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

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.

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.

Multiple species delimitation approaches with COI barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae)

DNA taxonomy including barcoding and metabarcoding is widely used to explore the diversity in biodiversity hotspots. In most of these hotspot areas, chafers are represented by a multitude of species, which are well defined by the complex shape of male genitalia. Here, we explore how well COI barcode data reflect morphological species entities and thus their usability for accelerated species inventorization. We conducted dedicated field surveys in Sri Lanka to collect the species‐rich and highly endemic Sericini chafers (Coleoptera: Scarabaeidae). Congruence among results of a series of protocols for de novo species delimitation and with morphology‐based species identifications was investigated. Different delimitation methods, such as the Poisson tree processes (PTP) model, Statistical Parsimony Analysis (TCS), Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), and Barcode Index Number (BIN) assignments, resulted in different numbers of molecular operational taxonomic units (MOTUs). All methods showed both over‐splitting and lumping of morphologically identified species. Only 18 of the observed 45 morphospecies perfectly matched MOTUs from all methods. The congruence of delimitation between MOTUs and morphospecies expressed by the match ratio was low, ranging from 0.57 to 0.67. TCS and multirate PTP (mPTP) showed the highest match ratio, while (BIN) assignment resulted in the lowest match ratio and most splitting events. mPTP lumped more species than any other method. Principal coordinate analysis (PCoA) on a match ratio‐based distance matrix revealed incongruent outcomes of multiple DNA delimitation methods, although applied to the same data. Our results confirm that COI barcode data alone are unlikely to correctly delimit all species, in particular, when using only a single delimitation approach. We encourage the integration of various approaches and data, particularly morphology, to validate species boundaries.

Review of Ophioplinthaca Verrill, 1899 (Echinodermata, Ophiuroidea, Ophiacanthidae), description of new species in Ophioplinthaca and Ophiophthalmus, and new records from the Northwest Pacific and the South China Sea

The ophiuroid genus Ophioplinthaca is well characterized by the deep incisions in the disc. Prior to this study, it contained 32 accepted species, but species limits and geographic distributions were not well understood. The manned submersible vehicle 'Shenhaiyongshi' was used to collect ophiuroid specimens from the deep-sea seamounts and cold seeps in the South China Sea and Northwest Pacific at 602-3600 m depth, during 2018 to 2020. The genus Ophioplinthaca was reviewed using both morphological data and a phylogenetic analysis, based on COI sequences. The taxonomic status of the genus Ophiophthalmus Matsumoto, 1917, a junior homonym of Ophiophthalmus Fitzinger, 1843 (a reptile) was clarified by proving prevailing usage of the ophiuroid name. A total of eight species were identified, including two new species, described asOphioplinthacabrachispina sp. nov. and Ophiophthalmusserratus sp. nov., and two new records. The new species are characterized by unique features of the arm skeletons. Tabular keys to all Ophioplinthaca and Ophiophthalmus species are provided. Interspecific and intraspecific genetic distance of Ophioplinthaca species ranged from 2.32% to 19.72%, and from 0.26% to 0.90%, respectively. The data suggest that species of the genus Ophioplinthaca are more widely spread around the Northwest Pacific region deep-sea seamounts than previously known.

Order Euryalida (Echinodermata, Ophiuroidea), new species and new records from the South China Sea and the Northwest Pacific seamounts

Ophiuroids were collected by the manned submersible ‘Shenhaiyongshi’ from the deep-sea seamounts in the South China Sea and Northwest Pacific regions at 602–1920 m depth, during 2018 to 2020. A total of nine species was identified, including two new species and seven new records from the South China Sea and one new record from the Northwest Pacific region. Two new species are described as Asteroschemashenhaiyongshiisp. nov. and Asteroschemadomogranulatumsp. nov. The seven new records included five species from the genus Asteroschema, and one species each from the genera Asterostegus and Astrodendrum. Comprehensive descriptions of morphological features are provided, including characteristics of the arm skeleton, as well as a phylogenetic analysis based on 16S and COI sequences. Intraspecific genetic distance ranges of Euryalida species from the present study were 0.34% to 1.38%, which was relatively low compared to other orders in the class Ophiuroidea. The present study suggests a high probability that species of the order Euryalida are more widely spread around the Indo-Pacific region than previously expected.

Diversity investigation by application of DNA barcoding: A case study of lepidopteran insects in Xinjiang wild fruit forests, China

To investigate the species diversity of lepidopteran insects in Xinjiang wild fruit forests, establish insect community monitoring systems, and determine the local species pool, we test the applicability of DNA barcoding based on cytochrome c oxidase subunit I (COI) gene for accurate and rapid identification of insect species. From 2017 to 2019, a total of 212 samples with ambiguous morphological identification were selected for DNA barcoding analysis. Five sequence-based methods for species delimitation (ABGD, BINs, GMYC, jMOTU, and bPTP) were conducted for comparison to traditional morphology-based identification. In total, 2,422 samples were recorded, representing 143 species of 110 genera in 17 families in Lepidoptera. The diversity analysis showed that the richness indices for Noctuidae was the highest (54 species), and for Pterophoridae, Cossidae, Limacodidae, Lasiocampidae, Pieridae, and Lycaenidae were the lowest (all with 1 species). The Shannon-Wiener species diversity index (H') and Pielou's evenness (J') of lepidopteran insects first increased and then decreased across these 3 years, while the Simpson diversity index showed a trend of subtracted then added. For molecular-based identification, 67 lepidopteran species within 61 genera in 14 families were identified through DNA barcoding. Neighbor-joining (NJ) analysis showed that conspecific individuals were clustered together and formed monophyletic groups with a high support value, except for Lacanobia contigua (Denis & Schiffermüller, 1775) (Noctuidae: Hadeninae). Sixty-seven morphospecies were classified into various numbers of MOTUs based on ABGD, BINs, GMYC, jMOTU, and bPTP (70, 96, 2, 71, and 71, respectively). In Xinjiang wild fruit forests, the family with the largest number of species is Noctuidae, followed by Geometridae, Crambidae, and the remaining families. The highest Shannon diversity index is observed for the family Noctuidae. Our results indicate that the distance-based methods (ABGD and jMOTU) and character-based method (bPTP) outperform GMYC. BINs is inclined to overestimate species diversity compared to other methods.

Cryptic Species Diversity and Phylogenetic Relationship in the Rust Genus Chrysomyxa from China

Chrysomyxa rusts are fungal pathogens widely distributed in the Northern hemisphere, causing spruce needle and cone rust diseases, and they are responsible for significant economic losses in China. Taxonomic delimitation and precise species identification are difficult within this genus because some characters often overlap in several species. Adequate species delimitation, enhanced by the use of DNA-based methodologies, will help to establish well-supported species boundaries and enable the identification of cryptic species. Here, we explore the cryptic species diversity in the rust genus Chrysomyxa from China. Species delimitation analyses are conducted using a distance-based method (ABGD) and three tree-based methods (GMYC, bPTP, and mPTP) based on combined LSU and ITS sequences of over 60 specimens. Although there is some incongruence among species delimitation methods, two new species and three putative cryptic species are identified. The key to 20 Chrysomyxa species distributed in China is presented. These results suggest that a significant level of undiscovered cryptic diversity is likely to be found in Chrysomyxa from China. Future studies should consider multiple analytical methods when dealing with multi-locus datasets.

Description of a New Brooding Species of Ophiodelos (Echinodermata: Ophiuroidea) from Japan

A new species of brittle star, Ophiodelos okayoshitakai, is described from two specimens collected in Sagami Bay, central-eastern Japan. Photographic examination of the holotype specimen of the sole other congener, Ophiodelos insignis Koehler, 1930, indicates that Ophiodelos okayoshitakai sp. nov. is distinguished from O. insignis by i) the disc stumps covering on the dorsal side of the disc, ii) the dorsal and ventral arm plates being separated from each other on the proximal arm regions, iii) the dorsal arm plate being smooth, iv) the arm spines at proximal portion of the arm being six in number and smooth in shape, and v) the number and shape of the tentacle scales at proximal portion of the arm being up to two and spine-shaped adradially and oval abradially. Detailed morphological observations of this new species suggest the inclusion of Ophiodelos, whose familial affiliation remains unclear, in the suborder Ophiacanthina. More than 10 juveniles of various sizes were found in the disc of Ophiodelos okayoshitakai sp. nov., indicating a brooding reproduction. This is the first report of the genus Ophiodelos from Japanese waters. We also provided a nucleotide sequence for part of the cytochrome c oxidase subunit I (COI) gene in O. okayoshitakai sp. nov. for future studies of DNA barcoding and phylogeny.

Description of three species of ophioplinthacids, including a new species, from a deep seamount in the Northwest Pacific Ocean

Five specimens of brittle star were collected from a deep-sea seamount in the Northwest Pacific, and identified into three species. One which is new to science, Ophioplinthaca grandisquama n. sp., can be easily distinguished from its congeners by the distinctly elongated and stout tentacle scales, stout and long disc spines, capitate with typically elongate to flaring head bearing numerous distinct thorns, radial shields roughly triangular and contiguous distally. One specimen was identified as Ophioplinthaca semele (Clark, 1949), which had been reported in Hawaii seamounts, is a new record of this species in the Northwest Pacific. The remaining specimen was an unknown species of Ophioplinthaca, with some different characteristics from other species of Ophioplinthaca. However, we, herein, prefer not to attach a name to this specimen until more morphological characteristics are available. The finding of this new species and two new records further enriches the distribution of Ophioplinthaca in the seamount of Northwest Pacific, providing useful information for marine protection in the cobalt-rich area.

ASAP: assemble species by automatic partitioning

Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 10⁴ sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.

World Travelers: DNA Barcoding Unmasks the Origin of Cloning Asteroid Larvae from the Caribbean

AbstractThe identity of wild cloning sea star larvae has been a mystery since they were first documented in the Caribbean. The most commonly collected cloning species was thought to belong to the Oreasteridae, on the basis of similarity with sequences from Oreaster reticulatus and Oreaster clavatus. This larval form has recently been linked to a rare benthic juvenile. As part of two larger DNA barcoding projects, we collected cloning asteroid larvae from the Caribbean coast of Panama and compared them to a large reference database of tropical echinoderms. Morphological and DNA barcode data from the cytochrome c oxidase subunit I gene demonstrated that Panamanian larvae belonged to the same operational taxonomic unit as those recovered in previous studies of cloning larvae from the Caribbean. Much to our surprise, sequences from these larvae clearly identified them as belonging to Valvaster striatus, a species typically considered to be endemic to the Indo-West Pacific. A lineage of Mithrodia clavigera that occurs in both the Caribbean and the Indo-West Pacific also has cloning larvae, suggesting that this unusual life history has allowed larvae to pass around the Cape of Good Hope and the Benguela upwelling region, which is a barrier to dispersal for most tropical marine invertebrates.

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.

Dark offshoot: Phylogenomic data sheds light on the evolutionary history of a new species of cave brittle star

Caves are a useful system for testing evolutionary and biogeographic hypotheses, as they are isolated, and their environmental conditions have resulted in adaptive selection across different taxa. Although in recent years many more cave species have been discovered, cave-dwelling members of the class Ophiuroidea (brittle stars) remain scarce. Out of the more than two thousand species of brittle stars described to date, only three are regarded as true cave-dwellers. These occurrences represent rare colonising events, compared to other groups that are known to have successfully diversified in these systems. A third species from an anchihaline cave system in the Yucatan Peninsula, Mexico, has been previously identified from cytochrome oxidase I (COI) barcodes. In this study, we reassess the species boundaries of this putative cave species using a phylogenomic dataset (20 specimens in 13 species, 100 exons, 18.7 kbp). We perform species delimitation analyses using robust full-coalescent methods for discovery and validation of hypotheses on species boundaries, as well as infer its phylogenetic relationships with species distributed in adjacent marine regions, in order to investigate the origin of this cave-adapted species. We assess which hypotheses on the origin of subterranean taxa can be applied to this species by taking into account its placement within the genus Ophionereis and its demographic history. We provide a detailed description of Ophionereis commutabilis n. sp., and evaluate its morphological characters in the light of its successful adaptation to life in caves.

Cryptic Diversity, but to What Extent? Discordance Between Single-Locus Species Delimitation Methods Within Mainland Anoles (Squamata: Dactyloidae) of Northern Central America

Single-locus molecular barcoding is a useful method for identifying overlooked and undescribed biodiversity, providing the groundwork for further systematic study and taxonomic investigation. A variety of methods for delimiting species from barcoding libraries have been developed and applied, allowing for rapid estimates of species diversity in a broad range of taxa. However, tree-based and distance-based analyses can infer different group assignments, potentially over- or underestimating the number of putative species groups. Here, we explore diversity of mainland species of anole lizards from the Chortís Block biogeographical province of northern Central America using a DNA barcoding approach, generating and analyzing cytochrome oxidase subunit I (COI) sequences for over 400 samples assignable to 33 of 38 (86.8%) native and one introduced mainland species. We subsequently tested the effects different models of nucleotide substitution, different species-delimitation algorithms, and reducing our dataset had on species delimitation estimates. We performed of two distance-based (ABGD, RESL) and three tree-based (bPTP, mPTP, GMYC) analyses on both the full dataset and a dataset consisting only of unique halotypes. From 34 nominal taxa, analyses of the full dataset recovered between 34 and 64 operational taxonomic units (OTUs), while analyses of the reduced dataset inferred between 36 and 59. Reassigning individuals to either mPTP-inferred or ABGD clustered (7.2% threshold) groups improved the detection of a barcoding gap across three different models of nucleotide substitution, removing overlap between intra- and interspecific distances. Our results highlight the underestimated diversity of mainland Chortís Block anoles, but the lack of congruence between analyses demonstrates the importance of considering multiple analytical methods when dealing with single-locus datasets. We recommend future studies consider the effects of different models of nucleotide substitution on proposed barcoding gaps, as well as the effect reducing a dataset to unique haplotypes may have on proposed diversity estimates.

Phylogenomics, life history and morphological evolution of ophiocomid brittlestars

Brittlestars in the family Ophiocomidae are large and colourful inhabitants of tropical shallow water habitats across the globe. Here we use targeted capture and next-generation sequencing to generate robust phylogenomic trees for 39 of the 43 species in order to test the monophyly of existing genera. The large genus Ophiocoma, as currently constituted, is paraphyletic on our trees and required revision. Four genera are recognised herein: an expanded Ophiomastix (now including Ophiocoma wendtii, O. occidentalis, O. endeani, O. macroplaca, and Ophiarthrum spp), Ophiocomella (now including the non-fissiparous Ophiocoma pumila, aethiops and valenciae) and Breviturma (now including Ophiocoma pica, O. pusilla, O. paucigranulata and O. longispina) and a restricted Ophiocoma. The resulting junior homonym Ophiomastix elegans is renamed O. brocki. The genus Ophiomastix exhibits relatively high rates of morphological disparity compared to other lineages. Ophiomastix flaccida and O. (formerly Ophiarthrum) pictum have divergent mitochondrial genomes, characterised by gene-order rearrangements, strand recoding, enriched GT base composition, and a corresponding divergence of nuclear mitochondrial protein genes. The new phylogeny indicates that larval and developmental transitions occurred rarely. Larval culture trials show that species with abbreviated lecithotrophic larval development occur only within Ophiomastix, although the possible monophyly of these species is obscured by the rapid early radiation within this genus. Asexual reproduction by fission is limited to one species-complex within Ophiocomella, also characterised by elevated levels of allelic heterozygosity, and which has achieved a relatively rapid global distribution. The crown ages of the new genera considerably predate the closure of the Tethyan seaway and all four are distributed in both the Atlantic and Indo-Pacific Oceans. Two species pairs appear to reflect the closure of the Panama Seaway, although their fossil-calibrated node ages (12-14 ± 6 my), derived from both concatenated sequence and multispecies coalescent analyses, considerably predate the terminal closure event. Ophiocoma erinaceus has crossed the East Pacific barrier and is recorded from Clipperton Island, SW of Mexico.

Molecular approaches uncover cryptic diversity in intertidal Ligia isopods (Crustacea, Isopoda, Ligiidae) across the southern Africa coastline

Recent phylogeographic studies along the coastline of southern Africa have uncovered cryptic diversity in several coastal invertebrates, including direct developing crustaceans in the superorder Peracarida. These findings indicating the possible existence of additional cryptic diversity in other yet to be studied peracarids, particularly those known to harbor said cryptic diversity in other regions of the world. Isopods in the genus Ligia are one such taxon. They inhabit patchy rocky beaches, are direct developers, avoid the open water, and exhibit other biological traits that severely constrain their dispersal potential (e.g., poor desiccation resistance). These traits are thought to have led to long-term isolation of populations, and allopatric diversification in Ligia species around the world; however, Ligia species in southern Africa, where three endemic Ligia species of uncertain validity are known to exist, remain unstudied to date. In this study, we used mitochondrial and nuclear markers to characterize Ligia collected in 18 localities from Namibia to the KwaZulu-Natal region of South Africa. We report the presence of cryptic lineages within Ligia species in the region that suggest the need for taxonomic reevaluation of these isopod species.

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.