Exploring Canadian Echinoderm Diversity through DNA Barcodes

Unveiling ophiuroid biodiversity across North Atlantic habitats via an integrative perspective

The depths of the North Atlantic Ocean host a species-rich fauna providing heterogeneous habitats from thermal vent fields to cold-water coral reefs. With the increasing threat of destruction of deep-sea habitats due to human impacts, such as demersal fishing and the beginning of deep-sea mining, an analysis of the diversity and distribution of species is crucial for conservation efforts. Brittle stars occur in high biomasses, contributing to the biodiversity of the seafloor. Specimens were collected during several scientific expeditions to gain a more detailed insight into the brittle star diversity in the North Atlantic Ocean. An integrative approach to identify the species with DNA barcoding (mtCOI) in combination with morphological studies revealed 24 species. Most species have been previously identified in the North Atlantic, but sequences for 13 species are newly added to public repositories. Additionally, the MALDI-TOF-MS proteomic analysis was successfully applied for 197 specimens with known COI barcodes. Results are congruent with other molecular species delimitations demonstrating the functionality of proteomics for the identification of brittle stars. This dataset significantly expands our understanding of the taxonomic and genetic diversity of brittle stars and contributes to publicly available data. It emphasizes the importance of considering habitat heterogeneity for large scale patterns of biodiversity.

A pioneer morphological and genetic study of the intertidal fauna of the Gerlache Strait (Antarctic Peninsula)

The underexplored intertidal ecosystems of Antarctica are facing rapid changes in important environmental factors. Associated with temperature increase, reduction in coastal ice will soon expose new ice-free areas that will be colonized by local or distant biota. To enable detection of future changes in faunal composition, a biodiversity baseline is urgently required. Here, we evaluated intertidal faunal diversity at 13 locations around the Gerlache Strait (western Antarctic Peninsula), using a combination of a quadrat approach, morphological identification and genetic characterization. Our data highlight a community structure comprising four generally distributed and highly abundant species (the flatworm Obrimoposthia wandeli, the bivalve Kidderia subquadrata, and the gastropods Laevilitorina umbilicata and Laevilitorina caliginosa) as well as 79 rarer and less widely encountered species. The most abundant species thrive in the intertidal zone due to their ability to either survive overwinter in situ or to rapidly colonize this zone when conditions allow. In addition, we confirmed the presence of multiple trophic levels at nearly all locations, suggesting that complex inter-specific interactions occur within these communities. Diversity indices contrasted between sampling locations (from 3 to 32 species) and multivariate approaches identified three main groups. This confirms the importance of environmental heterogeneity in shaping diversity patterns within the investigated area. Finally, we provide the first genetic and photographic baseline of the Antarctic intertidal fauna (106 sequences, 137 macrophotographs), as well as preliminary insights on the biogeography of several species. Taken together, these results provide a timely catalyst to assess the diversity and to inform studies of the potential resilience of these intertidal communities.

Maximizing the reliability and the number of species assignments in metabarcoding studies using a curated regional library and a public repository

Biodiversity assessments relying on DNA have increased rapidly over the last decade. However, the reliability of taxonomic assignments in metabarcoding studies is variable and affected by the reference databases and the assignment methods used. Species level assignments are usually considered as reliable using regional libraries but unreliable using public repositories. In this study, we aimed to test this assumption for metazoan species detected in the Gulf of St. Lawrence in the Northwest Atlantic. We first created a regional library (GSL-rl) by data mining COI barcode sequences from BOLD, and included a reliability ranking system for species assignments. We then estimated 1) the accuracy and precision of the public repository NCBI-nt for species assignments using sequences from the regional library and 2) compared the detection and reliability of species assignments of a metabarcoding dataset using either NCBI-nt or the regional library and popular assignment methods. With NCBI-nt and sequences from the regional library, the BLAST-LCA (least common ancestor) method was the most precise method for species assignments, but the accuracy was higher with the BLAST-TopHit method (>80% over all taxa, between 70% and 90% amongst taxonomic groups). With the metabarcoding dataset, the reliability of species assignments was greater using GSL-rl compared to NCBI-nt. However, we also observed that the total number of reliable species assignments could be maximized using both GSL-rl and NCBI-nt with different optimized assignment methods. The use of a two-step approach for species assignments, i.e., using a regional library and a public repository, could improve the reliability and the number of detected species in metabarcoding studies.

Morphological Description and Molecular Analysis of Newly Recorded Asteroid, Henricia djakonovi Chichvarkhin, 2017 (Asteroidea: Spinulosida: Echinasteridae), from Dokdo Island, Korea

We recently collected the samples of Henricia from adjacent waters of Dokdo Island, Korea, using trimix SCUBA diving. Based on a combined result of morphological and molecular analysis, we identified our specimen as Henricia djakonovi Chichvarkhin, 2017, which is newly recorded in Korea. Morphologically, H. djakonovi has crescent abactinal plates bearing numerous pillar-shaped abactinal spines with a droplet-like apical tip. Moreover, molecular analysis based on the mitochondrial COI gene occurred that clearly distinguished H. djakonovi from other species of Henricia in the pairwise genetic distance and maximum likelihood analysis. Accordingly, 15 species of Henricia are recorded in Korean fauna, including H. djakonovi.

DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy

Echinoderms are marine water invertebrates that are represented by more than 7000 extant species, grouped in five classes and showing diverse morphologies (starfish, sea lilies, feather stars, sea urchins, sea cucumbers, brittle and basket stars). In an effort to further study their diversity, DNA barcodes (DNA fragments of the 5' end of the cytochrome c oxidase subunit I gene, COI) have been used to complement morphological examination in identifying evolutionary lineages. Although divergent clusters of COI sequences were reported to generally match morphological species delineations, they also revealed some discrepancies, suggesting overlooked species, ecophenotypic variation or multiple COI lineages within one species. Here, we sequenced COI fragments of 312 shallow-water echinoderms of the East Coast of South Africa (KwaZulu-Natal Province) and compared morphological identifications with species delimitations obtained with four methods that are exclusively based on COI sequences. We identified a total of 103 morphospecies including 18 that did not exactly match described species. We also report 46 COI sequences that showed large divergences (>5% p-distances) with those available to date and publish the first COI sequences for 30 species. Our analyses also identified discordances between morphological identifications and COI-based species delimitations for a considerable proportion of the morphospecies studied here (49/103). For most of them, further investigation is necessary to keep a sound connection between taxonomy and the growing importance of DNA-based research.

Trans-Arctic vicariance in Strongylocentrotus sea urchins

The sea urchins Strongylocentotus pallidus and S. droebachiensis first invaded the Atlantic Ocean from the Pacific following the opening of the Bering seaway in the late Miocene. While trans-Arctic dispersal during the Pleistocene is thought to have maintained species' integrity, a recent genomic analysis identified a reproductively isolated cryptic species within S. droebachiensis. Based on previous studies, the distribution of one of these lineages (S. droebachiensis W) includes the shallow water habitats of the northwest Atlantic and Pacific, while the other (S. droebachiensis E) is found throughout the shallow habitat in the northeast but is mostly restricted to deep habitats (>65 m) in the northwest Atlantic. However, since genetic variation within S. droebachiensis has been largely unstudied in the north Pacific and Arctic oceans, the biogeography of the cryptic species is not well known, and it is difficult to identify the mechanisms driving population subdivision and speciation. Here we use population genetic analyses to characterize the distribution of each species, and to test hypotheses about the role of vicariance in the evolution of systematic and genomic divergence within the genus. We collected individuals of all three Strongylocentrotus species (n = 365) from 10 previously unsampled locations in the northeast Pacific and north Atlantic (Labrador Sea and Norway), and generated mtDNA sequence data for a 418 bp fragment of cytochrome c oxidase subunit I (COI). To assess the biogeography of all three species, we combined our alignment with five previously published data sets (total n = 789) and used statistical parsimony and maximum likelihood to identify species and characterize their distribution within and among oceans. Patterns of haplotype sharing, pairwise F _ST , and hierarchical analyses of molecular variance (AMOVA) identified trans-Arctic dispersal in S. pallidus and S. droebachiensis W, but other than 5 previously reported singletons we failed to detect additional mtDNA haplotypes of S. droebachiensis E in the north Pacific. Within the Atlantic, patterns of habitat segregation suggests that temperature may play a role in limiting the distribution of S. droebachiensis E, particularly throughout the warmer coastal waters along the coast of Nova Scotia. Our results are consistent with the cycles of trans-Arctic dispersal and vicariance in S. pallidus and S. droebachiensis W, but we suggest that the evolution of Atlantic populations of S. droebachiensis E has been driven by persistent trans-Arctic vicariance that may date to the initial invasion in the late Pliocene.

Amplicon sequence variant-based meiofaunal community composition revealed by DADA2 tool is compatible with species composition

The present study is aimed at implementing the morphological identification-free amplicon sequence variant (ASV) concept for describing meiofaunal species composition, while strongly indicating reasonable compatibility with the underlying species. A primer pair was constructed and demonstrated to PCR amplify a 470-490 bp 18S barcode from a variety of meiofaunal taxa, high throughput sequenced using the Illumina 300 × 2 bps platform. Sixteen 18S multi-species HTS assemblies were created from meiofaunal samples and merged to one assembly of ~2,150,000 reads. Five quality scores (q = 35, 30, 25, 20, 15) were implemented to filter five 18S barcode assemblies, which served as inputs for the DADA2 software, ending with five reference ASV libraries. Each of these libraries was clustered, applying 3% dissimilarity threshold, revealed an average number of 1.38 ± 0.078 ASVs / cluster. Hence, demonstrating high level of ASV uniqueness. The libraries which were based on q ≤ 25 reached a near-asymptote number of ASVs which together with the low average number of ASVs / cluster, strongly indicated fair representation of the actual number of the underlying species. Hence, the q = 25 library was selected to be used as metabarcoding reference library. It contained 461 ASVs and 342-3% clusters with average number of 1.34 ± 1.036 ASV / cluster and their BLASTN annotation elucidated a variety of expected meiofaunal taxa. The sixteen assemblies of sample-specific paired reads were mapped to this reference library and sample ASV profiles, namely the list of ASVs and their proportional copy numbers were created and clustered.

New and Poorly Known Species of Peniagone (Holothuroidea, Elpidiidae) from the Northwest Pacific Ocean with Discussion on Phylogeny of the Genus

The northwest Pacific fauna of Peniagone includes at least seven species. In the present study we considered the following six species: Peniagone dubia and P. mus are re-described, P. minuta and P. saveljevae are described as new to science, additional information is provided on P. vitrea and P. cf. purpurea. Peniagone japonica was not included in the analysis. A potentially new species Peniagone sp. “miniatura” was distinguished based on morphological and molecular data but not formally described due to insufficient material. In the northwest Pacific, the species of Peniagone are distributed from 2400 to 8200 m. The bathymetric range of most of the species is narrow except for P. mus being also one of the deepest representatives of the genus. Only one species, P. vitrea, is known outside the northwest Pacific region. Partial sequences of COI and 16S rDNA were obtained for provisionally ten species of the genus (four of them from the northwest Pacific) and two other species of Elpidiidae which were used as an outgroup in phylogenetic analyses. The phylogenetic analyses results suggest that the northwest Pacific species of Peniagone are not closely related.

Testing small-scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding

DNA metabarcoding has been increasingly used to detail distributions of hundreds of species. Most analyses focus on creating molecular operational taxonomic units (MOTUs) from complex mixtures of DNA sequences, but much less common is use of the sequence diversity within these MOTUs. Here we use the diversity of COI haplotypes within MOTUs from a California kelp forest to infer patterns of population abundance, dispersal and population history from 527 species of animals and algae from 106 samples of benthic habitats in Monterey Bay. Using haplotypes as a unit we show fine-grained differences of abundance across locations for 15 species, and marked aggregation from sample to sample for most of the common species of plants and animals. Previous analyses could not distinguish these patterns from artefacts of amplification or sequence bias. Our haplotype data also reveal strong population genetic differentiation over small spatial scales for 48 species of red algae, sponges and Bryozoa. Last, phylogenetic analysis of mismatch frequencies among haplotypes show a wide variety of demographic histories from recent expansions to long, stable population sizes. These analyses show that abundant, small-bodied marine species that are often overlooked in ecological surveys can have strikingly different patterns of ecological and genetic structure leading to population, ecological and perhaps adaptive differences between habitats. MOTU diversity data from the same sequencing efforts that generate species-level analyses can greatly increase the scope and value of metabarcoding studies.

A new species of the genus Henricia (Asteroidea, Spinulosida, Echinasteridae) from South Korea

A new species of the genus Henricia Gray, 1840 that belongs to the family Echinasteridae is described from South Korea. Henriciaepiphysialissp. nov. has epiphyseal ossicles at the ends of the abactinal and lateral plates, and the abactinal and lateral spines form a hooked crown. The partial sequence of the mitochondrial COXI gene (537 bp) of H.epiphysialissp. nov. was obtained, and the new species was morphologically and genetically compared with other related Henricia species.

On the genus Crossaster (Echinodermata: Asteroidea) and its distribution

Several starfish (Echinodermata, Asteroidea) are keystone species of marine ecosystems, but some of the species are difficult to identify using morphological criteria only. The common sunstar, Crossaster papposus (Linnaeus, 1767), is a conspicuous species with a wide circumboreal distribution. In 1900, a closely similar species, C. squamatus (Döderlein, 1900) was described from the NE Atlantic Ocean, but subsequent authors have differed in their views on whether this is a valid taxon or rather an ecotype associated with temperature variations. We assessed the differentiating morphological characters of specimens from Norwegian and Greenland waters identified as C. papposus and C. squamatus and compared their distributions in the NE Atlantic as inferred from research cruises. The field data show that C. papposus is found mainly in temperate and shallow waters, whereas C. squamatus resides on the shelf-break in colder, mixed water masses. Intraspecific diversity and interspecific genetic differentiation of the two putative species, and their phylogenetic relationships to several Crossaster congeners worldwide, were explored using mitochondrial and nuclear DNA sequences. The molecular evidence suggests that C. papposus is the more diverse and geographically structured taxon, in line with its wide distribution. C. papposus and C. squamatus are closely related, yet clearly distinct taxa, while C. papposus and C. multispinus H.L. Clark, 1916, the latter from the South Pacific Ocean, are closely related, possibly sister taxa.

Complete mitochondrial genome of the taxonomically notorious sea star, Henricia leviuscula (Asteroidea, Spinulosida, Echinasteridae), from South Korea

In this study, next-generation sequencing was used to obtain the complete mitogenome of Henricia leviuscula (Stimpson, 1857). The mitogenome form was found to be a circular molecule 16,119-bp long with a 60.4% AT bias. The gene arrangement of H. leviuscula was exactly the same as that of previously reported mitogenome for another species of Echinasteridae, such as Echinaster (Othilia) brasiliensis, containing 37 genes (13 PCGs, 22 tRNAs, and 2 rRNAs). A phylogenetic tree was constructed using the 13 PCGs and 2 rRNA sequences. Henricia leviuscula formed a monophyletic clade with E. (O.) brasiliensis and this clade formed a larger clade with species of the Paxillosida and Valvatida.

A New Fissiparous Brittle Star, Ophiacantha scissionis sp. nov. (Echinodermata, Ophiuroidea, Ophiacanthida), from Jeju Island, Korea

A new species of Ophiuroidea, Ophiacantha scissionis sp. nov., is described. It was collected from Munseom Island, Jeju-do, South Korea at a depth of 28-36 m, by SCUBA diving. Ophiacantha scissionis has unique and distinct morphological characteristics: small disk, densely covered by small trifid spines, radial shields completely concealed by disk spines, six arms with four arm spines proximally, fissiparous. In addition, this species is clearly distinguished from other species of Ophiacantha by mitochondrial COI. This species is usually hexamerous and reproduces asexually by fissiparity. It is the first report of fissiparous reproduction in the genus Ophiacantha.

Sea stars of the genus Henricia Gray, 1840 (Echinodermata, Asteroidea) from Vostok Bay, Sea of Japan

We report seven species of the genus Henricia Gray, 1840 that were found in Vostok Bay, and two species from adjacent area, known from museum collection or seen in underwater footage. while existing literature reported no confirmed species from this area. Most of these species: H. djakonovi, H. alexeyi, H. densispina, H. hayashii, H. granulifera, H. pacifica, H. asiatica, and H. oculata robusta were reported from the Sea of Japan previously. H. nipponica, known from Japan, is reported from Russian seas for the first time. All studied taxa are re-described here using a range of morphological characters and partial 16S rRNA nucleotide sequences, life colorations of several species are reported for the first time, and an identification key is provided. Lectotype designations are fixed for studied series of species described by AM Djakonov.

Cryptic species diversity and reproductive isolation among sympatric lineages of Strongylocentrotus sea urchins in the northwest Atlantic

Distinguishing between intra- and inter-specific variation in genetic studies is critical to understanding evolution because the mechanisms driving change among populations are expected to be different than those that shape reproductive isolation among lineages. Genetic studies of north Atlantic green sea urchins Strongylocentrotus droebachiensis (Müller, 1776) have detected significant population substructure and asymmetric gene flow from Europe to Atlantic Canada and interspecific hybridization between S. droebachiensis and Strongylocentrotus pallidus (Sars, 1871). However, combined with patterns of divergence at mtDNA sequences, morphological divergence at gamete traits suggests that the European and North American lineages of S. droebachiensis may be cryptic species. Here, we use a combination of cytochrome c oxidase subunit I ( COI) sequences and single nucleotide polymorphisms (SNPs) to test for cryptic species within Strongylocentrotus sea urchins and hybrids between S. droebachiensis and S. pallidus populations. We detect striking patterns of habitat and reproductive isolation between two S. droebachiensis lineages, with offshore deep-water collections consisting of S. pallidus in addition to a cryptic lineage sharing genetic similarity with previously published sequences from eastern Atlantic S. droebachiensis. We detected only limited hybridization among all three lineages of sea urchins, suggesting that shared genetic differences previously reported may be a result of historical introgression or incomplete lineage sorting.

DNA barcoding of reef brittle stars (Ophiuroidea, Echinodermata) from the southwestern Indian Ocean evolutionary hot spot of biodiversity

In anticipation of the current biodiversity crisis, it has become critical to rapidly and accurately assess biodiversity. DNA barcoding has proved efficient in facilitating the discovery and description of thousands of species and also provides insight into the dynamics of biodiversity. Here, we sequenced a portion of the mitochondrial cytochrome c oxidase subunit I (COI) gene from all morphospecies of reef brittle stars collected during a large‐scale biodiversity survey in the southwestern Indian Ocean (SWIO). Three methods of species delineation (Automatic Barcode Gap Discovery, Generalized Mixed Yule Coalescent model, and Bayesian Poisson Tree Processes) showed concordant results and revealed 51 shallow reef species in the region. Mean intraspecific genetic distances (0.005–0.064) and mean interspecific genetic distances within genera (0.056–0.316) were concordant with previous echinoderm studies. This study revealed that brittle‐star biodiversity is underestimated by 20% within SWIO and by >40% when including specimens from the Pacific Ocean. Results are discussed in terms of endemism, diversification processes, and conservation implications for the Indo‐West Pacific marine biodiversity. We emphasize the need to further our knowledge on biodiversity of invertebrate groups in peripheral areas.