Phylogenomics resolves ambiguous relationships within Aciculata (Errantia, Annelida).

Aciculata (Eunicida + Phyllodocida) is among the largest clades of annelids, comprising almost half of the known diversity of all marine annelids. Despite the group's large size and biological importance, most phylogenomic studies on Annelida to date have had a limited sampling of this clade. The phylogenetic placement of many clades within Phyllodocida in particular has remained poorly understood. To resolve the relationships within Aciculata we conducted a large-scale phylogenomic analysis based on 24 transcriptomes (13 new), chosen to represent many family-ranked taxa that have never been included in a broad phylogenomic study. Our sampling also includes several enigmatic taxa with challenging phylogenetic placement, such as Histriobdella, Struwela, Lacydonia, Pilargis and the holopelagic worms Lopadorrhynchus, Travisiopsis and Tomopteris. Our robust phylogeny allows us to name and place some of these problematic clades and has significant implications on the systematics of the group. Within Eunicida we reinstate the names Eunicoidea and Oenonoidea. Within Phyllodocida we delineate Phyllodociformia, Glyceriformia, Nereidiformia, Nephtyiformia and Aphroditiformia. Phyllodociformia now includes: Lacydonia, Typhloscolecidae, Lopadorrhynchidae and Phyllodocidae. Nephtyiformia includes Nephtyidae and Pilargidae. We also broaden the delineation of Glyceriformia to include Sphaerodoridae, Tomopteridae and Glyceroidea (Glyceridae + Goniadidae). Furthermore, our study demonstrates and explores how conflicting, yet highly supported topologies can result from confounding signals in gene trees.

Spaghetti to a Tree: A Robust Phylogeny for Terebelliformia (Annelida) Based on Transcriptomes, Molecular and Morphological Data.

Terebelliformia-"spaghetti worms" and their allies-are speciose and ubiquitous marine annelids but our understanding of how their morphological and ecological diversity evolved is hampered by an uncertain delineation of lineages and their phylogenetic relationships. Here, we analyzed transcriptomes of 20 terebelliforms and an outgroup to build a robust phylogeny of the main lineages grounded on 12,674 orthologous genes. We then supplemented this backbone phylogeny with a denser sampling of 121 species using five genes and 90 morphological characters to elucidate fine-scale relationships. The monophyly of six major taxa was supported: Pectinariidae, Ampharetinae, Alvinellidae, Trichobranchidae, Terebellidae and Melinninae. The latter, traditionally a subfamily of Ampharetidae, was unexpectedly the sister to Terebellidae, and hence becomes Melinnidae, and Ampharetinae becomes Ampharetidae. We found no support for the recently proposed separation of Telothelepodidae, Polycirridae and Thelepodidae from Terebellidae. Telothelepodidae was nested within Thelepodinae and is accordingly made its junior synonym. Terebellidae contained the subfamily-ranked taxa Terebellinae and Thelepodinae. The placement of the simplified Polycirridae within Terebellinae differed from previous hypotheses, warranting the division of Terebellinae into Lanicini, Procleini, Terebellini and Polycirrini. Ampharetidae (excluding Melinnidae) were well-supported as the sister group to Alvinellidae and we recognize three clades: Ampharetinae, Amaginae and Amphicteinae. Our analysis found several paraphyletic genera and undescribed species. Morphological transformations on the phylogeny supported the hypothesis of an ancestor that possessed both branchiae and chaetae, which is at odds with proposals of a "naked" ancestor. Our study demonstrates how a robust backbone phylogeny can be combined with dense taxon coverage and morphological traits to give insights into the evolutionary history and transformation of traits.

Species delimitation in Amblyosyllis (Annelida, Syllidae).

Amblyosyllis is a worldwide distributed group of annelids mainly found in coastal environments. It is well known among the polychaete specialists mostly because of its notable beauty, showing bright colourful patterns and outstanding long and coiled appendices. Amblyosyllis is a monophyletic genus easy to identify due to its distinct diagnostic features; however, the species and their boundaries are, in most cases, not well defined. Herein, we provide an extensive sample of Amblyosyllis material (115 specimens) from several world geographic areas. We have studied the morphological features of each specimen and photographed them alive. Two mitochondrial DNA markers (COI and 16S) and one nuclear gene fragment (28S, D1 region) were sequenced. We performed phylogenetic analyses based on each DNA partition, as well as the combined data sets, obtaining congruent results. Species delimitation methods such as distance analyses, statistical parsimony networks and multi-rate Poisson tree processes were also applied. The combined results obtained from different methodologies and data sets are used to differentiate between, at least, 19 lineages compatible with the separately evolving meta-populations species concept. Four of these lineages are identified as nominal species, including the type species of Amblyosyllis, A. rhombeata. For three other lineages previously synonymized names are recovered, and seven lineages are described as new species. All of these species are described and supported by appropriate iconography. We recognize several morphological characters useful to identify species of Amblyosyllis, which in some cases should also be combined with molecular methods for species delineation. The genetic divergence in the genus is high, contrary to the morphological homogeneity observed. Two species show a wide geographical distribution, while the rest have a more restricted distribution. There are several examples of species with overlapping distribution patterns.

Phylogeny, evolution and mitochondrial gene order rearrangement in scale worms (Aphroditiformia, Annelida).

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.

Articulating "Archiannelids": Phylogenomics and Annelid Relationships, with Emphasis on Meiofaunal Taxa.

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.

Cryptic species of Archinome (Annelida: Amphinomida) from vents and seeps.

Since its description from the Galapagos Rift in the mid-1980s, Archinome rosacea has been recorded at hydrothermal vents in the Pacific, Atlantic and Indian Oceans. Only recently was a second species described from the Pacific Antarctic Ridge. We inferred the identities and evolutionary relationships of Archinome representatives sampled from across the hydrothermal vent range of the genus, which is now extended to cold methane seeps. Species delimitation using mitochondrial cytochrome c oxidase subunit I (COI) recovered up to six lineages, whereas concatenated datasets (COI, 16S, 28S and ITS1) supported only four or five of these as clades. Morphological approaches alone were inconclusive to verify the identities of species owing to the lack of discrete diagnostic characters. We recognize five Archinome species, with three that are new to science. The new species, designated based on molecular evidence alone, include: Archinome levinae n. sp., which occurs at both vents and seeps in the east Pacific, Archinome tethyana n. sp., which inhabits Atlantic vents and Archinome jasoni n. sp., also present in the Atlantic, and whose distribution extends to the Indian and southwest Pacific Oceans. Biogeographic connections between vents and seeps are highlighted, as are potential evolutionary links among populations from vent fields located in the east Pacific and Atlantic Oceans, and Atlantic and Indian Oceans; the latter presented for the first time.

Phylogeny of scale-worms (Aphroditiformia, Annelida), assessed from 18SrRNA, 28SrRNA, 16SrRNA, mitochondrial cytochrome c oxidase subunit I (COI), and morphology.

The phylogeny of scale-worms, benthic polychaetes carrying dorsal scales (elytra), including taxa from Acoetidae, Aphroditidae, Eulepethidae, Pholoidae, Pholoididae, Polynoidae and Sigalionidae (Aphroditiformia), is assessed from the nuclear markers 18SrRNA and 28SrRNA, and mitochondrial 16SrRNA and cytochrome c oxidase subunit I (COI), and 24 morphological characters. The data sets are analyzed both separately and combined, with Bayesian analyses, maximum likelihood and parsimony. In total, 56 terminal taxa are examined, including 48 taxa from all scale-worm families, and eight out-group species. The results indicate that Aphroditidae and Eulepethidae are the most basally placed families among the scale-worms. The Pholoididae and Pisionidae are positioned within and synonymized with the Sigalionidae, and Pholoidae may be part of the same group. The subfamily Iphioninae falls out as sister group to a clade consisting of Polynoidae and Acoetidae and is elevated to Iphionidae. The families now included in the Aphroditiformia are Acoetidae, Aphroditidae, Eulepethidae, Pholoidae, Polynoidae, Iphionidae and Sigalionidae, and the subfamily name Harmothoinae and Acholoinae are treated as a junior synonyms of Polynoinae.

From one to ten in a single stroke--resolving the European Eumidasanguinea (Phyllodocidae, Annelida) species complex.

We investigate the genetic structure of European lineages of the polychaete Eumida sanguinea with mitochondrial COI and nuclear ITS, and demonstrate the presence of ten cryptic species. Within the E. sanguinea species complex there are six different white pigmentation patterns but only three of these are unique for a single species. No other consistent morphological differences were observed. We give new species names to seven of the lineages from our study, providing examples of combined morphological and molecular diagnoses, apply the available name E. sanguinea to one species, and leave two lineages with single representatives unnamed. We also include new data and a diagnosis for the poorly known E. notata, which also belongs to the E. sanguinea species complex.

Deep-sea, swimming worms with luminescent "bombs".

By using remotely operated vehicles, we found seven previously unknown species of swimming annelid worms below 1800 meters. Specimens were large and bore a variety of elaborate head appendages. In addition, five species have pairs of ellipsoidal organs homologous to branchiae that produce brilliant green bioluminescence when autotomized. Five genes were used to determine the evolutionary relationships of these worms within Cirratuliformia. These species form a clade within Acrocirridae and were not closely related to either of the two known pelagic cirratuliforms. Thus, this clade represents a third invasion of the pelagic realm from Cirratuliformia. This finding emphasizes the wealth of discoveries to be made in pelagic and deep demersal habitats.

Progress in systematics: from Siboglinidae to Pogonophora and Vestimentifera and back to Siboglinidae.

We review the taxonomic history of pogonophores (frenulates and vestimentiferans), from the species in first described 1914 to the recently described bone-eating worm Osedax. Previous systematists have referred both groups to the rank of phylum, and the animals have been treated as deuterostomes with a dorsal nerve cord. Further knowledge on their embryology, the discovery of the previously overlooked posterior, segmented part provided with chaetae, and access to molecular data, have completely changed earlier views on their affinities. They are now referred to as a single family of polychaete annelids, Siboglinidae.

Phylogeny of benthic Phyllodocidae (Polychaeta) based on morphological and molecular data.

A combined molecular (18S rDNA, 28S rDNA, 16S rDNA and COI) and morphological analysis of the benthic phyllodocids is presented for the first time. Nineteen phyllodocids and two outgroup taxa are assessed using parsimony, maximum likelihood and Bayesian analyses. We demonstrate high degrees in homoplasy in the traditionally used morphological phyllodocid characters, and show that all the three current subfamilies Phyllodocinae, Eteoninae and Notophyllinae are non-monophyletic. The genera Eulalia, Eumida, Protomystides, Pseudomystides, Pterocirrus and Sige form a well-supported group, as does Mystides and Nereiphylla. Another clade with strong support includes Eteone and Paranaitis, although with Eteone nested within a paraphyletic Paranaitis. The relationship between these two taxa indicate that the unusual arrangement of modified cirri on the first segments in Eteone is due to a fusion of segment 1 and 2 where the cirri of segment 1 have been reduced. Eulalia is non-monophyletic and should be split, minimally into two groups. Our results are ambiguous regarding the ancestral phyllodocid condition of absence-presence of median antenna or nuchal papilla and uniramous or biramous parapodia, but shows that the absence of cirri on segment 3 (previously an apomorphy, for e.g., Mystides, Pseudomystides and Hesionura) is maximally homoplastic.

A molecular phylogeny of annelids.

We present parsimony analyses of annelids based on the largest taxon sample and most extensive molecular data set yet assembled, with two nuclear ribosomal genes (18S rDNA and the D1 region of 28S rDNA), one nuclear protein coding-gene (Histone H3) and one mitochondrial ribosomal gene (16S rDNA) from 217 terminal taxa. Of these, 267 sequences are newly sequenced, and the remaining were obtained from GenBank. The included taxa are based on the criteria that the taxon must have 18S rDNA or at least two other loci. Our analyses show that 68% of annelid family ranked taxa represented by more than one taxon in our study are supported by a jackknife value > 50%. In spite of the size of our data set, the phylogenetic signal in the deepest part of the tree remains weak and the majority of the currently recognized major polychaete clades (except Amphinomida and Aphroditiformia) could not be recovered. Terbelliformia is monophyletic (with the exclusion of Pectinariidae, for which only 18S data were available), whereas members of taxa such as Phyllodocida, Cirratuliformia, Sabellida and Scolecida are scattered over the trees. Clitellata is monophyletic, although Dinophilidae should possibly be included, and Clitellata has a sister group within the polychaetes. One major problem is the current lack of knowledge on the closest relatives to annelids and the position of the annelid root. We suggest that the poor resolution in the basal parts of the trees presented here may be due to lack of signal connected to incomplete data sets both in terms of terminal and gene sampling, rapid radiation events and/or uneven evolutionary rates and long-branch attraction.

Phylogeny of Aphroditiformia (Polychaeta) based on molecular and morphological data.

The phylogeny of Aphroditiformia, benthic polychaetes carrying dorsal elytra, is assessed from nuclear 18S rDNA, mitochondrial cytochrome c oxidase subunit I (COI), and 31 morphological characters. Two non-elytrabearing taxa, Palmyra and Pisione, are included to assess their relationship to the elytrabearers. The data are analysed both separately and combined, with parsimony, maximum likelihood and Bayesian analyses. In total, 19 terminal taxa are examined, including 12 elytrabearing taxa from all scale-worm groups, Palmyra, Pisione, and five outgroup taxa. The results show that Palmyra and Pisione are nested within Aphroditiformia. Palmyra is sister to Aphrodita, and both Pisione and Pholoe are positioned within Sigalionidae, suggesting that both family names Pisionidae and Pholoidae should be treated as junior synonyms of Sigalionidae.

Reproductive biology of a new hesionid polychaete from the Great Barrier Reef.

We describe Lizardia hirschi, a new hesionid genus and species, from shallow water on the Great Barrier Reef. It is characterized by small size (maximally around 2 mm long) and by males with paired penes on the last segment or the pygidium. The sperm are elongated, with a conical acrosome; extended, cylindrical nucleus; and three mitochondria. The females have three to four pairs of eggs in segments 10-13, up to 150 microm in diameter. The female reproductive system consists of spermathecae, situated in the notopodia of segments 10-12, and oviducts opening ventrally on segment 11. Fertilization may be internal. The female (but not the male) reproductive system appears to be homologous to that in another small hesionid, capricornia. The phylogenetic position of L. hirschi within Hesionidae is currently uncertain due to the retention of many apparently larval features in the adults.

The phylogenetic position of Siboglinidae (Annelida) inferred from 18S rRNA, 28S rRNA and morphological data.

We assess the phylogenetic position of Siboglinidae (previously known as the phyla Pogonophora and Vestimentifera, but now referred to Annelida) in parsimony analyses of 1100 bp from 18S rRNA, 320 bp from the D1 region of 28S rRNA, and 107 morphological characters, totaling 667 parsimony informative characters. The 34 terminal taxa, apart from six siboglinids, include polychaete members of Sabellida, Terbelliformia, Cirratuliformia and Spionida, plus two Aciculata polychaetes as outgroups. Our results contradict most recent hypotheses in showing a sistergroup relationship between Siboglinidae and Oweniidae, and in that the latter taxon is not a member of Sabellida. Furthermore, our results indicate that Sabellariidae is not closely related to Sabellida, that Serpulidae may be nested within Sabellidae, and that Alvinellidae is nested within Ampharetidae.

Position and Delineation of Chrysopetalidae and Hesionidae (Annelida, Polychaeta, Phyllodocida).

Previous studies suggest that the polychaete taxa Hesionidae and Chrysopetalidae may not represent separate groups, that Pilargidae constitute a subgroup within Hesionidae, and that Hesionides and Microphthalmus are highly derived hesionids. Phylogenetic systematic analyses of Phyllodocida and the subgroup Nereidiformia are presented in order to clarify the position and delineation of these taxa. The phyllodocida analysis includes 18 families representing the majority of the taxa in the group, is rooted with Onuphidae, and is based on 42 absent/present coded morphological characters, obtained mainly from literature. All 69 resulting shortest trees include the clade (Chrysopetalidae, Nereididae, Hesionidae), but with either Syllidae, Nautiliniellidae, Pilargidae or (Aphroditiformia, Pisionidae) as sister. In- and outgroup taxon selection for the Nereidiformia study is dictated by the outcome of Phyllodocida analysis, with scores based on examined species of two chrysopetalids, four hesionids, one nereid, one pilargid, one pisionid, one syllid, plus the putative hesionids Hesionides arenaria and Microphthalmus sp. It is based on 46 absent/present coded morphological characters. Two equally parsimonious trees indicate that chrysopetalids and hesionids are well delineated, that pilargids and hesionids are non-overlapping, and that Microphthalmus and Hesionides are not hesionids.