ORCID Profile
0000-0003-0885-6578
Current Organisation
Museum Victoria
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Publisher: Elsevier BV
Date: 2019
DOI: 10.1016/J.YMPEV.2018.10.003
Abstract: Brittlestars in the family Ophiocomidae are large and colourful inhabitants of tropical shallow water habitats across the globe. Here we use targeted capture and next-generation sequencing to generate robust phylogenomic trees for 39 of the 43 species in order to test the monophyly of existing genera. The large genus Ophiocoma, as currently constituted, is paraphyletic on our trees and required revision. Four genera are recognised herein: an expanded Ophiomastix (now including Ophiocoma wendtii, O. occidentalis, O. endeani, O. macroplaca, and Ophiarthrum spp), Ophiocomella (now including the non-fissiparous Ophiocoma pumila, aethiops and valenciae) and Breviturma (now including Ophiocoma pica, O. pusilla, O. paucigranulata and O. longispina) and a restricted Ophiocoma. The resulting junior homonym Ophiomastix elegans is renamed O. brocki. The genus Ophiomastix exhibits relatively high rates of morphological disparity compared to other lineages. Ophiomastix flaccida and O. (formerly Ophiarthrum) pictum have ergent mitochondrial genomes, characterised by gene-order rearrangements, strand recoding, enriched GT base composition, and a corresponding ergence of nuclear mitochondrial protein genes. The new phylogeny indicates that larval and developmental transitions occurred rarely. Larval culture trials show that species with abbreviated lecithotrophic larval development occur only within Ophiomastix, although the possible monophyly of these species is obscured by the rapid early radiation within this genus. Asexual reproduction by fission is limited to one species-complex within Ophiocomella, also characterised by elevated levels of allelic heterozygosity, and which has achieved a relatively rapid global distribution. The crown ages of the new genera considerably predate the closure of the Tethyan seaway and all four are distributed in both the Atlantic and Indo-Pacific Oceans. Two species pairs appear to reflect the closure of the Panama Seaway, although their fossil-calibrated node ages (12-14 ± 6 my), derived from both concatenated sequence and multispecies coalescent analyses, considerably predate the terminal closure event. Ophiocoma erinaceus has crossed the East Pacific barrier and is recorded from Clipperton Island, SW of Mexico.
Publisher: Elsevier BV
Date: 08-2011
Publisher: Frontiers Media SA
Date: 22-06-2015
Publisher: Wiley
Date: 11-2008
DOI: 10.1111/J.1755-0998.2008.02332.X
Abstract: DNA barcode sequences (a 657-bp segment of the mtDNA cytochrome oxidase I gene, COI) were collected from 191 species (503 specimens) of Echinodermata. All five classes were represented: Ophiuroidea, Asteroidea, Echinoidea, Holothuroidea and Crinoidea. About 30% of sequences were collected specifically for this study, the remainder came from GenBank. Fifty-one species were represented by multiple s les, with a mean intraspecific ergence of 0.62%. Several possible instances of cryptic speciation were noted. Thirty-two genera were represented by multiple species, with a mean congeneric ergence of 15.33%. One hundred and eighty-seven of the 191 species (97.9%) could be distinguished by their COI barcodes. Those that could not were from the echinoid genus Amblypneustes. Neighbour-joining trees of COI sequences generally showed low bootstrap support for anything other than shallow splits, although with very rare exceptions, members of the same class clustered together. Two ophiuran species, in both nucleotide and amino acid neighbour-joining trees, grouped loosely as sister taxa to Crinoidea rather than Ophiuroidea sequences of these two species appear to have evolved very quickly. Results suggest that DNA barcoding is likely to be an effective, accurate and useful method of species diagnosis for all five classes of Echinodermata.
Publisher: Springer Science and Business Media LLC
Date: 05-2016
DOI: 10.1038/NATURE17937
Abstract: The deep ocean is the largest and least-explored ecosystem on Earth, and a uniquely energy-poor environment. The distribution, drivers and origins of deep-sea bio ersity remain unknown at global scales. Here we analyse a database of more than 165,000 distribution records of Ophiuroidea (brittle stars), a dominant component of sea-floor fauna, and find patterns of bio ersity unlike known terrestrial or coastal marine realms. Both patterns and environmental predictors of deep-sea (2,000-6,500 m) species richness fundamentally differ from those found in coastal (0-20 m), continental shelf (20-200 m), and upper-slope (200-2,000 m) waters. Continental shelf to upper-slope richness consistently peaks in tropical Indo-west Pacific and Caribbean (0-30°) latitudes, and is well explained by variations in water temperature. In contrast, deep-sea species show maximum richness at higher latitudes (30-50°), concentrated in areas of high carbon export flux and regions close to continental margins. We reconcile this structuring of oceanic bio ersity using a species-energy framework, with kinetic energy predicting shallow-water richness, while chemical energy (export productivity) and proximity to slope habitats drive deep-sea ersity. Our findings provide a global baseline for conservation efforts across the sea floor, and demonstrate that deep-sea ecosystems show a bio ersity pattern consistent with ecological theory, despite being different from other planetary-scale habitats.
Publisher: Elsevier BV
Date: 08-2014
DOI: 10.1016/J.CUB.2014.06.060
Abstract: Our understanding of the origin, evolution, and biogeography of seafloor fauna is limited because we have insufficient spatial and temporal data to resolve underlying processes. The abundance and wide distribution of modern and disarticulated fossil Ophiuroidea, including brittle stars and basket stars, make them an ideal model system for global marine biogeography if we have the phylogenetic framework necessary to link extant and fossil morphology in an evolutionary context. Here we construct a phylogeny from a highly complete 425-gene, 61-taxa transcriptome-based data set covering 15 of the 18 ophiuroid families and representatives of all extant echinoderm classes. We calibrate our phylogeny with a series of novel fossil discoveries from the early Mesozoic. We confirm the traditional paleontological view that ophiuroids are sister to the asteroids and date the crown group Ophiuroidea to the mid-Permian (270 ± 30 mega-annum). We refute all historical classification schemes of the Ophiuroidea based on gross structural characters but find strong congruence with schemes based on lateral arm plate microstructure and the temporal appearance of various plate morphologies in the fossil record. The verification that these microfossils contain phylogenetically informative characters unlocks their potential to advance our understanding of marine biogeographical processes.
Publisher: Inter-Research Science Center
Date: 26-08-2010
DOI: 10.3354/MEPS08713
Publisher: Wiley
Date: 05-08-2013
DOI: 10.1111/DDI.12119
Publisher: Wiley
Date: 30-03-2010
DOI: 10.1002/AQC.1111
Publisher: Wiley
Date: 11-2000
Publisher: Cold Spring Harbor Laboratory
Date: 02-07-2023
DOI: 10.1101/2023.06.29.547001
Abstract: The widespread and abundant brooding brittle-star ( Amphipholis squamata ) is a simultaneous hermaphrodite with a complex mitochondrial phylogeography of multiple ergent overlapping mtDNA lineages and can exhibit high levels of inbreeding or clonality and unusual sperm morphology. We use exon-capture and transcriptome data to show that the nuclear genome comprises multiple ( ) ergent (π 6%) expressed components spread across the mitochondrial lineages, and encompassing several other genera, including diploid dioecious dimorphic species. We also report a massive sperm genome size in A. squamata , an order of magnitude larger than in the sperm of other brittle-star species, consistent with our genetic measures of elevated and variable ploidy ( ). We propose that A. squamata (and related taxa) is a hybrid polyploid complex with many independent hybrid origins, variable ploidy, and complex patterns of parental subgenomes. We hypothesize that A. squamata has facultative sperm-dependent asexual reproduction, where sperm is required for embryogenesis but the egg and sperm only occasionally undergo fertilisation, a process that has been associated with the formation of polyploid hybrid swarms in other taxa [1]. Unique amongst known marine allopolyploids, the A. squamata complex inhabits an extensive bathymetric as well as geographic range. A. squamata is a much-studied animal amenable to laboratory culture: appreciating it as a hybrid polyploid complex makes it even more interesting to the study of evolutionary biology.
Publisher: CSIRO Publishing
Date: 2001
DOI: 10.1071/MF00114
Abstract: Habitats defined by various biological and environmental variables are increasingly assumed to be surrogates for bio ersity. This study tested this assumption for temperate subtidal rocky reefs off south-eastern Australia by investigating the consistency of floral and faunal macrobenthic assemblages within habitats defined by dominant vegetation, substratum lithology, depth, wave exposure and region. Taxonomic groups included seagrasses, rhodophytes, chlorophytes, phaeophytes, hydroids, bryozoans, molluscs, polychaetes, pycnogonids and echinoderms. The results from multivariate statistical analyses indicated that, although variation between replicate s les is high, habitats as defined by dominant vegetation and, to a lesser extent, region supported consistent floral and faunal assemblages. The patterns did not emphasize a broad-scale biogeographic gradient, but rather the environmental heterogeneity of the coastline at scales of 10–100 km.
Publisher: Proceedings of the National Academy of Sciences
Date: 27-05-2014
Abstract: Tests of bio ersity theory have been controversial partly because alternative formulations of the same theory seemingly yield different conclusions. This has been a particular challenge for neutral theory, which has dominated tests of bio ersity theory over the last decade. Neutral theory attributes differences in species abundances to chance variation in in iduals’ fates, rather than differences in species traits. By identifying common features of different neutral models, we conduct a uniquely robust test of neutral theory across a global dataset of marine assemblages. Consistently, abundances vary more among species than neutral theory predicts, challenging the hypothesis that community dynamics are approximately neutral, and implicating species differences as a key driver of community structure in nature.
Publisher: Museums Victoria
Date: 2002
Publisher: Wiley
Date: 20-12-2008
Publisher: Cold Spring Harbor Laboratory
Date: 30-01-2015
DOI: 10.1101/014613
Abstract: We present an exon-capture system for an entire class of marine invertebrates, the Ophiuroidea, built upon a phylogenetically erse transcriptome foundation. The system captures ~90 percent of the 1552 exon target, across all major lineages of the quarter-billion year old extant crown group. Key features of our system are: 1) basing the target on an alignment of orthologous genes determined from 52 transcriptomes spanning the phylogenetic ersity and trimmed to remove anything difficult to capture, map or align, 2) use of multiple artificial representatives based on ancestral states rather than exemplars to improve capture and mapping of the target, 3) mapping reads to a multi-reference alignment, and 4) using patterns of site polymorphism to distinguish among paralogy, polyploidy, allelic differences and s le contamination. The resulting data gives a well-resolved tree (currently standing at 417 s les, 275,352 bp, 91% data-complete) that will transform our understanding of ophiuroid evolution and biogeography.
Publisher: Elsevier BV
Date: 09-2014
DOI: 10.1016/J.YMPEV.2014.05.020
Abstract: In this paper we examine the phylogeny and biogeography of the temperate genera of the Ophiocomidae (Echinodermata: Ophiuroidea) which have an interesting asymmetrical anti-tropical distribution, with two genera (Ophiocomina and Ophiopteris) previously considered to have a separate species in both the North and South hemispheres, and the third (Clarkcoma) ersifying in the southern Australian/New Zealand region. Our phylogeny, generated from one mitochondrial and two nuclear markers, revealed that Ophiopteris is sister to a mixed Ophiocomina/Clarkcoma clade. Ophiocomina was polyphyletic, with O. nigra and an undescribed species from the South Atlantic Ocean sister to a clade including Clarkcoma species and O. australis. The phylogeny also revealed a number of recently erged lineages occurring within Clarkcoma, some of which are considered to be cryptic species due to the similarity in morphology combined with the apparent absence of interbreeding in a sympatric distribution, while the status of others is less certain. The phylogeny provides support for two transequatorial events in the group under study. A molecular clock analysis places both events in the middle to late Miocene. The analysis excludes a tectonic vicariance hypothesis for the antitropical distribution associated with the breakup of Pangaea and also excludes the hypothesis of more recent gene flow associated with Plio/Pleistocene glacial cycling.
Publisher: The Royal Society
Date: 16-06-2021
Abstract: The deep-seafloor in the tropical Indo-Pacific harbours a rich and erse benthic fauna with numerous palaeoendemics. Here, we describe a new species, genus and family of brittle-star (Ophiuroidea) from a single eight-armed specimen collected from a depth between 360 and 560 m on Banc Durand, a seamount east of New Caledonia. Leveraging a robust, fossil-calibrated (265 kbp DNA) phylogeny for the Ophiuroidea, we estimate the new lineage erged from other ophiacanthid families in the Late Triassic or Jurassic (median = 187–178 Myr, 95% CI = 215–143 Myr), a period of elevated ersification for this group. We further report very similar microfossil remains from Early Jurassic (180 Myr) sediments of Normandy, France. The discovery of a new ancient lineage in the relatively well-known Ophiuroidea indicates the importance of ongoing taxonomic research in the deep-sea, an environment increasingly threatened by human activities.
Publisher: Pensoft Publishers
Date: 25-01-2016
DOI: 10.3897/BDJ.4.E7251
Publisher: Cold Spring Harbor Laboratory
Date: 19-09-2019
DOI: 10.1101/775585
Abstract: The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations, however their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 in iduals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including CCTα (Chaperonin Containing TCP-1 subunit α), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examined in silico local protein stability of CCTα across the ophiuroid tree of life (967 in iduals from 725 species) in a phylogenetically-corrected context and found that deep sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed by in silico global protein stability analyses. This suggests that CCTα not only displays structural but also functional adaptations to deep water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as ‘cold-shock’ protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, are key metabolic deep-sea adaptations.
Publisher: Frontiers Media SA
Date: 03-2023
DOI: 10.3389/FMARS.2023.1056282
Abstract: The Clarion Clipperton Zone (CCZ) in the Northeast Pacific Ocean holds the largest deposits of polymetallic nodules at abyssal depths. These nodules are rock formations containing valuable metals and minerals targeted for mining. They further provide erse habitat for a range of deep-sea species. Little is known so far on the taxonomy, natural history and biogeography of these deep-sea animals which is vital for accurate assessment of the risk of species extinctions from large-scale mining. One of the most abundant megafaunal groups in the CCZ is the Ophiuroidea (brittle stars), of which Ophiotholia is one of the more abundant genera found in the area. The genus Ophiotholia has a world-wide distribution and currently holds six species. Material collected from seven scientific cruises to the CCZ was examined, morphologically, together with comparative material from all the known species. The small size and the damage caused during s ling often impeded their identification. The specimens were also genetically analyzed using a fragment of the mitochondrial COI gene. Scanning Electron Microscope images of the key microstructural characters were made using selected specimens from CCZ as well as from the comparative material. One morphotype was identified as the known species Ophiotholia supplicans Lyman, 1880, while the second is new to science and is described in this paper. The umbrella spines and the arrangement of their articulations on the lateral arm plate, were selected as the most relevant morphological characters in the taxonomy of the genus Ophiotholia and a revised identification key of all characters from all known Ophiotholia species is provided as a table in the supplement material. The identification and description of such a little-known genus improves the evaluation of the bio ersity not only in the CCZ but also for the deep sea.
Publisher: Elsevier BV
Date: 02-2017
DOI: 10.1016/J.YMPEV.2016.12.006
Abstract: The power and throughput of next-generation sequencing is instigating a major transformation in our understanding of evolution and classification of life on our planet. The new trees of life are robust and comprehensive. Here we provide a landmark phylogeny of the living ophiuroids and use it as the basis for a major revision of the higher classification of this class of marine invertebrates. We used an exon-capture system to generate a 1484 exon (273kbp) data-matrix from DNA extracted from ethanol-preserved museum s les. We successfully obtained an average of 90% of our target sequence from 576 species spread across the known taxonomic ersity. The topology of the major lineages was robust to taxon s ling, exon-s ling, models and methods. However, estimates of node age were much less precise, varying by about a quarter of mean age. We used a combination of phylogenetic distinctiveness and temporal-banding to guide our revision of the family-level classification. Empirically, we determined that limiting family crown age to 110±10Ma (mid Cretaceous) selected phylogenetically distinct nodes while minimising disruption to the existing taxonomy. The resulting scheme of 32 families and six orders considerably expands the number of higher taxa. The families are generally longitudinally widespread across the world's oceans, although 17 are largely confined to temperate and equatorial latitudes and six to relatively shallow water (less than 1000m depth).
Publisher: Springer Science and Business Media LLC
Date: 18-09-2020
DOI: 10.1186/S41200-020-00194-1
Abstract: Our knowledge of the benthic fauna at lower bathyal to abyssal (LBA, 2000 m) depths off Eastern Australia was very limited with only a few s les having been collected from these habitats over the last 150 years. In May–June 2017, the IN2017_V03 expedition of the RV Investigator s led LBA benthic communities along the lower slope and abyss of Australia’s eastern margin from off mid-Tasmania (42°S) to the Coral Sea (23°S), with particular emphasis on describing and analysing patterns of bio ersity that occur within a newly declared network of offshore marine parks. The study design was to deploy a 4 m (metal) beam trawl and Brenke sled to collect s les on soft sediment substrata at the target seafloor depths of 2500 and 4000 m at every 1.5 degrees of latitude along the western boundary of the Tasman Sea from 42° to 23°S, traversing seven Australian Marine Parks. The biological s ling included 35 beam trawls, 28 Brenke sleds, 8 box cores, 20 surface meso-zooplankton tows, and 7 Deep Towed Camera transects. In total, 25,710 specimens were identified to 1084 taxonomic entities, including 847 species-level, 144 genus-level and 69 family-level and 24 higher-level taxa. Of the species-level taxa, only 457 were assigned species-level taxonomic names, which implies that up to 58% of the collected fauna is undescribed. In addition, the ranges of numerous species have been extended to include the western Tasman Sea. The lower bathyal and abyssal fauna of soft sediment seafloors off eastern Australia has been systematically surveyed for the first time. The resultant collections will provide the foundation for much future ecological, biogeographical, phylogenetic and taxonomic research.
Publisher: CSIRO Publishing
Date: 2004
DOI: 10.1071/MF04226
Abstract: Using mtDNA sequences we found that the Indo-Pacific teatfish fishery comprises at least three species, clarifying confusion on the taxonomic status of these commercially important holothurians. Traditional taxonomic characters, including the morphology of skeletal structures, could not be used to differentiate the species. Sequences of the COI gene (529 bp) distinguished three haplotype clusters, corresponding to distinct colour forms and, to some extent, previously described species. The white teatfish, Holothuria fuscogilva, comprises a range of colour morphs and has a wide distribution over the tropical Indo-Pacific region. The large sequence ergence indicates potential for the presence of several cryptic species in the white teatfish complex. In contrast to current taxonomy, we identified two species of black teatfish that appear to be allopatric: H. whitmaei is entirely black and has a Pacific distribution whereas H. nobilis has white ventro-lateral dots and only occurs in the Indian Ocean. There is evidence for allopatric speciation between the black teatfish species, possibly driven by separation of the oceans and altered current patterns during the Pliocene, resulting in relatively young species with low intraspecific sequence ergence. These results provide insight into speciation in these tropical holothurians and are crucial for their conservation management.
Publisher: Oxford University Press (OUP)
Date: 18-12-2019
Abstract: Bioregions are important tools for understanding and managing natural resources. Bioregions should describe locations of relatively homogenous assemblages of species occur, enabling managers to better regulate activities that might affect these assemblages. Many existing bioregionalization approaches, which rely on expert-derived, Delphic comparisons or environmental surrogates, do not explicitly include observed biological data in such analyses. We highlight that, for bioregionalizations to be useful and reliable for systems scientists and managers, the bioregionalizations need to be based on biological data to include an easily understood assessment of uncertainty, preferably in a spatial format matching the bioregions and to be scientifically transparent and reproducible. Statistical models provide a scientifically robust, transparent, and interpretable approach for ensuring that bioregions are formed on the basis of observed biological and physical data. Using statistically derived bioregions provides a repeatable framework for the spatial representation of bio ersity at multiple spatial scales. This results in better-informed management decisions and bio ersity conservation outcomes.
Publisher: Inter-Research Science Center
Date: 2001
DOI: 10.3354/MEPS213111
Publisher: Springer Science and Business Media LLC
Date: 2019
Publisher: Cambridge University Press (CUP)
Date: 27-01-2012
DOI: 10.1017/S1468109911000235
Abstract: The failure to reconcile views of the past and to address historical injustice has damaged inter-state relations in Northeast Asia. Joint committees, dialogues, and the participation of civil society have been used to address historical issues, but scholars in the disciplines of international relations and area studies have largely ignored these dialogues and deliberative forums. At the same time, there is an emergent theoretical literature on how deliberative democracy can address ethnic conflicts and historical injustice. There is a serious disconnect or distance between the theoretical literature on the resolution of conflicts via deliberation on the one hand, and empirical studies of deliberative approach in East Asia on the other. This article aims to address this shortcoming in the study of the politics of historical dispute in Northeast Asia by proposing a deliberative approach to history disputes and highlighting the achievements, limits, and dynamics of deliberation. Through mapping and comparative testing, we confirm that deliberation offers some potential for a departure from nationalist mentalities and a shift towards a consciousness of regional history in Northeast Asia. Our empirical test of the utility of the deliberative approach suggests that a new model for addressing regional disputes may be emerging.
Publisher: Pensoft Publishers
Date: 11-05-2017
DOI: 10.3897/BDJ.5.E11794
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.
Publisher: Public Library of Science (PLoS)
Date: 02-03-2012
Publisher: Cambridge University Press (CUP)
Date: 23-01-2018
DOI: 10.1017/S0025315416002009
Abstract: Canopy-forming fucoid algae have an important role as ecosystem engineers on rocky intertidal shores, where they increase the abundance of species otherwise limited by exposure during low tide. The facilitative relationship between Ascophyllum nodosum and associated organisms was explored using a frond breakage experiment (100%, 50%, 25%, 0% intact-frond treatments) in southern England, to assess the consequences of disturbance. Understorey substratum temperature was on average 3°C higher in 0% and 25% intact-frond treatments than in plots with 50% and 100% intact fronds. Light (as PAR during low tide) doubled in 0% intact-frond treatments in comparison to other treatments (which had similar light levels). Mobile invertebrate species richness declined by on average 1 species per m 2 in the treatments with only 25% and 0% intact fronds, and the abundance of Littorina obtusata declined by 2.4–4.2 in iduals per m 2 in the treatments with 25 and 0% intact fronds. Sessile taxa, including Osmundea pinnatifida and encrusting coralline algae, declined by half on average in the 0% intact-frond treatment. These results suggest that the ability of Ascophyllum to mediate environmental conditions to the understorey is the mechanism responsible for species distributed in the understorey (autogenic ecosystem engineering). The results of this study imply that a pulse disturbance resulting in a 50% breakage of Ascophyllum fronds significantly increases temperature and decreases the abundance of mobile invertebrates usually associated with Ascophyllum . Sessile taxa associated with Ascophyllum can, however, withstand disturbances down to 25% intact Ascophyllum fronds.
Publisher: Cold Spring Harbor Laboratory
Date: 23-02-2016
DOI: 10.1101/035543
Abstract: The qualification of orthology is a significant challenge when developing large, multiloci phylogenetic datasets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts, and mis-indexing, which pose problems to automated methods of orthology assessment. Here, we identify a set of orthologous single-copy genes from transcriptome assemblies for the land snails and slugs (Eupulmonata) using a thorough approach to orthology determination involving manual alignment curation, gene tree assessment and sequencing from genomic DNA. We qualified the orthology of 500 nuclear, protein coding genes from the transcriptome assemblies of 21 eupulmonate species to produce the most complete gene data matrix for a major molluscan lineage to date, both in terms of taxon and character completeness. Exon-capture targeting 490 of the 500 genes (those with at least one exon 120 bp) from 22 species of Australian Camaenidae successfully captured sequences of 2,825 exons (representing all targeted genes), with only a 3.7% reduction in the data matrix due to the presence of putative paralogs or pseudogenes. The automated pipeline Agalma retrieved the majority of the manually qualified 500 single-copy gene set and identified a further 375 putative single-copy genes, although it failed to account for fragmented transcripts resulting in lower data matrix completeness. This could potentially explain the minor inconsistencies we observed in the supported topologies for the 21 eupulmonate species between the manually curated and Agalma-equivalent dataset (sharing 458 genes). Overall, our study confirms the utility of the 500 gene set to resolve phylogenetic relationships at a broad range of evolutionary depths, and highlights the importance of addressing fragmentation at the homolog alignment stage for probe design.
Publisher: Elsevier BV
Date: 11-2011
DOI: 10.1016/J.YMPEV.2011.07.003
Abstract: The existing taxonomy of Euryalida, one of the two orders of the Ophiuroidea (Echinodermata), is uncertain and characterized by controversial delimitation of taxonomic ranks from genus to family-level. Their phylogeny was not studied in detail until now. We investigated a dataset of sequence from a mitochondrial gene (16S rRNA) and two nucleic genes (18S rRNA and 28S rRNA) for 49 euryalid ophiuroids and four outgroup species from the order Ophiurida. The monophyly of the order Euryalida was supported as was the monophyly of Asteronychidae, Gorgonocephalidae and an Asteroschematidae+Euryalidae clade. However, the group currently known as the Asteroschematidae was paraphyletic with respect to the Euryalidae. The Asteroschematidae+Euryalidae clade, which we recognise as an enlarged Euryalidae, contains three natural groups: the Asteroschematinae (Asteroschema and Ophiocreas), a new subfamily Astrocharinae (Astrocharis) and the Euryalinae with remaining genera. These subfamilies can be distinguished by internal ossicle morphology.
Publisher: Springer Science and Business Media LLC
Date: 09-09-2015
Publisher: CSIRO Publishing
Date: 2002
DOI: 10.1071/IT01034
Publisher: Wiley
Date: 04-06-2019
DOI: 10.1111/JBI.13620
Publisher: Wiley
Date: 13-07-2010
Publisher: Wiley
Date: 28-06-2023
DOI: 10.1111/ECOG.06627
Abstract: Delineating biogeographical regions can provide important insights into the processes shaping large‐scale species distribution patterns. Here we aimed to 1) identify global marine benthic biogeographical regions for ophiuroids extending from shallow waters to the deep sea and 2) quantify the importance of contemporary environmental conditions and geological features in shaping the delineated biogeographical regions. We delineated marine benthic biogeographical regions using a bipartite network analysis applied to a historical dataset of brittle stars. We then examined the faunal exchanges between the regions, and applied random forest models to evaluate the relative role of contemporary environmental conditions and tectonic configuration underlying the proposed biogeographic scheme. We propose ten main large biogeographical regions across the benthos. The biogeographical regions with the highest species richness and endemicity rates were found in the Indo‐Pacific region, Tropical West Atlantic and Southern Ocean, and South America. The key transition regions fall within the subarctic areas of the Pacific and the waters surrounding Southern Australia and New Zealand. Tectonic configuration, surface temperature and salinity were found to be the most important predictors of the ten delineated biogeographical regions. Our biogeographic delineation, including the deep sea, is in partial agreement with those proposed in previous studies. Our results suggest that contemporary environmental conditions (sea water temperature and salinity) strongly influence the modern distribution of ophiuroids, but that plate tectonics left a marked imprint on regional species pools. Future work based on multiple benthic taxa, and with a better understanding of the environmental conditions in the deep sea, are needed to evaluate the robustness of our proposed ision.
Publisher: CSIRO Publishing
Date: 2009
DOI: 10.1071/IS08021
Abstract: The biscuit star Tosia australis Gray, 1840 is a well known component of the shallow rocky reef fauna of south-eastern Australia. The putative T. australis species complex was subjected to reproductive, morphometric and molecular analyses. Molecular analyses of the data from three markers (mitochondrial COI and 16S rRNA and the nuclear non-coding region ITS2) confirmed the presence of a cryptic species, the morphology of which does not agree with any of the existing nominal species. Two separate reproductive modes were observed within the complex and documented via scanning electron microscopy. T. neossia, sp. nov., described herein from south-eastern Australia, is shown to release gametes from gonopores on the actinal surface. Embryos develop first into non-feeding, non-swimming brachiolaria, and then into tripod brachiolaria before metamorphosis. No surface cilia are present at any point throughout development of T. neossia. T. australis sensu stricto is shown to release gametes from the abactinal surface. Embryos develop into non-feeding, swimming brachiolaria before metamorphosis. Whereas T. australis var. astrologorum is confirmed as synonymous with T. australis, the status of the putative Western Australian taxon T. nobilis remains unresolved.
Publisher: Elsevier BV
Date: 04-2014
Publisher: Springer Science and Business Media LLC
Date: 31-07-1998
Publisher: Magnolia Press
Date: 12-06-2015
DOI: 10.11646/ZOOTAXA.3972.3.8
Abstract: The taxonomy of some ophiuroids reported from off Argentina, western Antarctica and the SW Atlantic Ocean is reviewed. The species Amphilepis sanmatiensis, known only from the small holotype, is a synonym of Amphioplus lucyae. This synonymy removes the only reported endemic ophiuroid from Argentina. The species name "Ophiacantha ingrata Koehler, 1923" used for specimens from South Georgia is invalid the specimens are likely to belong to one of two cryptic species within the O. vivipara complex. Specimens of Amphiura joubini reported from Argentina are re-identified as Amphiura princeps, and specimens of Ophiactis amator from the Antarctic Peninsula are re-identified as Ophiactis asperula.
Publisher: Magnolia Press
Date: 31-03-2022
DOI: 10.11646/ZOOTAXA.5124.1.1
Abstract: The ophiuroid fauna of the Île Amsterdam and Île Saint-Paul territories (SPA) is reviewed. Four new species are described: Ophiolebes felli, Ophiolebes paulensis, Ophiocomina arnaudi and Amphiura remota. Recent phylogenetic results required a partial reorganisation of Ophiacanthidae and Amphiuridae genera, including the transfer of some Ophiacantha and Ophiomitrella species to a new genus Ophiosabine (O. rosea, O. anomala, O. aristata, O. cuspidata, O. densispina, O. nodosa, O. notata, O. parcita, O. pentactis, O. vivipara, O. wolfarntzi) and existing genera Ophiosemnotes (O. conferta, O. ingrata, O. corynephora, O. clavigera, O. hamata) and Ophiolebes (O. yaldwyni), Ophiacantha spectabilis to Ophiotreta in the Ophiotomidae, and some Amphioplus species to Amphiura (A, acutus, A. ctenacantha, A. cipus). The combination Ophiophycis nixastrum is restored. The SPA endemic species Ophiocten lymani and Amphiura brevispina, and the southern Australian/New Zealand species Ophiactis cuspidata and Ophiocten australis, are recognised as valid species. The North Atlantic species Ophiura ljungmani, Ophiacantha veterna, Ophiosabine cuspidata, Ophiolimna bairdi and Ophiactis nidarosiensis are recorded from the southern Indian Ocean. Shallow water specimens of Ophiura ljungmani from the Western Atlantic are re-identified as O. fallax and O. acervata. The monotypic Ophiothauma heptactis from northern Australia is synonymised with Ophiocomella sexradia and thus the genus Ophiothauma with Ophiocomella. The biogeography of the ophiuroid fauna reflects the position of the islands near the eastward-flowing currents of the South Indian Ocean gyre. The closest affinities are with faunas in the SW Indian Ocean and SE Atlantic Ocean. Despite its proximity, no species are shared with the Kerguelen Plateau to the south. The large temperature gradient across the subtropical front between Île Saint-Paul and Kerguelen appears to be a distribution limit for littoral and upper bathyal invertebrates.
Publisher: Magnolia Press
Date: 20-04-2021
DOI: 10.11646/ZOOTAXA.4963.3.6
Abstract: The brittle star s les collected by the Danish cruise ‘Galathea II’ (1950–52) had not been studied completely. We examined the remaining deep-sea s les ( m) and present the species inventory, discussing taxonomic issues in relation to recent phylogenetic data. About 235 s les were examined, over 9,300 in iduals, from 67 species and 74 s ling localities, at depths of 425–5340 m. The species complex Amphiophiura bullata (Thomson, 1877) is morphologically not well separated, but molecular data suggest at least two clades. We propose to apply A. bullata for Atlantic and Australian populations and A. convexa (Lyman, 1878) for the North Pacific clade. We consider A. bullata pacifica Litvinova, 1971 conspecific with A. convexa. Ophiuroglypha irrorata (Lyman, 1878) and its subspecies are a polyphyletic group with unclear morphological boundaries. We propose to transfer Ophiura ossiculata (Koehler, 1908), Ophiura plana (Lütken & Mortensen, 1899) and Ophiura scomba Paterson, 1985 to Ophiuroglypha. Silax Fell, 1962, until now synonymised with Amphioplus Verrill, 1899, is proposed as a valid genus with the species S. verrilli (Lyman, 1879), S. consors (Koehler, 1908), S. daleus (Lyman, 1879), S. patulus (Lyman, 1879) and S. magnificus (Koehler, 1907). Triplodia Turner & Hallen, 2011 (a replacement name for Triodia A. M. Clark, 1970, due to homonymy) is synonymised with Silax, and possible specimens of its type species Triodia abdita A. M. Clark, 1970 are analysed. The species limits of Ophiacantha cosmica Lyman, 1879 and Ophiacantha pacifica Lütken & Mortensen, 1899 could not be confirmed morphologically, but published molecular data suggest two clades. We propose to apply O. pacifica to the Northern/Central Pacific population and O. cosmica to the Southern Pacific/Antarctic population.
Publisher: Wiley
Date: 11-2007
Publisher: Wiley
Date: 13-07-2010
Publisher: Elsevier BV
Date: 09-2014
DOI: 10.1016/J.YMPEV.2014.05.006
Abstract: The marine species of the southern coast of Australia have not been well studied with regard to molecular connectivity. Cryptic species are expected to be prevalent on this coastline. Here, we investigate the crinoid genus Cenolia (Echinodermata: Crinoidea: Comasteridae) using molecular methods to elucidate cryptic species and phylogenetic relationships. The genus Cenolia dominates the southern Australian crinoid fauna in shallow waters. Few studies have examined crinoids for cryptic species at a molecular level and these have been predominantly based on mitochondrial data. We employ the nuclear markers 28S rRNA and ITS-2 in addition to the mitochondrial COI. Six ergent mitochondrial clades were identified. Gene flow between confirmed clades was subsequently examined by the use of six novel microsatellite markers, showing that sympatric taxa with low mtDNA ergences (1.7% K2P) were not interbreeding in the wild. The type specimens of Cenolia benhami and C. spanoschistum were examined, as well as all six ergent clades. Morphological characters iding taxa were refined. Due to comb pinnule morphology, the New Zealand species benhami was determined to belong to the genus Oxycomanthus (nov. comb.). Three new species of Cenolia (including the Australian "benhami") require description.
Publisher: Springer Science and Business Media LLC
Date: 17-08-2020
DOI: 10.1038/S41598-020-70744-1
Abstract: The deep sea represents the largest and least explored biome on the planet. Despite the iconic status of the Galapagos Islands and being considered one of the most pristine locations on earth, the deep-sea benthic ecosystems of the archipelago are virtually unexplored in comparison to their shallow-water counterparts. In 2015, we embarked on a multi-disciplinary scientific expedition to conduct the first systematic characterization of deep-sea benthic invertebrate communities of the Galapagos, across a range of habitats. We explored seven sites to depths of over 3,300 m using a two-part Remotely Operated Vehicle (ROV) system aboard the E/V Nautilus, and collected 90 biological specimens that were preserved and sent to experts around the world for analysis. Of those, 30 taxa were determined to be undescribed and new to science, including members of five new genera (2 sponges and 3 cnidarians). We also systematically analysed image frame grabs from over 85 h of ROV footage to investigate patterns of species ersity and document the presence of a range of underwater communities between depths of 290 and 3,373 m, including cold-water coral communities, extensive glass sponge and octocoral gardens, and soft-sediment faunal communities. This characterization of Galapagos deep-sea benthic invertebrate megafauna across a range of ecosystems represents a first step to study future changes that may result from anthropogenic impacts to the planet’s climate and oceans, and informed the creation of fully protected deep-water areas in the Galapagos Marine Reserve that may help preserve these unique communities in our changing planet.
Publisher: Inter-Research Science Center
Date: 2001
DOI: 10.3354/MEPS213111
Publisher: Springer Science and Business Media LLC
Date: 22-11-2012
Publisher: Wiley
Date: 28-01-2020
DOI: 10.1111/DDI.13034
Publisher: Pensoft Publishers
Date: 16-09-2011
Publisher: Elsevier BV
Date: 06-2016
DOI: 10.1016/J.CUB.2016.04.051
Abstract: Dendrogramma was the iconic deep-sea animal of 2014, voted among the top-ten new species described that year [1]. The two species described are mushroom shaped animals, diploblastic, with an apparent gastrovascular system that extends from the base of the stalk to bifurcating canals that radiate through the flat disc [2]. The authors could not assign the new genus to any known animal group with certainty, leading to numerous media reports that it belonged to an entirely new phylum. Here we use phylogenomic data from newly collected specimens to show that Dendrogramma is a cnidarian, specifically a benthic siphonophore in the family Rhodaliidae. Although an entire Dendrogramma colony has not been found, we hypothesise that the mushroom-like bodies are bracts, possibly used to aid buoyancy or as defensive appendages to protect feeding gastrozooids or gonads.
Publisher: The Royal Society
Date: 09-2017
DOI: 10.1098/RSOB.170129
Abstract: Neuropeptides are a erse class of intercellular signalling molecules that mediate neuronal regulation of many physiological and behavioural processes. Recent advances in genome/transcriptome sequencing are enabling identification of neuropeptide precursor proteins in species from a growing variety of animal taxa, providing new insights into the evolution of neuropeptide signalling. Here, detailed analysis of transcriptome sequence data from three brittle star species, Ophionotus victoriae , Amphiura filiformis and Ophiopsila aranea , has enabled the first comprehensive identification of neuropeptide precursors in the class Ophiuroidea of the phylum Echinodermata. Representatives of over 30 bilaterian neuropeptide precursor families were identified, some of which occur as paralogues. Furthermore, homologues of endothelin/CCHamide, eclosion hormone, neuropeptide-F/Y and nucleobinin/nesfatin were discovered here in a deuterostome/echinoderm for the first time. The majority of ophiuroid neuropeptide precursors contain a single copy of a neuropeptide, but several precursors comprise multiple copies of identical or non-identical, but structurally related, neuropeptides. Here, we performed an unprecedented investigation of the evolution of neuropeptide copy number over a period of approximately 270 Myr by analysing sequence data from over 50 ophiuroid species, with reference to a robust phylogeny. Our analysis indicates that the composition of neuropeptide ‘cocktails’ is functionally important, but with plasticity over long evolutionary time scales.
Publisher: Elsevier BV
Date: 07-2020
Publisher: Oxford University Press (OUP)
Date: 14-09-2018
Publisher: Springer Science and Business Media LLC
Date: 2004
Publisher: Wiley
Date: 13-02-2017
Publisher: Cambridge University Press (CUP)
Date: 24-04-2020
DOI: 10.1017/S002531542000034X
Abstract: Since 2012, when Ophiothela was first described in the Atlantic, there has been no consensus regarding its identification. It has been described as O . mirabilis , O . cf. mirabilis , O . danae , or only Ophiothela sp. In order to fill these gaps, our aim was to test if specimens from Brazil are Ophiothela mirabilis and/or Ophiothela danae . Syntypes from the Museum of Comparative Zoology and United States National Museum, Smithsonian Institution, were used. We examined species boundaries of the small six-rayed brittle star Ophiothela using independent character sets utilizing morphology (external morphology and morphometry) and molecular data (16S and COI). Concordance was found between the analyses indicating that Ophiothela sp. from Brazil (BR), Ophiothela mirabilis and Ophiothela danae are closely related. We suggest that O . danae should be considered as a junior synonym of O . mirabilis . A detailed description of O . mirabilis BR is presented using external morphology and microstructural ossicles (arm plates, vertebra, dental and oral plates). This description includes new diagnostic features, particularly regarding its microstructures: (i) transspondylous articulation (first record in Ophiotrichidae) (ii) eight smooth knobs on the dorsal surface of the vertebrae (to date only in Ophiothela ) (iii) vertebrae with distal keel ided into two separate end processes matching the two large dorsal grooves proximally (first time in the literature) and (iv) an opening on both sides of the oral plate (as seen in other fissiparous species Ophiactis savignyi and Ophiocomella ophiactoides ).
Publisher: Public Library of Science (PLoS)
Date: 28-10-2015
Publisher: Elsevier BV
Date: 11-2019
DOI: 10.1016/J.CUB.2019.09.012
Abstract: The seafloor contains valuable mineral resources, including polymetallic (or manganese) nodules that form on offshore abyssal plains. The largest and most commercially attractive deposits are located in the Clarion Clipperton Fracture Zone (CCZ), in the eastern Pacific Ocean (EP) between Hawaii and Mexico, where testing of a mineral collection system is set to start soon [1]. The requirement to establish pre-mining environmental management plans has prompted numerous recent bio ersity and DNA barcoding surveys across these remote regions. Here we map DNA sequences from s led ophiuroids (brittle stars, including post-larvae) of the CCZ and Peru Basin onto a substantial tree of life to show unprecedented levels of abyssal ophiuroid phylogenetic ersity including at least three ancient (>70 Ma), previously unknown clades. While substantial dark (unobserved) bio ersity has been reported from various microbial meta-barcoding projects [2, 3], our data show that we have considerably under-estimated the bio ersity of even the most conspicuous mega-faunal invertebrates [4] of the EP abyssal plain.
No related grants have been discovered for Timothy O'Hara.