leads to more reliable demosponge trees. We show the influence of more sophisticated models on phylogenetic reconstructions of early-branching metazoans and the phylogenetic relationships of demosponge orders.
Mitochondrial Diversity of Early-Branching Metazoa Is Revealed by the Complete mt Genome of a Haplosclerid Demosponge
Publisher: Oxford University Press (OUP)
Date: 19-10-2006
Abstract: The first mitochondrial (mt) genomes of demosponges have recently been sequenced and appear to be markedly different from published eumetazoan mt genomes. Here we show that the mt genome of the haplosclerid demosponge Amphimedon queenslandica has features that it shares with both demosponges and eumetazoans. Although the A. queenslandica mt genome has typical demosponge features, including size, long noncoding regions, and bacterialike rRNA genes, it lacks atp9, which is found in the other demosponges sequenced to date. We found strong evidence of a recent transposon-mediated transfer of atp9 to the nuclear genome. In addition, A. queenslandica bears an incomplete tRNA set, unusual amino acid deletion patterns, and a putative control region. Furthermore, the arrangement of mt rRNA genes differs from that of other demosponges. These genes evolve at significantly higher rates than observed in other demosponges, similar to previously observed nuclear rRNA gene rates in other haplosclerid demosponges.
Persistent Gaps of Knowledge for Naming and Distinguishing Multiple Species of Crown-of-Thorns-Seastar in the Acanthaster planci Species Complex
Publisher: MDPI AG
Date: 12-05-2017
DOI: 10.3390/D9020022
A comprehensive approach towards the systematics of Cervidae
Publisher: PeerJ
Date: 28-03-2019
DOI: 10.7287/PEERJ.PREPRINTS.27618V1
Abstract: Systematic relationships of cervids have been controversial for decades. Despite new input from molecular systematics, consensus could only be partially reached. The initial, gross (sub)classification based on morphology and comparative anatomy was mostly supported by molecular data. The rich fossil record of cervids has never been extensively tested in phylogenetic frameworks concerning potential systematic relationships of fossil cervids to extant cervids. The aim of this work was to investigate the systematic relationships of extant and fossil cervids using molecular and morphological characters and make implications about their evolutionary history based on the phylogenetic reconstructions. To achieve these objectives, molecular data were compiled consisting of five nuclear markers and the complete mitochondrial genome of 50 extant and one fossil cervid species. Several analyses using different data partitions, taxon s ling, partitioning schemes, and optimality criteria were undertaken. In addition, the most extensive morphological character matrix for such a broad cervid taxon s ling was compiled including 168 cranial and dental characters of 41 extant and 29 fossil cervid species. The morphological and molecular data were analysed in a combined approach and other comprehensive phylogenetic reconstructions. The results showed that most of the Miocene cervids were more closely related to each other than to any other cervids. They were often positioned between the outgroup and all other cervids or as the sister taxon to Muntiacini. Two Miocene cervids were frequently placed within Muntiacini. Plio- and Pleistocene cervids could often be affiliated to Cervini, Odocoileini or Capreolini. The phylogenetic analyses of this work provide new insights into the evolutionary history of cervids. Several fossil cervids could be successfully related to living representatives, confirming previously assumed affiliations based on comparative morphology and introducing new hypotheses. New systematic relationships were observed, some uncertainties persisted and resolving systematics within certain taxa remained challenging.
A chemical view of the most ancient metazoa – biomarker chemotaxonomy of hexactinellid sponges
Publisher: Springer Science and Business Media LLC
Date: 10-01-2002
DOI: 10.1007/S00114-001-0284-9
Abstract: Hexactinellid sponges are often considered to be the most ancient metazoans. Lipid biomarkers from 23 species were studied for information on their phylogenetic properties, particularly their disputed relation to the two other sponge classes (Demospongiae, Calcarea). The most prominent lipid compounds in the Hexactinellida comprise C28 to C32 polyenoic fatty acids. Their structures parallel the unique patterns found in demosponge membrane fatty acids ('demospongic acids') and strongly support a close phylogenetic association of the Demospongiae and the Hexactinellida. Both taxa also show unusual mid-chain methylated fatty acids (C15-C25) and irregular C25- and C40-isoprenoid hydrocarbons, tracers for specific eubacteria and Archaea, respectively. These biomarkers indicate a similar, highly conservative symbiont community, although some shift in the abundance of the associated microbiota was observed. The lack of these features in calcareous sponges further contradicts the still common view that Calcarea and Demospongiae are more closely related to each other than either is to the Hexactinellida.
Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria)
Publisher: Wiley
Date: 12-2002
DOI: 10.1046/J.1365-294X.2002.01652.X
Abstract: Mitochondrial genes have been used extensively in population genetic and phylogeographical analyses, in part due to a high rate of nucleotide substitution in animal mitochondrial DNA (mtDNA). Nucleotide sequences of anthozoan mitochondrial genes, however, are virtually invariant among conspecifics, even at third codon positions of protein-coding sequences. Hence, mtDNA markers are of limited use for population-level studies in these organisms. Mitochondrial gene sequence ergence among anthozoan species is also low relative to that exhibited in other animals, although higher level relationships can be resolved with these markers. Substitution rates in anthozoan nuclear genes are much higher than in mitochondrial genes, whereas nuclear genes in other metazoans usually evolve more slowly than, or similar to, mitochondrial genes. Although several mechanisms accounting for a slow rate of sequence evolution have been proposed, there is not yet a definitive explanation for this observation. Slow evolution and unique characteristics may be common in primitive metazoans, suggesting that patterns of mtDNA evolution in these organisms differ from that in other animal systems.
The genome of the contractile demosponge Tethya wilhelma and the evolution of metazoan neural signalling pathways
Publisher: Cold Spring Harbor Laboratory
Date: 27-03-2017
DOI: 10.1101/120998
Abstract: Porifera are a erse animal phylum with species performing important ecological roles in aquatic ecosystems, and have become models for multicellularity and early-animal evolution. Demosponges form the largest class in sponges, but previous studies have relied on the only draft demosponge genome of Amphimedon queenslandica . Here we present the 125-megabase draft genome of a contractile laboratory demosponge Tethya wilhelma , sequenced to almost 150x coverage. We explore the genetic repertoire of transporters, receptors, and neurotransmitter metabolism across early-branching metazoans in the context of the evolution of these gene families. Presence of many genes is highly variable across animal groups, with many gene family expansions and losses. Three sponge classes show lineage-specific expansions of GABA-B receptors, far exceeding the gene number in vertebrates, while ctenophores appear to have secondarily lost most genes in the GABA pathway. Both GABA and glutamate receptors show lineage-specific domain rearrangements, making it difficult to trace the evolution of these gene families. Gene sets in the examined taxa suggest that nervous systems evolved independently at least twice and either changed function or were lost in sponges. Changes in gene content are consistent with the view that ctenophores and sponges are the earliest-branching metazoan lineages and provide additional support for the proposed clade of Placozoa/Cnidaria/Bilateria.
Low variation in partial cytochrome oxidase subunit I (COI) mitochondrial sequences in the coralline demosponge Astrosclera willeyana across the Indo-Pacific
Publisher: Springer Science and Business Media LLC
Date: 09-11-2005
Phylogeny and Evolution of Glass Sponges (Porifera, Hexactinellida)
Publisher: Oxford University Press (OUP)
Date: 06-2008
DOI: 10.1080/10635150802161088
Abstract: Reconstructing the phylogeny of sponges (Porifera) is one of the remaining challenges to resolve the metazoan Tree of Life and is a prerequisite for understanding early animal evolution. Molecular phylogenetic analyses for two of the three extant classes of the phylum, Demospongiae and Calcarea, are largely incongruent with traditional classifications, most likely because of a paucity of informative morphological characters and high levels of homoplasy. For the third class, Hexactinellida (glass sponges)--predominantly deep-sea inhabitants with unusual morphology and biology--we present the first molecular phylogeny, along with a cladistic analysis of morphological characters. We collected 18S, 28S, and mitochondrial 16S ribosomal DNA sequences of 34 glass sponge species from 27 genera, 9 families, and 3 orders and conducted partitioned Bayesian analyses using RNA secondary structure-specific substitution models (paired-sites models) for stem regions. Bayes factor comparisons of different paired-sites models against each other and conventional (independent-sites) models revealed a significantly better fit of the former but, contrary to previous predictions, the least parameter-rich of the tested paired-sites models provided the best fit to our data. In contrast to Demospongiae and Calcarea, our rDNA phylogeny agrees well with the traditional classification and a previously proposed phylogenetic system, which we ascribe to a more informative morphology in Hexactinellida. We find high support for a close relationship of glass sponges and Demospongiae sensu stricto, though the latter may be paraphyletic with respect to Hexactinellida. Homoscleromorpha appears to be the sister group of Calcarea. Contrary to most previous findings from rDNA, we recover Porifera as monophyletic, although support for this clade is low under paired-sites models.
Deep Phylogeny and Evolution of Sponges (Phylum Porifera)
Publisher: Elsevier
Date: 2012
Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies
Publisher: Elsevier BV
Date: 12-2004
DOI: 10.1016/J.YMPEV.2004.07.005
Abstract: The internal transcribed spacer regions (ITS1 and ITS2) of the tandemly repeated nuclear ribosomal DNA clusters are frequently used as markers for fine scale analyses in erse animals. In certain taxa, ITS is nearly exclusively used for population level or inter-specific studies, despite the frequent presence of ergent paralogs within in idual genomes that can be phylogenetically misleading. For the first time we survey erse marine sponges to determine the extent and phylogenetic implications of intragenomic polymorphisms (IGPs) exhibited at their ITS loci. We discover that the extent of IGP varies greatly between taxa (with most taxa exhibiting very few) and cannot be predicted by taxonomy. Furthermore, we demonstrate that ITS can be phylogenetically informative between species when moderate levels of IGPs are detected, but that ITS paralogy can interfere with population level studies. We caution against the routine use of ITS in phylogenetic studies of sponges without (1) screening for IGPs in specimens from every population s led (2) including all ergent paralogs in phylogenetic analyses (3) testing ITS data using other single-copy, unlinked loci (such as nuclear introns).
The Role of Homology and Orthology in the Phylogenomic Analysis of Metazoan Gene Content
Publisher: Oxford University Press (OUP)
Date: 28-01-2019
Abstract: Resolving the relationships of animals (Metazoa) is crucial to our understanding of the origin of key traits such as muscles, guts, and nerves. However, a broadly accepted metazoan consensus phylogeny has yet to emerge. In part, this is because the genomes of deeply erging and fast-evolving lineages may undergo significant gene turnover, reducing the number of orthologs shared with related phyla. This can limit the usefulness of traditional phylogenetic methods that rely on alignments of orthologous sequences. Phylogenetic analysis of gene content has the potential to circumvent this orthology requirement, with binary presence/absence of homologous gene families representing a source of phylogenetically informative characters. Applying binary substitution models to the gene content of 26 complete animal genomes, we demonstrate that patterns of gene conservation differ markedly depending on whether gene families are defined by orthology or homology, that is, whether paralogs are excluded or included. We conclude that the placement of some deeply erging lineages may exceed the limit of resolution afforded by the current methods based on comparisons of orthologous protein sequences, and novel approaches are required to fully capture the evolutionary signal from genes within genomes.
rRNA depletion for holobiont metatranscriptome profiling across demosponges
Publisher: Cold Spring Harbor Laboratory
Date: 14-08-2022
DOI: 10.1101/2022.08.12.503726
Abstract: The pervasive association of demosponges with erse bacterial communities has been a research topic since the late 1970s. Studies characterizing these bacterial communities have detected over 40 bacterial phyla associated with sponges and determined that sponge microbiomes differ from the bacterioplankton of the surrounding water and include sponges-specific bacterial associates. Despite the large body of information available on the ersity of the sponge microbiome, the molecular mechanisms used by sponges to interact with their bacterial symbionts and vice versa remain poorly understood. Yet, studying how sponges interact with their microbiomes is pivotal to understanding how these systems react to environmental changes and when these changes lead to a disruption of sponge-microbe associations. An important factor h ering the characterization of the sponge-microbiome molecular cross-talk mechanisms is the lack of broadly applicable molecular methods to, for instance, efficiently sequence meta-transcriptomes across a broad range of sponge species. To overcome this limitation, we implemented a hybrid-capture strategy capable of depleting both sponge and bacterial rRNA from total RNA extracts of highly ergent demosponges with microbiomes of different complexity. Our pan-demosponge rRNA depletion strategy allows for the efficient characterization of the metatranscriptome of erse demosponge holobionts and the simultaneous quantification of gene expression in both the host and its microbiome.
Exploring the mitochondrial response to oxidative DNA damage in octocorals
Publisher: PeerJ
Date: 02-2017
DOI: 10.7287/PEERJ.PREPRINTS.2770V1
Abstract: Mitochondrial response to oxidative stress is intricately related to cellular homeostasis due to the high susceptibility of the mitochondrial genome to oxidative damage. Octocoral mitogenomes possess a unique DNA repair gene, mtMutS, potentially capable of counteracting the effects of oxidative stress induced mtDNA damage. Despite this unique feature, the response of octocoral mitochondria to increased oxidative stress remains unexplored. Here we explore the response of the octocoral Sinularia cf. cruciata to elevated temperature and low-pH stress and its ability to reverse acute oxidative mtDNA damage caused by exogenous agents like hydrogen peroxide (H 2 O 2 ). The differential transcriptional response to these climate change-related stresses was recorded for two mtDNA-encoded genes and three stress biomarkers. Only HSP70 was significantly upregulated during thermal stress whereas significant reduction in the expression levels of HSP70 , GPX , and COI was observed along with an increased number of mtMutS transcripts during low-pH stress. Damage to mtDNA was evident, accompanied by changes in mtDNA copy number. Damage caused by H 2 O 2 toxicity was reversed within 5 hours and initial mtDNA copy number apparently influenced damage reversal. Our results indicate that different stress-specific resilience strategies are used by this octocoral species and its mitochondria to reverse oxidative stress and associated mtDNA damage. These experiments provide the first account on the response of octocoral mitochondria with its unique gene repertoire among animals to different stressors and highlight its potential role in conferring resilience to the host cells during different climate change scenarios.
Spatial variability of microbial communities of the coralline demosponge Astrosclera willeyana across the Indo-Pacific
Publisher: Inter-Research Science Center
Date: 24-02-2015
DOI: 10.3354/AME01732
Never Ending Analysis of a Century Old Evolutionary Debate: “Unringing” the Urmetazoon Bell
Publisher: Frontiers Media SA
Date: 04-02-2016
Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model
Publisher: Springer Science and Business Media LLC
Date: 18-07-2018
New cervid cytochrome b sequences, new conundrums in cervid systematics
Publisher: Springer Science and Business Media LLC
Date: 09-2016
Identification and first insights into the structure and biosynthesis of chitin from the freshwater sponge Spongilla lacustris
Publisher: Elsevier BV
Date: 09-2013
DOI: 10.1016/J.JSB.2013.06.015
Abstract: This work demonstrates that chitin is an important structural component within the skeletal fibers of the freshwater sponge Spongilla lacustris. Using a variety of analytical techniques ((13)C solid state NMR, FT-IR, Raman, NEXAFS, ESI-MS, Morgan-Elson assay and Calcofluor White Staining) we show that this sponge chitin is much closer to α-chitin, known to be present in other animals, than to β-chitin. Genetic analysis confirmed the presence of chitin synthases, which are described for the first time in a sponge. The presence of chitin in both marine (demosponges and hexactinellids) and freshwater sponges indicates that this important structural biopolymer was already present in their common ancestor.
Zootaxa 20 years: Phylum Porifera
Publisher: Magnolia Press
Date: 28-05-2021
DOI: 10.11646/ZOOTAXA.4979.1.8
Abstract: The peer-reviewed journal Zootaxa has accelerated the rate of sponge (Porifera) species discoveries in 289 peer-reviewed papers published between 2002 up until the end of 2020, describing 725 new species, six new subspecies, 27 new genera, four new subgenera, and 123 new species and genus names needed to resolve existing homonyms. Zootaxa has been the most prolific of all taxonomic journals in its contributions to describing new taxa of Porifera in modern times. This present article analyses these taxonomic contributions over the past 20 years of Zootaxa, including their trends and highlights pertaining to sponge publications.
Author response: The last common ancestor of animals lacked the HIF pathway and respired in low-oxygen environments
Publisher: eLife Sciences Publications, Ltd
Date: 27-11-2017
Correlation betweenHoxcode and vertebral morphology in archosaurs
Publisher: The Royal Society
Date: 07-07-2015
Abstract: The relationship between developmental genes and phenotypic variation is of central interest in evolutionary biology. An excellent ex le is the role of Hox genes in the anteroposterior regionalization of the vertebral column in vertebrates. Archosaurs (crocodiles, dinosaurs including birds) are highly variable both in vertebral morphology and number. Nevertheless, functionally equivalent Hox genes are active in the axial skeleton during embryonic development, indicating that the morphological variation across taxa is likely owing to modifications in the pattern of Hox gene expression. By using geometric morphometrics, we demonstrate a correlation between vertebral Hox code and quantifiable vertebral morphology in modern archosaurs, in which the boundaries between morphological subgroups of vertebrae can be linked to anterior Hox gene expression boundaries. Our findings reveal homologous units of cervical vertebrae in modern archosaurs, each with their specific Hox gene pattern, enabling us to trace these homologies in the extinct sauropodomorph dinosaurs, a group with highly variable vertebral counts. Based on the quantifiable vertebral morphology, this allows us to infer the underlying genetic mechanisms in vertebral evolution in fossils, which represents not only an important case study, but will lead to a better understanding of the origin of morphological disparity in recent archosaur vertebral columns.
Cloning, characterization and sulfonamide inhibition studies of an α-carbonic anhydrase from the living fossil sponge Astrosclera willeyana
Publisher: Elsevier BV
Date: 02-2012
DOI: 10.1016/J.BMC.2012.01.007
Abstract: The α-carbonic anhydrase (CA, EC 4.2.1.1) Astrosclerin-3 previously isolated from the living fossil sponge Astrosclera willeyana (Jackson et al., Science 2007, 316, 1893), was cloned, kinetically characterized and investigated for its inhibition properties with sulfonamides and sulfamates. Astrosclerin-3 has a high catalytic activity for the CO(2) hydration reaction to bicarbonate and protons (k(cat) of 9.0×10(5) s(-1) and k(cat)/K(m) of 1.1×10(8) M(-1) × s(-1)), and is inhibited by various aromatic/heterocyclic sulfonamides and sulfamates with inhibition constants in the range of 2.9 nM-8.85 μM. Astrosclerin, and the human isoform CA II, display similar kinetic properties and affinities for sulfonamide inhibitors, despite more than 550 million years of independent evolution. Because Astrosclerin-3 is involved in biocalcification, the inhibitors characterized here may be used to gain insights into such processes in other metazoans.
Molecular phylogeny and DNA barcoding of tropical eastern Pacific shallow-water gorgonian octocorals
Publisher: Springer Science and Business Media LLC
Date: 23-02-2014
Modified parallel strategies for preparation of heteroduplex plasmids for in vitro mismatch repair assays
Publisher: Elsevier BV
Date: 09-2018
Abstract: We present efficient and reproducible parallel strategies for preparing large quantities of pure heteroduplex plasmids containing defined mismatches. The strategies described involve the use of synthetic oligonucleotides, the commercially available pGEM-T plasmid, and nicking enzymes to prepare prerequisite ssDNA. Alternatively, bacterial packaging cell lines containing an engineered phagemid construct to produce ssDNA without the need of a helper phage were utilized, hence providing added flexibility and choice. These integrated approaches help to construct different mismatch substrates of choice in large quantities, thus enhancing the usability of mismatch repair assays and extending their range and accessibility to wider research groups.
Dating early animal evolution using phylogenomic data
Publisher: Springer Science and Business Media LLC
Date: 15-06-2017
DOI: 10.1038/S41598-017-03791-W
Abstract: Information about the geological timeframe during which animals radiated into their major subclades is crucial to understanding early animal ecology and evolution. Unfortunately, the pre-Cambrian fossil record is sparse and its interpretation controversial. Relaxed molecular-clock methods provide an alternative means of estimating the timing of cladogenesis deep in the metazoan tree of life. So far, thorough molecular clock studies focusing specifically on Metazoa as a whole have been based on relatively small datasets or incomplete representation of the main non-bilaterian lineages (such as sponges and ctenophores), which are fundamental for understanding early metazoan evolution. Here, we use a previously published phylogenomic dataset that includes a fair s ling of all relevant groups to estimate the timing of early animal evolution with Bayesian relaxed-clock methods. According to our results, all non-bilaterian phyla, as well as total-group Bilateria, evolved in an ancient radiation during a geologically relatively short time span, before the onset of long-term global glaciations (“Snowball Earth” ~720–635 Ma). Importantly, this result appears robust to alterations of a number of important analytical variables, such as models of among-lineage rate variation and sets of fossil calibrations used.
The Skeleton Forming Proteome of an Early Branching Metazoan: A Molecular Survey of the Biomineralization Components Employed by the Coralline Sponge Vaceletia Sp.
Publisher: Public Library of Science (PLoS)
Date: 04-11-2015
Molecular biodiversity of Iranian shallow water sponges
Publisher: Informa UK Limited
Date: 17-02-2020
Comparative genomics and the nature of placozoan species
Publisher: Public Library of Science (PLoS)
Date: 31-07-2018
Sponges as bioindicators for microparticulate pollutants
Publisher: Cold Spring Harbor Laboratory
Date: 28-05-2020
DOI: 10.1101/2020.05.26.116012
Abstract: Amongst other threats, the world’s oceans are faced with man-made pollution, including an increasing number of microparticulate pollutants. Sponges, aquatic filter-feeding animals, are able to incorporate fine foreign particles, and thus may be a potential bioindicator for microparticulate pollutants. To address this question, 15 coral reef demosponges s led around Bangka Island (North Sulawesi, Indonesia) were analyzed for the nature of their foreign particle content using traditional histological methods, advanced light microscopy, and Raman spectroscopy. S led sponges accumulated and embedded the very fine sediment fraction ( 200 µm), absent in the surrounding sand, in the ectosome (outer epithelia) and spongin fibers (skeletal elements), which was confirmed by two-photon microscopy. A total of 34 different particle types were identified, of which degraded man-made products, i.e., polystyrene, cotton, titanium dioxide and blue-pigmented particles, were incorporated by eight specimens at concentrations between 91 to 612 particle/g dry sponge tissue. As sponges can weigh several hundreds of grams, we conservatively extrapolate that sponges can incorporate on average 10,000 microparticulate pollutants in their tissue. The uptake of particles, however, appears independent of the material, which suggests that the fluctuation in material ratios is due to the spatial variation of surrounding microparticles. Therefore, sponges have a strong potential to biomonitor microparticulate pollutants, such as microplastics and other degraded industrial products.
Identification of an aquaculture poriferan “Pest with Potential” and its phylogenetic implications
Publisher: PeerJ
Date: 24-09-2018
DOI: 10.7717/PEERJ.5586
Abstract: Correct identification and classification of sponges is challenging due to ambiguous or misleading morphological features. A particular case is a blue keratose sponge occasionally referred to as the “Blue Photo Sponge” among aquarists, which appears frequently (and in several cases unintended) in private aquaria. This spicule-less species, occasionally specified as Collospongia auris Bergquist, Cambie & Kernan 1990, not only displays a high phenotypic plasticity in growth form and colour, it also proliferates in aquacultures under standard conditions unlike most other sponges. Therefore, this species is regarded as a pest for most aquarists. In turn, the ease of cultivation and propagation in aquacultures qualifies this species as a model organism for a wide array of scientific applications. For these purposes, correct identification and classification are indispensable. We reconstructed ribosomal gene trees and determined this species as Lendenfeldia chondrodes (De Laubenfels, 1954) (Phyllospongiinae), distant to Collospongia auris , and corroborated by skeletal features. Additionally, the resulting phylogeny corroborated major shortcomings of the current Phyllospongiinae classification—its consequences are discussed.
Precious coral and rock sponge gardens on the deep aphotic fore-reef of Osprey Reef (Coral Sea, Australia)
Publisher: Springer Science and Business Media LLC
Date: 31-07-2011
Volcanic ash supports a diverse bacterial community in a marine mesocosm
Publisher: Wiley
Date: 03-03-2017
DOI: 10.1111/GBI.12231
Beyond corals and fish: the effects of climate change on noncoral benthic invertebrates of tropical reefs
Publisher: Wiley
Date: 18-11-2008
TransPi—a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly
Publisher: Wiley
Date: 18-02-2022
Abstract: The use of RNA sequencing (RNA‐Seq) data and the generation of de novo transcriptome assemblies have been pivotal for studies in ecology and evolution. This is especially true for nonmodel organisms, where no genome information is available. In such organisms, studies of differential gene expression, DNA enrichment bait design and phylogenetics can all be accomplished with de novo transcriptome assemblies. Multiple tools are available for transcriptome assembly, but no single tool can provide the best assembly for all data sets. Therefore, a multi‐assembler approach, followed by a reduction step, is often sought to generate an improved representation of the assembly. To reduce errors in these complex analyses while at the same time attaining reproducibility and scalability, automated workflows have been essential in the analysis of RNA‐Seq data. However, most of these tools are designed for species where genome data are used as reference for the assembly process, limiting their use in nonmodel organisms. We present TransPi, a comprehensive pipeline for de novo transcriptome assembly, with minimum user input but without losing the ability of a thorough analysis. A combination of different model organisms, k‐mer sets, read lengths and read quantities was used for assessing the tool. Furthermore, a total of 49 nonmodel organisms, spanning different phyla, were also analysed. Compared to approaches using single assemblers only, TransPi produces higher BUSCO completeness percentages, and a concurrent significant reduction in duplication rates. TransPi is easy to configure and can be deployed seamlessly using Conda, Docker and Singularity.
First report on chitinous holdfast in sponges (Porifera)
Publisher: The Royal Society
Date: 07-07-2013
Abstract: A holdfast is a root- or basal plate-like structure of principal importance that anchors aquatic sessile organisms, including sponges, to hard substrates. There is to date little information about the nature and origin of sponges’ holdfasts in both marine and freshwater environments. This work, to our knowledge, demonstrates for the first time that chitin is an important structural component within holdfasts of the endemic freshwater demosponge Lubomirskia baicalensis . Using a variety of techniques (near-edge X-ray absorption fine structure, Raman, electrospray ionization mas spectrometry, Morgan–Elson assay and Calcofluor White staining), we show that chitin from the sponge holdfast is much closer to α-chitin than to β-chitin. Most of the three-dimensional fibrous skeleton of this sponge consists of spicule-containing proteinaceous spongin. Intriguingly, the chitinous holdfast is not spongin-based, and is ontogenetically the oldest part of the sponge body. Sequencing revealed the presence of four previously undescribed genes encoding chitin synthases in the L. baicalensis sponge. This discovery of chitin within freshwater sponge holdfasts highlights the novel and specific functions of this biopolymer within these ancient sessile invertebrates.
Deceptive Desmas: Molecular Phylogenetics Suggests a New Classification and Uncovers Convergent Evolution of Lithistid Demosponges
Publisher: Public Library of Science (PLoS)
Date: 07-01-2015
Lock, Stock and Two Different Barrels: Comparing the Genetic Composition of Morphotypes of the Indo-Pacific Sponge Xestospongia testudinaria
Publisher: Public Library of Science (PLoS)
Date: 12-09-2013
Deep genetic divergences among Indo-Pacific populations of the coral reef sponge Leucetta chagosensis (Leucettidae): Founder effects, vicariance, or both?
Publisher: Springer Science and Business Media LLC
Date: 2008
An evolutionary fast‐track to biocalcification
Publisher: Wiley
Date: 13-05-2010
DOI: 10.1111/J.1472-4669.2010.00236.X
Abstract: The ability to construct mineralized shells, spicules, spines and skeletons is thought to be a key factor that fuelled the expansion of multicellular animal life during the early Cambrian. The genes and molecular mechanisms that control the process of biomineralization in disparate phyla are gradually being revealed, and it is broadly recognized that an insoluble matrix of proteins, carbohydrates and other organic molecules are required for the initiation, regulation and inhibition of crystal growth. Here, we show that Astrosclera willeyana, a living representative of the now largely extinct stromatoporid sponges (a polyphyletic grade of poriferan bauplan), has apparently bypassed the requirement to evolve many of these mineral-regulating matrix proteins by using the degraded remains of bacteria to seed CaCO(3) crystal growth. Because stromatoporid sponges formed extensive reefs during the Paelozoic and Mesozoic eras (fulfilling the role that stony corals play in modern coral reefs), and fossil evidence suggests that the same process of bacterial skeleton formation occurred in these stromatoporid ancestors, we infer that some ancient reef ecosystems might have been founded on this microbial-metazoan relationship.
Mitochondrial DNA of Clathrina clathrus (Calcarea, Calcinea): Six Linear Chromosomes, Fragmented rRNAs, tRNA Editing, and a Novel Genetic Code
Publisher: Oxford University Press (OUP)
Date: 06-12-2012
Abstract: Sponges (phylum Porifera) are a large and ancient group of morphologically simple but ecologically important aquatic animals. Although their body plan and lifestyle are relatively uniform, sponges show extensive molecular and genetic ersity. In particular, mitochondrial genomes from three of the four previously studied classes of Porifera (Demospongiae, Hexactinellida, and Homoscleromorpha) have distinct gene contents, genome organizations, and evolutionary rates. Here, we report the mitochondrial genome of Clathrina clathrus (Calcinea, Clathrinidae), a representative of the fourth poriferan class, the Calcarea, which proves to be the most unusual. Clathrina clathrus mitochondrial DNA (mtDNA) consists of six linear chromosomes 7.6-9.4 kb in size and encodes at least 37 genes: 13 protein codings, 2 ribosomal RNAs (rRNAs), and 24 transfer RNAs (tRNAs). Protein genes include atp9, which has now been found in all major sponge lineages, but no atp8. Our analyses further reveal the presence of a novel genetic code that involves unique reassignments of the UAG codons from termination to tyrosine and of the CGN codons from arginine to glycine. Clathrina clathrus mitochondrial rRNAs are encoded in three (srRNA) and ≥6 (lrRNA) fragments distributed out of order and on several chromosomes. The encoded tRNAs contain multiple mismatches in the aminoacyl acceptor stems that are repaired posttranscriptionally by 3'-end RNA editing. Although our analysis does not resolve the phylogenetic position of calcareous sponges, likely due to their high rates of mitochondrial sequence evolution, it confirms mtDNA as a promising marker for population studies in this group. The combination of unusual mitochondrial features in C. clathrus redefines the extremes of mtDNA evolution in animals and further argues against the idea of a "typical animal mtDNA."
Profiling cellular diversity in sponges informs animal cell type and nervous system evolution
Publisher: American Association for the Advancement of Science (AAAS)
Date: 05-11-2021
Abstract: Sponges represent our distant animal relatives. They do not have a nervous system but do have a simple body for filter feeding. Surveying the cell types in the freshwater sponge Spongilla lacustris , Musser et al . found that many genes important in synaptic communication are expressed in cells of the small digestive chambers. They found secretory machinery characteristic of the presynapse in small multipolar cells contacting all other cells and also the receptive apparatus of the postsynapse in the choanocytes that generate water flow and digest microbial food. These results suggest that the first directed communication in animals may have evolved to regulate feeding, serving as a starting point on the long path toward nervous system evolution. —BAP
Horny sponges and their affairs: On the phylogenetic relationships of keratose sponges
Publisher: Elsevier BV
Date: 06-2012
DOI: 10.1016/J.YMPEV.2012.02.024
Abstract: The demosponge orders Dictyoceratida and Dendroceratida are historically assigned to the keratose (or "horny") sponges, which are mostly devoid of primary skeletal elements, but possess an elaborate skeleton of organic fibres instead. This paucity of complex mineral skeletal elements makes their unambiguous classification and phylogenetic reconstruction based on morphological features difficult. Here we present the most comprehensive molecular phylogeny to date for the Dendroceratida, Dictyoceratida, and also other sponge orders that largely lack a mineral skeleton or skeletal elements at all (i.e. Verongida, Halisarcida, Chondrosida), based on independent mitochondrial and nuclear markers. We used molecular data to validate the coherence of all recognised orders, families and subfamilies that are currently defined using morphological characteristics. We discussed the significance of morphological and chemotaxonomic characters for keratose sponges, and suggested adapted definitions for the classification of dendroceratid, dictyoceratid, and verongid higher taxa. Also, we found that chondrosid sponges are non-monophyletic with respect to Halisarcida. Verongida and Dendroceratida were monophyletic, however most of their classically recognised families were not recovered. This indicated that the current distinction between dendritic and mesh-like fibre skeletons is not significant at this level of classification. Dysideidae were found to be the sister-group to the remaining Dictyoceratida. Irciniidae formed a distinct clade, however Thorectidae and Spongiidae could not be separated with the molecular markers used. Finally, we are establishing the name Verongimorpha for the clade combining verongid, chondrosid and halisarcid taxa and readjust the content of its sister-clade Keratosa.
Dynamic expression of ancient and novel molluscan shell genes during ecological transitions
Publisher: Springer Science and Business Media LLC
Date: 10-09-2007
Abstract: The Mollusca constitute one of the most morphologically and ecologically erse metazoan phyla, occupying a wide range of marine, terrestrial and freshwater habitats. The evolutionary success of the molluscs can in part be attributed to the evolvability of the external shell. Typically, the shell first forms during embryonic and larval development, changing dramatically in shape, colour and mineralogical composition as development and maturation proceeds. Major developmental transitions in shell morphology often correlate with ecological transitions (e.g. from a planktonic to benthic existence at metamorphosis). While the genes involved in molluscan biomineralisation are beginning to be identified, there is little understanding of how these are developmentally regulated, or if the same genes are operational at different stages of the mollusc's life. Here we relate the developmental expression of nine genes in the tissue responsible for shell production – the mantle – to ecological transitions that occur during the lifetime of the tropical abalone Haliotis asinina (Vetigastropoda). Four of these genes encode evolutionarily ancient proteins, while four others encode secreted proteins with little or no identity to known proteins. Another gene has been previously described from the mantle of another haliotid vetigastropod. All nine genes display dynamic spatial and temporal expression profiles within the larval shell field and juvenile mantle. These expression data reflect the regulatory complexity that underlies molluscan shell construction from larval stages to adulthood, and serves to highlight the different ecological demands placed on each stage. The use of both ancient and novel genes in all stages of shell construction also suggest that a core set of shell-making genes was provided by a shared metazoan ancestor, which has been elaborated upon to produce the range of molluscan shell types we see today.
Comparative Proteomics of Octocoral and Scleractinian Skeletomes and the Evolution of Coral Calcification
Publisher: Oxford University Press (OUP)
Date: 06-08-2020
DOI: 10.1093/GBE/EVAA162
Abstract: Corals are the ecosystem engineers of coral reefs, one of the most bio erse marine ecosystems. The ability of corals to form reefs depends on the precipitation of calcium carbonate (CaCO3) under biological control. However, several mechanisms underlying coral biomineralization remain elusive, for ex le, whether corals employ different molecular machineries to deposit different CaCO3 polymorphs (i.e., aragonite or calcite). Here, we used tandem mass spectrometry (MS/MS) to compare the proteins occluded in the skeleton of three octocoral and one scleractinian species: Tubipora musica and Sinularia cf. cruciata (calcite sclerites), the blue coral Heliopora coerulea (aragonitic skeleton), and the scleractinian aragonitic Montipora digitata. Reciprocal Blast analysis revealed extremely low overlap between aragonitic and calcitic species, while a core set of proteins is shared between octocorals producing calcite sclerites. However, the carbonic anhydrase CruCA4 is present in the skeletons of both polymorphs. Phylogenetic analysis highlighted several possible instances of protein co-option in octocorals. These include acidic proteins and scleritin, which appear to have been secondarily recruited for calcification and likely derive from proteins playing different functions. Similarities between octocorals and scleractinians included presence of a galaxin-related protein, carbonic anhydrases, and one hephaestin-like protein. Although the first two appear to have been independently recruited, the third appear to share a common origin. This work represents the first attempt to identify and compare proteins associated with coral skeleton polymorph ersity, providing several new research targets and enabling both future functional and evolutionary studies aimed at elucidating the origin and evolution of coral biomineralization.
Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov
Publisher: Springer Science and Business Media LLC
Date: 05-08-2019
Genetic structure of the Crown-of-Thorns seastar in the Pacific Ocean, with focus on Guam
Publisher: PeerJ
Date: 04-03-2016
DOI: 10.7287/PEERJ.PREPRINTS.1167V3
Abstract: Population outbreaks of the corallivorous crown-of-thorns seastar (COTS), Acanthaster ‘planci’ L. , are among the most important biological disturbances of tropical coral reefs. Over the past 50 years, several devastating outbreaks have been documented around Guam, an island in the western Pacific Ocean. Previous analyses have shown that in the Pacific Ocean, COTS larval dispersal may be geographically restricted to certain regions. Here, we assess the genetic structure of Pacific COTS populations and compared s les from around Guam with a number of distant localities in the Pacific Ocean, and focused on determining the degree of genetic structure among populations previously considered to be isolated. Using microsatellites, we document substantial genetic structure between 14 localities from different geographical regions in the Pacific Ocean. Populations from the 14 locations s led were found to be structured in three significantly differentiated groups: (1) all locations immediately around Guam, as well as Kingman Reef and Swains Island (2) Japan, Philippines, GBR and Vanuatu and (3) Johnston Atoll, which was significantly different from all other localities. The most stark ergence of these groupings from previous studies is the lack of genetic differentiation between Guam and extremely distant populations from Kingman Reef and Swains Island. These findings suggest potential long-range dispersal of COTS in the Pacific, and highlight the importance of ecological determinants in shaping genetic structure.
Insights into the evolution of freshwater sponges (Porifera: Demospongiae: Spongillina): Barcoding and phylogenetic data from Lake Tanganyika endemics indicate multiple invasions and unsettle existing
Publisher: Elsevier BV
Date: 10-2011
DOI: 10.1016/J.YMPEV.2011.05.021
Abstract: Sponges are a conspicuous element in many benthic habitats including in Africa's oldest, deepest lake, Lake Tanganyika. Despite their prevalence and pivotal ecological role as filter feeders, knowledge of the evolutionary history of sponges is in its infancy. Here, we provide the first molecular analysis targeting the evolution of sponges from Lake Tanganyika. Independent markers indicate the occurrence of several colonisation events which have shaped the current Tanganyikan lacustrine sponge bio ersity. This is in contrast to a range of previously studied organisms that have ersified within the lake from single lineages. Our tree reconstructions indicate the presence of two genera, Oncosclera and Eunapius, which are globally distributed. Therefore, we reject the hypothesis of monophyly for the sponges from Lake Tanganyika and challenge existing higher taxonomic structure for freshwater sponges.
The mitochondrial genomes of sponges provide evidence for multiple invasions by Repetitive Hairpin-forming Elements (RHE)
Publisher: Springer Science and Business Media LLC
Date: 2009
A horizontal gene transfer supported the evolution of an early metazoan biomineralization strategy
Publisher: Springer Science and Business Media LLC
Date: 12-08-2011
The genome of the reef-building glass sponge Aphrocallistes vastus provides insights into silica biomineralization
Publisher: The Royal Society
Date: 06-2023
DOI: 10.1098/RSOS.230423
Abstract: Well-annotated and contiguous genomes are an indispensable resource for understanding the evolution, development, and metabolic capacities of organisms. Sponges, an ecologically important non-bilaterian group of primarily filter-feeding sessile aquatic organisms, are underrepresented with respect to available genomic resources. Here we provide a high-quality and well-annotated genome of Aphrocallistes vastus , a glass sponge (Porifera: Hexactinellida) that forms large reef structures off the coast of British Columbia (Canada). We show that its genome is approximately 80 Mb, small compared to most other metazoans, and contains nearly 2500 nested genes, more than other genomes. Hexactinellida is characterized by a unique skeletal architecture made of amorphous silicon dioxide (SiO 2 ), and we identified 419 differentially expressed genes between the osculum, i.e. the vertical growth zone of the sponge, and the main body. Among the upregulated ones, mineralization-related genes such as glassin, as well as collagens and actins, dominate the expression profile during growth. Silicateins, suggested being involved in silica mineralization, especially in demosponges, were not found at all in the A. vastus genome and suggests that the underlying mechanisms of SiO 2 deposition in the Silicea sensu stricto (Hexactinellida + Demospongiae) may not be homologous.
Genomic data do not support comb jellies as the sister group to all other animals
Publisher: Proceedings of the National Academy of Sciences
Date: 30-11-2015
Abstract: Clarifying the phylogeny of animals is fundamental to understanding their evolution. Traditionally, sponges have been considered the sister group of all other extant animals, but recent genomic studies have suggested comb jellies occupy that position instead. Here, we analyzed the current genomic evidence from comb jellies and found no convincing support for this hypothesis. Instead, when analyzed with appropriate methods, recent genomic data support the traditional hypothesis. We conclude that the alternative scenario of animal evolution according to which ctenophores evolved morphological complexity independently from cnidarians and bilaterians or, alternatively, sponges secondarily lost a nervous system, muscles, and other characters, is not supported by the available evidence.
Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships
Publisher: Oxford University Press (OUP)
Date: 08-04-2010
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