ORCID Profile
0000-0002-6305-4749
Current Organisation
University of Melbourne
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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)
Phycology (incl. Marine Grasses) | Genomics | Phylogeny and Comparative Analysis | Marine and Estuarine Ecology (incl. Marine Ichthyology) | Microbial Ecology | Plant Biology | Microbiology | Evolutionary Biology
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Marine Flora, Fauna and Biodiversity | Effects of Climate Change and Variability on Australia (excl. Social Impacts) | Climate and Climate Change not elsewhere classified |
Related Links
Publications
Bio‐ORACLE v2.0: Extending marine data layers for bioclimatic modelling
Publisher: Wiley
Date: 29-12-2017
DOI: 10.1111/GEB.12693
Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae
Publisher: Springer Science and Business Media LLC
Date: 22-08-2016
DOI: 10.1038/SREP31508
Abstract: Bacteria, fungi and green algae are common inhabitants of coral skeletons. Their ersity is poorly characterized because they are difficult to identify with microscopy or environmental sequencing, as common metabarcoding markers have low phylogenetic resolution and miss a large portion of the bio ersity. We used a cost-effective protocol and a combination of markers ( tuf A, 16S rDNA, 18S rDNA and 23S rDNA) to characterize the microbiome of 132 coral skeleton s les. We identified a wide range of prokaryotic and eukaryotic organisms, many never reported in corals before. We additionally investigated the phylogenetic ersity of the green algae—the most abundant eukaryotic member of this community, for which previous literature recognizes only a handful of endolithic species. We found more than 120 taxonomic units (near species level), including six family-level lineages mostly new to science. The results suggest that the existence of lineages with an endolithic lifestyle predates the existence of modern scleractinian corals by ca . 250my and that this particular niche was independently invaded by over 20 lineages in green algae evolution. These results highlight the potential of the multi-marker approach to assist in species discovery and, when combined with a phylogenetic framework, clarify the evolutionary origins of host-microbiota associations.
Biodiversity of endolithic fungi in coral skeletons and other reef substrates revealed with 18S rDNA metabarcoding
Publisher: Springer Science and Business Media LLC
Date: 30-11-2019
Molecular systematics of the siphonous green algal genus codium in Eastern Victoria, Australia
Publisher: Museum National d'Histoire Naturelle, Paris, France
Date: 11-2018
PSEUDOCODIUM MUCRONATUM, A NEW SPECIES FROM NEW CALEDONIA, AND AN ANALYSIS OF THE EVOLUTION OF CLIMATIC PREFERENCES IN THE GENUS (BRYOPSIDALES, CHLOROPHYTA)1
Publisher: Wiley
Date: 08-2009
DOI: 10.1111/J.1529-8817.2009.00717.X
Abstract: A new species, Pseudocodium mucronatum, is described from the Chesterfield platform off the west coast of New Caledonia. The species differs from its congeners in having mucronate utricules. A phylogenetic analysis of rbcL and tufA sequences showed that P. mucronatum is most closely associated with P. natalense De Clerck, Coppejans et Verbruggen and P. devriesii Weber Bosse, with which it shares compressed axes, depressed apices, and plastids in the utricles and the medullar siphons. We studied the evolution of climatic and ecological preferences in the genus using an interdisciplinary approach consisting of relaxed molecular clock analysis, extraction of macroecological data from satellite imagery in a geographic information system (GIS) framework, and ancestral character state estimation. It was shown that the genus originated in tropical waters during the Early Mesozoic. Whereas the P. floridanum-okinawense lineage remained tropical, the lineage including P. natalense, P. devriesii, and P. mucronatum gradually invaded more temperate waters during Cenozoic times. Except for P. devriesii, which occurs in shallow and intertidal habitats, all Pseudocodium species grow in deep-water habitats, and this ecological preference appears to be ancestral.
Macroecology meets macroevolution: evolutionary niche dynamics in the seaweed Halimeda
Publisher: Wiley
Date: 10-06-2009
Systematics of the genus Halimeda (Bryopsidales, Chlorophyta) in Brazil including the description of Halimeda jolyana sp. nov.
Publisher: Informa UK Limited
Date: 07-2017
DOI: 10.2216/16-77.1
Genetic patterns in the calcified tropical seaweeds Halimeda opuntia, H-distorta, H-hederacea, and H-minima (Bryopsidales, Chlorophyta) provide insights in species boundaries and interoceanic dispersal
Publisher: Wiley
Date: 31-01-2005
Chloroplast and mitochondrial genomes of Balbiania investiens (Balbianiales, Nemaliophycidae)
Publisher: Informa UK Limited
Date: 08-03-2019
MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis
Publisher: Research Square Platform LLC
Date: 09-2023
DOI: 10.21203/RS.3.RS-1999920/V1
Abstract: MetaGenePipe (MGP) is an efficient, flexible, portable, and scalable metagenomics pipeline that uses performant bioinformatics software suites and genomic databases to create an accurate taxonomic and functional characterization of the prokaryotic fraction of sequenced microbiomes. Written in the Workflow Definition Language (WDL), MGP produces output that is useful in its default form, or that can be used for further downstream analysis. MGP is a pipeline-development best practice tool which uses Singularity for containerization and includes a setup script that downloads the necessary databases for setup. The source code for MGP is freely available and is distributed under the Apache 2.0 license.
DNA barcodes and morphometric data indicate that Codium fragile (Bryopsidales, Chlorophyta) may consist of two species
Publisher: Informa UK Limited
Date: 2017
DOI: 10.2216/16-54.1
Whole genome population structure of North Atlantic kelp confirms high‐latitude glacial refugia
Publisher: Wiley
Date: 27-10-2022
DOI: 10.1111/MEC.16714
Abstract: Coastal refugia during the Last Glacial Maximum (~21,000 years ago) have been hypothesized at high latitudes in the North Atlantic, suggesting marine populations persisted through cycles of glaciation and are potentially adapted to local environments. Here, whole‐genome sequencing was used to test whether North Atlantic marine coastal populations of the kelp Alaria esculenta survived in the area of southwestern Greenland during the Last Glacial Maximum. We present the first annotated genome for A. esculenta and call variant positions in 54 in iduals from populations in Atlantic Canada, Greenland, Faroe Islands, Norway and Ireland. Differentiation across populations was reflected in ~1.9 million single nucleotide polymorphisms, which further revealed mixed ancestry in the Faroe Islands in iduals between putative Greenlandic and European lineages. Time‐calibrated organellar phylogenies suggested Greenlandic populations were established during the last interglacial period more than 100,000 years ago, and that the Faroe Islands population was probably established following the Last Glacial Maximum. Patterns in population statistics, including nucleotide ersity, minor allele frequencies, heterozygosity and linkage disequilibrium decay, nonetheless suggested glaciation reduced Canadian Atlantic and Greenlandic populations to small effective sizes during the most recent glaciation. Functional differentiation was further reflected in exon read coverage, which revealed expansions unique to Greenland in 337 exons representing 162 genes, and a modest degree of exon loss (103 exons from 56 genes). Altogether, our genomic results provide strong evidence that A. esculenta populations were resilient to past climatic fluctuations related to glaciations and that high‐latitude populations are potentially already adapted to local conditions as a result.
Meridionella gen. nov., a New Genus of Cystocloniaceae (Gigartinales, Rhodophyta) from the Southern Hemisphere, Including M. obtusangula comb. nov. and M. antarctica sp. nov.
Publisher: Wiley
Date: 18-03-2021
DOI: 10.1111/JPY.13127
Abstract: The classification of Cystoclonium obtusangulum has been questioned since the species was first described by Hooker and Harvey as Gracilaria? obtusangula . The objective of this study was to provide the first comprehensive taxonomic analysis of Cystoclonium obtusangulum , based on DNA sequences coupled with morphological observations made on syntype specimens and new collections. Sequence ergences of rbc L, UPA, and COI‐5P, and maximum‐likelihood phylogenies for rbc L and 18S demonstrated that specimens identified as Cystoclonium obtusangulum represent a clade of two distinct species that are distantly related to the generitype Cystoclonium purpureum . A new genus, Meridionella gen. nov., is proposed for this clade. The two species placed in this new genus were morphologically indistinguishable cryptic species, but have disjunct distributions, with Meridionella obtusangula comb. nov. found from temperate to cold coasts of South America and the Falkland Islands and Meridionella antarctica sp. nov., occurring in Antarctic waters. Vegetative and reproductive characters of Meridionella gen. nov. are described, and implications of our results for the biogeography of the family Cystocloniaceae are discussed.
Phylogeography of the mediterranean green seaweed Halimeda tuna (Ulvophyceae, Chlorophyta)
Publisher: Wiley
Date: 22-05-2020
DOI: 10.1111/JPY.13006
Resolving the taxonomy of the Polysiphonia scopulorum complex and the Bryocladia lineage (Rhodomelaceae, Rhodophyta)
Publisher: Wiley
Date: 25-10-2023
DOI: 10.1111/JPY.13402
Analysis of chloroplast genomes and a supermatrix inform reclassification of the Rhodomelaceae (Rhodophyta)
Publisher: Wiley
Date: 11-07-2017
DOI: 10.1111/JPY.12553
Abstract: With over a thousand species, the Rhodomelaceae is the most species-rich family of red algae. While its genera have been assigned to 14 tribes, the high-level classification of the family has never been evaluated with a molecular phylogeny. Here, we reassess its classification by integrating genome-scale phylogenetic analysis with observations of the morphological characters of clades. In order to resolve relationships among the main lineages of the family we constructed a phylogeny with 55 chloroplast genomes (52 newly determined). The majority of branches were resolved with full bootstrap support. We then added 266 rbcL, 125 18S rRNA gene and 143 cox1 sequences to construct a comprehensive phylogeny containing nearly half of all known species in the family (407 species in 89 genera). These analyses suggest the same sub ision into higher-level lineages, but included many branches with moderate or poor support. The circumscription for nine of the 13 previously described tribes was supported, but the Lophothalieae, Polysiphonieae, Pterosiphonieae and Herposiphonieae required revision, and five new tribes and one resurrected tribe were segregated from them. Rhizoid anatomy is highlighted as a key diagnostic character for the morphological delineation of several lineages. This work provides the most extensive phylogenetic analysis of the Rhodomelaceae to date and successfully resolves the relationships among major clades of the family. Our data show that organellar genomes obtained through high-throughput sequencing produce well-resolved phylogenies of difficult groups, and their more general application in algal systematics will likely permit deciphering questions about classification at many taxonomic levels.
The marine flora of Rodrigues (Republic of Mauritius, Indian Ocean): an island with low habitat diversity or one in the process of colonization?
Publisher: Informa UK Limited
Date: 12-2004
DNA taxonomy in morphologically plastic taxa: Algorithmic species delimitation in the Boodlea complex (Chlorophyta: Cladophorales)
Publisher: Elsevier BV
Date: 10-2009
DOI: 10.1016/J.YMPEV.2009.06.004
Abstract: DNA-based taxonomy provides a convenient and reliable tool for species delimitation, especially in organisms in which morphological discrimination is difficult or impossible, such as many algal taxa. A group with a long history of confusing species circumscriptions is the morphologically plastic Boodlea complex, comprising the marine green algal genera Boodlea, Cladophoropsis, Phyllodictyon and Struveopsis. In this study, we elucidate species boundaries in the Boodlea complex by analysing nrDNA internal transcribed spacer sequences from 175 specimens collected from a wide geographical range. Algorithmic methods of sequence-based species delineation were applied, including statistical parsimony network analysis, and a maximum likelihood approach that uses a mixed Yule-coalescent model and detects species boundaries based on differences in branching rates at the level of species and populations. Sequence analyses resulted in the recognition of 13 phylogenetic species, although we failed to detect sharp species boundaries, possibly as a result of incomplete reproductive isolation. We found considerable conflict between traditional and phylogenetic species definitions. Identical morphological forms were distributed in different clades (cryptic ersity), and at the same time most of the phylogenetic species contained a mixture of different morphologies (indicating intraspecific morphological variation). S ling outside the morphological range of the Boodlea complex revealed that the enigmatic, sponge-associated Cladophoropsis (Spongocladia) vaucheriiformis, also falls within the Boodlea complex. Given the observed evolutionary complexity and nomenclatural problems associated with establishing a Linnaean taxonomy for this group, we propose to discard provisionally the misleading morphospecies and genus names, and refer to clade numbers within a single genus, Boodlea.
Algivore or Phototroph? Plakobranchus ocellatus (Gastropoda) Continuously Acquires Kleptoplasts and Nutrition from Multiple Algal Species in Nature
Publisher: Public Library of Science (PLoS)
Date: 25-07-2012
MORPHOLOGICAL COMPLEXITY, PLASTICITY, AND SPECIES DIAGNOSABILITY IN THE APPLICATION OF OLD SPECIES NAMES IN DNA-BASED TAXONOMIES
Publisher: Wiley
Date: 02-2014
DOI: 10.1111/JPY.12155
Systematics and biogeography of the genus Pseudocodium (Bryopsidales, Chlorophyta), including the description of P. natalense sp. nov. from South Africa
Publisher: Informa UK Limited
Date: 12-03-2008
DOI: 10.2216/07-79.1
Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds
Publisher: Proceedings of the National Academy of Sciences
Date: 07-01-2020
Abstract: The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focuses on the evolutionary origins of green seaweeds, which play an important ecological role in the benthos of modern sunlit oceans and likely played a crucial part in the evolution of early animals by structuring benthic habitats and providing novel niches. By applying a phylogenomic approach, we resolve deep relationships of the core Chlorophyta (Ulvophyceae or green seaweeds, and freshwater or terrestrial Chlorophyceae and Trebouxiophyceae) and unveil a rapid radiation of Chlorophyceae and the principal lineages of the Ulvophyceae late in the Neoproterozoic Era. Our time-calibrated tree points to an origin and early ersification of green seaweeds in the late Tonian and Cryogenian periods, an interval marked by two global glaciations with strong consequent changes in the amount of available marine benthic habitat. We hypothesize that unicellular and simple multicellular ancestors of green seaweeds survived these extreme climate events in isolated refugia, and ersified in benthic environments that became increasingly available as ice retreated. An increased supply of nutrients and biotic interactions, such as grazing pressure, likely triggered the independent evolution of macroscopic growth via different strategies, including true multicellularity, and multiple types of giant-celled forms.
Systematics of the marine microfilamentous green algaeUronema curvatumandUrospora microscopica(Chlorophyta)
Publisher: Informa UK Limited
Date: 11-2009
Reference datasets of tuf A and UPA markers to identify algae in metabarcoding surveys
Publisher: Elsevier BV
Date: 04-2017
Climate change impact on seaweed meadow distribution in the North Atlantic rocky intertidal
Publisher: Wiley
Date: 12-04-2013
DOI: 10.1002/ECE3.541
The bacterial microbiome of the coral skeleton algal symbiontOstreobiumshows preferential associations and signatures of phylosymbiosis
Publisher: Cold Spring Harbor Laboratory
Date: 13-12-2022
DOI: 10.1101/2022.12.13.520198
Abstract: Ostreobium , the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria (2) enriched tightly attached and potential intracellular bacteria and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with erse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include taxa known as nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton s les, we show that the Ostreobium -bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives.
Phylogenetic analysis ofCodiumspecies from Brazil, with the description of the new speciesC. pernambucensis(Bryopsidales, Chlorophyta)
Publisher: Informa UK Limited
Date: 11-2012
Evolutionary dynamics of chloroplast genomes in low light: A case study of the endolithic green alga ostreobium quekettii
Publisher: Oxford University Press (OUP)
Date: 25-08-2016
DOI: 10.1093/GBE/EVW206
Abstract: Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species’ genomes. Here, we present the chloroplast genomes of four green algae (Bryopsidales, Ulvophyceae), including the endolithic (limestone-boring) alga Ostreobium quekettii, which is a low light specialist. We use phylogenetic models and comparative genomic tools to investigate whether the chloroplast genome of Ostreobium corresponds to our expectations of how low light would affect genome evolution. Ostreobium has the smallest and most gene-dense chloroplast genome among Ulvophyceae reported to date, matching our expectation that light limitation would impose resource constraints reflected in the chloroplast genome architecture. Rates of molecular evolution are significantly slower along the phylogenetic branch leading to Ostreobium, in agreement with the expected effects of low light and energy levels on molecular evolution. We expected the ability of Ostreobium to perform photosynthesis in very low light to be associated with positive selection in genes related to the photosynthetic machinery, but instead, we observed that these genes may be under stronger purifying selection. Besides shedding light on the genome dynamics associated with a low light lifestyle, this study helps to resolve the role of environmental factors in shaping the ersity of genome architectures observed in nature.
A time-calibrated multi-gene phylogeny of the diatom genus Pinnularia
Publisher: Elsevier BV
Date: 12-2011
DOI: 10.1016/J.YMPEV.2011.08.031
Abstract: Pinnularia is an ecologically important and species-rich genus of freshwater diatoms (Bacillariophyceae) showing considerable variation in frustule morphology. Interspecific evolutionary relationships were inferred for 36 Pinnularia taxa using a five-locus dataset. A range of fossil taxa, including newly discovered Middle Eocene forms of Pinnularia, was used to calibrate a relaxed molecular clock analysis and investigate temporal aspects of the genus' ersification. The multi-gene approach resulted in a well-resolved phylogeny of three major clades and several subclades that were frequently, but not universally, delimited by valve morphology. The genus Caloneis was not recovered as monophyletic, confirming that, as currently delimited, this genus is not evolutionarily meaningful and should be merged with Pinnularia. The Pinnularia-Caloneis complex is estimated to have erged between the Upper Cretaceous and the early Eocene, implying a ghost range of at least 10 million year (Ma) in the fossil record.
Reassessment of the classification of Bryopsidales (Chlorophyta) based on chloroplast phylogenomic analyses
Publisher: Elsevier BV
Date: 2019
DOI: 10.1016/J.YMPEV.2018.09.009
Abstract: The Bryopsidales is a morphologically erse group of mainly marine green macroalgae characterized by a siphonous structure. The order is composed of three suborders - Ostreobineae, Bryopsidineae, and Halimedineae. While previous studies improved the higher-level classification of the order, the taxonomic placement of some genera in Bryopsidineae (Pseudobryopsis and Lambia) as well as the relationships between the families of Halimedineae remains uncertain. In this study, we re-assess the phylogeny of the order with datasets derived from chloroplast genomes, drastically increasing the taxon s ling by sequencing 32 new chloroplast genomes. The phylogenies presented here provided good support for the major lineages (suborders and most families) in Bryopsidales. In Bryopsidineae, Pseudobryopsis hainanensis was inferred as a distinct lineage from the three established families allowing us to establish the family Pseudobryopsidaceae. The Antarctic species Lambia antarctica was shown to be an early-branching lineage in the family Bryopsidaceae. In Halimedineae, we revealed several inconsistent phylogenetic positions of macroscopic taxa, and several entirely new lineages of microscopic species. A new classification scheme is proposed, which includes the merger of the families Pseudocodiaceae, Rhipiliaceae and Udoteaceae into a more broadly circumscribed Halimedaceae, and the establishment of tribes for the different lineages found therein. In addition, the deep-water genus Johnson-sea-linkia, currently placed in Rhipiliopsis, was reinstated based on our phylogeny.
Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium
Publisher: Elsevier BV
Date: 04-2021
DOI: 10.1016/J.CUB.2021.01.018
Abstract: The green alga Ostreobium is an important coral holobiont member, playing key roles in skeletal decalcification and providing photosynthate to bleached corals that have lost their dinoflagellate endosymbionts. Ostreobium lives in the coral's skeleton, a low-light environment with variable pH and O
The South African estuarine specialist Codium tenue (Bryopsidales, Chlorophyta) discovered in a south-western Australian estuary
Publisher: Walter de Gruyter GmbH
Date: 05-11-2015
Abstract: Codium tenue , previously known reliably only from estuarine habitats in South Africa, is recorded from a similar habitat in the Walpole and Nornalup Inlet system, on the south coast of Western Australia. The Australian C. tenue has a repeatedly aricately dichotomously branched thallus to 11.5 cm in height, with markedly compressed axes up to 1 cm in width at branch dichotomies, but distally attenuating to terete branch apices. Structurally, thalli have cortices with distinctive cuneate utricles up to 1310 μm long and 650 μm in diameter. Both the habit and structural morphology essentially agree with C. tenue as known in South Africa. Sequences generated from the Australian specimens are also wholly comparable with those of South African specimens newly generated in this study. While similarly disjunct South African/Western Australian distributions are known for other algae, that of C. tenue is particularly remarkable in that the species is apparently an estuarine specialist.
Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta)
Publisher: Oxford University Press (OUP)
Date: 16-03-2018
DOI: 10.1093/GBE/EVY063
Species boundaries and phylogenetic relationships within the green algal genus Codium (Bryopsidales) based on plastid DNA sequences
Publisher: Elsevier BV
Date: 07-2007
DOI: 10.1016/J.YMPEV.2007.01.009
Abstract: Despite the potential model role of the green algal genus Codium for studies of marine speciation and evolution, there have been difficulties with species delimitation and a molecular phylogenetic framework was lacking. In the present study, 74 evolutionarily significant units (ESUs) are delimited using 227 rbcL exon 1 sequences obtained from specimens collected throughout the genus' range. Several morpho-species were shown to be poorly defined, with some clearly in need of lumping and others containing pseudo-cryptic ersity. A phylogenetic hypothesis of 72 Codium ESUs is inferred from rbcL exon 1 and rps3-rpl16 sequence data using a conventional nucleotide substitution model (GTR+Gamma+I), a codon position model and a covariotide (covarion) model, and the fit of a multitude of substitution models and alignment partitioning strategies to the sequence data is reported. Molecular clock tree rooting was carried out because outgroup rooting was probably affected by phylogenetic bias. Several aspects of the evolution of morphological features of Codium are discussed and the inferred phylogenetic hypothesis is used as a framework to study the biogeography of the genus, both at a global scale and within the Indian Ocean.
Rhipidosiphon lewmanomontiae sp. nov. (Bryopsidales, Chlorophyta), a calcified udoteacean alga from the central Indo-Pacific based on morphological and molecular investigations
Publisher: Informa UK Limited
Date: 07-2011
DOI: 10.2216/10-90.1
MORPHOMETRIC TAXONOMY OF SIPHONOUS GREEN ALGAE: A METHODOLOGICAL STUDY WITHIN THE GENUS HALIMEDA (BRYOPSIDALES)1
Publisher: Wiley
Date: 31-01-2005
Host Traits and Phylogeny Contribute to Shaping Coral-Bacterial Symbioses
Publisher: American Society for Microbiology
Date: 26-04-2022
DOI: 10.1128/MSYSTEMS.00044-22
Abstract: The rapid decline of coral reefs, driven by climate changes, calls for manipulative interventions such as the use of probiotics, which can assist the resilience of these ecosystems.
Organization of plastid genomes in the freshwater red algal order Batrachospermales (Rhodophyta).
Publisher: Wiley
Date: 22-11-2018
DOI: 10.1111/JPY.12602
Abstract: Little is known about genome organization in members of the order Batrachospermales, and the infra-ordinal relationship remains unresolved. Plastid (cp) genomes of seven members of the freshwater red algal order Batrachospermales were sequenced, with the following aims: (i) to describe the characteristics of cp genomes and compare these with other red algal groups (ii) to infer the phylogenetic relationships among these members to better understand the infra-ordinal classification. Cp genomes of Batrachospermales are large, with several cases of gene loss, they are gene-dense (high gene content for the genome size and short intergenic regions) and have highly conserved gene order. Phylogenetic analyses based on concatenated nucleotide genome data roughly supports the current taxonomic system for the order. Comparative analyses confirm data for members of the class Florideophyceae that cp genomes in Batrachospermales is highly conserved, with little variation in gene composition. However, relevant new features were revealed in our study: genome sizes in members of Batrachospermales are close to the lowest values reported for Florideophyceae differences in cp genome size within the order are large in comparison with other orders (Ceramiales, Gelidiales, Gracilariales, Hildenbrandiales, and Nemaliales) and members of Batrachospermales have the lowest number of protein-coding genes among the Florideophyceae. In terms of gene loss, apcF, which encodes the allophycocyanin beta subunit, is absent in all sequenced taxa of Batrachospermales. We reinforce that the interordinal relationships between the freshwater orders Batrachospermales and Thoreales within the Nemaliophycidae is not well resolved due to limited taxon s ling.
A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): Investigating the evolutionary nature of the “brown algal crown radiation”
Publisher: Elsevier BV
Date: 08-2010
DOI: 10.1016/J.YMPEV.2010.04.020
Abstract: The most conspicuous feature in previous phaeophycean phylogenies is a large polytomy known as the brown algal crown radiation (BACR). The BACR encompasses 10 out of the 17 currently recognized brown algal orders. A recent study has been able to resolve a few nodes of the BACR, suggesting that it may be a soft polytomy caused by a lack of signal in molecular markers. The present work aims to refine relationships within the BACR and investigate the nature and timeframe of the ersification in question using a dual approach. A multi-marker phylogeny of the brown algae was built from 10 mitochondrial, plastid and nuclear loci (>10,000 nt) of 72 phaeophycean taxa, resulting in trees with well-resolved inter-ordinal relationships within the BACR. Using Bayesian relaxed molecular clock analysis, it is shown that the BACR is likely to represent a gradual ersification spanning most of the Lower Cretaceous rather than a sudden radiation. Non-molecular characters classically used in ordinal delimitation were mapped on the molecular topology to study their evolutionary history.
The marine red algae of Rodrigues (Mauritius, Indian Ocean)
Publisher: Informa UK Limited
Date: 12-2004
Kraftionema allantoideum, a new genus and family of Ulotrichales (Chlorophyta) adapted for survival in high intertidal pools
Publisher: Wiley
Date: 08-09-2016
DOI: 10.1111/JPY.12447
Abstract: The marine, sand-dwelling green alga Kraftionema allantoideum gen. et sp. nov. is described from clonal cultures established from s les collected in coastal, high intertidal pools from south eastern Australia. The species forms microscopic, uniseriate, unbranched, 6-8 μm wide filaments surrounded by a gelatinous capsule of varying thickness. Filaments are twisted, knotted, and variable in length from 4 to 50 cells in field s les but straighter and much longer in culture, up to 1.5 mm in length. Cell ision occurs in several planes, resulting in daughter cells of varying shape, from square to rectangular to triangular, giving rise to gnarled filaments. Mature cells become allantoid, elongate with rounded ends, before iding one time to form bicells comprised of two domed cells. Adjacent bicells separate from one another and mature filaments appeared as a string of loosely arranged sausages. A massive, single, banded chloroplast covered 3/4 of the wall circumference, and contained a single large pyrenoid encased in a starch envelope that measures 1.5-2.5 μm. Filaments were not adhesive nor did they produce specialized adhesive cells or structures. Reproduction was by fragmentation with all cells capable of producing a new filament. No motile or reproductive cells were observed. Filaments in culture grew equally well in freshwater or marine media, as well as at high salinity, and cells quickly recovered from desiccation. Phylogenetic analysis based on the nuclear-encoded small subunit ribosomal RNA (18S) shows the early branching nature of the Kraftionema lineage among Ulotrichales, warranting its recognition as a family (Kraftionemaceae).
Evolution and phylogeography of Halimeda section Halimeda (Bryopsidales, Chlorophyta)
Publisher: Elsevier BV
Date: 12-2005
DOI: 10.1016/J.YMPEV.2005.06.015
Abstract: Nuclear ribosomal and plastid DNA sequences of specimens belonging to section Halimeda of the pantropical green seaweed genus Halimeda show that the group under scrutiny contains many more genetically delineable species than those recognized by classical taxonomy. Discordances between phylograms inferred from nuclear and plastid DNA sequences suggest that reticulate evolution has been involved in speciation within the clade. Nonetheless, our data do not allow ruling out certain alternative explanations for the discordances. Several pseudo-cryptic species are restricted to the margins of the generic distribution range. In a clade of H. cuneata sibling species from widely separated subtropical localities in the Indian Ocean, the South African sibling branches off first, leaving the Arabian and West Australian species as closest relatives. We hypothesize that geographic isolation of the siblings may have taken place following Pleistocene or Pliocene periods of climatic cooling during which subtropical species occupied larger distribution ranges. A more basal separation of Atlantic, Indo-Pacific, and Mediterranean species indicates vicariance. The alternative events that could have caused this vicariance are discussed.
Ecological niche models of invasive seaweeds
Publisher: Wiley
Date: 23-07-2015
DOI: 10.1111/JPY.12322
Abstract: Ecological niche models (ENMs) are commonly used to calculate habitat suitability from species' occurrence and macroecological data. In invasive species biology, ENMs can be applied to anticipate whether invasive species are likely to establish in an area, to identify critical routes and arrival points, to build risk maps and to predict the extent of potential spread following an introduction. Most studies using ENMs focus on terrestrial organisms and applications in the marine realm are still relatively rare. Here, we review some common methods to build ENMs and their application in seaweed invasion biology. We summarize methods and concepts involved in the development of niche models, show ex les of how they have been applied in studies on algae and discuss the application of ENMs in invasive algae research and to predict effects of climate change on seaweed distributions.
Building trees of algae: some advances in phylogenetic and evolutionary analysis
Publisher: Informa UK Limited
Date: 08-2008
Gene‐rich plastid genomes of two parasitic red algal species, Laurencia australis and L. verruciformis (Rhodomelaceae, Ceramiales), and a taxonomic revision of Janczewskia
Publisher: Wiley
Date: 28-08-2023
DOI: 10.1111/JPY.13373
Abstract: Parasitic red algae are an interesting system for investigating the genetic changes that occur in parasites. These parasites have evolved independently multiple times within the red algae. The functional loss of plastid genomes can be investigated in these multiple independent ex les, and fine‐scale patterns may be discerned. The only plastid genomes from red algal parasites known so far are highly reduced and missing almost all photosynthetic genes. Our study assembled and annotated plastid genomes from the parasites Janczewskia tasmanica and its two Laurencia host species ( Laurencia elata and one unidentified Laurencia sp. A25) from Australia and Janczewskia verruciformis , its host species ( Laurencia catarinensis ), and the closest known free‐living relative ( Laurencia obtusa ) from the Canary Islands (Spain). For the first time we show parasitic red algal plastid genomes that are similar in size and gene content to free‐living host species without any gene loss or genome reduction. The only exception was two pseudogenes ( moe B and ycf 46) found in the plastid genome of both isolates of J. tasmanica , indicating potential for future loss of these genes. Further comparative analyses with the three highly reduced plastid genomes showed possible gene loss patterns, in which photosynthetic gene categories were lost followed by other gene categories. Phylogenetic analyses did not confirm monophyly of Janczewskia , and the genus was subsumed into Laurencia . Further investigations will determine if any convergent small‐scale patterns of gene loss exist in parasitic red algae and how these are applicable to other parasitic systems.
The Plastid Genome in Cladophorales Green Algae Is Encoded by Hairpin Chromosomes
Publisher: Elsevier BV
Date: 12-2017
DOI: 10.1016/J.CUB.2017.11.004
Abstract: Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100 and 200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates, where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin chromosomes. Short- and long-read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1- to 7-kb DNA contigs with an exceptionally high GC content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin chromosomes. The Boodlea chloroplast genes are highly ergent from their corresponding orthologs, and display an alternative genetic code. The origin of this highly deviant chloroplast genome most likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes, and highlights unexpected variation in plastid genome architecture.
Contrasting Geographical Distributions as a Result of Thermal Tolerance and Long-Distance Dispersal in Two Allegedly Widespread Tropical Brown Algae
Publisher: Public Library of Science (PLoS)
Date: 26-01-2012
CHARACTERIZATION OF CELL WALL POLYSACCHARIDES OF THE COENCOCYTIC GREEN SEAWEED BRYOPSIS PLUMOSA (BRYOPSIDACEAE, CHLOROPHYTA) FROM THE ARGENTINE COAST1
Publisher: Wiley
Date: 19-03-2012
DOI: 10.1111/J.1529-8817.2012.01131.X
Abstract: Bryopsis sp. from a restricted area of the rocky shore of Mar del Plata (Argentina) on the Atlantic coast was identified as Bryopsis plumosa (Hudson) C. Agardh (Bryopsidales, Chlorophyta) based on morphological characters and rbcL and tufA DNA barcodes. To analyze the cell wall polysaccharides of this seaweed, the major room temperature (B1) and 90°C (X1) water extracts were studied. By linkage analysis and NMR spectroscopy, the structure of a sulfated galactan was determined, and putative sulfated rhamnan structures and furanosidic nonsulfated arabinan structures were also found. By anion exchange chromatography of X1, a fraction (F4), comprising a sulfated galactan as major structure was isolated. Structural analysis showed a linear backbone constituted of 3-linked β-d-galactose units, partially sulfated on C-6 and partially substituted with pyruvic acid forming an acetal linked to O-4 and O-6. This galactan has common structural features with those of green seaweeds of the genus Codium (Bryopsidales, Chlorophyta), but some important differences were also found. This is the first report about the structure of the water-soluble polysaccharides biosynthesized by seaweeds of the genus Bryopsis. These sulfated galactans and rhamnans were in situ localized mostly in two layers, one close to the plasma membrane and the other close to the apoplast, leaving a middle amorphous, unstained cell wall zone. In addition, fibrillar polysaccharides, comprising (1→3)-β-d-xylans and cellulose, were obtained by treatment of the residue from the water extractions with an LiCl/DMSO solution at high temperature. These polymers were also localized in a bilayer arrangement.
Complete mitochondrial genomes of six species of the freshwater red algal order Batrachospermales (Rhodophyta)
Publisher: Informa UK Limited
Date: 23-05-2018
Evolutionary dynamics of algal traits and diversity
Publisher: Schweizerbart
Date: 06-2014
ANALYSIS OF A PLASTID MULTIGENE DATA SET AND THE PHYLOGENETIC POSITION OF THE MARINE MACROALGA CAULERPA FILIFORMIS (CHLOROPHYTA)1
Publisher: Wiley
Date: 10-2009
DOI: 10.1111/J.1529-8817.2009.00731.X
Abstract: Molecular phylogenetic relationships within the Chlorophyta have relied heavily on rRNA data. These data have revolutionized our insight in green algal evolution, yet some class relationships have never been well resolved. A commonly used class within the Chlorophyta is the Ulvophyceae, although there is not much support for its monophyly. The relationships among the Ulvophyceae, Trebouxiophyceae, and Chlorophyceae are also contentious. In recent years, chloroplast genome data have shown their utility in resolving relationships between the main green algal clades, but such studies have never included marine macroalgae. We provide partial chloroplast genome data (∼30,000 bp, 23 genes) of the ulvophycean macroalga Caulerpa filiformis (Suhr) K. Herig. We show gene order conservation for some gene combinations and rearrangements in other regions compared to closely related taxa. Our data also revealed a pseudogene (ycf62) in Caulerpa species. Our phylogenetic results, based on analyses of a 23-gene alignment, suggest that neither Ulvophyceae nor Trebouxiophyceae are monophyletic, with Caulerpa being more closely related to the trebouxiophyte Chlorella than to Oltmannsiellopsis and Pseudendoclonium.
Metaphor—A workflow for streamlined assembly and binning of metagenomes
Publisher: Oxford University Press (OUP)
Date: 28-12-2022
DOI: 10.1093/GIGASCIENCE/GIAD055
Abstract: Recent advances in bioinformatics and high-throughput sequencing have enabled the large-scale recovery of genomes from metagenomes. This has the potential to bring important insights as researchers can bypass cultivation and analyze genomes sourced directly from environmental s les. There are, however, technical challenges associated with this process, most notably the complexity of computational workflows required to process metagenomic data, which include dozens of bioinformatics software tools, each with their own set of customizable parameters that affect the final output of the workflow. At the core of these workflows are the processes of assembly—combining the short-input reads into longer, contiguous fragments (contigs)—and binning, clustering these contigs into in idual genome bins. The limitations of assembly and binning algorithms also pose different challenges depending on the selected strategy to execute them. Both of these processes can be done for each s le separately or by pooling together multiple s les to leverage information from a combination of s les. Here we present Metaphor, a fully automated workflow for genome-resolved metagenomics (GRM). Metaphor differs from existing GRM workflows by offering flexible approaches for the assembly and binning of the input data and by combining multiple binning algorithms with a bin refinement step to achieve high-quality genome bins. Moreover, Metaphor generates reports to evaluate the performance of the workflow. We showcase the functionality of Metaphor on different synthetic datasets and the impact of available assembly and binning strategies on the final results.
A morphological and molecular study supports the recognition of Rhipilia psammophila sp. nov. and Rhipilia baculifera comb. nov. (Halimedaceae, Chlorophyta) from southern Australia
Publisher: CSIRO Publishing
Date: 2023
DOI: 10.1071/SB23016
Fast-spreading green beds of recently introduced Halimeda incrassata invade Mallorca island (NW Mediterranean Sea)
Publisher: Inter-Research Science Center
Date: 25-10-2016
DOI: 10.3354/MEPS11869
Cladophora rhodolithicolasp. nov. (Cladophorales, Chlorophyta), a diminutive species from European maerl beds
Publisher: Informa UK Limited
Date: 05-2009
Taxonomic Reshuffling of the Cladophoraceae
Publisher: Wiley
Date: 12-2016
DOI: 10.1111/JPY.12459
Gain and loss of elongation factor genes in green algae
Publisher: Springer Science and Business Media LLC
Date: 2009
A multi-locus time-calibrated phylogeny of the siphonous green algae
Publisher: Elsevier BV
Date: 03-2009
DOI: 10.1016/J.YMPEV.2008.12.018
Abstract: The siphonous green algae are an assemblage of seaweeds that consist of a single giant cell. They comprise two sister orders, the Bryopsidales and Dasycladales. We infer the phylogenetic relationships among the siphonous green algae based on a five-locus data matrix and analyze temporal aspects of their ersification using relaxed molecular clock methods calibrated with the fossil record. The multi-locus approach resolves much of the previous phylogenetic uncertainty, but the radiation of families belonging to the core Halimedineae remains unresolved. In the Bryopsidales, three main clades were inferred, two of which correspond to previously described suborders (Bryopsidineae and Halimedineae) and a third lineage that contains only the limestone-boring genus Ostreobium. Relaxed molecular clock models indicate a Neoproterozoic origin of the siphonous green algae and a Paleozoic ersification of the orders into their families. The inferred node ages are used to resolve conflicting hypotheses about species ages in the tropical marine alga Halimeda.
Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium
Publisher: Cold Spring Harbor Laboratory
Date: 22-07-2020
DOI: 10.1101/2020.07.21.211367
Abstract: The green alga Ostreobium is an important coral holobiont member, playing key roles in skeletal decalcification and providing photosynthate to bleached corals that have lost their dinoflagellate endosymbionts. Ostreobium lives in the coral’s skeleton, a low-light environment with variable pH and O□ availability. We present the Ostreobium nuclear genome and a metatranscriptomic analysis of healthy and bleached corals to improve our understanding of Ostreobium ’s adaptations to its extreme environment and its roles as a coral holobiont member. The Ostreobium genome has 10,663 predicted protein-coding genes and shows adaptations for life in low and variable light conditions and other stressors in the endolithic environment. This alga presents a rich repertoire of light-harvesting complex proteins but lacks many genes for photoprotection and photoreceptors. It also has a large arsenal of genes for oxidative stress response. An expansion of extracellular peptidases suggests that Ostreobium may supplement its energy needs by feeding on the organic skeletal matrix, and a erse set of fermentation pathways allow it to live in the anoxic skeleton at night. Ostreobium depends on other holobiont members for vitamin B12, and our metatranscriptomes identify potential bacterial sources. Metatranscriptomes showed Ostreobium becoming a dominant agent of photosynthesis in bleached corals and provided evidence for variable responses among coral s les and different Ostreobium genotypes. Our work provides a comprehensive understanding of the adaptations of Ostreobium to its extreme environment and an important genomic resource to improve our comprehension of coral holobiont resilience, bleaching and recovery.
The marine green and brown algae of Rodrigues (Mauritius, Indian Ocean)
Publisher: Informa UK Limited
Date: 12-2004
Molecular survey of the red algal family Rhodomelaceae (Ceramiales, Rhodophyta) in Australia reveals new introduced species
Publisher: Springer Science and Business Media LLC
Date: 07-11-2019
Molecular phylogeny of the Siphonocladales (Chlorophyta: Cladophorophyceae)
Publisher: Elsevier BV
Date: 09-2007
DOI: 10.1016/J.YMPEV.2007.04.016
Abstract: The Siphonocladales are tropical to warm-temperate, marine green macro-algae characterized by a wide variety of thallus morphologies, ranging from branched filaments to pseudo-parenchymatous plants. Phylogenetic analyses of partial large subunit (LSU) rDNA sequences s led from 166 isolates revealed nine well-supported siphonocladalean clades. Analyses of a concatenated dataset of small subunit (SSU) and partial LSU rDNA sequences greatly clarified the phylogeny of the Siphonocladales. However, the position of the root of the Siphonocladales could not be determined unambiguously, as outgroup rooting and molecular clock rooting resulted in a different root placement. Different phylogenetic methods (likelihood, parsimony and distance) yielded similar tree topologies with comparable internal node resolution. Likewise, analyses under more realistic models of sequence evolution, taking into account differences in evolution between stem and loop regions of rRNA, did not differ markedly from analyses using standard four-state models. The molecular phylogeny revealed that all siphonocladalean architectures may be derived from a single Cladophora-like ancestor. Parallel and convergent evolution of various morphological characters (including those traditionally employed to circumscribe the families and genera) have occurred in the Siphonocladales. Consequently, incongruence with traditional classifications, including non-monophyly in all families and most genera, was shown.
The plastid genome of the red alga Laurencia.
Publisher: Wiley
Date: 04-05-2015
DOI: 10.1111/JPY.12297
Abstract: We present the 174,935 nt long plastid genome of the red alga Laurencia sp. JFC0032. It is the third plastid genome characterized for the largest order of red algae (Ceramiales). The circular-mapping plastid genome is small compared to most florideophyte red algae, and our comparisons show a trend toward smaller plastid genome sizes in the family Rhodomelaceae, independent from a similar trend in Cyanidiophyceae. The Laurencia genome is densely packed with 200 annotated protein-coding genes (188 widely conserved, 3 open reading frames shared with other red algae and 9 hypothetical coding regions). It has 29 tRNAs, a single-copy ribosomal RNA cistron, a tmRNA, and the RNase P RNA.
Research note: Identity of the Qingdao algal bloom
Publisher: Wiley
Date: 26-05-2009
One hundred years later, resurrection ofTydemania gardineriA. Gepp & E. Gepp (Udoteaceae, Chlorophyta) based on molecular and morphological data
Publisher: Informa UK Limited
Date: 09-10-2019
The new species Codium recurvatum from Tanzania
Publisher: Informa UK Limited
Date: 24-07-2012
Every refuge has its price: Ostreobium as a model for understanding how algae can live in rock and stay in business
Publisher: Elsevier BV
Date: 2022
Tightly Constrained Genome Reduction and Relaxation of Purifying Selection during Secondary Plastid Endosymbiosis
Publisher: Oxford University Press (OUP)
Date: 06-10-2021
Abstract: Endosymbiosis, the establishment of a former free-living prokaryotic or eukaryotic cell as an organelle inside a host cell, can dramatically alter the genomic architecture of the endosymbiont. Plastids or chloroplasts, the light-harvesting organelle of photosynthetic eukaryotes, are excellent models to study this phenomenon because plastid origin has occurred multiple times in evolution. Here, we investigate the genomic signature of molecular processes acting through secondary plastid endosymbiosis—the origination of a new plastid from a free-living eukaryotic alga. We used phylogenetic comparative methods to study gene loss and changes in selective regimes on plastid genomes, focusing on green algae that have given rise to three independent lineages with secondary plastids (euglenophytes, chlorarachniophytes, and Lepidodinium). Our results show an overall increase in gene loss associated with secondary endosymbiosis, but this loss is tightly constrained by the retention of genes essential for plastid function. The data show that secondary plastids have experienced temporary relaxation of purifying selection during secondary endosymbiosis. However, this process is tightly constrained, with selection relaxed only relative to the background in primary plastids. Purifying selection remains strong in absolute terms even during the endosymbiosis events. Selection intensity rebounds to pre-endosymbiosis levels following endosymbiosis events, demonstrating the changes in selection efficiency during different origin phases of secondary plastids. Independent endosymbiosis events in the euglenophytes, chlorarachniophytes, and Lepidodinium differ in their degree of relaxation of selection, highlighting the different evolutionary contexts of these events. This study reveals the selection–drift interplay during secondary endosymbiosis and evolutionary parallels during organellogenesis.
Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures
Publisher: MDPI AG
Date: 19-10-2020
DOI: 10.3390/V12101180
Abstract: Our knowledge of the ersity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured s les from two major groups of microbial algae: the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to the Tombusviridae and Amalgaviridae viral families commonly associated with land plants. This suggests that the evolutionary history of these viruses extends to ergence events between algae and land plants. Seven Ostreobium sp-associated viruses exhibited sequence similarity to the mitoviruses most commonly found in fungi, compatible with horizontal virus transfer between algae and fungi. We also document, for the first time, RNA viruses associated with chlorarachniophytes, including the first negative-sense (bunya-like) RNA virus in microalgae, as well as a distant homolog of the plant virus Virgaviridae, potentially signifying viral inheritance from the secondary chloroplast endosymbiosis that marked the origin of the chlorarachniophytes. More broadly, these data suggest that the scarcity of RNA viruses in algae results from limited investigation rather than their absence.
Arctic marine forest distribution models showcase potentially severe habitat losses for cryophilic species under climate change
Publisher: Wiley
Date: 08-03-2022
DOI: 10.1111/GCB.16142
Abstract: The Arctic is among the fastest‐warming areas of the globe. Understanding the impact of climate change on foundational Arctic marine species is needed to provide insight on ecological resilience at high latitudes. Marine forests, the underwater seascapes formed by seaweeds, are predicted to expand their ranges further north in the Arctic in a warmer climate. Here, we investigated whether northern habitat gains will compensate for losses at the southern range edge by modelling marine forest distributions according to three distribution categories: cryophilic (species restricted to the Arctic environment), cryotolerant (species with broad environmental preferences inclusive but not limited to the Arctic environment), and cryophobic (species restricted to temperate conditions) marine forests. Using stacked MaxEnt models, we predicted the current extent of suitable habitat for contemporary and future marine forests under Representative Concentration Pathway Scenarios of increasing emissions (2.6, 4.5, 6.0, and 8.5). Our analyses indicate that cryophilic marine forests are already ubiquitous in the north, and thus cannot expand their range under climate change, resulting in an overall loss of habitat due to severe southern range contractions. The extent of marine forests within the Arctic basin, however, is predicted to remain largely stable under climate change with notable exceptions in some areas, particularly in the Canadian Archipelago. Succession may occur where cryophilic and cryotolerant species are extirpated at their southern range edge, resulting in ecosystem shifts towards temperate regimes at mid to high latitudes, though many aspects of these shifts, such as total biomass and depth range, remain to be field validated. Our results provide the first global synthesis of predicted changes to pan‐Arctic coastal marine forest ecosystems under climate change and suggest ecosystem transitions are unavoidable now for some areas.
Highly structured prokaryote communities exist within the skeleton of coral colonies
Publisher: Springer Science and Business Media LLC
Date: 20-10-2018
Multigene Phylogeny, Morphological Observation and Re-examination of the Literature Lead to the Description of the Phaeosacciophyceae Classis Nova and Four New Species of the Heterokontophyta SI Clade
Publisher: Elsevier BV
Date: 12-2020
Complex noncalcified macroalgae from the Silurian of Cornwallis Island, Arctic Canada
Publisher: Cambridge University Press (CUP)
Date: 2011
DOI: 10.1666/10-025.1
Abstract: Thin beds of silty limestone within a Ludlovian (Ludfordian) section of the Cape Phillips Formation on Cornwallis Island, Arctic Canada, contain numerous specimens of noncalcified macroalgae in association with dendroid and graptoloid graptolites, brachiopods, and trilobites. The algal material, preserved as carbonaceous compressions, represents three new taxa, each characterized by a central axis surrounded by laterals. Laterals of Eocladus xiaoi n. gen. n. sp. are thin and branch to the fifth order whereas those of Chaetocladus captitatus n. sp. are un ided and form a distinctive capitulum. Thalli of Palaeocymopolia nunavutensis n. gen. n. sp. have a branched, serial-segmented form and a corticated structure. On the basis of thallus architecture, all three taxa are assigned to the extant green algal order Dasycladales. Parallels exist between this macroalgal assemblage and a modern macroalgal association in Florida Bay.
The recognition of Caulerpa integerrima (Zanardini) comb. et stat. nov (Bryopsidales, Chlorophyta) from the Red Sea
Publisher: Informa UK Limited
Date: 07-2009
DOI: 10.2216/08-78.1
Divergence times and plastid phylogenomics within the intron-rich order Erythropeltales (Compsopogonophyceae, Rhodophyta)
Publisher: Wiley
Date: 13-04-2021
DOI: 10.1111/JPY.13159
Abstract: The advent of high‐throughput sequencing (HTS) has allowed for the use of large numbers of coding regions to produce robust phylogenies. These phylogenies have been used to highlight relationships at ancient ersifications (subphyla, class) and highlight the evolution of plastid genome structure. The Erythropeltales are an order in the Compsopogonophyceae, a group with unusual plastid genomes but with low taxon s ling. We use HTS to produce near complete plastid genomes of all genera, and multiple species within some genera, to produce robust phylogenies to investigate character evolution, dating of ergence in the group, and plastid organization, including intron patterns. Our results produce a fully supported phylogeny of the genera in the Erythropeltales and suggest that morphologies (upright versus crustose) have evolved multiple times. Our dated phylogeny also indicates that the order is very old (~800 Ma), with ersification occurring after the ice ages of the Cryogenian period (750–635 Ma). Plastid gene order is congruent with phylogenetic relationships and suggests that genome architecture does not change often. Our data also highlight the abundance of introns in the plastid genomes of this order. We also produce a nearly complete plastid genome of Tsunamia transpacifica (Stylonematophyceae) to add to the taxon s ling of genomes of this class. The use of plastid genomes clearly produces robust phylogenetic relationships that can be used to infer evolutionary events, and increased taxon s ling, especially in less well‐known red algal groups, will provide additional insights into their evolution.
Phylogeny and Evolution of the Brown Algae
Publisher: Informa UK Limited
Date: 03-07-2020
Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae
Publisher: Cold Spring Harbor Laboratory
Date: 05-10-2021
DOI: 10.1101/2021.10.04.463119
Abstract: The genomic ersity underpinning high ecological and species ersity in the green algae (Chlorophyta) remains little known. Here, we aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage-specific innovations of the Core Chlorophyta. We generated a high-quality nuclear genome for pedinophyte YPF701, a sister lineage to others in the Core Chlorophyta, and incorporated this genome in a comparative analysis with 25 other genomes from erse Viridiplantae taxa. The nuclear genome of pedinophyte YPF701 has an intermediate size and gene number between those of most early- erging prasinophytes and the remainder of the Core Chlorophyta. Our results suggest positive selection for genome streamlining in Pedinophyceae, independent from genome minimisation observed among prasinophyte lineages. Genome expansion was predicted along the branch leading to the UTC clade (classes Ulvophyceae, Trebouxiophyceae and Chlorophyceae) after ergence from their common ancestor with pedinophytes, with genomic novelty implicated in a range of basic biological functions. These results emphasise multiple independent signals of genome minimisation within the Chlorophyta, as well as the genomic novelty arising prior to ersification in the UTC clade, which may underpin the success of this species-rich clade in a ersity of habitats.
Multigene phylogeny of the red algal subclass Nemaliophycidae
Publisher: Elsevier BV
Date: 2016
DOI: 10.1016/J.YMPEV.2015.10.015
Abstract: The red algae (Rhodophyta) are a lineage of primary endosymbionts whose ancestors represent some of the first photosynthetic eukaryotes on the planet. They primarily inhabit marine ecosystems, with only ∼5% of species found in freshwater systems. The subclass Nemaliophycidae is very erse in ecological and life history features and therefore a useful model to study these traits, but the phylogenetic relationships among the orders are, for the most part, poorly resolved. To elucidate the phylogeny of the Nemaliophycidae, we constructed a nine-gene dataset comprised of nuclear, plastid, and mitochondrial markers for 67 red algal specimens. The resulting maximum likelihood (ML) phylogeny confirmed the monophyly of all orders. The sister relationship of the Acrochaetiales and Palmariales received high support and the relationship of the Balliales with Balbianiales and Entwisleiales with Colaconematales was moderately supported. The Nemaliales, Entwisleiales, Colaconematales, Palmariales and Acrochaetiales formed a highly supported clade. Unfortunately, all other relationships among the orders had low bootstrap support. Although the ML analysis did not resolve many of the relationships, further analyses suggested that a resolution is possible. A Phycas analysis supported a dichotomously branching tree and Bayesian analysis showed a similar topology with all relationships highly supported. Simulations extrapolating the number of nucleotide characters beyond the current size of the dataset suggested that most nodes in the phylogeny would be resolved if more data become available. Phylogenomic approaches will be necessary to provide a well-supported phylogeny of this subclass with all relationships resolved such that the evolution of freshwater species from marine ancestors as well as reproductive traits can be explored.
Phylogenomic analysis of pseudocryptic diversity reveals the new genus Deltalsia (Rhodomelaceae, Rhodophyta)
Publisher: Wiley
Date: 02-01-2023
DOI: 10.1111/JPY.13311
Abstract: Molecular analyses, in combination with morphological studies, provide invaluable tools for delineating red algal taxa. However, molecular datasets are incomplete and taxonomic revisions are often required once additional species or populations are sequenced. The small red alga Conferva parasitica was described from the British Isles in 1762 and then reported from other parts of Europe. Conferva parasitica was traditionally included in the genus Pterosiphonia (type species P. cloiophylla in Schmitz and Falkenberg 1897), based on its morphological characters, and later transferred to Symphyocladia and finally to Symphyocladiella using molecular data from an Iberian specimen. However, although morphological differences have been observed between specimens of Symphyocladiella parasitica from northern and southern Europe they have yet to be investigated in a phylogenetic context. In this study, we collected specimens from both regions, studied their morphology and analyzed rbc L and cox 1 DNA sequences. We determined the phylogenetic position of a British specimen using a phylogenomic approach based on mitochondrial and plastid genomes. Northern and southern European populations attributed to S. parasitica represent different species. Symphyocladiella arecina sp. nov. is proposed for specimens from southern Europe, but British specimens were resolved as a distant sister lineage to the morphologically distinctive Amplisiphonia , so we propose the new genus Deltalsia for this species. Our study highlights the relevance of using materials collected close to the type localities for taxonomic reassessments, and showcases the utility of genome‐based phylogenies for resolving classification issues in the red algae.
Chloroplast Genome Traits Correlate With Organismal Complexity and Ecological Traits in Chlorophyta
Publisher: Frontiers Media SA
Date: 08-12-2021
Abstract: A positive relationship between cell size and chloroplast genome size within chloroplast-bearing protists has been hypothesized in the past and shown in some case studies, but other factors influencing chloroplast genome size during the evolution of chlorophyte algae have been less studied. We study chloroplast genome size and GC content as a function of habitats and cell size of chlorophyte algae. The chloroplast genome size of green algae in freshwater, marine and terrestrial habitats was differed significantly, with terrestrial algae having larger chloroplast genome sizes in general. The most important contributor to these enlarged genomes in terrestrial species was the length of intergenic regions. There was no clear difference in the GC content of chloroplast genomes from the three habitats categories. Functional morphological categories also showed differences in chloroplast genome size, with filamentous algae having substantially larger genomes than other forms of algae, and foliose algae had lower GC content than other groups. Chloroplast genome size showed no significant differences among the classes Ulvophyceae, Trebouxiophyceae, and Chlorophyceae, but the GC content of Chlorophyceae chloroplast genomes was significantly lower than that of Ulvophyceae and Trebouxiophyceae. There was a certain positive relationship between chloroplast genome size and cell size for the Chlorophyta as a whole and within each of three major classes. Our data also confirmed previous reports that ancestral quadripartite architecture had been lost many times independently in Chlorophyta. Finally, the comparison of the phenotype of chlorophytes algae harboring plastids uncovered that most of the investigated Chlorophyta algae housed a single plastid per cell.
Atypical development of Chaetomorpha antennina in culture (Cladophorales, Chlorophyta)
Publisher: Wiley
Date: 27-01-2011
SPECIES DELIMITATION, TAXONOMY, AND BIOGEOGRAPHY OF DICTYOTA IN EUROPE (DICTYOTALES, PHAEOPHYCEAE)1
Publisher: Wiley
Date: 02-11-2010
Morphological evolution and classification of the red algal order Ceramiales inferred using plastid phylogenomics
Publisher: Elsevier BV
Date: 08-2019
DOI: 10.1016/J.YMPEV.2019.04.022
Abstract: The order Ceramiales contains about one third of red algal ersity and it was classically classified into four families according to morphology. The first phylogenies based on one or two molecular markers were poorly supported and failed to resolve these families as monophyletic. Nine families are currently recognized, but relationships within and among them are poorly understood. We produced a well-resolved phylogeny for the Ceramiales using plastid genomes for 80 (28 newly sequenced) representative species of the major lineages. Three of the previously recognized families were resolved as independent monophyletic lineages: Ceramiaceae, Wrangeliaceae and Rhodomelaceae. By contrast, our results indicated that the other six families require reclassification. We propose the new order Inkyuleeales, a new circumscription of the Callithamniaceae to include the Spyridiaceae, and a new concept of the Delesseriaceae that includes the Sarcomeniaceae and the Dasyaceae. We also investigated the evolution of the thallus structure, which has been important in the classical delineation of families. The ancestor of the Ceramiales was a monosiphonous filament that evolved into more complex morphologies several times independently during the evolutionary history of this hyper erse lineage.
Unique biodiversity in Arctic marine forests is shaped by diverse recolonization pathways and far northern glacial refugia
Publisher: Proceedings of the National Academy of Sciences
Date: 25-08-2020
Abstract: Our work challenges the existing paradigm that marine Arctic ecosystems are depauperate extensions of southerly (temperate) communities established in the wake of recent glaciation, fundamentally changing how these systems should be viewed and interpreted. We forward hypotheses regarding the history of Arctic marine systems, particularly with regards to endemism being an integral feature of Arctic biomes, and present a firm framework for future evolutionary research in this system typically viewed as “ecologically immature.”
Molecular diversity of the Caulerpa racemosa–Caulerpa peltata complex (Caulerpaceae, Bryopsidales) in New Caledonia, with new Australasian records for C. racemosa var. cylindra
Publisher: Informa UK Limited
Date: 2013
DOI: 10.2216/11-116.1
AN UNRECOGNIZED ANCIENT LINEAGE OF GREEN PLANTS PERSISTS IN DEEP MARINE WATERS1
Publisher: Wiley
Date: 27-09-2010
Plastid phylogenomics with broad taxon sampling further elucidates the distinct evolutionary origins and timing of secondary green plastids
Publisher: Springer Science and Business Media LLC
Date: 24-01-2018
DOI: 10.1038/S41598-017-18805-W
Abstract: Secondary plastids derived from green algae occur in chlorarachniophytes, photosynthetic euglenophytes, and the dinoflagellate genus Lepidodinium . Recent advances in understanding the origin of these plastids have been made, but analyses suffer from relatively sparse taxon s ling within the green algal groups to which they are related. In this study we aim to derive new insights into the identity of the plastid donors, and when in geological time the independent endosymbiosis events occurred. We use newly sequenced green algal chloroplast genomes from carefully chosen lineages potentially related to chlorarachniophyte and Lepidodinium plastids, combined with recently published chloroplast genomes, to present taxon-rich phylogenetic analyses to further pinpoint plastid origins. We integrate phylogenies with fossil information and relaxed molecular clock analyses. Our results indicate that the chlorarachniophyte plastid may originate from a precusor of siphonous green algae or a closely related lineage, whereas the Lepidodinium plastid originated from a pedinophyte. The euglenophyte plastid putatively originated from a lineage of prasinophytes within the order Pyramimonadales. Our molecular clock analyses narrow in on the likely timing of the secondary endosymbiosis events, suggesting that the event leading to Lepidodinium likely occurred more recently than those leading to the chlorarachniophyte and photosynthetic euglenophyte lineages.
MOLECULAR AND MORPHOMETRIC DATA PINPOINT SPECIES BOUNDARIES IN HALIMEDA SECTION RHIPSALIS (BRYOPSIDALES, CHLOROPHYTA)1
Publisher: Wiley
Date: 18-05-2005
A new marine prasinophyte genus alternates between a flagellate and a dominant benthic stage with microrhizoids for adhesion
Publisher: Wiley
Date: 09-10-2019
DOI: 10.1111/JPY.12909
Abstract: Prasinophytes (Chlorophyta) are a erse, paraphyletic group of planktonic microalgae for which benthic species are largely unknown. Here, we report a sand-dwelling, marine prasinophyte with several novel features observed in clonal cultures established from numerous locations around Australia. The new genus and species, which we name Microrhizoidea pickettheapsiorum (Mamiellophyceae), alternates between a benthic palmelloid colony, where cell ision occurs, and a planktonic flagellate. Flagellates are short lived, settle and quickly resorb their flagella, the basal bodies then nucleate novel tubular appendages, termed "microrhizoids", that lack an axoneme and function to anchor benthic cells to the substratum. To our knowledge, microrhizoids have not been observed in any other green alga or protist, are slightly smaller in diameter than flagella, generally contain nine microtubules, are long (3-5 times the length of flagella) and are not encased in scales. Following settlement, cell isions result in a loose, palmelloid colony, each cell connected to the substratum by two microrhizoids. Flagellates are round to bean-shaped with two long, slightly uneven flagella. Both benthic cells and flagellates, along with their flagella, are encased in thin scales. Phylogenies based on the complete chloroplast genome of Microrhizoidea show that it is clearly a member of the Mamiellophyceae, most closely related to Dolichomastix tenuilepsis. More taxon-rich phylogenetic analyses of the 18S rRNA gene, including metabarcodes from the Tara Oceans and Ocean S ling Day projects, confidently show the distinctive nature of Microrhizoidea, and that the described bio ersity of the Mamiellophyceae is a fraction of its real bio ersity. The discovery of a largely benthic prasinophyte changes our perspective on this group of algae and, along with the observation of other potential benthic lineages in environmental sequences, illustrates that benthic habitats can be a rich ground for algal biodiscovery.
The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns
Publisher: PeerJ
Date: 03-01-2020
DOI: 10.7717/PEERJ.8273
Abstract: Within the siphonous green algal order Bryopsidales, the size and gene arrangement of chloroplast genomes has been examined extensively, while mitochondrial genomes have been mostly overlooked. The recently published mitochondrial genome of Caulerpa lentillifera is large with expanded noncoding DNA, but it remains unclear if this is characteristic of the entire order. Our study aims to evaluate the evolutionary forces shaping organelle genome dynamics in the Bryopsidales based on the C. lentillifera and Ostreobium quekettii mitochondrial genomes. In this study, the mitochondrial genome of O. quekettii was characterised using a combination of long and short read sequencing, and bioinformatic tools for annotation and sequence analyses. We compared the mitochondrial and chloroplast genomes of O. quekettii and C. lentillifera to examine hypotheses related to genome evolution. The O. quekettii mitochondrial genome is the largest green algal mitochondrial genome sequenced (241,739 bp), considerably larger than its chloroplast genome. As with the mtDNA of C. lentillifera , most of this excess size is from the expansion of intergenic DNA and proliferation of introns. Inflated mitochondrial genomes in the Bryopsidales suggest effective population size, recombination and/or mutation rate, influenced by nuclear-encoded proteins, differ between the genomes of mitochondria and chloroplasts, reducing the strength of selection to influence evolution of their mitochondrial genomes.
Molecular survey of Codium species diversity in southern Madagascar
Publisher: Museum National d'Histoire Naturelle, Paris, France
Date: 05-2015
The Forgotten genusPseudoderbesia(Bryopsidales, Chlorophyta)
Publisher: Museum National d'Histoire Naturelle, Paris, France
Date: 08-2014
Molecular analyses resolve the phylogenetic position of Polysiphonia adamsiae (Rhodomelaceae, Rhodophyta) and reveal a strong phylogeographic structure in Australia
Publisher: Informa UK Limited
Date: 09-2018
DOI: 10.2216/18-36.1
The Organelle Genomes in the Photosynthetic Red Algal Parasite Pterocladiophila hemisphaerica (Florideophyceae, Rhodophyta) Have Elevated Substitution Rates and Extreme Gene Loss in the Plastid Genome
Publisher: Wiley
Date: 20-04-2020
DOI: 10.1111/JPY.12996
Improving Transferability of Introduced Species’ Distribution Models: New Tools to Forecast the Spread of a Highly Invasive Seaweed
Publisher: Public Library of Science (PLoS)
Date: 28-06-2013
Six Newly Sequenced Chloroplast Genomes From Trentepohliales: The Inflated Genomes, Alternative Genetic Code and Dynamic Evolution
Publisher: Frontiers Media SA
Date: 08-12-2021
Abstract: Cephaleuros is often known as an algal pathogen with 19 taxonomically valid species, some of which are responsible for red rust and algal spot diseases in vascular plants. No chloroplast genomes have yet been reported in this genus, and the limited genetic information is an obstacle to understanding the evolution of this genus. In this study, we sequenced six new Trentepohliales chloroplast genomes, including four Cephaleuros and two Trentepohlia . The chloroplast genomes of Trentepohliales are large compared to most green algae, ranging from 216 to 408 kbp. They encode between 93 and 98 genes and have a GC content of 26–36%. All new chloroplast genomes were circular-mapping and lacked a quadripartite structure, in contrast to the previously sequenced Trentepohlia odorata , which does have an inverted repeat. The duplicated trnD -GTC , petD , and atpA genes in C. karstenii may be remnants of the IR region and shed light on its reduction. Chloroplast genes of Trentepohliales show elevated rates of evolution, strong rearrangement dynamics and several genes display an alternative genetic code with reassignment of the UGA/UAG codon presumably coding for arginine. Our results present the first whole chloroplast genome of the genus Cephaleuros and enrich the chloroplast genome resources of Trentepohliales.
Extensive cryptic diversity in the widely distributed Polysiphonia scopulorum (Rhodomelaceae, Rhodophyta): Molecular species delimitation and morphometric analyses
Publisher: Elsevier BV
Date: 11-2020
Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae.
Publisher: Wiley
Date: 06-01-2022
DOI: 10.1111/NPH.17926
Abstract: The genomic ersity underpinning high ecological and species ersity in the green algae (Chlorophyta) remains little known. Here, we aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage-specific innovations of the core Chlorophyta. We generated a high-quality nuclear genome for pedinophyte YPF701, a sister lineage to others in the core Chlorophyta and incorporated this genome in a comparative analysis with 25 other genomes from erse Viridiplantae taxa. The nuclear genome of pedinophyte YPF701 has an intermediate size and gene number between those of most prasinophytes and the remainder of the core Chlorophyta. Our results suggest positive selection for genome streamlining in the Pedinophyceae, independent from genome minimisation observed among prasinophyte lineages. Genome expansion was predicted along the branch leading to the UTC clade (classes Ulvophyceae, Trebouxiophyceae and Chlorophyceae) after ergence from their last common ancestor with pedinophytes, with genomic novelty implicated in a range of basic biological functions. Results emphasise multiple independent signals of genome minimisation within the Chlorophyta, as well as the genomic novelty arising before ersification in the UTC clade, which may underpin the success of this species-rich clade in a ersity of habitats.
Multiple techniques point to oxygenic phototrophs dominating the Isopora palifera skeletal microbiome
Publisher: Springer Science and Business Media LLC
Date: 15-02-2021
High-throughput sequencing for algal systematics
Publisher: Informa UK Limited
Date: 18-04-2018
Metaphor - A workflow for streamlined assembly and binning of metagenomes
Publisher: Cold Spring Harbor Laboratory
Date: 10-02-2023
DOI: 10.1101/2023.02.09.527784
Abstract: Recent advances in bioinformatics and high-throughput sequencing have enabled the large-scale recovery of genomes from metagenomes. This has the potential to bring important insights as researchers can bypass cultivation and analyse genomes sourced directly from environmental s les. There are, however, technical challenges associated with this process, most notably the complexity of computational workflows required to process metagenomic data, which include dozens of bioinformatics software tools, each with their own set of customisable parameters that affect the final output of the workflow. At the core of these workflows are the processes of assembly - combining the short input reads into longer, contiguous fragments (contigs), and binning - clustering these contigs into in idual genome bins. Both processes can be done for each s le separately or by pooling together multiple s les to leverage information from a combination of s les. Here we present Metaphor, a fully-automated workflow for genome-resolved metagenomics (GRM). Metaphor differs from existing GRM workflows by offering flexible approaches for the assembly and binning of the input data, and by combining multiple binning algorithms with a bin refinement step to achieve high quality genome bins. Moreover, Metaphor generates reports to evaluate the performance of the workflow. We showcase the functionality of Metaphor on different synthetic datasets, and the impact of available assembly and binning strategies on the final results. The workflow is freely available at inisalazar/metaphor . We present Metaphor, a user-friendly, automated workflow for the recovery of genomes from metagenomes. Our tool offers flexible options for assembling and binning metagenomic contigs, that may be adjusted according to the characteristics of the input data and available computational resources, and a combination of binning algorithms, which improves the quantity and quality of resulting genome bins. We showcase the performance of Metaphor on synthetic benchmarking datasets and discuss the implication of methodological decisions regarding the strategy for assembling and binning metagenomic contigs.
Permanent residents or temporary lodgers: characterizing intracellular bacterial communities in the siphonous green alga Bryopsis
Publisher: The Royal Society
Date: 07-03-2013
Abstract: The ecological success of giant celled, siphonous green algae in coastal habitats has repeatedly been linked to endophytic bacteria living within the cytoplasm of the hosts. Yet, very little is known about the relative importance of evolutionary and ecological factors controlling the intracellular bacterial flora of these seaweeds. Using the marine alga Bryopsis (Bryopsidales, Chlorophyta) as a model, we explore the ersity of the intracellular bacterial communities and investigate whether their composition is controlled by ecological and biogeographic factors rather than the evolutionary history of the host. Using a combination of 16S rDNA clone libraries and denaturing gradient gel electrophoresis analyses, we show that Bryopsis harbours a mixture of relatively few but phylogenetically erse bacterial species. Variation partitioning analyses show a strong impact of local environmental factors on the presence of Rickettsia and Mycoplasma in their association with Bryopsis . The presence of Flavobacteriaceae and Bacteroidetes, on the other hand, reflects a predominant imprint of host evolutionary history, suggesting that these bacteria are more specialized in their association. The results highlight the importance of interpreting the presence of in idual bacterial phylotypes in the light of ecological and evolutionary principles such as phylogenetic niche conservatism to understand complex endobiotic communities and the parameters shaping them.
The Ulvophyceae (Chlorophyta) of eastern Sorsogon, Philippines, including Halimeda magnicuneata sp. nov. (Bryopsidales)
Publisher: Walter de Gruyter GmbH
Date: 31-08-2020
Abstract: The marine algal flora of eastern Sorsogon has been intensively collected and is generally considered as the richest in the Philippines. A trend of species records in the area has been dominated by rhodophytes (red algae) with significantly fewer similar studies for other algal groups (green and brown algae). In this study we present an updated catalogue of the green seaweeds (Ulvophyceae) of eastern Sorsogon. A checklist, including notes on taxonomy, is given of the 103 species. Twenty-six species are newly recorded locally of which five represent new records for the Philippines: Avrainvillea amadelpha , Caulerpa buginensis, an unidentified Caulerpa species, Codium cf. latum , and one taxon new to science. The new species is described as Halimeda magnicuneata Verbruggen et Dumilag based on morpho-anatomy and DNA sequence data. The number of ulvophycean species recorded in eastern Sorsogon is found to be the highest in the Philippines. This may be a result of the high collection effort in the region, as well as eastern Sorsogon’s erse habitats providing favourable conditions for a wide range of seaweed species.
NICHE PARTITIONING AND THE COEXISTENCE OF TWO CRYPTIC DICTYOTA (DICTYOTALES, PHAEOPHYCEAE) SPECIES FROM THE CANARY ISLANDS1
Publisher: Wiley
Date: 02-11-2010
Halimeda pygmaea and Halimeda pumila(Bryopsidales,Chlorophyta): two new dwarf species from fore reef slopes in Fiji and the Bahamas
Publisher: Informa UK Limited
Date: 04-09-2007
DOI: 10.2216/07-01.1
DNA sequencing and anatomy demonstrate that Pacific Codium simulans is a genetically variable species found in the floras of Bermuda and Florida
Publisher: Wiley
Date: 16-07-2020
DOI: 10.1111/PRE.12396
Into the deep: New discoveries at the base of the green plant phylogeny
Publisher: Wiley
Date: 11-07-2011
Abstract: Recent data have provided evidence for an unrecognised ancient lineage of green plants that persists in marine deep-water environments. The green plants are a major group of photosynthetic eukaryotes that have played a prominent role in the global ecosystem for millions of years. A schism early in their evolution gave rise to two major lineages, one of which ersified in the world's oceans and gave rise to a large ersity of marine and freshwater green algae (Chlorophyta) while the other gave rise to a erse array of freshwater green algae and the land plants (Streptophyta). It is generally believed that the earliest- erging Chlorophyta were motile planktonic unicellular organisms, but the discovery of an ancient group of deep-water seaweeds has challenged our understanding of the basal branches of the green plant phylogeny. In this review, we discuss current insights into the origin and ersification of the green plant lineage.
Outstanding Challenges in the Transferability of Ecological Models
Publisher: Elsevier BV
Date: 10-2018
DOI: 10.1016/J.TREE.2018.08.001
Abstract: Predictive models are central to many scientific disciplines and vital for informing management in a rapidly changing world. However, limited understanding of the accuracy and precision of models transferred to novel conditions (their 'transferability') undermines confidence in their predictions. Here, 50 experts identified priority knowledge gaps which, if filled, will most improve model transfers. These are summarized into six technical and six fundamental challenges, which underlie the combined need to intensify research on the determinants of ecological predictability, including species traits and data quality, and develop best practices for transferring models. Of high importance is the identification of a widely applicable set of transferability metrics, with appropriate tools to quantify the sources and impacts of prediction uncertainty under novel conditions.
Patterns and drivers of species diversity in the Indo‐Pacific red seaweed Portieria
Publisher: Wiley
Date: 22-07-2018
DOI: 10.1111/JBI.13410
Organellar genomics: a useful tool to study evolutionary relationships and molecular evolution in Gracilariaceae (Rhodophyta)
Publisher: Wiley
Date: 12-09-2018
DOI: 10.1111/JPY.12765
Abstract: Gracilariaceae has a worldwide distribution including numerous economically important species. We applied high-throughput sequencing to obtain organellar genomes (mitochondria and chloroplast) from 10 species of Gracilariaceae and, combined with published genomes, to infer phylogenies and compare genome architecture among species representing main lineages. We obtained similar topologies between chloroplast and mitochondrial genomes phylogenies. However, the chloroplast phylogeny was better resolved with full support. In this phylogeny, Melanthalia intermedia is sister to a monophyletic clade including Gracilaria and Gracilariopsis, which were both resolved as monophyletic genera. Mitochondrial and chloroplast genomes were highly conserved in gene synteny, and variation mainly occurred in regions where insertions of plasmid-derived sequences (PDS) were found. In mitochondrial genomes, PDS insertions were observed in two regions where the transcription direction changes: between the genes cob and trnL, and trnA and trnN. In chloroplast genomes, PDS insertions were in different positions, but generally found between psdD and rrs genes. Gracilariaceae is a good model system to study the impact of PDS in genome evolution due to the frequent presence of these insertions in organellar genomes. Furthermore, the bacterial leuC/leuD operon was found in chloroplast genomes of Gracilaria tenuistipitata, G. chilensis, and M. intermedia, and in extrachromosomal plasmid of G. vermiculophylla. Phylogenetic trees show two different origins of leuC/leuD: genes found in chloroplast and plasmid were placed with proteobacteria, and genes encoded in the nucleus were close to Viridiplantae and cyanobacteria.
Rhodenigma contortum, an obscure new genus and species of Rhodogorgonales (Rhodophyta) from Western Australia
Publisher: Wiley
Date: 14-04-2016
DOI: 10.1111/JPY.12402
Abstract: An unknown microscopic, branched filamentous red alga was isolated into culture from coral fragments collected in Coral Bay, Western Australia. It grew well unattached or attached to glass with no reproduction other than fragmentation of filaments. Cells of some branch tips became slightly contorted and digitated, possibly as a substrate-contact-response seen at filament tips of various algae. Attached multicellular compact disks on glass had a very different cellular configuration and size than the free filaments. In culture the filaments did not grow on or in coral fragments. Molecular phylogenies based on four markers (rbcL, cox1, 18S, 28S) clearly showed it belongs to the order Rhodogorgonales, as a sister clade of Renouxia. Based on these results, the alga is described as the new genus and species Rhodenigma contortum in the Rhodogorgonaceae. It had no morphological similarity to either of the other genera in Rhodogorgonaceae and illustrates the unknown ersity in cryptic habitats such as tropical coral rubble.
Molecular analyses of turf algae reveal a new species and an undetected introduction in the Pterosiphonieae (Rhodomelaceae, Rhodophyta)
Publisher: Wiley
Date: 04-05-2023
DOI: 10.1111/JPY.13336
Abstract: Introduced seaweeds and undescribed species often remain undetected because marine regional floras are as yet poorly understood. DNA sequencing facilitates their detection, but databases are incomplete, so their improvement will continue to lead the discovery of these species. Here we aim to clarify the taxonomy of two turf‐forming red algal Australian species that morphologically resemble the European Aphanocladia stichidiosa . We also aim to elucidate whether either of these species could have been introduced in Europe or Australia. We studied their morphology, analyzed 17 rbc L sequences of European and Australian specimens, examined their generic assignment using a phylogeny based on 24 plastid genomes, and investigated their biogeography using a taxon‐rich phylogeny including 52 rbc L sequences of species in the Pterosiphonieae. The rbc L sequences of one of the Australian species were identical to A. stichidiosa from Europe, considerably expanding its known distribution. Unexpectedly, our phylogenetic analyses resolved this species in the Lophurella clade rather than in Aphanocladia and the new combination L. stichidiosa is proposed. The other Australian species is described as L. pseudocorticata sp. nov. Although L. stichidiosa was originally described in the Mediterranean ca. 70 years ago, our phylogenetic analyses placed it in a lineage restricted to the southern hemisphere, showing that it is native to Australia and introduced to Europe. This study confirms that further work using molecular tools is needed to characterize seaweed ersity, especially among the poorly explored algal turfs, and showcases the usefulness of phylogenetic approaches to uncover introduced species and to determine their native ranges.
Whole‐genome sequencing reveals forgotten lineages and recurrent hybridizations within the kelp genus Alaria (Phaeophyceae)
Publisher: Wiley
Date: 12-10-2021
DOI: 10.1111/JPY.13212
Abstract: The genomic era continues to revolutionize our understanding of the evolution of bio ersity. In phycology, emphasis remains on assembling nuclear and organellar genomes, leaving the full potential of genomic datasets to answer long‐standing questions about the evolution of bio ersity largely unexplored. Here, we used whole‐genome sequencing (WGS) datasets to survey species ersity in the kelp genus Alaria , compare phylogenetic signals across organellar and nuclear genomes, and specifically test whether phylogenies behave like trees or networks. Genomes were sequenced from across the global distribution of Alaria (including Alaria crassifolia , A. praelonga , A. crispa , A. marginata , and A. esculenta ), representing over 550 GB of data and over 2.2 billion paired reads. Genomic datasets retrieved 3,814 and 4,536 single‐nucleotide polymorphisms (SNPs) for mitochondrial and chloroplast genomes, respectively, and upwards of 148,542 high‐quality nuclear SNPs. WGS revealed an Arctic lineage of Alaria , which we hypothesize represents the synonymized taxon A. grandifolia . The SNP datasets also revealed inconsistent topologies across genomic compartments, and hybridization (i.e., phylogenetic networks) between Pacific A . praelonga , A . crispa , and putative A . grandifolia , and between some lineages of the A . marginata complex. Our analysis demonstrates the potential for WGS data to advance our understanding of evolution and bio ersity beyond licon sequencing, and that hybridization is potentially an important mechanism contributing to novel lineages within Alaria . We also emphasize the importance of surveying phylogenetic signals across organellar and nuclear genomes, such that models of mixed ancestry become integrated into our evolutionary and taxonomic understanding.
Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera
Publisher: Research Square Platform LLC
Date: 26-07-2022
DOI: 10.21203/RS.3.RS-1890655/V1
Abstract: At present our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed towards the millimetre-thin coral tissue, leaving the erse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals' Porites lutea and Isopora palifera , through a compendium of ~ 400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 microbial classes. Skeletal microbiomes harboured a erse array of stress response genes, including dimethylsulfoniopropionate synthesis ( dsy B) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulphate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.
Diversity of Halimeda (Bryopsidales, Chlorophyta) in New Caledonia: a Combined Morphological and Molecular Study
Publisher: Wiley
Date: 16-11-2012
DOI: 10.1111/JPY.12002
Abstract: Halimeda is a genus of calcified and segmented green macroalgae in the order Bryopsidales. In New Caledonia, the genus is abundant and represents an important part of the reef flora. Previous studies recorded 19 species that were identified using morphological criteria. The aim of this work was to reassess the ersity of the genus in New Caledonia using morpho-anatomical examinations and molecular analyses of the plastid tufA and rbcL genes. Our results suggest the occurrence of 22 species. Three of these are reported for the first time from New Caledonia: Halimeda kanaloana, H. xishaensis, and an entity resembling H. stuposa. DNA analyses revealed that the species H. fragilis exhibits cryptic or pseudocryptic ersity in New Caledonia. We also show less conclusive evidence for cryptic species within H. taenicola.
Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera
Publisher: Oxford University Press (OUP)
Date: 28-12-2022
DOI: 10.1093/GIGASCIENCE/GIAC127
Abstract: At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the erse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a erse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.
Three new cryptogenic species in the tribes Polysiphonieae and Streblocladieae (Rhodomelaceae, Rhodophyta)
Publisher: Informa UK Limited
Date: 11-2017
DOI: 10.2216/17-17.1
The phylogenetic position of the morphologically unusual Pleurostichidium falkenbergii (Rhodomelaceae, Rhodophyta) based on plastid phylogenomics
Publisher: Informa UK Limited
Date: 07-03-2019
The Bacterial Microbiome of the Coral Skeleton Algal Symbiont Ostreobium Shows Preferential Associations and Signatures of Phylosymbiosis
Publisher: Springer Science and Business Media LLC
Date: 31-03-2023
DOI: 10.1007/S00248-023-02209-7
Abstract: Ostreobium , the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria, (2) enriched tightly attached and potential intracellular bacteria, and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with erse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include known nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs, and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton s les, we show that the Ostreobium -bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives.
Codium pulvinatum (Bryopsidales, Chlorophyta), a new species from the Arabian Sea, recently introduced into the Mediterranean Sea
Publisher: Informa UK Limited
Date: 2018
DOI: 10.2216/17-74.1
Tracing the introduction history of the brown seaweed Dictyota cyanoloma (Phaeophyceae, Dictyotales) in Europe
Publisher: Informa UK Limited
Date: 02-01-2017
Structure and formation of the perforated theca defining the Pelagophyceae (Heterokonta), and three new genera that substantiate the diverse nature of the class
Publisher: Wiley
Date: 22-12-2022
DOI: 10.1111/JPY.13294
Abstract: The pelagophytes, a morphologically erse class of marine heterokont algae, have been historically united only by DNA sequences. Recently we described a novel perforated theca (PT) encasing cells from the Pelagophyceae and hypothesized it may be the first morphological feature to define the class. Here we consolidate that observation, describing a PT for the first time in an additional seven pelagophyte genera, including three genera new to science. We established clonal cultures of pelagophytes collected from intertidal pools located around Australia, and established phylogenetic trees based on nuclear 18S rDNA and plastid rbc L, psa A, psa B, psb A and psb C gene sequences that led to the discovery of three new species: Wyeophycus julieharrissiae and Chromopallida australis form a distinct lineage along with Ankylochrysis lutea within the Pelagomonadales, while Pituiglomerulus capricornicus is sister genus to Chrysocystis fragilis in the Chrysocystaceae (Sarcinochrysidales). Using fixation by high‐pressure freezing for electron microscope observations, a distinctive PT was observed in the three new genera described in this paper, as well as four genera not previously investigated: Chrysoreinhardia , Sargassococcus , Sungminbooa and Andersenia . The mechanism of PT formation is novel, being fabricated from rafts in Golgi‐derived vesicles before being inserted into an established PT. Extracellular wall and/or mucilage layers assemble exterior to the PT in most pelagophytes, the materials likewise secreted by Golgi‐derived vesicles, though the mechanism of secretion is novel. Secretory vesicles never fuse with the plasma membrane as in classic secretion and deposition, but rather relocate extracellularly beneath the PT and disintegrate, the contents having to pass through the PT prior to wall and/or mucilage synthesis. This study substantiates the erse nature of pelagophytes, and provides further evidence that the PT is a sound morphological feature to define the Pelagophyceae, with all 14 of the 20 known genera studied to date by TEM possessing a PT.
Beneath the surface: community assembly and functions of the coral skeleton microbiome
Publisher: Springer Science and Business Media LLC
Date: 12-2019
DOI: 10.1186/S40168-019-0762-Y
Abstract: Coral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue and the underlying skeleton are home to a rich bio ersity of eukaryotic, bacterial and archaeal species that form an integral part of the coral holobiont. New techniques now enable detailed studies of the endolithic habitat, and our knowledge of the skeletal microbial community and its eco-physiology is increasing rapidly, with multiple lines of evidence for the importance of the skeletal microbiota in coral health and functioning. Here, we review the roles these organisms play in the holobiont, including nutritional exchanges with the coral host and decalcification of the host skeleton. Microbial metabolism causes steep physico-chemical gradients in the skeleton, creating micro-niches that, along with dispersal limitation and priority effects, define the fine-scale microbial community assembly. Coral bleaching causes drastic changes in the skeletal microbiome, which can mitigate bleaching effects and promote coral survival during stress periods, but may also have detrimental effects. Finally, we discuss the idea that the skeleton may function as a microbial reservoir that can promote recolonization of the tissue microbiome following dysbiosis and help the coral holobiont return to homeostasis.
The importance of offshore origination revealed through ophiuroid phylogenomics
Publisher: The Royal Society
Date: 05-07-2017
Abstract: Our knowledge of macro-evolutionary processes in the deep sea is poor, leading to much speculation about whether the deep sea is a source or sink of evolutionary adaptation. Here, we use a phylogenetic approach, on large molecular (688 species, 275 kbp) and distributional datasets (104 513 records) across an entire class of marine invertebrates (Ophiuroidea), to infer rates of bathymetric range shift over time between shallow and deep water biomes. Biome conservation is evident through the phylogeny, with the majority of species in most clades distributed within the same bathome. Despite this, bathymetric shifts have occurred. We inferred from ancestral reconstructions that eurybathic or intermediate distributions across both biomes were a transitional state and direct changes between shallow and deep sea did not occur. The macro-evolutionary pattern of bathome shift appeared to reflect micro-evolutionary processes of bathymetric speciation. Results suggest that most of the oldest clades have a deep-sea origin, but multiple colonization events indicate that the evolution of this group conforms neither to a simple onshore–offshore hypothesis, nor the opposite pattern. Both shallow and deep bathomes have played an important role in generating the current ersity of this major benthic class.
Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds
Publisher: Cold Spring Harbor Laboratory
Date: 12-06-2019
DOI: 10.1101/668475
Abstract: The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focusses on the evolutionary origins of green seaweeds, which play an important ecological role in the benthos of modern sunlit oceans and likely played a crucial part in the evolution of early animals by structuring benthic habitats and providing novel niches. By applying a phylogenomic approach, we resolve deep relationships of the core Chlorophyta (Ulvophyceae or green seaweeds, and freshwater or terrestrial Chlorophyceae and Trebouxiophyceae) and unveil a rapid radiation of Chlorophyceae and the principal lineages of the Ulvophyceae late in the Neoproterozoic Era. Our time-calibrated tree points to an origin and early ersification of green seaweeds in the late Tonian and Cryogenian periods, an interval marked by two global glaciations, with strong consequent changes in the amount of available marine benthic habitat. We hypothesize that the unicellular and simple multicellular ancestors of green seaweeds survived these extreme climate events in isolated refugia, and ersified following recolonization of benthic environments that became increasingly available as sea ice retreated. An increased supply of nutrients and biotic interactions such as grazing pressure has likely triggered the independent evolution of macroscopic growth via different strategies, including both true multicellularity, and multiple types of giant celled forms. Green seaweeds are important primary producers along coastlines worldwide, and likely played a key role in the evolution of animals. To understand their origin and ersification, we resolve key relationships among extant green algae using a phylotranscriptomic approach. We calibrate our tree using available fossil data, to reconstruct important evolutionary events such as transitions to benthic environments, and evolution of macroscopic growth. We estimate green seaweeds to have originated in the late Tonian/Cryogenian Period, followed by a marked Ordovician ersification of macroscopic forms. This ancient proliferation of green seaweeds likely modified shallow marine ecosystems, which set off an evolutionary arms race between ever larger seaweeds and grazers.
Marine Benthic Plants of Western Australia's Shelf-Edge Atolls
Publisher: Western Australian Museum
Date: 2009
Bio‐ORACLE: a global environmental dataset for marine species distribution modelling
Publisher: Wiley
Date: 24-03-2011
The plastid genome in Cladophorales green algae is encoded by hairpin plasmids
Publisher: Cold Spring Harbor Laboratory
Date: 02-06-2017
DOI: 10.1101/145037
Abstract: Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100-200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin plasmids. Short and long read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1-7 kb DNA contigs with an exceptionally high GC-content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin plasmids. The Boodlea chloroplast genes are highly ergent from their corresponding orthologs. The origin of this highly deviant chloroplast genome likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes and highlights unexpected variation in the plastid genome architecture.
DNA-based species delimitation in algae
Publisher: Informa UK Limited
Date: 03-04-2014
Phylogeny and Molecular Evolution of the Green Algae
Publisher: Informa UK Limited
Date: 2012
Ten Ostreobium (Ulvophyceae) strains from Great Barrier Reef corals as a resource for algal endolith biology and genomics
Publisher: Informa UK Limited
Date: 06-05-2022
PHYLOGENETIC ANALYSIS OF PSEUDOCHLORODESMIS STRAINS REVEALS CRYPTIC DIVERSITY ABOVE THE FAMILY LEVEL IN THE SIPHONOUS GREEN ALGAE (BRYOPSIDALES, CHLOROPHYTA)1
Publisher: Wiley
Date: 06-2009
DOI: 10.1111/J.1529-8817.2009.00690.X
Abstract: The genus Pseudochlorodesmis (Bryopsidales) is composed of diminutive siphons of extreme morphological simplicity. The discovery of Pseudochlorodesmis-like juveniles in more complex Bryopsidales (e.g., the Halimeda microthallus stage) jeopardized the recognition of this genus. Confronted with this uncertainty, taxonomists transferred many simple siphons into a new genus, Siphonogramen. In this study, we used a multimarker approach to clarify the phylogenetic and taxonomic affinities of the Pseudochlorodesmis-Siphonogramen (PS) complex within the more morphologically complex bryopsidalean taxa. Our analyses reveal a new layer of ersity largely distinct from the lineages containing the structurally complex genera. The PS complex shows profound cryptic ersity exceeding the family level. We discuss a potential link between thallus complexity and the prevalence and profundity of cryptic ersity. For taxonomic simplicity and as a first step toward clarifying the taxonomy of these simple siphons, we propose to maintain Pseudochlorodesmis as a form genus and subsume Siphonogramen and Botryodesmis therein.
A REVISED CLASSIFICATION OF THE DICTYOTEAE (DICTYOTALES, PHAEOPHYCEAE) BASED ON rbcL AND 26S RIBOSOMAL DNA SEQUENCE ANALYSES1
Publisher: Wiley
Date: 16-11-2006
Global biogeographic structuring of tropical shallow‐water brittle stars
Publisher: Wiley
Date: 04-06-2019
DOI: 10.1111/JBI.13620
High-throughput sequencing of the kelp Alaria (Phaeophyceae) reveals epi-endobiotic associations, including a likely phaeophycean parasite
Publisher: Informa UK Limited
Date: 12-04-2021
MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis
Publisher: The Open Journal
Date: 20-02-2023
DOI: 10.21105/JOSS.04851
Application of multigene phylogenetics and site-stripping to resolve intraordinal relationships in the Rhodymeniales (Rhodophyta)
Publisher: Wiley
Date: 28-04-2016
DOI: 10.1111/JPY.12418
Abstract: Previous molecular assessments of the red algal order Rhodymeniales have confirmed its monophyly and distinguished the six currently recognized families (viz. Ch iaceae, Faucheaceae, Fryeellaceae, Hymenocladiaceae, Lomentariaceae, and Rhodymeniaceae) however, relationships among most of these families have remained unresolved possibly as a result of substitution saturation at deeper phylogenetic nodes. The objective of the current study was to improve rhodymenialean systematics by increasing taxonomic representation and using a more robust multigene dataset of mitochondrial (COB, COI/COI-5P), nuclear (LSU, EF2) and plastid markers (psbA, rbcL). Additionally, we aimed to prevent phylogenetic inference problems associated with substitution saturation (particularly at the interfamilial nodes) by removing fast-evolving sites and analyzing a series of progressively more conservative alignments. The Rhodymeniales was resolved as two major lineages: (i) the Fryeellaceae as sister to the Faucheaceae and Lomentariaceae and (ii) the Rhodymeniaceae allied to the Ch iaceae and Hymenocladiaceae. Support at the interfamilial nodes was highest when 20% of variable sites were removed. Inclusion of Binghamiopsis, Chamaebotrys, and Minium, which were absent in previous phylogenetic investigations, established their phylogenetic affinities while assessment of two genera consistently polyphyletic in phylogenetic analyses, Erythrymenia and Lomentaria, resulted in the proposition of the novel genera Perbella and Fushitsunagia. The taxonomic position of Drouetia was reinvestigated with re-examination of holotype material of D. coalescens to clarify tetrasporangial development in this genus. In addition, we added three novel Australian species to Drouetia as a result of ongoing DNA barcoding assessments-D. aggregata sp. nov., D. scutellata sp. nov., and D. viridescens sp. nov.
Widely distributed red algae often represent hidden introductions, complexes of cryptic species or species with strong phylogeographic structure
Publisher: Wiley
Date: 19-09-2018
DOI: 10.1111/JPY.12778
Abstract: Despite studies suggesting that most seaweeds are poor dispersers, many red algal species are reported to have circumglobal distributions. Such distributions have mostly been based on morphological identifications, but molecular data have revealed a range of issues with morphologically defined species boundaries. Consequently, the real distribution of such reportedly circumglobal species must be questioned. In this study, we analyzed molecular data sets (rbcL gene) of nine species in the Rhodomelaceae for which s les were available from widely spaced geographical locations. Three overall patterns were identified: (i) species showing strong phylogeographic structure (i.e., phylogenetic similarity correlates with geographical provenance), often to the point that populations from different locations could be considered as different species (Lophosiphonia obscura, Ophidocladus simpliciusculus, Polysiphonia villum, and Xiphosiphonia pinnulata) (ii) species with a broad distribution that is explained, in part, by putative human-mediated transport (Symphyocladia dendroidea and Polysiphonia devoniensis) and (iii) non-monophyletic complexes of cryptic species, most with a more restricted distribution than previously thought (Herposiphonia tenella, Symphyocladia dendroidea, and the Xiphosiphonia pennata complex that includes the species Xiphosiphonia pinnulata and Symphyocladia spinifera). This study shows that widely distributed species are the exception in marine red algae, unless they have been spread by humans.
Chloroplast genomes as a tool to resolve red algal phylogenies: a case study in the Nemaliales.
Publisher: Springer Science and Business Media LLC
Date: 10-10-2016
Identification of polycistronic transcriptional units and non-canonical introns in green algal chloroplasts based on long-read RNA sequencing data
Publisher: Springer Science and Business Media LLC
Date: 23-04-2021
DOI: 10.1186/S12864-021-07598-Y
Abstract: Chloroplasts are important semi-autonomous organelles in plants and algae. Unlike higher plants, the chloroplast genomes of green algal linage have distinct features both in organization and expression. Despite the architecture of chloroplast genome having been extensively studied in higher plants and several model species of algae, little is known about the transcriptional features of green algal chloroplast-encoded genes. Based on full-length cDNA (Iso-Seq) sequencing, we identified widely co-transcribed polycistronic transcriptional units (PTUs) in the green alga Caulerpa lentillifera. In addition to clusters of genes from the same pathway, we identified a series of PTUs of up to nine genes whose function in the plastid is not understood. The RNA data further allowed us to confirm widespread expression of fragmented genes and conserved open reading frames, which are both important features in green algal chloroplast genomes. In addition, a newly fragmented gene specific to C. lentillifera was discovered, which may represent a recent gene fragmentation event in the chloroplast genome. With the newly annotated exon-intron boundary information, gene structural annotation was greatly improved across the siphonous green algae lineages. Our data also revealed a type of non-canonical Group II introns, with a deviant secondary structure and intronic ORFs lacking known splicing or mobility domains. These widespread introns have conserved positions in their genes and are excised precisely despite lacking clear consensus intron boundaries. Our study fills important knowledge gaps in chloroplast genome organization and transcription in green algae, and provides new insights into expression of polycistronic transcripts, freestanding ORFs and fragmented genes in algal chloroplast genomes. Moreover, we revealed an unusual type of Group II intron with distinct features and conserved positions in Bryopsidales. Our data represents interesting additions to knowledge of chloroplast intron structure and highlights clusters of uncharacterized genes that probably play important roles in plastids.
Pseudoderbesia Eckloniae, sp. nov. (Bryopsidaceae, Ulvophyceae) from Western Australia
Publisher: Museum National d'Histoire Naturelle, Paris, France
Date: 04-03-2020
Beneath the surface: community assembly and functions of the coral skeleton microbiome
Publisher: California Digital Library (CDL)
Date: 21-05-2019
Host specificity and coevolution of Flavobacteriaceae endosymbionts within the siphonous green seaweed Bryopsis
Publisher: Elsevier BV
Date: 06-2013
DOI: 10.1016/J.YMPEV.2013.02.025
Abstract: The siphonous green seaweed Bryopsis harbors complex intracellular bacterial communities. Previous studies demonstrated that certain species form close, obligate associations with Flavobacteriaceae. A predominant imprint of host evolutionary history on the presence of these bacteria suggests a highly specialized association. In this study we elaborate on previous results by expanding the taxon s ling and testing for host-symbiont coevolution Therefore, we optimized a PCR protocol to directly and specifically lify Flavobacteriaceae endosymbiont 16S rRNA gene sequences, which allowed us to screen a large number of algal s les without the need for cultivation or surface sterilization. We analyzed 146 Bryopsis s les, and 92 additional s les belonging to the Bryopsidales and other orders within the class Ulvophyceae. Results indicate that the Flavobacteriaceae endosymbionts are restricted to Bryopsis, and only occur within specific, warm-temperate and tropical clades of the genus. Statistical analyses (AMOVA) demonstrate a significant non-random host-symbiont association. Comparison of bacterial 16S rRNA and Bryopsis rbcL phylogenies, however, reveal complex host-symbiont evolutionary associations, whereby closely related hosts predominantly harbor genetically similar endosymbionts. Bacterial genotypes are rarely confined to a single Bryopsis species and most Bryopsis species harbored several Flavobacteriaceae, obscuring a clear pattern of coevolution.
Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks
Publisher: Springer Science and Business Media LLC
Date: 16-02-2023
DOI: 10.1038/S41598-023-27816-9
Abstract: Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but the majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects to identify potential microalgal-bacterial associations in aquatic ecosystems. A high degree of clustering was observed in microalgal-bacterial modules, indicating densely connected neighbourhoods. Proteobacteria and Bacteroidetes predominantly co-occurred with microalgae and represented hubs of most modules. Our results also indicated that species-specificity may be a global characteristic of microalgal associated microbiomes. Several previously known associations were recovered from our network modules, validating that biologically meaningful results can be inferred using this approach. A range of previously unknown associations were recognised such as co-occurrences of Bacillariophyta with uncultured Planctomycetes OM190 and Deltaproteobacteria order NB1-j . Planctomycetes and Verrucomicrobia were identified as key associates of microalgae due to their frequent co-occurrences with several microalgal taxa. Despite no clear taxonomic pattern, bacterial associates appeared functionally similar across different environments. To summarise, we demonstrated the potential of 16S rRNA gene-based co-occurrence networks as a hypothesis-generating framework to guide more focused research on microalgal-bacterial associations.
Morphological characterization of lineages within the calcified tropical seaweed genus Halimeda (Bryopsidales, Chlorophyta)
Publisher: Informa UK Limited
Date: 05-2004
Diversity and stability of coral endolithic microbial communities at a naturally high pCO2 reef
Publisher: Wiley
Date: 24-08-2017
DOI: 10.1111/MEC.14268
Abstract: The health and functioning of reef-building corals is dependent on a balanced association with prokaryotic and eukaryotic microbes. The coral skeleton harbours numerous endolithic microbes, but their ersity, ecological roles and responses to environmental stress, including ocean acidification (OA), are not well characterized. This study tests whether pH affects the ersity and structure of prokaryotic and eukaryotic algal communities associated with skeletons of Porites spp. using targeted licon (16S rRNA gene, UPA and tufA) sequencing. We found that the composition of endolithic communities in the massive coral Porites spp. inhabiting a naturally high pCO
Global biogeography and diversification of a group of brown seaweeds (Phaeophyceae) driven by clade‐specific evolutionary processes
Publisher: Wiley
Date: 07-01-2021
DOI: 10.1111/JBI.14047
Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks
Publisher: Cold Spring Harbor Laboratory
Date: 06-01-2022
DOI: 10.1101/2022.01.05.475147
Abstract: Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but the majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects to identify potential microalgal-bacterial associations in aquatic ecosystems. A high degree of clustering was observed in microalgal-bacterial modules, indicating densely connected neighbourhoods. Proteobacteria and Bacteroidetes predominantly co-occurred with microalgae and represented hubs of most modules. Our results also indicated that species-specificity may be a global characteristic of microalgal associated microbiomes. Several previously known associations were recovered from our network modules, validating that biologically meaningful results can be inferred using this approach. A range of previously unknown associations were recognised such as co-occurrences of Bacillariophyta with uncultured Planctomycetes OM190 and Deltaproteobacteria order NB1-j. Planctomycetes and Verrucomicrobia were identified as key associates of microalgae due to their frequent co-occurrences with several microalgal taxa. Despite no clear taxonomic pattern, bacterial associates appeared functionally similar across different environments. To summarise, we demonstrated the potential of 16S rRNA gene-based co-occurrence networks as a hypothesis-generating framework to guide more focused research on microalgal-bacterial associations.
New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data
Publisher: Frontiers Media SA
Date: 17-10-2014
Evolution and Cytological Diversification of the Green Seaweeds (Ulvophyceae)
Publisher: Oxford University Press (OUP)
Date: 05-04-2010
Abstract: The Ulvophyceae, one of the four classes of the Chlorophyta, is of particular evolutionary interest because it features an unrivaled morphological and cytological ersity. Morphological types range from unicells and simple multicellular filaments to sheet-like and complex corticated thalli. Cytological layouts range from typical small cells containing a single nucleus and chloroplast to giant cells containing millions of nuclei and chloroplasts. In order to understand the evolution of these morphological and cytological types, the present paper aims to assess whether the Ulvophyceae are monophyletic and elucidate the ancient relationships among its orders. Our approach consists of phylogenetic analyses (maximum likelihood and Bayesian inference) of seven nuclear genes, small subunit nuclear ribosomal DNA and two plastid markers with carefully chosen partitioning strategies, and models of sequence evolution. We introduce a procedure for fast site removal (site stripping) targeted at improving phylogenetic signal in a particular epoch of interest and evaluate the specificity of fast site removal to retain signal about ancient relationships. From our phylogenetic analyses, we conclude that the ancestral ulvophyte likely was a unicellular uninucleate organism and that macroscopic growth was achieved independently in various lineages involving radically different mechanisms: either by evolving multicellularity with coupled mitosis and cytokinesis (Ulvales-Ulotrichales and Trentepohliales), by obtaining a multinucleate siphonocladous organization where every nucleus provides for its own cytoplasmic domain (Cladophorales and Blastophysa), or by developing a siphonous organization characterized by either one macronucleus or millions of small nuclei and cytoplasmic streaming (Bryopsidales and Dasycladales). We compare different evolutionary scenarios giving rise to siphonous and siphonocladous cytologies and argue that these did not necessarily evolve from a multicellular or even multinucleate state but instead could have evolved independently from a unicellular ancestor.
Phylogeny and taxonomy of Halimeda incrassata, including descriptions of H. kanaloana and H. heteromorpha spp. nov. (Bryopsidales, Chlorophyta)
Publisher: Informa UK Limited
Date: 08-2006
The golden paradox - a new heterokont lineage with chloroplasts surrounded by two membranes.
Publisher: Wiley
Date: 31-01-2019
DOI: 10.1111/JPY.12822
Abstract: A marine, sand-dwelling, golden-brown alga is described from clonal cultures established from a high intertidal pool in southeastern Australia. This tiny, unicellular species, which we call the "golden paradox" (Chrysoparadoxa australica gen. et sp. nov.), is benthic, surrounded by a multilayered cell wall and attached to the substratum by a complex adhesive plug. Each vegetative cell gives rise to a single, naked zoospore with heterokont flagella that settles and may become briefly amoeboid prior to iding. Daughter cells are initially amoeboid, then either permanently attach and return to the benthic stage or become motile again prior to final settlement. Two deeply lobed chloroplasts occupy opposite ends of the cell and are surrounded by only two membranes. The outer chloroplast membrane is continuous between the two chloroplasts via the outer membrane of the nuclear envelope. Only two membranes occupy the chloroplast-nucleus interface, the inner membrane of the nuclear envelope and the inner chloroplast membrane. A small pyrenoid is found in each chloroplast and closely abuts the nucleus or protrudes into it. It contains an unusual, membrane-bound inclusion that stains with SYBR green but is unlikely to be a nucleomorph. Phylogenies inferred from a 10-gene concatenated alignment show an early-branching position within the PX clade. The unusual morphological features and phylogenetic position indicate C. australica should be classified as a new class, Chrysoparadoxophyceae. Despite an atypical plastid, exploration of the C. australica transcriptome revealed typical heterokont protein targeting to the plastid.
Multigene analyses resolve early diverging lineages in the Rhodymeniophycidae (Florideophyceae, Rhodophyta)
Publisher: Wiley
Date: 27-06-2016
DOI: 10.1111/JPY.12426
Abstract: Multigene phylogenetic analyses were directed at resolving the earliest ergences in the red algal subclass Rhodymeniophycidae. The inclusion of key taxa (new to science and/or previously lacking molecular data), additional sequence data (SSU, LSU, EF2, rbcL, COI-5P), and phylogenetic analyses removing the most variable sites (site stripping) have provided resolution for the first time at these deep nodes. The earliest erging lineage within the subclass was the enigmatic Catenellopsis oligarthra from New Zealand (Catenellopsidaceae), which is here placed in the Catenellopsidales ord. nov. In our analyses, Atractophora hypnoides was not allied with the other included Bonnemaisoniales, but resolved as sister to the Peyssonneliales, and is here assigned to Atractophoraceae fam. nov. in the Atractophorales ord. nov. Inclusion of Acrothesaurum gemellifilum gen. et sp. nov. from Tasmania has greatly improved our understanding of the Acrosymphytales, to which we assign three families, the Acrosymphytaceae, Acrothesauraceae fam. nov. and Schimmelmanniaceae fam. nov.
Extensive cryptic species diversity and fine-scale endemism in the marine red alga Portieria in the Philippines
Publisher: The Royal Society
Date: 22-02-2013
Abstract: We investigated species ersity and distribution patterns of the marine red alga Portieria in the Philippine archipelago. Species boundaries were tested based on mitochondrial, plastid and nuclear encoded loci, using a general mixed Yule-coalescent (GMYC) model-based approach and a Bayesian multilocus species delimitation method. The outcome of the GMYC analysis of the mitochondrial encoded cox 2-3 dataset was highly congruent with the multilocus analysis. In stark contrast with the current morphology-based assumption that the genus includes a single, widely distributed species in the Indo-West Pacific ( Portieria hornemannii ), DNA-based species delimitation resulted in the recognition of 21 species within the Philippines. Species distributions were found to be highly structured with most species restricted to island groups within the archipelago. These extremely narrow species ranges and high levels of intra-archipelagic endemism contrast with the wide-held belief that marine organisms generally have large geographical ranges and that endemism is at most restricted to the archipelagic level. Our results indicate that speciation in the marine environment may occur at spatial scales smaller than 100 km, comparable with some terrestrial systems. Our finding of fine-scale endemism has important consequences for marine conservation and management.
The genera Melanothamnus Bornet & Falkenberg and Vertebrata S.F. Gray constitute well-defined clades of the red algal tribe Polysiphonieae (Rhodomelaceae, Ceramiales)
Publisher: Informa UK Limited
Date: 02-01-2017
Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life
Publisher: Springer Science and Business Media LLC
Date: 2010
Complex phylogenetic distribution of a non-canonical genetic code in green algae
Publisher: Springer Science and Business Media LLC
Date: 2010
Reassessment of the genus Lophurella (Rhodomelaceae, Rhodophyta) from Australia and New Zealand reveals four cryptic species
Publisher: Informa UK Limited
Date: 14-10-2020
RHIPILIA COPPEJANSII, A NEW CORAL REEF‐ASSOCIATED SPECIES FROM GUAM (BRYOPSIDALES, CHLOROPHYTA)1
Publisher: Wiley
Date: 10-07-2012
DOI: 10.1111/J.1529-8817.2012.01199.X
Abstract: The new species Rhipilia coppejansii is described from Guam. This species, which has the external appearance of a Chlorodesmis species, features tenacula upon microscopical examination, a diagnostic character of Rhipilia. This unique morphology, along with the tufA and rbcL data presented herein, set this species apart from others in the respective genera. Phylogenetic analyses show that the taxon is nested within the Rhipiliaceae. We discuss the ersity and possible adaptation of morphological types in the Udoteaceae and Rhipiliaceae.
Phylogenetic position of the coral symbiont Ostreobium (Ulvophyceae) inferred from chloroplast genome data
Publisher: Wiley
Date: 12-05-2017
DOI: 10.1111/JPY.12540
Abstract: The green algal genus Ostreobium is an important symbiont of corals, playing roles in reef decalcification and providing photosynthates to the coral during bleaching events. A chloroplast genome of a cultured strain of Ostreobium was available, but low taxon s ling and Ostreobium's early-branching nature left doubt about its phylogenetic position. Here, we generate and describe chloroplast genomes from four Ostreobium strains as well as Avrainvillea mazei and Neomeris sp., strategically s led early-branching lineages in the Bryopsidales and Dasycladales respectively. At 80,584 bp, the chloroplast genome of Ostreobium sp. HV05042 is the most compact yet found in the Ulvophyceae. The Avrainvillea chloroplast genome is ~94 kbp and contains introns in infA and cysT that have nearly complete sequence identity except for an open reading frame (ORF) in infA that is not present in cysT. In line with other bryopsidalean species, it also contains regions with possibly bacteria-derived ORFs. The Neomeris data did not assemble into a canonical circular chloroplast genome but a large number of contigs containing fragments of chloroplast genes and showing evidence of long introns and intergenic regions, and the Neomeris chloroplast genome size was estimated to exceed 1.87 Mb. Chloroplast phylogenomics and 18S nrDNA data showed strong support for the Ostreobium lineage being sister to the remaining Bryopsidales. There were differences in branch support when outgroups were varied, but the overall support for the placement of Ostreobium was strong. These results permitted us to validate two suborders and introduce a third, the Ostreobineae.
Algal taxonomy: a road to nowhere?
Publisher: Wiley
Date: 26-12-2012
DOI: 10.1111/JPY.12020
Abstract: The widespread view of taxonomy as an essentially retrogressive and outmoded science unable to cope with the current bio ersity crisis stimulated us to analyze the current status of cataloguing global algal ersity. Contrary to this largely pessimistic belief, species description rates of algae through time and trends in the number of active taxonomists, as revealed by the web resource AlgaeBase, show a much more positive picture. More species than ever before are being described by a large community of algal taxonomists. The lack of any decline in the rate at which new species and genera are described, however, is indicative of the large proportion of undiscovered ersity and bears heavily on any prediction of global algal species ersity and the time needed to catalogue it. The saturation of accumulation curves of higher taxa (family, order, and classes) on the other hand suggest that at these taxonomic levels most ersity has been discovered. This reasonably positive picture does not imply that algal taxonomy does not face serious challenges in the near future. The observed levels of cryptic ersity in algae, combined with the shift in methods used to characterize them, have resulted in a r ant uncertainty about the status of many older species. As a consequence, there is a tendency in phycology to move gradually away from traditional names to a more informal system whereby clade-, specimen- or strain-based identifiers are used to communicate biological information. Whether these informal names for species-level clades represent a temporary situation stimulated by the lag between species discovery and formal description, or an incipient alternative or parallel taxonomy, will be largely determined by how well we manage to integrate historical collections into modern taxonomic research. Additionally, there is a pressing need for a consensus about the organizational framework to manage the information about algal species names. An eventual strategy should preferably come out of an international working group that includes the various databases as well as the various phycological societies. In this strategy, phycologists should link up to major international initiatives that are currently being developed, such as the compulsory registration of taxonomic and nomenclatural acts and the introduction of Life Science Identifiers.
DNA-assisted identification of Caulerpa (Caulerpaceae, Chlorophyta) reduces species richness estimates for the Eastern Tropical Pacific
Publisher: Magnolia Press
Date: 14-03-2016
DOI: 10.11646/PHYTOTAXA.252.3.2
Abstract: Taxonomy and species richness estimates for the genus Caulerpa have proven challenging due to the difficulty of assessing morphological species limits. In the present study we evaluate the taxonomy of the genus and assess species distributions in the Eastern Tropical Pacific (ETP), based on morphology and tufA sequence data. Molecular analyses revealed six species-level clades: C. verticillata, C. sertularioides, C. cupressoides, C. serrulata, C. racemosa and C. chemnitzia (part of C. racemosa-peltata complex). Our results reduce species richness estimates throughout the ETP by over 54% (from 13 to 6). In accordance with recent studies, our morphological and DNA results warrant the recognition of C. chemnitzia to comprise the morphological entities C. laetevirens, C. peltata and C. vanbossea complex. We continue the use of ecads as a practical identification tool for morphological ersity below the species level present in the ETP. In addition we formally recognize the synonymy of C. racemosa var. macrophysa with the lineage of C. racemosa proposed in recent studies. The six species of Caulerpa found in this study are of pantropical in distribution. Within the ETP region, four species have restricted distributions (C. verticillata, C. cupressoides, C. serrulata, C. racemosa), while two show a wide latitudinal distribution (C. chemnitzia and C. sertularioides).
New pelagophytes show a novel mode of algal colony development and reveal a perforated theca that may define the class
Publisher: Wiley
Date: 12-2021
DOI: 10.1111/JPY.13074
Taxonomic revision of Halimeda (Bryopsidales, Chlorophyta) in south-Western Australia
Publisher: CSIRO Publishing
Date: 2016
DOI: 10.1071/SB15043
Abstract: Halimeda J.V.Lamour. is a green algal genus that is an important component of tropical reefs and lagoons. Although it does not generally occur outside the tropics, the range of one putatively widespread species, Halimeda cuneata Hering, in Western Australia extends southward past Cape Leeuwin to its southern extreme at Cape Howe and around to its most easterly record at Middle Island of the Recherche Archipelago. Previous molecular studies have shown that H. cuneata as recorded worldwide encompasses cryptic species ersity, with most of the cryptic entities being geographically isolated from the others. Halimeda cuneata has been the name consistently applied to specimens from the south-western coast of Australia, where it has been regarded as the only representative of its genus in the region. Using a combination of morphological features and assessment of species boundaries based on a plastid gene (tufA) and a nuclear protein-coding gene (HSP90), we have reassessed the supposed presence of H. cuneata in south-western Australia. Our results showed the existence of two species in the region, namely, H. versatilis J.Agardh, to which the name H. cuneata has been misapplied, and H. gigas W.R.Taylor, a central-Pacific species previously recorded only from tropical Australia.
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