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Abstract: A consensus on molluscan relationships has yet to be achieved, largely because of conflicting morphological and molecular hypotheses. Monoplacophora show marked seriality of ctenidia, atria, muscles and nephridia and this has been interpreted as plesiomorphic for Mollusca, reflecting a segmented ancestry. More recently this seriality, also partly seen in Polyplacophora, has been seen as a derived condition. Analysis of the first published monoplacophoran DNA sequence from Laevilipilina antarctica Warén & Hain, 1992 [Giribet, G., Okusu, A., Lindgren, A.R., Huff, S., Schrödl, M., Nishiguchi, M.K., 2006. Evidence for a clade composed of molluscs with serially repeated structures: Monoplacophorans are related to chitons. Proc. Natl. Acad. Sci. USA 103, 7723–7728. 10.1073/pnas.0602578103], showed Monoplacophora inside Polyplacophora. These taxa were then grouped under the name Serialia, reflecting the hypothesis that their seriality is a synapomorphy. Subsequent examination revealed that part of the L. antarctica published sequence was the result of contamination with Polyplacophora (Giribet, Supplementary Material S1). We collected and sequenced another monoplacophoran, Laevipilina hyalina McLean, 1979, resulting in the first multi-gene dataset representing all molluscan classes. Our analyses did not show unambiguous support for Serialia. Model-based approaches strongly supported Serialia as a clade, however, parsimony analyses under dynamic and static homology did not resolve the position of Monoplacophora. Although our study provides support for Serialia and none for Conchifera, it appears that further resolution of molluscan relationships will require large increases of data. [Copyright &y& Elsevier]

Chromodoris is a genus of colourful nudibranchs that feed on sponges and is found across the Indo-Pacific. While this was once the most diverse chromodorid genus, recent work has shown that the genus should be restricted to a monophyletic lineage that contains only 22 species, all of which exhibit black pigmentation and planar spawning behaviour. Earlier phylogenies of this group are poorly resolved and thus additional work is needed to clarify species boundaries within Chromodoris . This study presents a maximum-likelihood phylogeny based on mitochondrial loci (COI, 16S) for 345 Chromodoris specimens, including data from 323 new specimens and 22 from GenBank, from across the Indo-Pacific. Species hypotheses and phylogenetic analysis uncovered 39 taxa in total containing 18 undescribed species, with only five of 39 taxa showing stable colour patterns and distinct morphotypes. This study also presents the first evidence for regional mimicry in this genus, with C. colemani and C. joshi displaying geographically-based variation in colour patterns which appear to match locally abundant congenerics, highlighting the flexibility of these colour patterns in Chromodoris nudibranchs. The current phylogeny contains short branch lengths, polytomies and poor support at interior nodes, which is indicative of a recent radiation. As such, future work will employ a transcriptome-based exon capture approach for resolving the phylogeny of this group. In all, this study included 21 of the 22 described species in the Chromodoris sensu stricto group with broad sampling coverage from across the Indo-Pacific, constituting the most comprehensive sampling of this group to date. This work highlights several cases of undocumented diversity, ultimately expanding our knowledge of species boundaries in this group, while also demonstrating the limitations of colour patterns for species identification in this genus. [ABSTRACT FROM AUTHOR]

Abstract: Although the status of Crinoidea (sea lilies and featherstars) as sister group to all other living echinoderms is well-established, relationships among crinoids, particularly extant forms, are debated. All living species are currently placed in Articulata, which is generally accepted as the only crinoid group to survive the Permian–Triassic extinction event. Recent classifications have recognized five major extant taxa: Isocrinida, Hyocrinida, Bourgueticrinina, Comatulidina and Cyrtocrinida, plus several smaller groups with uncertain taxonomic status, e.g., Guillecrinus, Proisocrinus and Caledonicrinus. Here we infer the phylogeny of extant Crinoidea using three mitochondrial genes and two nuclear genes from 59 crinoid terminals that span the majority of extant crinoid diversity. Although there is poor support for some of the more basal nodes, and some tree topologies varied with the data used and mode of analysis, we obtain several robust results. Cyrtocrinida, Hyocrinida, Isocrinida are all recovered as clades, but two stalked crinoid groups, Bourgueticrinina and Guillecrinina, nest among the featherstars, lending support to an argument that they are paedomorphic forms. Hence, they are reduced to families within Comatulida. Proisocrinus is clearly shown to be part of Isocrinida, and Caledonicrinus may not be a bourgueticrinid. Among comatulids, tree topologies show little congruence with current taxonomy, indicating that much systematic revision is required. Relaxed molecular clock analyses with eight fossil calibration points recover Articulata with a median date to the most recent common ancestor at 231–252mya in the Middle to Upper Triassic. These analyses tend to support the hypothesis that the group is a radiation from a small clade that passed through the Permian–Triassic extinction event rather than several lineages that survived. Our tree topologies show various scenarios for the evolution of stalks and cirri in Articulata, so it is clear that further data and taxon sampling are needed to recover a more robust phylogeny of the group. [Copyright &y& Elsevier]

• Hybrid capture is a useful large-scale phylogenomic reconstructions. • We perform the largest phylogenomic reconstruction of Scleractinia. • Phylogenetic relationships are resolved, but paraphyletic families remain. • Taxonomic uncertainty is rife, and revisions are urgently required. A well-supported evolutionary tree representing most major lineages of scleractinian corals is in sight with the development and application of phylogenomic approaches. Specifically, hybrid-capture techniques are shedding light on the evolution and systematics of corals. Here, we reconstructed a broad phylogeny of Scleractinia to test previous phylogenetic hypotheses inferred from a few molecular markers, in particular, the relationships among major scleractinian families and genera, and to identify clades that require further research. We analysed 449 nuclear loci from 422 corals, comprising 266 species spanning 26 families, combining data across whole genomes, transcriptomes, hybrid capture and low-coverage sequencing to reconstruct the largest phylogenomic tree of scleractinians to date. Due to the large number of loci and data completeness (less than 38% missing data), node supports were high across shallow and deep nodes with incongruences observed in only a few shallow nodes. The "Robust" and "Complex" clades were recovered unequivocally, and our analyses confirmed that Micrabaciidae Vaughan, 1905 is sister to the "Robust" clade, transforming our understanding of the "Basal" clade. Several families remain polyphyletic in our phylogeny, including Deltocyathiidae Kitahara, Cairns, Stolarski & Miller, 2012, Caryophylliidae Dana, 1846, and Coscinaraeidae Benzoni, Arrigoni, Stefani & Stolarski, 2012, and we hereby formally proposed the family name Pachyseridae Benzoni & Hoeksema to accommodate Pachyseris Milne Edwards & Haime, 1849, which is phylogenetically distinct from Agariciidae Gray, 1847. Results also revealed species misidentifications and inconsistencies within morphologically complex clades, such as Acropora Oken, 1815 and Platygyra Ehrenberg, 1834, underscoring the need for reference skeletal material and topotypes, as well as the importance of detailed taxonomic work. The approach and findings here provide much promise for further stabilising the topology of the scleractinian tree of life and advancing our understanding of coral evolution. [ABSTRACT FROM AUTHOR]

Predicting biotic resistance to highly invasive strains of “killer algae” ( Caulerpa spp.) requires understanding the diversity and feeding preferences of native consumers, including sea slugs in family Oxynoidae. Past studies reported low algal host specificity for Oxynoe (6 spp.) and Lobiger (4 spp.), but these taxonomically challenging slugs may represent species complexes of unrecognized specialists that prefer different Caulerpa spp. Here, we assess global diversity of these genera by integrating gene sequences with morphological data from microscopic teeth and internal shells, the only hard parts in these soft-bodied invertebrates. Four delimitation methods applied to datasets comprising mtDNA and/or nuclear alleles yielded up to 16 species hypotheses for samples comprising five nominal taxa, including five highly divergent species in Lobiger and five in Oxynoe . Depending on the analysis, a further four to six species were recovered in the O. antillarum-viridis complex, a clade in which mitochondrial divergence was low and nuclear alleles were shared among lineages. Bayesian species delimitation using only morphological data supported most candidate species, however, and integrative analyses combining morphological and genetic data fully supported all complex members. Collectively, our findings double the recognized biodiversity in Oxynoidae, and illustrate the value of including data from traits that mediate fast-evolving ecological interactions during species delimitation. Preference for Caulerpa spp. and radular tooth characteristics covaried among newly delimited species, highlighting an unappreciated degree of host specialization and coevolution in these taxa that may help predict their role in containing outbreaks of invasive algae. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

[Display omitted] Scleractinian corals are a diverse group of ecologically important yet highly threatened marine invertebrates, which can be challenging to identify to the species level. An influx of molecular studies has transformed scleractinian systematics, highlighting that cryptic species may be more common than previously understood. In this study, we test the hypothesis that Plesiastrea versipora (Lamarck, 1816), a species currently considered to occur throughout the Indo-Pacific in tropical, sub-tropical and temperate waters, is a single species. Molecular and morphological analyses were conducted on 80 samples collected from 31 sites spanning the majority of the species putative range and twelve mitogenomes were assembled to identify informative regions for phylogenetic reconstruction. Congruent genetic data across three gene regions supports the existence of two monophyletic clades aligning with distinct tropical and temperate provenances. Multivariate macromorphological analyses based on 13 corallite characters provided additional support for the phylogeographic split, with the number of septa and corallite density varying across this biogeographic divide. Furthermore, micromorphological and microstructural analyses identified that the temperate representatives typically develop sub-cerioid corallites with sparse or absent coenosteal features and smooth septal faces. In contrast, tropical representatives typically develop plocoid corallites separated by a porous dissepimental coenosteum and have granulated septal faces. These data suggest that at least two species exist within the genus Plesiastrea Milne Edwards & Haime, 1848. Based on examination of type material, we retain the name Plesiastrea versipora (Lamarck, 1816) for the temperate representatives of the genus and resurrect the name Plesiastrea peroni Milne Edwards & Haime, 1857 for the tropical members. This study highlights how broadly distributed hard coral taxa still need careful re-examination through an integrated systematics approach to better understand their phylogeographic patterns. Furthermore, it demonstrates the utility of integrating micro-, macro-morphological and genetic datasets, and the importance of type specimens when dealing with taxonomic revisions of scleractinian taxa. [ABSTRACT FROM AUTHOR]

[Display omitted] • We evaluate the evolutionary history of Southern Ocean and South American Tritoniidae. • Molecular data of 167 specimens of Tritonia and Tritoniella are provided. • We found 13 + species versus five traditionally recognised species. • Restricted distribution and endemicity is driven by specific ecological and historical processes. • Tritoniidae species are yet another example of underrecognized diversity in the Southern Ocean. The Tritoniidae provides one of the most famous model species for neurophysiology and behaviour, yet a well-developed phylogenetic framework for this family is still incomplete. In this study, we explored the species-level taxonomy, phylogenetic relationships, and geographic distributions of the tritoniid nudibranchs. During numerous expeditions, specimens from southern South America, Sub-Antarctic Islands, and Antarctica were collected, documented alive, and fixed for anatomical descriptions and genetic sequencing. DNA from 167 specimens were extracted and sequenced for mitochondrial (COI, 16S) and nuclear (H3) markers. An additional 109 sequences of all available tritoniids plus additional outgroups were downloaded from GenBank for comparative purposes. Maximum Likelihood under the GHOST model of evolution and Bayesian inference using the GTR + GAMMA model produced congruent topologies from concatenated alignments. The results of ABGD, GMYC, bPTP, and mPTP species delimitation analyses suggest many separately evolving units that do not coincide with traditionally recognized species limits. Southern Ocean Tritoniella and Tritonia species split into several previously unrecognized species. This result is in accordance with the limited dispersal abilities of some southern tritoniids. Along with the most complete phylogeny of Tritoniidae to date, we also provided many taxonomic notes at the species and genus level. Tritoniidae species are yet another example of under-recognized diversity in the Southern Ocean. [ABSTRACT FROM AUTHOR]

[Display omitted] • First DNA barcoding survey of Acastinae sponge-inhabiting barnacles. • Results reveal highly speciose group of barnacles inhabit the sponge order Dictyoceratida. • Surveyed barnacles are typically host specialists. • Phylogenetic reconstruction show host usage is phylogenetically conserved. Sponges represent one of the most species-rich hosts for commensal barnacles yet host utilisation and diversity have not been thoroughly examined. This study investigated the diversity and phylogenetic relationships of sponge-inhabiting barnacles within a single, targeted host group, primarily from Western Australian waters. Specimens of the sponge order Dictyoceratida were surveyed and a total of 64 host morphospecies, representing four families, were identified as barnacle hosts during the study. Utilising molecular (COI , 12S) and morphological methods 42 molecular operational taxonomic units (MOTUs) of barnacles, representing Acasta , Archiacasta , Euacasta and Neoacasta were identified. Comparing inter- and intra-MOTU genetic distances showed a barcode gap between 2.5% and 5% for COI , but between 1% and 1.5% in the 12S dataset, thus demonstrating COI as a more reliable barcoding region. These sponge-inhabiting barnacles were demonstrated to show high levels of host specificity with the majority being found in a single sponge species (74%), a single genus (83%) or a single host family (93%). Phylogenetic relationships among the barnacles were reconstructed using mitochondrial (12S , COI) and nuclear (H3 , 28S) markers. None of the barnacle genera were recovered as monophyletic. Euacasta was paraphyletic in relation to the remaining Acastinae genera, which were polyphyletic. Six well-supported clades of molecular operational taxonomic units, herein considered to represent species complexes, were recovered, but relationships between them were not well supported. These complexes showed differing patterns of host usage, though most were phylogenetically conserved with sister lineages typically occupying related hosts within the same genus or family of sponge. The results show that host specialists are predominant, and the dynamics of host usage have played a significant role in the evolutionary history of the Acastinae. [ABSTRACT FROM AUTHOR]

• Transcriptomic data provide a robust phylogeny for bubble snails (Cephalaspidea). • Well-supported tree topology largely congruent across analytical methods. • Topology robust to amino acid compositional heterogeneity. • Cephalaspidean shell loss concentrated within the superfamily Philinoidea. Cephalaspidea is an order of marine gastropods found worldwide, often in sandy or muddy habitats, which has a convoluted taxonomic history based on convergent or ill-defined morphological characters. The cephalaspidean shell—which can be external and robust, internal, or altogether absent in the adult—is of particular interest in this group, and a well-resolved phylogeny can give us greater insight into the evolution of this character. Molecular data have clarified many relationships within Cephalaspidea, but studies involving few Sanger sequenced phylogenetic markers remain limited in the resolution they provide. Here we take a phylogenomic approach, the first to address internal cephalaspidean relationships, sequencing and assembling transcriptomes de novo from 22 ingroup taxa—representing the five currently accepted superfamilies, 10 of the 21 currently recognized families, and 21 genera—and analyzing these along with publicly available data. We generated two main datasets varying by a minimum taxon occupancy threshold (50% and 75%), and analyzed these using maximum likelihood, Bayesian inference and a coalescence-based method. We find a consistent, well-supported topology, with full support across most nodes including at the family and genus level, which also appears to be robust to the effect of compositional heterogeneity among amino acids in the dataset. Our analyses find Newnesioidea as the sister group to the rest of Cephalaspidea. Within the rest of the order, Philinoidea is the sister group to a clade that comprises (Bulloidea (Haminoeoidea, Cylichnoidea)). There is strong support for several previously suggested, but tenuously supported relationships such as the genus Odontoglaja nesting within the family Aglajidae, and a sister group relationship between Gastropteridae and Colpodaspididae, with Philinoglossidae as their sister group. We discuss these results and their implications in the context of current cephalaspidean taxonomy and evolution. Genomic-scale data give a backbone to this group of snails and slugs, and hold promise for a completely resolved Cephalaspidea. [ABSTRACT FROM AUTHOR]