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Figure A1. Morphology of Alvinellidae. (A) Paralvinella fijiensis, juvenile (SIO-BIC A8627). (B) Alvinella caudata (SIO-BIC A8618), anterior body with filamentous branchiae carrying lamellae as secondary structures. (C) Paralvinella fijiensis (SIO-BIC A8627), head with tentacles retracted into the mouth and the filamentous branchiae carrying smaller filaments as secondary structures. (D) Paralvinella fijiensis, closeup of notopodia with spines and cirri. (E) Paralvinella palmiformis (SIO-BIC A1104, 630×), uncini from posterior thorax with the characteristic single prominent tooth over the rostrum. (F) Paralvinella grasslei (SIO-BIC A1093, 200×), notopodial ramus with a notpodial cirrus and both smooth and serrated capillary chaetae. (G) Alvinella caudata (SIO-BIC A1092, 200×), capillary chaetae from mid thorax with serrated rims. Abbreviations: pe—peristomium, pr—prostomium, te—buccal palps or tentacles. Roman numerals designate segment counts.
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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 ro...
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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 Phyllod...
Citations
... Even though robust molecular phylogenetic studies are common for other annelid groups (e.g. Aguado et al., 2012;Eilertsen et al., 2017;Li et al., 2015Li et al., , 2017Stiller et al., 2020;Weigert et al., 2014), a large-scale molecular phylogenetic assessment across the breadth of Spionidae is still lacking and limiting our understanding about the evolution of one of the most diverse groups of annelids (Abe & Sato-Okoshi, 2021;Blake, 2006). ...
Most efforts at improving accuracy in phylogenomic reconstructions have focused on improving tree-building methods or orthology determination. Even though the use of whole genome sequence or transcriptome data is increasing, the degree to which accurate genome assembly and annotation influence phylogenetic inference has not been well explored. Here, we use low-coverage whole genome sequencing of spionid annelids to explore the impact of different assemblers and annotation strategies on tree reconstruction. We also produce a phylogenetic hypothesis that spans the breadth of Spionidae, examining the current systematics of the group, which is based on morphological parsimony analyses and classical taxonomy. Our results show that both assembly and annotation can have important consequences for the pool of loci that may be available for tree reconstruction. When an identical phylogenomic pipeline is used, differences in assembly and annotation can account for variation in reconstructed topologies. Interestingly, the completeness and depth of the data used for training annotation software (i.e. data from model systems) appear to be more important, by some measures, than the degree of phylogenetic relatedness of the organism from which training data are drawn. Despite variation in recovered topologies, the recognized subfamily Spioninae is nested within Nerininae, suggesting that diagnostic characters of Nerininae (e.g. thick egg membrane, short-headed sperm) are symplesiomorphies of Spionidae rather than apomorphies of a particular sub-clade. With the increased use of genomic data, our results advocate for a broader consideration of how assembly and annotation may impact data matrices used in phylogenomic analyses. K E Y W O R D S genome, loci, phylogeny, reconstruction, Spionidae
... If this is the case then the rostrum in Osedax's chaetae would be reduced. The rostrum is also reduced within other sedentarian annelids such as Pectinariidae [38], a familyranked taxon well nested within Terebellida, which otherwise primarily possess hooked chaetae with a rostrum [1,16,39]. Recent insights into annelid phylogeny coupled with new observations of remarkably different hook ultrastructure and formation [40], challenge the homology of all annelid hooks and substructures hereof. Nonetheless, targeted comparisons of chaetogenesis within closely related taxa and distinct monophyletic clades offer a framework for testing and potentially substantiating hypotheses of homology. ...
Background
This study sheds light on the genetic blueprints of chaetogenesis (bristle formation), a complex biomineralization process essential not only for the diverse group of bristle worms (annelids) but also for other spiralians. We explore the complex genetic mechanisms behind chaetae formation in Osedax japonicus, the bone-devouring deep-sea worm known for its unique ecological niche and morphological adaptations.
Results
We characterized the chaetal structure and musculature using electron microscopy and immunohistochemistry, and combined RNAseq of larval stages with in-situ hybridization chain reaction (HCR) to reveal gene expression patterns integral to chaetogenesis. Our findings pinpoint a distinct surge in gene expression during the larval stage of active chaetogenesis, identifying specific genes and cells involved.
Conclusions
Our research underscores the value of studying on non-model, "aberrant" organisms like Osedax, whose unique, temporally restricted chaetogenesis provided insights into elevated gene expression across specific larval stages and led to the identification of genes critical for chaetae formation. The genes identified as directly involved in chaetogenesis lay the groundwork for future comparative studies across Annelida and Spiralia, potentially elucidating the homology of chaetae-like chitinous structures and their evolution.
... hutchings et al. , b, Nogueira et al. 2013. In contrast, Stiller et al. (2020) concluded, based on transcriptomes, molecular, and morphological data, that trichobranchidae and terebellidae are sister groups. Accordingly, within the terebellidae there are two subfamilies, the terebellinae and the thelopodinae. ...
... One representative of the telothelepodidae was nested within the thelepodidae, and Polycirridae within terebellinae. In addition, Stiller et al. (2020) found four well-defined clades within the terebellinae, which are ranked as tribes, namely Procleini, Polycirrini, terebellini and lanicini. ...
Three new terebellid species with two pairs of arborescent branchiae, serrated notochaetae with bulbous wings and avicular uncini in completely separate double rows are described from the Namibian coast, SW Africa, found during different expeditions between 2004 and 2022. These species were assigned to the genus Amphitritides, A. jirkovi sp. nov., A. namibiensis sp. nov. and A. skeletonensis sp. nov. The main diagnostic characters of these species are discussed, especially in the light of the ongoing discussion of synonymising Amphitritides with Amphitrite and Paramphitrite. The features of the three newly described species are compared in a table. An identification key for all known species of Amphitritides is also provided.
... Amplified products were sent to Macrogen Company to obtain sequences, using same set of primers as used for PCR. The paratype SIO-BIC A15677 COI was sequenced using methods in Stiller et al. (2020). ...
... Sequences homologous to Eisenia fetida a-amylases (treated as reference sequences) were identified by BLASTp search. Additional sequences were also retrieved from other sources: NCBI Transcriptome Shotgun Assembly Sequence Database, GenBank, J ekely lab transcriptomes databases for Platynereis dumerilii and Alvinella pomepjana (http://jekelylab.ex.ac.uk/blast/) [49,50], and supplementary data from another paper [51]. Moreover, in a few cases (Aporrectodea caliginosa, Enchytraeus crypticus, Lepidonotus clava, and Metaphire vulgaris), homologous sequences were identified by tBLASTn hit in genomes available at the NCBI Assembly database and predicted with AUGUSTUS [52] integrated in Omics-Box suite. ...
... Homologous sequences of sufficient length (complete or almost complete 5 0 -partial sequences) were recovered from 45 out of a total of 94 SRA-derived transcriptomes. The remaining sequences were retrieved from TSA (9 sequences), Stiller et al. [51] supplementary data (9 sequences), GenBank (7 sequences), AUGUSTUS gene prediction for selected Annelida genomes (6 sequences), and J ekely lab transcriptomes (5 sequences). Resulting sequences were screened against GenBank using BLASTp, while Eisenia fetida aamylases (Acc. ...
Although enchytraeids have gained popularity in scientific research, fundamental questions regarding their feeding ecology and biology remain largely unexplored. This study investigates α-amylases, major digestive enzymes responsible for hydrolyzing starch and similar polysaccharides into sugars, in Enchytraeus albidus. Genetic data related to α-amylases is currently lacking for the family Enchytraeidae but also for the entire Annelida. To detect and identify coding sequences of the expressed α-amylase genes in COI-monohaplotype culture (PL-A strain) of E. albidus, we used classical “gene fishing” and transcriptomic approaches. We also compared coding sequence variants of α-amylase retrieved from transcriptomic data related to freeze-tolerant strains. Our results reveal that E. albidus possesses two distinct α-amylase genes (Amy I and Amy II) that are homologs to earthworm Eisenia fetida Ef-Amy genes. Different strains of E. albidus possess distinctive alleles of α-amylases with unique SNP patterns specific to a particular strain. Unlike Amy II, Amy I seems to be a highly polymorphic and multicopy gene. The domain architecture of the putative Amy proteins was found the same as for classical animal α-amylases with ABC-domains. A characteristic feature of Amy II is the lack of GHGA motif in the flexible loop region, similarly to many insect amylases. We identified “Enchytraeus-Eisenia type” α-amylase homologs in other clitellates and polychaetes, indicating the ancestral origin of Amy I/II proteins in Annelida. This study provides the first insight into the endogenous non-proteolytic digestive enzyme genes in potworms, discusses the evolution of Amy α-amylases in Annelida, and explores phylogenetic implications.
... Improved molecular techniques have enhanced analyses of specimens from both new and old collections for genetic barcoding (e.g. Poitrimol et al., 2022;Stiller et al., 2020). In general, greater sampling tends to extend and infill species ranges in poorly sampled systems. ...
Aim
Deep‐sea hydrothermal vent habitats support a low‐diversity fauna in which most species are unique to the ecosystem. To inform conservation planning around this vulnerable marine ecosystem, we examine species distributions over a wide area to assess the underlying beta‐diversity components and to examine biogeographic patterns. We assess the concept of a highly connected fauna that would repopulate areas of local extinction from distal locations.
Location
Western Pacific Ocean from Japan to New Zealand.
Methods
We assemble a database of 295 confirmed species records for 11 western Pacific vent systems. The SET beta‐diversity framework supports query of the distribution of pairwise pattern components in comparisons among vent systems. We build a network based in graph theory to examine connectivity among vent systems based on shared species similarity. A bipartite network revealed the relative role of each species in linkages among vent system nodes. We assess the importance of sampling bias and distance between systems.
Results
Overall, two‐thirds of the taxa are restricted to a single basin or arc. The Mariana Trough system has the highest corrected weighted endemism for vent‐specific species, followed by that of the Okinawa Trough. Species replacement is the dominant feature of beta‐diversity. Eleven vent systems form seven network modules with stronger connectivity in the Southwest than Northwest Pacific. The Manus Basin vent system emerges as a network ‘hub’ reflecting its central geographic near the equator.
Main Conclusion
Two western Pacific biogeographic provinces arise, north and south of the equator that few species transcend. Local and regional conservation plans should consider the low network connectivity and high system endemism in management of hydrothermal vent ecosystems in the event of seabed mining. Species recruitment is unlikely to transcend vent system boundaries. We identify Okinawa Trough, Mariana Trough, Manus Basin, Feni‐Tabar Arc and Kermadec Arc for development of conservation plans that initiate or expand protection.
... Despite its great ecological importance, little is known about its biology and population ecology. In addition, the few DNA sequences available in the GenBank come from extensive phylogenetic studies with little emphasis on morphological and taxonomic aspects Stiller et al. 2020). ...
... The clade of Amythas is sister to Samytha sexcirrata under strong support (BI: 1, ML: 100%; Fig. 3). The relationships among other species are well resolved and according with recent studies Stiller et al. 2020). ...
Amythas membranifera was originally described through a single and incomplete specimen found in Commonwealth Bay, Adélie Land, Antarctica, at ~ 600 m depth. The species occurs exclusively in Antarctic waters and has a great ecological and biological value to benthic dynamics in some Antarctic areas. We collected several specimens of A. membranifera at Marian Cove, Maxwell Bay (King George Island) during a cruise of the project “CHAnges in Coastal Marine Systems of the Antarctic Peninsula: a 2050 Outlook (CHAMP2050)”. We present here a detailed study of A. membranifera from new specimens collected during this cruise, including morphological redescription, morphometry, molecular biology studies and aspects of their distribution, reproduction and feeding. A. membranifera specimens present an intraovarian oogenesis with blood vessel association for yolk precursor transference, with mature oocytes with 180–260 µm in diameter. Our data may suggest a broadcast spawner strategy. The spermiogenesis follows with the maturation of spermatids in spermatozoids in smaller clusters of cells and stored freely in the coelom prior to spawn ect-aquasperms. Finally, we point that one of the most intriguing aspects to date is its distribution, since most recent records were made in the West Antarctic Peninsula region while few records were made in the region of the original description (East Antarctic). This is our contribution to the knowledge of this species encompassing different scientific topics in a integrative perspective.
... Relationships among Polynoidae groups or subfamilies were recognized early on in phylogenetic studies as being "taxonomically entangled" and in need of major revision (see Fauchald and Rouse 1997). Early studies, like Struck et al. (2005) and Wiklund et al. (2005) were limited in their taxon sampling and group representation, yet still recovered paraphyly across Polynoidae. As representation of taxa grew across phylogenetic studies (see Gonzalez et al., 2018;Norlinder et al., 2012;Zhang et al., 2018b), so did the number of subfamilies and genera recovered as paraphyletic. ...
... Phylotranscriptomic datasets have previously been used across Annelida in order to understand the systematic relationships among major groups or subfamilies (e.g., Struck et al. 2011;Weigert et al. 2014), but despite their large diversity and biological importance, transcriptomic sampling to infer systematic relationships within annelid families remains limited (Stiller et al., 2020;Tilic et al., 2022). Weigert et al. (2014) were the first to include transcriptomic data from representatives of Aphroditiformia, specifically Harmothoe extenuata (Grube, 1840) and Sthenelais boa (Johnston, 1833), however, in-depth phylogenomic examination of Aphroditiformia or its families is lacking. ...
Polynoidae is the most diverse radiation of Aphroditiformia and one of the most successful groups of all Annelida in terms of diversity and habitats colonized. With such an unmatched diversity, phylogenetic investigations have struggled to understand their evolutionary relationships. Previous phylogenetic analyses have slowly increased taxon sampling and employed methodologies, but despite their diversity and biological importance, large genomic sampling is limited. To investigate the internal relationships within Polynoidae, we conducted the first phylogenomic analyses of the group based on 12 transcriptomes collected from species inhabiting a broad array of habitats, including shallow and deep waters, as well as hydrothermal vents, anchialine caves and the midwater. Our phylogenomic analyses of Polynoidae recovered congruent tree topologies representing the clades Polynoinae, Macellicephalinae and Lepidonotopodinae. Members of Polynoinae and Macellicephalinae clustered in well supported and independent clades. In contrast, Lepidonotopodinae taxa were always recovered nested within Macellicephalinae. Though our sampling only covers a small proportion of the species known for Polynoidae, our results provide a robust phylogenomic framework to build from, emphasizing previously hypothesized relationships between Macellicephalinae and Lepidonotopodinae taxa, while providing new insights on the origin of enigmatic cave and pelagic lineages.
... Traditionally, Melinninae Chamberlin, 1919 and Ampharet inae Malmgren, 1866 were treated as two subfamilies within the family Ampharetidae Malmgren, 1866 andEbbe &Purschke (2021) who provided a brief description of the family Ampharetidae accepted these two subfamilies. However, Stiller et al. (2020) undertook a phylogenetic analysis of a selected number of Terebelliformia using both molecular and morphological data. They found that the subfamily Melinninae was sister to the Terebellidae Johnston, 1846 and not closely related to other ampharetids. ...
... Thus, they raised Melinninae to a new family, Melinnidae. This new family includes all the five genera previously included in the subfamily Melinninae, although molecular data for Melinninae used in Stiller et al. (2020) was limited. The authors used molecular data from 41 taxa of Ampharetinae and only six taxa of Melinninae. ...
... The authors used molecular data from 41 taxa of Ampharetinae and only six taxa of Melinninae. All other genera previously classified in the Ampharetinae have been elevated to the Ampharetidae and, within this, Stiller et al. (2020) recognized three clades: Ampharetinae, Amaginae, and Amphicteinae, although it is unclear if these should be considered as subfamilies, given the limited numbers of species in this family sequenced. ...
A new species of Melinna (family Melinnidae) is described from the abyssal depths off the east coast of Australia. All material was collected during the RV Investigator voyage "Sampling the abyss" (IN2017_V03) in May-June 2017 from Bass Strait, Tasmania/Victoria using a beam trawl at 4197-4133 m depth. The new species Melinna hamulus sp. nov. differs from all other species of Melinna by having around 45 abdominal segments, dorsal membrane with 13-17 projections, four pairs of branchiae completely free and occurring in depths of over 4000 m. Phylogenetic relationships between our new species and other species within the family Melinnidae were assessed using the nuclear 18S and the mitochondrial 16S and cytochrome oxidase subunit I (COI) gene fragments. The results revealed that Melinna hamulus sp. nov. was genetically distinct from all other species of Melinnidae. This is the first species of Melinna to be described from Australian waters. We provide a new standard for description of species of Melinna and provide further detail on three existing species: Melinna albicincta Mackie & Pleijel, 1995, Melinna elisabethae McIntosh, 1914 and the type species of the genus Melinna cristata (Sars, 1851) using morphological characters illustrated with light and scanning electron microscopy photographs. We provide a table with the main diagnostic characters of all described species of Melinna together with type localities and depths.. 2023. New species of Melinna (Melinnidae, Annelida) from the Australian abyss with comments on M. albicincta, M. cristata and M. elisabethae. In RV Investigator-Abyssal Annelida, ed. E. K. Kupriyanova and L. M. Gunton. Records of the Australian Museum 75(3): 125-154. https://doi.
... Unlike other genera of Terebelliformia, the members of Polycirrus do not make solid tubes, and they are found in shallow to deep waters, inhabiting environments such as sandy to muddy sediments, maerl or seagrass beds, the interior of sponges and the cracks of rocky or coral substrates [18,[21][22][23]. The classification of this genus and its 'family' has been the subject of much debate based on morphological and molecular data [21,[24][25][26]. Since this study does not focus on higher-level classification, we will treat Polycirrus as a genus of Terebelliformia without mentioning its family level. ...
Bioluminescence, a phenomenon observed widely in organisms ranging from bacteria to metazoans, has a significant impact on the behaviour and ecology of organisms. Among bioluminescent organisms, Polycirrus, which has unique emission wavelengths, has received attention, and advanced studies such as RNA-Seq have been conducted, but they are limited to a few cases. In addition, accurate species identification is difficult due to lack of taxonomic organization. In this study, we conducted comprehensive taxonomic survey of Japanese Polycirrus based on multiple specimens from different locations and described as three new species: Polycirrus onibi sp. nov., P. ikeguchii sp. nov. and P. aoandon sp. nov. The three species can be distinguished from the known species based on the following characters: (i) arrangement of mid-ventral groove, (ii) arrangement of notochaetigerous segments, (iii) type of neurochaetae uncini, and (iv) arrangement of nephridial papillae. By linking the bioluminescence phenomenon with taxonomic knowledge, we established a foundation for future bioluminescent research development. We also provide a brief phylogenetic tree based on cytochrome c oxidase subunit I (COI) sequences to discuss the evolution of bioluminescence and the direction of future research.
