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Koch, NM, Coppard SE, Lessios HA, Briggs DEG, Mooi R, Rouse GW.  2018.  A phylogenomic resolution of the sea urchin tree of life. Bmc Evolutionary Biology. 18   10.1186/s12862-018-1300-4   AbstractWebsite

BackgroundEchinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a variety of morphological data, molecular attempts have relied on only a handful of genes. Both of these approaches have had limited success at resolving the deepest nodes of the tree, and their disagreement over the positions of a number of clades remains unresolved.ResultsWe performed de novo sequencing and assembly of 17 transcriptomes to complement available genomic resources of sea urchins and produce the first phylogenomic analysis of the clade. Multiple methods of probabilistic inference recovered identical topologies, with virtually all nodes showing maximum support. In contrast, the coalescent-based method ASTRAL-II resolved one node differently, a result apparently driven by gene tree error induced by evolutionary rate heterogeneity. Regardless of the method employed, our phylogenetic structure deviates from the currently accepted classification of echinoids, with neither Acroechinoidea (all euechinoids except echinothurioids), nor Clypeasteroida (sand dollars and sea biscuits) being monophyletic as currently defined. We show that phylogenetic signal for novel resolutions of these lineages is strong and distributed throughout the genome, and fail to recover systematic biases as drivers of our results.ConclusionsOur investigation substantially augments the molecular resources available for sea urchins, providing the first transcriptomes for many of its main lineages. Using this expanded genomic dataset, we resolve the position of several clades in agreement with early molecular analyses but in disagreement with morphological data. Our efforts settle multiple phylogenetic uncertainties, including the position of the enigmatic deep-sea echinothurioids and the identity of the sister clade to sand dollars. We offer a detailed assessment of evolutionary scenarios that could reconcile our findings with morphological evidence, opening up new lines of research into the development and evolutionary history of this ancient clade.

Moore, JM, Carvajal JI, Rouse GW, Wilson NG.  2018.  The Antarctic Circumpolar Current isolates and connects: Structured circumpolarity in the sea star Glabraster antarctica. Ecology and Evolution. 8:10621-10633.   10.1002/ece3.4551   AbstractWebsite

Aim The Antarctic Circumpolar Current (ACC) connects benthic populations by transporting larvae around the continent, but also isolates faunas north and south of the Antarctic Convergence. We test circumpolar panmixia and dispersal across the Antarctic Convergence barrier in the benthic sea star Glabraster antarctica. Location The Southern Ocean and south Atlantic Ocean, with comprehensive sampling including the Magellanic region, Scotia Arc, Antarctic Peninsula, Ross Sea, and East Antarctica. Methods The cytochrome c oxidase subunit I (COI) gene (n = 285) and the internal transcribed spacer region 2 (ITS2; n = 33) were sequenced. We calculated haplotype networks for each genetic marker and estimated population connectivity and the geographic distribution of genetic structure using phi(ST) for COI data. Results Glabraster antarctica is a single circum-Antarctic species with instances of gene flow between distant locations. Despite the homogenizing potential of the ACC, population structure is high (phi(ST) = 0.5236), and some subpopulations are genetically isolated. Genetic breaks in the Magellanic region do not align with the Antarctic Convergence, in contrast with prior studies. Connectivity patterns in East Antarctic sites are not uniform, with some regional isolation and some surprising affinities to the distant Magellanic and Scotia Arc regions. Main conclusions Despite gene flow over extraordinary distances, there is strong phylogeographic structuring and genetic barriers evident between geographically proximate regions (e.g., Shag Rocks and South Georgia). Circumpolar panmixia is rejected, although some subpopulations show a circumpolar distribution. Stepping-stone dispersal occurs within the Scotia Arc but does not appear to facilitate connectivity across the Antarctic Convergence. The patterns of genetic connectivity in Antarctica are complex and should be considered in protected area planning for Antarctica.

Rouse, GW, Carvajal JI, Pleijel F.  2018.  Phylogeny of Hesionidae (Aciculata, Annelida), with four new species from deep-sea eastern Pacific methane seeps, and resolution of the affinity of Hesiolyra . Invertebrate Systematics. 32:1050-1068.   10.1071/is17092   AbstractWebsite

Hesionidae Grube, 1850 currently comprises over 175 species in 28 genera, placed in several subfamilies. Discoveries in recent years have largely been of deep-sea taxa. Here we describe a further four new hesionid species, mainly from methane cold' seeps at around 1000-1800 m depths off the Pacific coast of Costa Rica and new record of another species. Several of these taxa also occur at methane seeps in the Guaymas Basis (Mexico) and off the USA west coast (California and Oregon). The phylogenetic relationships within Hesionidae are reassessed via maximum parsimony and maximum likelihood analyses of DNA sequences from nuclear (18S rRNA and 28SrRNA) and mitochondrial (16SrRNA and Cytochrome c oxidase I) loci for the new samples. On the basis of these results, we refer one of the new species to Gyptis Marion & Bobretzky in Marion, 1874, one to Neogyptis Pleijel, Rouse, Sundkvist & Nygren, 2012, and two to Sirsoe Pleijel, 1998. The new species Gyptis robertscrippsi n. sp., Neogyptis jeffruoccoi n. sp., Sirsoe dalailamai n. sp. and Sirsoe munki n. sp. We refer to a collection of individuals from seeps ranging from Oregon to Costa Rica as Amphiduropsis cf. axialensis (Blake & Hilbig, 1990), even though this species was described from hydrothermal vents off Oregon. Neogyptis jeffruoccoi n. sp. was generally found living inside the solemyid clam Acharax johnsoni (Dall, 1891). The position of Hesiolyra bergi Blake, 1985 is resolved on the basis of newly-collected specimens from near the type locality and, as a result, Hesiolyrinae Pleijel, 1998 is synonymized with Gyptini Pleijel, 1998 (and Gyptinae Pleijel, 1998).

Leiva, C, Riesgo A, Avila C, Rouse GW, Taboada S.  2018.  Population structure and phylogenetic relationships of a new shallow-water Antarctic phyllodocid annelid. Zoologica Scripta. 47:714-726.   10.1111/zsc.12313   AbstractWebsite

Shallow-water polychaetes are abundant and diverse components of the Southern Ocean benthic communities, and although they have been widely studied, new species that are relatively common are still discovered. Here, we report the discovery of Pterocirrus giribeti sp. n., a new and abundant intertidal and upper-subtidal Antarctic phyllodocid. To establish the phylogenetic relationships of the new species, we sequenced two nuclear (18S and 28S) and two mitochondrial (COI and 16S) markers. Although the phylogenetic relationships obtained for the family Phyllodocidae were not fully resolved, we assigned our new phyllodocid to the genus Pterocirrus based on both its phylogenetic position and its morphological characters. Using COI and 16S sequences of 126 and 118 individuals, respectively, from eight populations across the South Shetland Islands and the Antarctic Peninsula, we also investigated the genetic diversity and gene flow patterns of this new species. Our results suggested that all populations were panmictic, likely due to the presence of planktotrophic larvae allowing long-distance dispersal. Interestingly, some genetic substructure was detected despite panmixis, and we identified a semipermeable barrier coinciding with an oceanic front produced by the intrusion into the Bransfield Strait of a tongue of water from the Weddell Sea. This front produced signatures of differentiation on populations at the tip of the West Antarctic Peninsula. Moreover, our results indicated a recent demographic expansion throughout the sampled area, in agreement with the glacial refugium hypothesis stated for other Antarctic shallow-water invertebrates.

McCowin, MF, Rouse GW.  2018.  A new Lamellibrachia species and confirmed range extension for Lamellibrachia barhami (Siboglinidae, Annelida) from Costa Rica methane seeps. Zootaxa. 4504:1-22.   10.11646/zootaxa.4504.1.1   Abstract

Lamellibrachia Webb, 1969 has eight currently recognized species reported from chemosynthetic environments in the Pacific, Atlantic, and Mediterranean. Of these, Lamellibrachia barhami Webb, 1969 has been reported in the eastern Pacific from Canada to Costa Rica. In this study, phylogenetic analyses of Lamellibrachia tubeworms sampled from the Costa Rica margin confirm the large geographic range of L. barhami and reveal a new Lamellibrachia species from a single methane seep between 999 and 1,040 meters. Lamellibrachia donwalshi sp. nov. differs genetically and morphologically from all congeneric species. Despite its geographic proximity to the eastern Pacific L. barhami, L. donwalshi sp. nov. formed a Glade with Atlantic and Mediterranean Lamellibrachia species. This suggests a vicariant event may have occurred after an Atlantic radiation of Lamellibrachia.

Martin, JW, Wall AR, Shank T, Cha H, Seid CA, Rouse GW.  2018.  A new species of Alvinocaris (Crustacea: Decapoda: Caridea: Alvinocarididae) from Costa Rican methane seeps. Zootaxa. 4504:418-430.   10.11646/zootaxa.4504.3.7   AbstractWebsite

A new caridean shrimp, Alvinocaris costaricensis, is described from methane seeps in the eastern Pacific off Costa Rica. The new species is the 16th described species of the genus, and by molecular analysis appears closest to Alvinocaris komaii from the Lau Basin, southwestern Pacific, but shares certain morphological characters with A. lusca from the Galapagos Rift and A. muricola from the West Florida Escarpment, as well as with A. kexueae from the Manus Basin in the Southwest Pacific.

McCowin, MF, Rouse GW.  2018.  Phylogeny of hydrothermal vent Iphionidae, with the description of a new species (Aphroditiformia, Annelida). Zookeys. 779:89-107.   10.3897/zookeys.779.24781   Abstract

The scale-worm family Iphionidae consists of four genera. Of these, Thermiphione has two accepted species, both native to hydrothermal vents in the Pacific Ocean; T. fijiensis Miura, 1994 (West Pacific) and T. tufari Hartmann-Schroder, 1992 (East Pacific Rise). Iphionella is also known from the Pacific, and has two recognized species; Iphionella risensis Pettibone, 1986 (East Pacific Rise, hydrothermal vents) and I. philippinensis Pettibone, 1986 (West Pacific, deep sea). In this study, phylogenetic analyses of Iphionidae from various hydrothermal vent systems of the Pacific Ocean were conducted utilizing morphology and mitochondrial (COI and 16S rRNA) and nuclear (18S and 28S rRNA) genes. The results revealed a new iphionid species, described here as Thermiphione rapanui sp. n. The analyses also demonstrated the paraphyly of Thermiphione, requiring Iphionella risensis to be referred to the genus, as Thermiphione risensis (Pettibone, 1986).

Rouse, GW, Goffredi SK, Johnson SB, Vrijenhoek RC.  2018.  An inordinate fondness for Osedax (Siboglinidae: Annelida): Fourteen new species of bone worms from California. Zootaxa. 4377:451–489.   10.11646/zootaxa.4377.4.1   AbstractOpen Access

We incorporate DNA sequences from a comprehensive sampling of taxa to provide an updated phylogeny of Osedax and discuss the remarkable diversity of this clade of siboglinids. We formally describe 14 new species of Osedax from Monterey Bay, California, USA, raising the total number of properly named Osedax species to 25. These new species had formerly been recognized by informal names in various publications, and on GenBank. The descriptions document the occurrence of dwarf males in five of the new species. The distribution for the 19 species of Osedax known to occur in Monterey Bay across depths from 385 to 2898 meters and various bone substrates is documented. The exploitation of extant bird and marine turtle bones by Osedax is reported for the first time.

Zhang, Y, Sun J, Rouse GW, Wiklund H, Pleijel F, Watanabe HK, Cheng C, Qian P-Y, Qiu J-W.  2018.  Phylogeny, evolution and mitochondrial gene order rearrangement in scale worms (Aphroditiformia, Annelida): Insights from low-coverage genome sequencing. Molecular Phylogenetics and Evolution. 125:220-231. Abstract

Next-generation sequencing (NGS) has become a powerful tool in phylogenetic and evolutionary studies. Here we applied NGS to recover two ribosomal RNA genes (18S and 28S) from 16 species and 15 mitochondrial genomes from 16 species of scale worms representing six families in the suborder Aphroditiformia (Phyllodocida, Annelida), a complex group of polychaetes characterized by the presence of dorsal elytra or scales. The phylogenetic relationship of the several groups of scale worms remains unresolved due to insufficient taxon sampling and low resolution of individual gene markers. Phylogenetic tree topology based on mitochondrial genomes is comparable with that based on concatenated sequences from two mitochondrial genes (cox1 and 16S) and two ribosomal genes (18S and 28S) genes, but has higher statistical support for several clades. Our analyses show that Aphroditiformia is monophyletic, indicating the presence of elytra is an apomorphic trait. Eulepethidae and Aphroditidae together form the sister group to all other families in this suborder, whereas Acoetidae is sister to Iphionidae. Polynoidae is monophyletic, but within this family the deep-sea subfamilies Branchinotogluminae and Macellicephalinae are paraphyletic. Mitochondrial genomes in most scale-worm families have a conserved gene order, but within Polynoidae there are two novel arrangement patterns in the deep-sea clade. Mitochondrial protein-coding genes in polynoids as a whole have evolved under strong purifying selection, but substitution rates in deep-sea species are much higher than those in shallow-water species, indicating that purifying selection is relaxed in deep-sea polynoids. There are positive selected amino acids for some mitochondrial genes of the deep-sea clade, indicating they may involve in the adaption of deep-sea polynoids. Overall, our study (1) provided more evidence for reconstruction of the phylogeny of Aphroditiformia, (2) provided evidence to refute the assumption that mitochondrial gene order in Errantia is conserved, and (3) indicated that the deep-sea extreme environment may have affected the mitochondrial genome evolution rate and gene order arrangement in Polynoidae.

Taylor, KH, Rouse GW, Messing CG.  2018.  Revising Mariametridae: the genera Dichrometra, Lamprometra, and Liparometra (Echinodermata, Crinoidea, Comatulida). Systematics and Biodiversity. 16:142-159.   10.1080/14772000.2017.1375044   AbstractWebsite

The featherstar genera, Dichrometra A.H. Clark, 1909a, Lamprometra A.H. Clark, 1913, and Liparometra A.H. Clark, 1913 (Comatulida: Mariametridae), are currently diagnosed only on the basis of the relative lengths of their proximal three pairs of pinnules. Previous published descriptions and a morphological re-examination indicate that this character is inconsistent and phenotypically variable. Distinctions amongst most of the 11 currently recognized species within each of these three genera are similarly ambiguous. This study compared currently accepted diagnostic characters amongst members of these three genera and incorporated mitochondrial DNA and nuclear DNA sequencing to assess taxonomic distinctions. Specimens were obtained from throughout the range of all three genera. Molecular data supported a monophyletic grouping, which we have placed under the senior generic name Dichrometra, based on a level of intraspecies divergence similar to that in other featherstar taxa, with four distinct species-level clades: palmata Müller, 1841, flagellata Müller, 1841, gyges Bell, 1884, and brachypecha H.L. Clark, 1915, the latter two resurrected from synonymy under palmata. Amongst these, proportions of proximal pinnules contributed only to the diagnosis of D. brachypecha. These species and the genus are redescribed. However, new diagnostic morphological characters remain, because they are needed to corroborate the four clades distinguished by molecular data. Because no sequence data were available from specimens identifiable as the remaining nine nominal species, we maintain them as accepted, pending further information.

Kerbl, A, Vereide EH, Gonzalez BC, Rouse GW, Worsaae K.  2018.  Two new meiofaunal species of Trilobodrilus (Dinophilidae, Annelida) from California, USA. European Journal of Taxonomy. 421:1-18. AbstractWebsite

We describe two new species of the annelid genus Trilobodrilus Remane, 1925 (Dinophilidae Verill, 1892) from an intertidal and a subtidal location in San Diego, California. These two species show morphological and molecular divergences between each other and the previously described, geographically distant species. Intertidal T. windansea sp. nov. differs from subtidal T. ellenscrippsae sp. nov. most remarkably in the number and pattern of ciliary tufts and bands on the prostomium and along the body length, besides showing ca. 15% difference in gene fragments of COI and CytB. Trilobodrilus windansea sp. nov., though nesting with T. ellenscrippsae sp. nov. in the molecular phylogenetic analyses, morphologically resembles the Japanese T. itoi Kajihara, Ikoma, Yamasaki & Hiruta, 2015 most closely, but still differs from this species in the higher number of apical ciliary tufts, an additional ciliary row posterior to the second ciliary band, and by lacking a forth ciliary band and segmentally arranged lateral ciliary tufts. Trilobodrilus ellenscrippsae sp. nov. is morphologically most similar to the Japanese T. nipponicus Uchida & Okuda, 1943, but is much shorter, has more apical ciliary tufts, and less regularly arranged lateral ciliary tufts along the body. All species differ significantly in all compared gene fragments, and no obvious correlation was found between habitat and the species morphology or relationships.

Taylor, KH, Rouse GW, Messing CG.  2017.  Systematics of Himerometra (Echinodermata: Crinoidea: Himerometridae) based on morphology and molecular data.. Zoological Journal of the Linnean Society. 181:342–356.   Abstract

One of the most common genera of feather stars found on tropical Indo-western Pacific reefs, Himerometra A.H.Clark, 1907, has previously included six accepted species, distinguished chiefly by variations in the enlarged proximal pinnules. This study examined new and existing specimens using molecular (mtDNA and nuDNA) techniques and morphological characters to revise the genus. Both approaches support placing H. magnipinna and H. martensi as junior synonyms of H. robustipinna. Sequence data for specimens attributed to H. bartschi also place this species as a junior synonym of H. robustipinna, despite some morphological disparity. Himerometra sol is retained as distinct despite morphological congruence with H. robustipinna, because the two known specimens were collected outside the known range of the latter, with no molecular data currently available. Himerometra persica is herein transferred to Heterometra: the type specimens were incorrectly identified. The species treated as valid are redescribed. This study illustrates the importance of re-examining crinoid species boundaries for established taxa without molecular corroboration and demonstrates that diversity in this particular feather star clade might be lower than previously thought.

Millan-Aguinaga, N, Chavarria KL, Ugalde JA, Letzel AC, Rouse GW, Jensen PR.  2017.  Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations. Scientific Reports. 7   10.1038/s41598-017-02845-3   AbstractWebsite

Bacteria represent the most genetically diverse kingdom of life. While great progress has been made in describing this diversity, it remains difficult to identify the phylogenetic and ecological characteristics that delineate groups of bacteria that possess species-like properties. One major challenge associated with species delineations is that not all shared genes have the same evolutionary history, and thus the choice of loci can have a major impact on phylogenetic reconstruction. Sequencing the genomes of large numbers of closely related strains provides new opportunities to distinguish ancestral from acquired alleles and assess the effects of recombination on phylogenetic inference. Here we analyzed the genomes of 119 strains of the marine actinomycete genus Salinispora, which is currently comprised of three named species that share 99% 16S rRNA gene sequence identity. While 63% of the core genome showed evidence of recombination, this had no effect on species-level phylogenomic resolution. Recombination did however blur intra-species relationships and biogeographic resolution. The genome-wide average nucleotide identity provided a new perspective on Salinispora diversity, revealing as many as seven new species. Patterns of orthologous group distributions reveal a genetic basis to delineation the candidate taxa and insight into the levels of genetic cohesion associated with bacterial species.

Summers, MM, Messing CG, Rouse GW.  2017.  The genera and species of Comatulidae (Comatulida: Crinoidea): a molecular and morphological guide. Zootaxa. 4268:151–190.   10.11646/zootaxa.4268.2.1   Abstract

We provide a guide for identification of Comatulidae, a family of crinoid echinoderms, incorporating morphological and molecular evidence. A non-dichotomous key for all genera is included, as well as photographs of species most likely to be encountered in the tropical western Pacific Ocean. Based on sequencing of cytochrome oxidase subunit I (COI), and other genes when necessary, we identified four cases where taxonomic revision was needed. We synonymized Comaster nobilis under Comaster schlegelii, and Clarkcomanthus exilis under Clarkcomanthus comanthipinnus, and re-described Clarkcomanthus albinotus. We also showed the variation of COI sequences within and among species, which varies from lineage to lineage. In some cases, specimens with obvious morphological disparity possessed very little intraspecific molecular diversity (<1%). In others, specimens with nearly identical external appearances exhibited quite divergent COI sequences (up to 6%). These results, combined with the non-dichotomous key herein, offer guidelines for identification and discussion of existing and new species of Comatulidae.

Stiller, J, Wilson NG, Donnellan S, Rouse GW.  2017.  The leafy seadragon, Phycodurus eques, a flagship species with low but structured genetic variability. Journal of Heredity. 108:152-162.   10.1093/jhered/esw075   AbstractWebsite

The leafy seadragon (Phycodurus eques, Syngnathidae), is a charismatic endemic of Australia's temperate coast. The species exhibits remarkable camouflage in its kelp and seagrass habitat. These habitats have been retreating throughout the range of the species, leading to concerns about the persistence of leafy seadragons. Despite being a popular aquarium display and a flagship for coastal conservation, little is known about leafy seadragon biology. We used 7 microsatellite markers and 2 mitochondrial DNA fragments to investigate the population structuring and genetic diversity of 71 individuals. Bayesian cluster analysis identified 2 main genetic partitions, one in Western Australia and the other in South Australia. Shallower, yet significant, differentiation of mitochondrial DNA (phi(ST)) and microsatellites (F-ST, F'(ST), D) was found on the smaller geographic scales in South Australia. Distinct groups were supported in Encounter Bay, on both shores of Gulf St Vincent, and in Spencer Gulf. Sample sizes were too small in the eastern Great Australian Bight and in the westernmost locality to address genetic differentiation in these regions. Overall genetic diversity was moderate to low, but particularly low levels were found in the Western Australian cluster. This latter point needs confirmation at other sites in Western Australia. In South Australia, signatures of demographic changes were detected, which may have been caused by a population expansion due to post-glacial reflooding of the gulfs. The Western Australian and South Australian clusters appeared as demographically independent units. Conservation actions should focus on preserving genetic diversity at local scales and maintaining habitat connectivity.

Wilson, NG, Stiller J, Rouse GW.  2017.  Barriers to gene flow in common seadragons (Syngnathidae: Phyllopteryx taeniolatus). Conservation Genetics. 18:53-66.   10.1007/s10592-016-0881-y   AbstractWebsite

The common seadragon is an iconic fish with presumed limited dispersal, because juveniles hatch directly from the tail of the male parent. Nothing is presently known of their phylogeographic structure, despite conservation concerns and a distribution spanning southern Australia. Here, we sequenced mitochondrial genes from 201 common seadragons in Western Australia, South Australia, Victoria, Tasmania and New South Wales. We show that common seadragon populations are highly structured geographically, and that genetic variation varies significantly. The historical Bassian Isthmus appears to have left a strong imprint on population structure. Populations east of the Bassian Isthmus are low in diversity and appear more connected than those in the west, although this is likely caused by a recent expansion from a common source after the Last Glacial Maximum. All individuals from Eden, Bicheno and Hobart are represented by only two haplotypes. Populations west of the Bassian Isthmus are more diverse, with the highest diversity indices shown by Western Australian and Spencer Gulf populations. A large sampling gap across the Great Australian Bight is yet to be resolved; the west versus east break here may be an artifact of this gap. Almost all sampled populations can be inferred to have limited gene flow among them, which has implications for recovery after local extinction. Populations thought to be in decline (Sydney, Hobart) showed low genetic diversity, which may make them vulnerable to further reductions.

Rouse, GW, Stiller J, Wilson NG.  2017.  First live records of the ruby seadragon (Phyllopteryx dewysea, Syngnathidae). Marine Biodiversity Records. 10:2.   10.1186/s41200-016-0102-x   Abstract

Until recently, only two species of seadragon were known, Phycodurus eques (the leafy seadragon) and Phyllopteryx taeniolatus (the common seadragon), both from Australia. In 2015, we described a new species of seadragon, Phyllopteryx dewysea (the ruby seadragon). Although the leafy and common seadragons are well known and commonly seen in aquarium exhibits world-wide, the ruby seadragon was known only from four preserved specimens, leaving many aspects of its biology unknown. Based on specimen records, it was speculated that the ruby seadragon normally lives at depths beyond recreational SCUBA diving limits, which may also explain why it went undiscovered for so long. The ruby seadragon also bears a superficial resemblance to the common seadragon, with a number of specimens misidentified in museum collections. The only recent live-collected specimen was trawled from the Recherche Archipelago, a cluster of over 100 islands in Western Australia. We took a small remotely operated vehicle (miniROV) to this locality to obtain the first images of live ruby seadragons. We made observations on the seadragon habitat and behavior, including feeding. We also provide new key observations on their morphology, notably that they lack dermal appendages and have a prehensile tail. We recommend that the ruby seadragon be protected as soon as practicable.

Messing, CG, Hoggett AK, Vail LL, Rouse GW, Rowe FWE.  2017.  Chapter 7. Class Crinoidea.. Australian Echinoderms: Biology, Ecology & Evolution. ( Byrne M, O'Hara T, Eds.)., Melbourne: CSIRO Publishing
Eilertsen, MH, Kongsrud JA, Alvestad T, Stiller J, Rouse GW, Rapp HT.  2017.  Do ampharetids take sedimented steps between vents to seeps? Phylogeny and habitat-use of Ampharetidae (Annelida, Terebelliformia) in chemosynthesis-based ecosystems. BMC Evolutionary Biology. 17:222.   10.1186/s12862-017-1065-1   Abstract

A range of higher animal taxa are shared across various chemosynthesis-based ecosystems (CBEs), which demonstrates the evolutionary link between these habitats, but on a global scale the number of species inhabiting multiple CBEs is low. The factors shaping the distributions and habitat specificity of animals within CBEs are poorly understood, but geographic proximity of habitats, depth and substratum have been suggested as important. Biogeographic studies have indicated that intermediate habitats such as sedimented vents play an important part in the diversification of taxa within CBEs, but this has not been assessed in a phylogenetic framework. Ampharetid annelids are one of the most commonly encountered animal groups in CBEs, making them a good model taxon to study the evolution of habitat use in heterotrophic animals. Here we present a review of the habitat use of ampharetid species in CBEs, and a multi-gene phylogeny of Ampharetidae, with increased taxon sampling compared to previous studies.

Forrest, MJ, Stiller J, King TL, Rouse GW.  2017.  Between hot rocks and dry places: The status of the Dixie Valley toad. Western North American Naturalist. 77:162-175. Abstract

In Dixie Valley, Nevada, an isolated population of toads has been the subject of proactive conservation measures by the Nevada Department of Wildlife and the U.S. Fish and Wildlife Service since 2008 due to concerns about potential habitat degradation resulting from exploitation of nearby geothermal energy resources. These toads appear to belong within the Anaxyrus boreas species group but are commonly referred to as Dixie Valley toads (DVTs). The DVT is currently confined to an extremely narrow habitat range (370 ha) that is geographically isolated from any other A. boreas population. In this study, genetic variations in mitochondrial genes and 11 microsatellite loci were used to assess the affinities of DVTs in relation to members of the A. boreas species group. We compared results from DVTs with previously published data spanning much of the range of A. boreas in the United States and new data from a nearby toad population within Dixie Valley. Data from both mitochondrial DNA and microsatellites placed DVTs inside the A. boreas species group. In particular, DVTs fell into a cluster of A. boreas from Washington and California, along with other species from the A. boreas species group, namely A. nelsoni, A. canorus, and A. exsul. Genetic differentiation of DVTs was lowest between A. boreas populations in Washington and California. However, allele frequencies were significantly different between DVTs and all other populations, including a nearby locality within Dixie Valley. This genetic differentiation, along with the DVT’s geographical isolation and restricted habitat, warrants recognition of the DVT as a distinct management unit.

Pasulka, AL, Goffredi SK, Tavormina PL, Dawson KS, Levin LA, Rouse GW, Orphan VJ.  2017.  Colonial tube-dwelling ciliates influence methane cycling and microbial diversity within methane seep ecosystems.. Frontiers in Marine Science-Aquatic Microbiology. 3:276.   10.3389/fmars.2016.00276   Abstract

In a variety of marine ecosystems, microbial eukaryotes play important ecological roles; however, our knowledge of their importance in deep-sea methane seep ecosystems is limited. Microbial eukaryotes have the potential to influence microbial community composition and diversity by creating habitat heterogeneity, and may contribute to carbon cycling through grazing or symbiotic associations with microorganisms. In this study, we characterized the distribution, substrate variability and ecology of a particular group of microbial eukaryotes, known as folliculinid ciliates, at methane seeps along the eastern Pacific margin. Folliculinid ciliates were recently recognized as an abundant and ecologically important component of hydrothermal vent ecosystems, but their ecology in methane seeps has not been examined. Folliculinid ciliates inhabited methane seeps from Costa Rica to Oregon, suggesting a broad distribution in the eastern Pacific. Using phylogenetic analyses of the 18S rRNA gene, two different species of folliculinid were identified and are formally described here. Folliculinids occupied a range of physical substrates, including authigenic carbonate rocks, shells of dead vesicomyid clams, polychaete tubes and gastropod shells. Molecular analysis of the folliculinid-associated microorganisms (16S rRNA and particular methane monoxygenase) revealed that these ciliates not only influence overall microbial diversity, but also have a specific relationship with bacteria in the “Deep sea-2” methanotroph clade. Natural δ13C isotope signatures of the folliculinids (−35 ) and their 13C-enrichment patterns in shipboard 13CH4 stable isotope-probing experiments indicated these ciliates and their associated microbes are involved in cycling methane-derived carbon. Folliculinids were significantly enriched in 13C after the addition of 13CH4 over short-term (3–8 day) incubations. Together, these results suggest that folliculinid ciliates represent a previously overlooked contributor to the ecology and biogeochemical cycling at deep-sea methane seep ecosystems.

Xu, T, Sun J, Lv J, Li T, Zou W, Watanabe H, Rouse GW, Wang S, Qian P-Y, Bao Z, Qiu J-W.  2017.  Genome-wide discovery of single nucleotide polymorphisms (SNPs) and single nucleotide variants (SNVs) in deep-sea mussels: Potential use in population genomics and cross-species application.. Deep Sea Research II. 137:318-326. Abstract

The present study aimed to generate genome-wide single nucleotide polymorphisms (SNPs) for the deep-sea mussel Bathymodiolus platifrons via a combination of genome survey sequencing and the type IIB endonuclease restriction-site associated DNA (2b-RAD) sequencing, assess the potential use of SNPs in detecting fine-sale population genetic structure and signatures of divergent selection, as well as their cross-species application in other bathymodioline mussels. Genome survey sequencing was conducted for one individual of B. platifrons. De novo assembly resulted in 781,720 sequences with a scaffold N50 of 2.9 kb. Using these sequences as a reference, 9307 genome-wide SNPs were identified by 2b-RAD for 28 B. platifrons individuals collected from a seep and a vent population. Among these SNPs, nine outliers showed significant evidence for divergent selection, and their positions in the genes or scaffolds were identified. The FST estimated based on the putative neutral SNPs was low (0.0126) indicating the two B. platifrons populations having a high genetic connectivity. However, the permutation test detected sig- nificant differences (Po0.00001), indicating the two populations having clearly detectable genetic dif- ferentiation. The Bayesian clustering analyses and principle component analyses (PCA) performed based on either the putative neutral or outlier SNPs also showed that these two populations were genetically differentiated. In addition, 2b-RAD was also conducted to detect 10,199, 6429, and 3811 single nucleotide variants (SNVs) respectively in the bathymodioline mussels Bathymodiolus japonicus, Bathymodiolus aduloides and Idas sp. with different phylogenetic distances from B. platifrons. Overall, our study has demonstrated the feasibility and effectiveness of combining genome survey sequencing and 2b-RAD to rapidly generate genomic resources for use in fine-scale population genetic studies, and various cross- species applications.

Goffredi, S.K., Johnson S, Tunnicliffe V, Caress D, Clague D, Escobar E, Lundsten L, Paduan JB, Rouse GW, Salcedo DL, Soto LA, Spelz-Madero R, Zierenberg R, Vrijenhoek R.  2017.  Hydrothermal vent fields discovered in the southern Gulf of California clarify role of habitat in augmenting regional diversity.. Proc. R. Soc. B . 284:20170817. Abstract

Hydrothermal vent communities are distributed along mid-ocean spreading ridges as isolated patches. While distance is a key factor influencing connectivity among sites, habitat characteristics are also critical. The Pescadero Basin (PB) and Alarcón Rise (AR) vent fields, recently discovered in the southern Gulf of California, are bounded by previously known vent localities (e.g. Guaymas Basin and 21° N East Pacific Rise); yet, the newly discovered vents differ markedly in substrata and vent fluid attributes. Out of 116 macrofaunal species observed or collected, only three species are shared among all four vent fields, while 73 occur at only one locality. Foundation species at basalt-hosted sulfide chimneys on the AR differ from the functional equivalents inhabiting sediment-hosted carbonate chimneys in the PB, only 75 km away. The dominant species of symbiont-hosting tubeworms and clams, and peripheral suspension-feeding taxa, differ between the sites. Notably, the PB vents host a limited and specialized fauna in which 17 of 26 species are unknown at other regional vents and many are new species. Rare sightings and captured larvae of the 'missing' species revealed that dispersal limitation is not responsible for differences in community composition at the neighbouring vent localities. Instead, larval recruitment-limiting habitat suitability probably favours species differentially. As scenarios develop to design conservation strategies around mining of seafloor sulfide deposits, these results illustrate that models encompassing habitat characteristics are needed to predict metacommunity structure.

Miller, AK, Kerr AM, Paulay G, Reich M, Wilson NG, Carvajal JI, Rouse GW.  2017.  Molecular phylogeny of extant Holothuroidea (Echinodermata).. Molecular Phylogenetics and Evolution. 111:110-131. Abstract

Sea cucumbers (Holothuroidea) are a morphologically diverse, ecologically important, and economically valued clade of echinoderms; however, the understanding of the overall systematics of the group remains controversial. Here, we present a phylogeny of extant Holothuroidea assessed with maximum parsimony, maximum likelihood, and Bayesian approaches using approximately 4.3 kb of mt- (COI, 16S, 12S) and nDNA (H3, 18S, 28S) sequences from 82 holothuroid terminals representing 23 of the 27 widely- accepted family-ranked taxa. Currently five holothuroid taxa of ordinal rank are accepted. We find that three of the five orders are non-monophyletic, and we revise the taxonomy of the groups accordingly. Apodida is sister to the rest of Holothuroidea, here considered Actinopoda. Within Actinopoda, Elasipodida in part is sister to the remaining Actinopoda. This latter clade, comprising holothuroids with respiratory trees, is now called Pneumonophora. The traditional Aspidochirotida is paraphyletic, with representatives from three orders (Molpadida, Dendrochirotida, and Elasipodida in part) nested within. Therefore, we discontinue the use of Aspidochirotida and instead erect Holothuriida as the sister group to the remaining Pneumonophora, here termed Neoholothuriida. We found four well-supported major clades in Neoholothuriida: Dendrochirotida, Molpadida and two new clades, Synallactida and Persiculida. The mapping of traditionally-used morphological characters in holothuroid systematics onto the phylogeny revealed marked homoplasy in most characters demonstrating that further taxonomic revision of Holothuroidea is required. Two time-tree analyses, one based on calibrations for uncontroversial crown group dates for Eleutherozoa, Echinozoa and Holothuroidea and another using these calibrations plus four more from within Holothuroidea, showed major discrepancies, suggesting that fossils of Holothuroidea may need reassessment in terms of placing these forms with existing crown clades.

Zhang, D-sheng, Zhou Y-dong, Wang C-sheng, Rouse GW.  2017.  A new species of Ophryotrocha (Annelida: Eunicida: Dorvilleidae) from hydrothermal vents on the Southwest Indian Ridge. Zookeys. 687:1-9. AbstractWebsite

Dorvilleids were collected from hydrothermal vents on the Southwest Indian Ridge by manned submersible Jiaolong. These represent a new species of Ophryotrocha that is here described as Ophryotrocha jiaolongi sp. n. This is the first dorvilleid described from vents on the Southwest Indian Ridge. It most closely resembles another vent species, Ophryotrocha akessoni Blake, 1985 from the Galapagos Rift, but can be distinguished by its antennae, palps, jaw structure. The new species has particularly distinctive mandibles, which allow it to be easily identified.

Moore, JM, Nishi E, Rouse GW.  2017.  Phylogenetic analyses of Chaetopteridae (Annelida).. Zoologica Scripta. 46:596-610.   10.1111/zsc.12238   Abstract

Phylogenetic relationships within Chaetopteridae were assessed using parsimony cladistic analysis of 43 external morphological characters and molecular phylogenetic analysis of three genes: mitochondrial cytochrome oxidase subunit I DNA (COI) and nuclear 28S and 18S ribosomal DNA. The group currently comprises four accepted genera: Chaetopterus Cuvier, Spiochaetopterus Sars, Phyllochaetopterus Grube and Mesochaetopterus Potts, with 97 available species names. We selected 79 species and one subspecies with adequately detailed data for morphological comparison. Sixteen additional unidentified chaetopterid species were included to enhance representation of the morphological and genetic diversity of the family. The morphological matrix was coded chiefly from the original descriptions, as well as revisions, type specimens and newly collected specimens. Chaetopteridae was mono- phyletic in the molecular phylogeny, and united by a number of morphological features, including a single pair of grooved peristomial palps, three morphologically distinct tagmata (A, B, C) and the presence of stout, modified cutting chaetae on anterior chaetiger 4 (A4). Chaetopterus and Mesochaetopterus formed well-supported sister clades based on sequence data; however, the reciprocal monophyly of these genera was not supported by morphologi- cal data. Spiochaetopterus and Phyllochaetopterus were paraphyletic/polyphyletic as currently defined, and the status of these and other available generic names is discussed.

Linchangco, GV, Foltz DW, Reid R, Williams J, Nodzak C, Kerr AM, Miller AK, Hunter R, Wilson NG, Nielsen WJ, Mah CL, Rouse GW, Wray GA, Janies DA.  2017.  The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics.. Molecular Phylogenetics and Evolution. 115:161-170. Abstract

Multi-locus phylogenetic studies of echinoderms based on Sanger and RNA-seq technologies and the fossil record have provided evidence for the Asterozoa-Echinozoa hypothesis. This hypothesis posits a sister relationship between asterozoan classes (Asteroidea and Ophiuroidea) and a similar relationship between echinozoan classes (Echinoidea and Holothuroidea). Despite this consensus around Asterozoa-Echinozoa, phylogenetic relationships within the class Asteroidea (sea stars or starfish) have been controversial for over a century. Open questions include relationships within asteroids and the status of the enigmatic taxon Xyloplax. Xyloplax is thought by some to represent a newly discovered sixth class of echinoderms – and by others to be an asteroid. To address these questions, we applied a novel workflow to a large RNA-seq dataset that encompassed a broad taxonomic and genomic sample. This study included 15 species sampled from all extant orders and 13 families, plus four ophiuroid species as an outgroup. To expand the taxonomic coverage, the study also incorporated five previously published transcriptomes and one previously published expressed sequence tags (EST) dataset. We developed and applied methods that used a range of alignment parameters with increasing permissiveness in terms of gap characters present within an alignment. This procedure facilitated the selection of phylogenomic data subsets from large amounts of transcriptome data. The results included 19 nested data subsets that ranged from 37 to 4,281 loci. Tree searches on all data subsets reconstructed Xyloplax as a velatid asteroid rather than a new class. This result implies that asteroid morphology remains labile well beyond the establishment of the body plan of the group. In the phylogenetic tree with the highest average asteroid nodal support several monophyletic groups were recovered. In this tree, Forcipulatida and Velatida are monophyletic and form a clade that includes Brisingida as sister to Forcipulatida. Xyloplax is consistently recovered as sister to Pteraster. Paxillosida and Spinulosida are each monophyletic, with Notomyotida as sister to the Paxillosida. Valvatida is recovered as paraphyletic. The results from other data subsets are largely consistent with these results. Our results support the hypothesis that the earliest divergence event among extant asteroids separated Velatida and Forcipulatacea from Valvatacea and Spinulosida.

Álvarez-Campos, P, Giribet G, Martín GS, Rouse GW, Riesgo A.  2017.  Straightening the striped chaos: systematics and evolution of Trypanosyllis and the case of its pseudo-cryptic type species Trypanosyllis krohnii (Annelida, Syllidae).. Zoological Journal of the Linnean Society. 179:492-540. Abstract

All members of the syllid genus Trypanosyllis show distinctive flattened, ribbon-like bodies and a pharynx armed with a trepan; however, the phylogenetic relationships within this genus remain unsettled, especially with respect to the genera Eurysyllis and Xenosyllis (morphologically similar). To resolve this systematic uncertainty we analysed the phylogenetic relationships of a worldwide sampling of specimens of Trypanosyllis and three related genera using multiple molecular markers. We show that Trypanosyllis as presently construed is paraphyletic, and identify a clade of striped species that were previously all considered to be Trypanosyllis zebra (Grube, 1860). We outline the case to consider Trypanosyllis krohnii Clapar ede, 1864 as the type species of the genus, instead of Trypanosyllis zebra. Trypanosyllis krohnii (interpreted as Trypanosyllis zebra by recent authors) was previously believed to be cosmopolitan, but we show that it includes at least seven cryptic and pseudocryptic species, five of which are described herein: Trypanosyllis kalkin sp. nov., Trypanosyllis californiensis sp. nov., Trypanosyllis luquei sp. nov., Trypanosyllis leivai sp. nov., and Trypanosyllis taboadai sp. nov. In addition, Trypanedenta gemmipara (Johnson, 1901) comb. nov. and Trypanedenta gigantea (McIntosh, 1885) comb. nov., previously included in Trypanosyllis, are here transferred to Trypanedenta Imajima & Hartman, 1964, and Pseudosyllis brevipennis Grube, 1863 [previously named Trypanosyllis coeliaca (Clapar ede, 1868)] is transferred to the resurrected genus Pseudosyllis Grube, 1863. Overall our results show a complex scenario of speciation, with cases of pseudocryptic species that correspond to geographically restricted lineages.

Rouse, GW, Lanterbecq D, Summers MM, Eeckhaut I.  2016.  Four new species of Mesomyzostoma (Myzostomida: Annelida). Journal of Natural History. 50:1-23.   10.1080/00222933.2015.1056266   AbstractWebsite

Mesomyzostoma Remscheid, 1918 currently includes three described species that live in the coelom and/or gonads of comatulid crinoids: Mesomyzostoma reichenspergeri Remscheid, 1918, Mesomyzostoma katoi Okada, 1933 and Mesomyzostoma lanterbecqae Summers and Rouse, 2014 in Summers, Al-Hakim et al. 2014. Here we describe four new species of Mesomyzostoma and assess their phylogenetic relation- ships using 18S rRNA, cytochrome oxidase subunit I and 16S rRNA sequence data. We also designate a neotype for M. katoi as the original types appear to be lost. We record M. reichenspergeri from the Australian Great Barrier Reef and from northern Papua New Guinea, but samples from the type locality (Aru Islands, Indonesia) and pre- viously recorded host are needed for confirmation. The new species of Mesomyzostoma are one Japanese species: Mesomyzostoma okadai sp. nov., and three Australian species: Mesomyzostoma lobus sp. nov., Mesomyzostoma leukos sp. nov. and Mesomyzostoma botulus sp. nov. The first infects the coelom of crinoid arms and pinnules, and the other three are found in crinoid oral discs. We also record M. leukos sp. nov. and M. botulus sp. nov. from Papua New Guinea. Phylogenetic analyses suggest that M. okadai sp. nov. is the sister group to all other Mesomyzostoma.

Watson, C, Carvajal JI, Sergeeva NG, Pleijel F, Rouse GW.  2016.  Free-living calamyzin chrysopetalids (Annelida) from methane seeps, anoxic basins, and whale falls. Zoological Journal of the Linnean Society. 177:700-719.   10.1111/zoj.12390   AbstractWebsite

Members of Calamyzinae, a clade of free-living and ectoparasitic chrysopetalids, are mainly associated with deep-sea chemosynthetic environments. The three currently known free-living calamyzin species are placed in Vigtorniella. A new free-living calamyzin species similar to these is described here. Phylogenetic analyses of Calamyzinae using mitochondrial (cytochrome c oxidase subunit I and 16S rDNA) and nuclear (Histone H3 and 18S rDNA) loci showed that Vigtorniella and the new species form a grade with respect to an ectoparasitic clade, requiring two new genera to be erected. All free-living calamyzins show a similar anterior end and chaetal morphology. Micospina auribohnorum gen. et sp. nov. is described for the small-bodied new species from deep-sea whale falls off California and methane seeps off Costa Rica. The maximum-likelihood and Bayesian analyses show Micospina gen. nov. as sister to the ectoparasitic clade. Boudemos gen. nov. is named for the clade of two larger-bodied species: Boudemos flokati gen. et comb. nov. and Boudemos ardabilia gen. et comb. nov., which is sister group to all other Calamyzinae. Vigtorniella is retained for the type species, Vigtorniella zaikai (Kiseleva, 1992), with the adults found amongst bacterial mats at the boundary of the hydrogen sulphide zone in the Black Sea. Micospina gen. nov., Boudemos gen. nov., and Vigtorniella form a grade of free-living taxa that is associated with feeding on organic-enriched sediments, and the latter two taxa display ontogenetic jaw change. Jaws are absent in Micospina auribohnorum gen. et sp. nov. and most of the calamyzin clade of parasitic forms. (C) 2016 The Linnean Society of London

Rouse, GW, Wilson NG, Carvajal JI, Vrijenhoek RC.  2016.  New deep-sea species of Xenoturbella and the position of Xenacoelomorpha. Nature. 530:94-97.   10.1038/nature16545   AbstractWebsite

The discovery of four new Xenoturbella species from deep waters of the eastern Pacific Ocean is reported here. The genus and two nominal species were described from the west coast of Sweden(1,2), but their taxonomic placement remains unstable(3,4). Limited evidence placed Xenoturbella with molluscs(5,6), but the tissues can be contaminated with prey(7,8). They were then considered deuterostomes(9-13). Further taxon sampling and analysis have grouped Xenoturbella with acoelomorphs (= Xenacoelomorpha) as sister to all other Bilateria (= Nephrozoa)(14,15), or placed Xenacoelomorpha inside Deuterostomia with Ambulacraria (Hemichordata + Echinodermata)(16). Here we describe four new species of Xenoturbella and reassess those hypotheses. A large species (> 20 cm long) was found at cold-water hydrocarbon seeps at 2,890 m depth in Monterey Canyon and at 1,722 m in the Gulf of California (Mexico). A second large species (similar to 10 cm long) also occurred at 1,722 m in the Gulf of California. The third large species (similar to 15 cm long) was found at similar to 3,700 m depth near a newly discovered carbonate-hosted hydrothermal vent in the Gulf of California. Finally, a small species (similar to 2.5 cm long), found near a whale carcass at 631 m depth in Monterey Submarine Canyon (California), resembles the two nominal species from Sweden. Analysis of whole mitochondrial genomes places the three larger species as a sister clade to the smaller Atlantic and Pacific species. Phylogenomic analyses of transcriptomic sequences support placement of Xenacoelomorpha as sister to Nephrozoa or Protostomia.

TIlic, E, Bartolomaeus T, Rouse GW.  2016.  Chaetal type diversity increases during evolution of Eunicida (Annelida). Organisms Diversity & Evolution. 16:105-119.   10.​1007/​s13127-015-0257-z   Abstract

Annelid chaetae are a superior diagnostic character on species and supraspecific levels, because of their structural variety and taxon specificity. A certain chaetal type, once evolved, must be passed on to descendants, to become characteristic for supraspecific taxa. Therefore, one would expect that chaetal diversity increases within a monophyletic group and that additional chaetae types largely result from transformation of plesiomorphic chaetae. In order to test these hypotheses and to explain potential losses of diversity, we take up a systematic approach in this paper and investigate chaetation in Eunicida. As a backbone for our analysis, we used a three-gene (COI, 16S, 18S) molecular phylogeny of the studied eunicidan species. This phylogeny largely corresponds to previous assessments of the phylogeny of Eunicida. Presence or absence of chaetal types was coded for each species included into the molecular analysis and transformations for these characters were then estimated using the mK1 likelihood model. Our results show that chaetal type diversity does indeed increase within eunicids and provide possible explanations for the homology, convergence, and loss of chaetal types in eunicidan subtaxa.

Lan, Y, Sun J, Bartlett DH, Rouse GW, Tabata HG, Qian P-Y.  2016.  The deepest mitochondrial genome; sequenced from Mariana Trench Hirondellea gigas (Amphipoda). Mitochondrial DNA Part B: Resources. 1:802-803.   10.1080/23802359.2016.1214549   Abstract

Hirondellea gigas is an amphipod that is a dominant animal resident living in the Challenger Deep (∼11,000m depth) of the Mariana Trench, which is the world deepest point in the ocean. Here we report a nearly complete mitochondrial genome of H. gigas, the world deepest mitogenome. The genome consists of two contigs with lengths of 8,603 bp and 6,984 bp, respectively, and it includes 13 complete protein-coding genes, 2 rRNA genes, and 21 tRNA genes. The ends of both contigs are highly repetitive and AT rich. The gene order of H. gigas is similar to another amphipod (Onisimus nanseni) in the same superfamily, Lysianassoidea. Phylogenetic analysis showed that Lysianassoidea is grouped with Gammaroidea and Calliopioidea in the same clade. Our result also suggested that the H. gigas collected from Izu-Bonin Trench and Japan Trench are indeed the same species as those from the Mariana Trench. These results will contribute to a better understanding of the phylogeny of amphipod and other hadal species.

Levin, LA, Baco AR, Bowden DA, Colaco A, Cordes EE, Cunha MR, Demopoulos AWJ, Gobin J, Grupe BM, Le J, Metaxas A, Netburn AN, Rouse GW, Thurber AR, Tunnicliffe V, Vandover CL, Vanreusel A, Watling L.  2016.  Hydrothermal Vents and Methane Seeps: Rethinking the Sphere of Influence.. Frontiers in Marine Science. 3:72.   10.3389/fmars.2016.00072   Abstract

Although initially viewed as oases within a barren deep ocean, hydrothermal vents and methane seep chemosynthetic communities are now recognized to interact with surrounding ecosystems on the sea floor and in the water column, and to affect global geochemical cycles. The importance of understanding these interactions is growing as the potential rises for disturbance of the systems from oil and gas extraction, seabed mining and bottom trawling. Here we synthesize current knowledge of the nature, extent and time and space scales of vent and seep interactions with background systems. We document an expanded footprint beyond the site of local venting or seepage with respect to elemental cycling and energy flux, habitat use, trophic interactions, and connectivity. Heat and energy are released, global biogeochemical and elemental cycles are modified, and particulates are transported widely in plumes. Hard and biotic substrates produced at vents and seeps are used by “benthic background” fauna for attachment substrata, shelter, and access to food via grazing or through position in the current, while particulates and fluid fluxes modify planktonic microbial communities. Chemosynthetic production provides nutrition to a host of benthic and planktonic heterotrophic background species through multiple horizontal and vertical transfer pathways assisted by flow, gamete release, animal movements, and succession, but these pathways remain poorly known. Shared species, genera and families indicate that ecological and evolutionary connectivity exists among vents, seeps, organic falls and background communities in the deep sea; the genetic linkages with inactive vents and seeps and background assemblages however, are practically unstudied. The waning of venting or seepage activity generates major transitions in space and time that create links to surrounding ecosystems, often with identifiable ecotones or successional stages. The nature of all these interactions is dependent on water depth, as well as regional oceanography and biodiversity. Many ecosystem services are associated with the interactions and transitions between chemosynthetic and background ecosystems, for example carbon cycling and sequestration, fisheries production, and a host of non-market and cultural services. The quantification of the sphere of influence of vents and seeps could be beneficial to better management of deep-sea environments in the face of growing industrialization.

Worsaae, K, Rimskaya-Korsakova NN, Rouse GW.  2016.  Neural reconstruction of bone-eating Osedax spp. (Annelida) and evolution of the siboglinid nervous system. BMC Evolutionary Biology. 16:83.   10.1186/s12862-016-0639-7   Abstract

Bone-devouring Osedax worms were described over a decade ago from deep-sea whale falls. The gutless females (and in one species also the males) have a unique root system that penetrates the bone and nourishes them via endosymbiotic bacteria. Emerging from the bone is a cylindrical trunk, which is enclosed in a transparent tube, that generally gives rise to a plume of four palps (or tentacles). In most Osedax species, dwarf males gather in harems along the female’s trunk and the nervous system of these microscopic forms has been described in detail. Here, the nervous system of bone-eating Osedax forms are described for the first time, allowing for hypotheses on how the abberant ventral brain and nervous system of Siboglinidae may have evolved from a ganglionated nervous system with a dorsal brain, as seen in most extant annelids.

Warén, A, Rouse GW.  2016.  A new genus and species of Cataegidae (Gastropoda; Seguenzioidea) from eastern Pacific Ocean methane seeps.. Novaplex. 17:59-66. AbstractLink

A new genus, Kanoia, n. gen., is erected for an unnamed seguenzioid gastropod species, now known from several methane seeps off California, in Gulf of California and off Costa Rica, and named Kanoia myronfeinbergi n. sp. It differs from K. meroglypta (n. comb.) a Caribbean species, mainly in having fewer spiral ridges on the shell, a lower spire and more distinct crenulation on the apical spiral cords.

Rouse, GW.  2016.  Phylum Annelida: The Segmented (and Some Unsegmented) Worms. Invertebrates, Third Edition. ( Brusca RC, Moore W, Schuster S, Eds.)., Sunderland: Sinauer Associates
Andrade, SCS, Novo M, Kawauchi GY, Worsaae K, Pleijel F, Giribet G, Rouse GW.  2015.  Articulating "archiannelids": Phylogenomics and annelid relationships, with emphasis on meiofaunal taxa. Molecular Biology and Evolution. 32:2860-2875.   10.1093/molbev/msv157   AbstractWebsite

Annelid disparity has resulted in morphological-based classifications that disagree with phylogenies based on Sanger sequencing and phylogenomic analyses. However, the data used for the latter studies came from various sources and technologies, involved poorly occupied matrices and lacked key lineages. Here, we generated a new Illumina-based data set to address annelid relationships from a fresh perspective, independent from previously generated data and with nearly fully occupied matrices. Our sampling reflects the span of annelid diversity, including two symbiotic annelid groups (Myzostomida and Spinther) and five meiofaunal groups once referred to as part of Archiannelida (three from Protodrilida, plus Dinophilus and Polygordius). As well as the placement of these unusual annelids, we sought to address the overall phylogeny of Annelida, and provide a new perspective for naming of major clades. Our results largely corroborate the phylogenomic results of Weigert et al. (2014; Illuminating the base of the annelid tree using transcriptomics. Mol Biol Evol. 31: 1391-1401), with "Magelona + Owenia" and Chaetopteridae forming a grade with respect to all other annelids. Echiura and Sipuncula are supported as being annelid groups, with Sipuncula closest to amphinomids as sister group to Sedentaria and Errantia. We recovered the three Protodrilida terminals as sister clade to Phyllodocida and Eunicida (=clade Aciculata). We therefore place Protodrilida as part of Errantia. Polygordius was found to be sister group to the scaleworm terminal and the possibility that it is a simplified scaleworm clade, as has been shown for the former family Pisionidae, is discussed. Our results were equivocal with respect to Dinophilus, Myzostomida, and Spinther possibly owing to confounding long-branch effects.

Kupriyanova, EK, Sun YA, ten Hove HA, Wong E, Rouse GW.  2015.  Serpulidae (Annelida) of Lizard Island, Great Barrier Reef, Australia. Zootaxa. 4019:275-353. AbstractWebsite

Serpulidae are obligatory sedentary polychaetes inhabiting calcareous tubes that are most common in subtropical and tropical areas of the world. This paper describes serpulid polychaetes collected from Lizard Island, Great Barrier Reef, Australia in 1983-2013 and deposited in Australian museums and overseas. In total, 17 serpulid genera were recorded, but although the study deals with 44 nominal taxa, the exact number of species remains unclear because a number of genera (i.e., Salmacina, Protula, Serpula, Spirobranchus, and Vermiliopsis) need world-wide revisions. Some species described herein are commonly found in the waters around Lizard Island, but had not previously been formally reported. A new species of Hydroides (H. lirs) and two new species of Semivermilia (S. annehoggettae and S. lylevaili) are described. A taxonomic key to all taxa found at Lizard Island is provided.

Capa, M, Rouse GW.  2015.  Sphaerodoridae (Annelida) from Lizard Island, Great Barrier Reef, Australia, including the description of two new species and reproductive notes. Zootaxa. 4019:168-183. AbstractWebsite

Sphaerodorids are scarce at Lizard Island archipelago and other localities in the Great Barrier Reef, Australia. Intensive collections at a variety of habitats within the Lizard Island archipelago over the last four decades have resulted in a total of just 11 specimens. Nevertheless, they represent two new species and a new record for Lizard Island. Sphaerodoropsis aurantica n. sp. is characterised by nine longitudinal rows of sessile and spherical dorsal macrotubercles, arranged in a single transverse row per segment; parapodia with around 10 spherical papillae; and compound chaetae with thin shafts and long blades. Sphaerodoropsis plurituberculata n. sp. is characterised by more than 12 more or less clearly arranged longitudinal rows of sessile spherical dorsal tubercles (variable in size), in four transverse rows per segment; parapodia lacking papillae; and semi-compound chaetae with distally enlarged shaft and short blades. Ephesiella australiensis is reported for the first time in Lizard Island. Laboratory observations of live specimens of Sphaerodoropsis plurituberculata n. sp., revealed the use of spermatophores by males. These were found attached externally to the body surface of both sexes, indicating pseudo-copulation.

Summers, M, Pleijel F, Rouse GW.  2015.  Whale falls, multiple colonisations of the deep, and the phylogeny of Hesionidae (Annelida). Invertebrate Systematics. 29:105-123.   10.1071/is14055   AbstractWebsite

Phylogenetic relationships within Hesionidae Grube, 1850 are assessed via maximum parsimony and maximum likelihood analyses of mitochondrial (cytochrome c oxidase subunit I and 16S rRNA) and nuclear (18S rRNA, and 28S rRNA) data. The analyses are based on 42 hesionid species; six of these being new species that are described here. The new species, all from deep (>200m depth) benthic environments (including whale falls) in the eastern Pacific, are Gyptis shannonae, sp. nov., Neogyptis julii, sp. nov., Sirsoe sirikos, sp. nov., Vrijenhoekia ketea, sp. nov., Vrijenhoekia falenothiras, sp. nov., and Vrijenhoekia ahabi, sp. nov. The molecular divergence among the new members of Vrijenhoekia is pronounced enough to consider them cryptic species, even though we cannot distinguish among them morphologically. Our results also showed that the subfamily Hesioninae Grube, 1850, as traditionally delineated, was paraphyletic. We thus restrict Hesioninae to include only Hesionini Grube, 1850 and refer the remaining members to Psamathinae Pleijel, 1998. The present study increases the number of hesionid species associated with whale falls from one to six and markedly increases the number of described deep-sea hesionid taxa. There appear to have been multiple colonisations of the deep sea from shallow waters by hesionids, though further sampling is warranted.

Levin, LA, Mendoza GF, Grupe BM, Gonzalez JP, Jellison B, Rouse G, Thurber AR, Waren A.  2015.  Biodiversity on the rocks: Macrofauna inhabiting authigenic carbonate at Costa Rica methane seeps. PLoS ONE. 10:e0131080.: Public Library of Science   10.1371/journal.pone.0131080   Abstract

The activity of anaerobic methane oxidizing microbes facilitates precipitation of vast quantities of authigenic carbonate at methane seeps. Here we demonstrate the significant role of carbonate rocks in promoting diversity by providing unique habitat and food resources for macrofaunal assemblages at seeps on the Costa Rica margin (400–1850 m). The attendant fauna is surprisingly similar to that in rocky intertidal shores, with numerous grazing gastropods (limpets and snails) as dominant taxa. However, the community feeds upon seep-associated microbes. Macrofaunal density, composition, and diversity on carbonates vary as a function of seepage activity, biogenic habitat and location.

Zhang, YJ, Rouse GW, Qiu JW.  2015.  A new species of Mesochaetopterus (Annelida, Chaetopteridae) from Hong Kong, with comments on the phylogeny of the family. Zootaxa. 3974:495-506. AbstractWebsite

We described a new species, Mesochaetopterus tingkokensis, based on 14 specimens collected from an intertidal area in Hong Kong. This species is large (body length of complete specimens 17.9-24.1 cm), with 9, 2 and 36-41 chaetigers in region A, B and C, respectively. It belongs to a small group of Mesochaetopterus species with an expanded wing-shaped notopodia in chaetiger B2. The new species can be distinguished from other Mesochaetopterus species in this group by having a pair of palps with two longitudinal stripes formed by suture-like discontinuous orange bands, more teeth in the uncini of region B and C neuropodia, and presence of a bundle of simple chaetae in region C notopodia. Comparison with other chaetopterids based on partial cytochrome oxidase I (COI), 18S and 28S rRNA gene sequences confirmed the placement of M. tingkokensis n. sp. within Mesochaetopterus and its distinction from other members of this genus with the available DNA sequences. The phylogenetic tree base on COI showed that Mesochaetopterus and Chaetopterus are paraphyletic, but that based on concatenated data, 18S and 28S showed they are monophyletic with low supporting values.

Martinez, A, Di Domenico M, Rouse GW, Worsaae K.  2015.  Phylogeny and systematics of Protodrilidae (Annelida) inferred with total evidence analyses. Cladistics. 31:250-276.   10.1111/cla.12089   AbstractWebsite

Protodrilidae is a group of small, superficially simple-looking annelids, lacking chaetae and appendages, except for two prostomial palps. Originally considered to be one of the primitive archiannelid families, its affinity within Annelida is still highly debated. Protodrilids are found worldwide in the interstices of intertidal and subtidal marine sediments. Despite their simple appearance they constitute one of the most species-rich interstitial families, with 36 described species in two genera, Protodrilus and the gutless Astomus. Here we present the first phylogenetic study of Protodrilidae employing five gene fragments, 55 morphological characters and 73 terminals (including seven outgroups) analysed under direct optimization and parsimony as well as model-based methods. The large data set includes all 36 described species of Protodrilidae (17 of which are represented only by the morphological partition) as well as 30 undescribed or uncertain species (represented by both morphology and molecules). This comprehensive, inclusive and combined analysis revealed a new perspective on the phylogeny of Protodrilidae: the family is shown to contain six cosmopolitan subclades, each supported by several morphological apomorphies, and with the genus Astomus consistently nested among the other five clades rather than next to these. Consequently, the diagnosis of Protodrilus is emended, Astomus remains unchanged and the four remaining lineages are diagnosed and named Megadrilus n. gen, Meiodrilus gen. nov., Claudrilus n. gen and Lindrilus gen. nov. Character transformations showed that large size and presence of pigmentation, oviducts and eyes are plesiomorphies of the family, retained in Protodrilus, Megadrilus gen. nov. and Lindrilus gen. nov. These features are secondarily lost in the gutless Astomus with epidermal uptake of nutrients, as well as in Meiodrilus gen. nov. and some species of Claudrilus n. gen, with smaller size correlated to life in interstices of finer sediments.

Borda, E, Yanez-Rivera B, Ochoa GM, Kudenov JD, Sanchez-Ortiz C, Schulze A, Rouse GW.  2015.  Revamping Amphinomidae (Annelida: Amphinomida), with the inclusion of Notopygos. Zoologica Scripta. 44:324-333.   10.1111/zsc.12099   AbstractWebsite

This study revises the taxonomic status of the formerly monotypic Archinomidae, which is nested within paraphyletic Amphinomidae according to recent phylogenetic work. We focused our taxonomic sampling to evaluate the affinities of Notopygos and genera classified as fusiform' in body shape, including Archinome and Chloeia. Prior to this study, the phylogenetic placement of Notopygos had not been evaluated. We inferred the phylogenetic relationships of Notopygos within Amphinomidae based on nuclear and mitochondrial markers, and cytochrome c oxidase subunit I genetic divergences of five Notopygos species, including the newly described Notopygos kekooa sp. n. from the Gulf of California. The phylogenetic and morphological evidence, now including Notopygos species, justified the establishment of two subfamilies within Amphinomidae. In accordance with ICZN Article 36 (Principle of Coordination), both subfamilies are presented as status novus in the nomenclature ranks.

Rouse, GW, Wilson NG, Worsaae K, Vrijenhoek RC.  2015.  A dwarf male reversal in bone-eating worms. Current Biology. 25:236-241.   10.1016/j.cub.2014.11.032   AbstractWebsite

Darwin [1] hypothesized that sexes in a species should be similar unless sexual selection, fecundity selection, or resource partitioning has driven them apart. Male dwarfism has evolved multiple times in a range of animals, raising questions about factors that drive such extreme size dimorphism [2-4]. Ghiselin [5] noted that dwarf males are more common among smaller marine animals, and especially among sedentary and sessile species living at low densities, where mates are difficult to find, or in deep-sea environments with limited energy sources. These benefits of male dwarfism apply well to Osedax (Annelida: Siboglinidae), bone-eating marine worms [6]. Osedax males, notable for extreme sexual size dimorphism (SSD), are developmentally arrested larvae that produce sperm from yolk reserves. Harems of dwarf males reside in the lumen of the tube surrounding a female. Herein, we describe Osedax priapus n. sp., a species that deviates remarkably by producing males that anchor into, and feed on, bone via symbiont-containing "roots," just like female Osedax. Phylogenetic analyses revealed O. priapus n. sp. as a derived species, and the absence of dwarf males represents a character reversal for this genus. Some dwarf male features are retained due to functional and morphological constraints. Since O. priapus n. sp. males are anchored in bone, they possess an extensible trunk that allows them to roam across the bone to contact and inseminate females. Evolutionary and ecological implications of a loss of male dwarfism are discussed.

Burkett, AM, Rathburn AE, Perez ME, Levin LA, Cha H, Rouse GW.  2015.  Phylogenetic placement of Cibicidoides wuellerstorfi (Schwager, 1866) from methane seeps and non-seep habitats on the Pacific margin. Geobiology. 13:44-52.   10.1111/gbi.12118   AbstractWebsite

Benthic foraminifera are among the most abundant groups found in deep-sea habitats, including methane seep environments. Unlike many groups, no endemic foraminiferal species have been reported from methane seeps, and to our knowledge, genetic data are currently sparse for Pacific deep-sea foraminifera. In an effort to understand the relationships between seep and non-seep populations of the deep-sea foraminifera Cibicidoides wuellerstorfi, a common paleo-indicator species, specimens from methane seeps in the Pacific were analyzed and compared to one another for genetic similarities of small subunit rDNA (SSU rDNA) sequences. Pacific Ocean C. wuellerstorfi were also compared to those collected from other localities around the world (based on 18S gene available on Genbank, e.g., Schweizer et al., 2009). Results from this study revealed that C. wuellerstorfi living in seeps near Costa Rica and Hydrate Ridge are genetically similar to one another at the species level. Individuals collected from the same location that display opposite coiling directions (dextral and sinstral) had no species level genetic differences. Comparisons of specimens with genetic information available from Genbank (SSU rDNA) showed that Pacific individuals, collected for this study, are genetically similar to those previously analyzed from the North Atlantic and Antarctic. These observations provide strong evidence for the true cosmopolitan nature of C. wuellerstorfi and highlight the importance of understanding how these microscopic organisms are able to maintain sufficient genetic exchange to remain within the same species between seep and non-seep habitats and over global distances.

Taboada, S, Riesgo A, Bas M, Arnedo MA, Cristobo J, Rouse GW, Avila C.  2015.  Bone-eating worms spread: Insights into shallow-water Osedax (Annelida, Siboglinidae) from Antarctic, Subantarctic, and Mediterranean waters. PLoS ONE. 10:e0140341. Abstract


Dietz, L, Arango CP, Halanych K, Harder AM, Held C, Mahon AR, Mayer C, Melzer RR, Rouse GW, Weis A, Wilson NG, Leese F.  2015.  Regional differentiation and extensive hybridisation between mitochondrial clades of the Southern Ocean giant sea spider Colossendeis megalonyx. Royal Society Open Science.   10.1098/rsos.140424   Abstract

Assessing the enormous diversity of Southern Ocean benthic species and their evolutionary histories is a central task in the era of global climate change. Based on mitochondrial markers, it was recently suggested that the circumpolar giant sea spider Colossendeis megalonyx comprises a complex of at least six cryptic species with mostly small and non-overlapping distribution ranges. Here, we expand the sampling to include over 500 mitochondrial COI sequences of specimens from around the Antarctic. Using multiple species delimitation approaches, the number of distinct mitochondrial OTUs increased from six to 15–20 with our larger dataset. In contrast to earlier studies, many of these clades show almost circumpolar distributions. Additionally, analysis of the nuclear internal transcribed spacer region for a subset of these specimens showed incongruence between nuclear and mitochondrial results. These mito-nuclear discordances suggest that several of the divergent mitochondrial lineages can hybridize and should not be interpreted as cryptic species. Our results suggest survival of C. megalonyx during Pleistocene glaciations in multiple refugia, some of them probably located on the Antarctic shelf, and emphasize the importance of multi-gene datasets to detect the presence of cryptic species, rather than their inference based on mitochondrial data alone.

Stiller, J, Wilson NG, Rouse GW.  2015.  A spectacular new species of seadragon (Syngnathidae). Royal Society Open Science. 2(2):140458.   10.1098/rsos.140458   Abstract

The exploration of Earth's biodiversity is an exciting and ongoing endeavour. Here, we report a new species of seadragon from Western Australia with substantial morphological and genetic differences to the only two other known species. We describe it as Phyllopteryx dewysea n. sp. Although the leafy seadragon (Phycodurus eques) and the common seadragon (Phyllopteryx taeniolatus) occur along Australia's southern coast, generally among relatively shallow macroalgal reefs, the new species was found more offshore in slightly deeper waters. The holotype was trawled east of the remote Recherche Archipelago in 51 m; additional specimens extend the distribution west to Perth in 72 m. Molecular sequence data show clear divergence from the other seadragons (7.4–13.1% uncorrected divergence in mitochondrial DNA) and support a placement as the sister-species to the common seadragon. Radiographs and micro-computed tomography were used on the holotype of the new species and revealed unique features, in addition to its unusual red coloration. The discovery provides a spectacular example of the surprises still hidden in our oceans, even in relatively shallow waters.