Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs

Circumtropical distribution and cryptic species of the meiofaunal enteropneust Meioglossus (Harrimaniidae, Hemichordata)

Hemichordata has always played a central role in evolutionary studies of Chordata due to their close phylogenetic affinity and shared morphological characteristics. Hemichordates had no meiofaunal representatives until the surprising discovery of a microscopic, paedomorphic enteropneust Meioglossus psammophilus (Harrimaniidae, Hemichordata) from the Caribbean in 2012. No additional species have been described since, questioning the broader distribution and significance of this genus. However, being less than a millimeter long and superficially resembling an early juvenile acorn worm, Meioglossus may easily be overlooked in both macrofauna and meiofauna surveys. We here present the discovery of 11 additional populations of Meioglossus from shallow subtropical and tropical coralline sands of the Caribbean Sea, Red Sea, Indian Ocean, and East China Sea. These geographically separated populations show identical morphology but differ genetically. Our phylogenetic reconstructions include four gene markers and support the monophyly of Meioglossus. Species delineation analyses revealed eight new cryptic species, which we herein describe using DNA taxonomy. This study reveals a broad circumtropical distribution, supporting the validity and ecological importance of this enigmatic meiobenthic genus. The high cryptic diversity and apparent morphological stasis of Meioglossus may exemplify a potentially common evolutionary 'dead-end' scenario, where groups with highly miniaturized and simplified body plan lose their ability to diversify morphologically.

Green armoured tardigrades (Echiniscidae: Viridiscus), including a new species from the Southern Nearctic, exemplify problems with tardigrade variability research

Ranges of tardigrade intraspecific and interspecific variability are not precisely defined, both in terms of morphology and genetics, rendering descriptions of new taxa a cumbersome task. This contribution enhances the morphological and molecular dataset available for the heterotardigrade genus Viridiscus by supplying new information on Southern Nearctic populations of V. perviridis, V. viridianus, and a new species from Tennessee. We demonstrate that, putting aside already well-documented cases of significant variability in chaetotaxy, the dorsal plate sculpturing and other useful diagnostic characters, such as morphology of clavae and pedal platelets, may also be more phenotypically plastic characters at the species level than previously assumed. As a result of our integrative analyses, V. viridianus is redescribed, V. celatus sp. nov. described, and V. clavispinosus designated as nomen inquirendum, and its junior synonymy with regard to V. viridianus suggested. Morphs of three Viridiscus species (V. perviridis, V. viridianus, and V. viridissimus) are depicted, and the implications for general echiniscid taxonomy are drawn. We emphasise that taxonomic conclusions reached solely through morphological or molecular analyses lead to a distorted view on tardigrade α-diversity.

Seven new “cryptic” species of Discodorididae (Mollusca, Gastropoda, Nudibranchia) from New Caledonia

The study of a well-preserved collection of discodorid nudibranchs collected in Koumac, New Caledonia, revealed the presence of seven species new to science belonging to the genera Atagema, Jorunna, Rostanga, and Sclerodoris, although some of the generic assignments are tentative as the phylogeny of Discodorididae remains unresolved. Moreover, a poorly known species of Atagema originally described from New Caledonia is re-described and the presence of Sclerodoris tuberculata in New Caledonia is confirmed with molecular data. All the species described herein are highly cryptic on their food source and in the context of the present study the term “cryptic” is used to denote such species. This paper highlights the importance of comprehensive collecting efforts to identify and document well-camouflaged taxa.

Comparative molecular and morphological species delineation of Halammohydra Remane, 1927 (Hydrozoa)—with the description of four new species

Whereas most cnidarians are macrofaunal, a few microscopic lineages have evolved, and some of them inhabit marine sediments. The meiofaunal genus with the most species is Halammohydra, comprising nine nominal species. Species are described with high intraspecific variability in, e.g., the number of tentacles and statocysts and the shape and length of tentacles and body, complicating morphological identification to species level. Additionally, there is not much molecular data available. This study aims to revise already described species with morphological and molecular methods, as well as, to delineate potential new species answering questions about their geographical distribution. For this, specimens were sampled at 16 locations in the Northwest Atlantic and two localities in the East Atlantic, documented with light microscopy, and fixed individually for sequencing (16S, 18S, and CO1). Herewith, morphological characters were linked to a specific sequence, enabling the testing of character variation within one molecular phylogenetic group. Phylogenetic analyses were conducted (Bayesian Interference and Maximum Likelihood) in combination with species delimitation tests (ABGD, GMYC, and bPTP). Four already described species were identified in the data sets, and all of these were found at multiple localities. Four new species are described. Overall, the combined molecular and morphological data acquisition revealed multiple new species and a high degree of sympatry in Halammohydra. This, together with the confirmed excessive intraspecific variation in morphological traits, underlines the necessity of molecular sequencing for the taxonomy and species identification of Halammohydra.

Reappraisal of the hyperdiverse

Morphologically similar species are often overlooked but molecular techniques have been effective in signalling potential hidden diversity, boosting the documentation of unique evolutionary lineages and ecological diversity. Platynereis dumerilii and Platynereis massiliensis are part of a recognised species complex, where differences in the reproductive biology have mainly been highlighted to date. Analyses of DNA sequence data (COI, 16S rDNA and D2 region of the 28S rDNA) of populations of the apparent morphotype of P. dumerilii obtained from a broader sampling area along European marine waters, including the Azores and Webbnesia islands (Madeira and Canaries), provided compelling evidence for the existence of at least 10 divergent evolutionary lineages. Complementing the genetic data, morphological observations of the better represented lineages revealed two major groups with distinctive paragnath patterns. Two new Platynereis species were erected: P. nunezi sp. nov., widespread in the Azores and Webbnesia islands, and P. jourdei sp. nov., restricted to the western Mediterranean. The new combination P. agilis is also proposed for Nereis agilis, previously unaccepted for one of the lineages present both in the Northeast Atlantic and western Mediterranean. Platynereis dumerilii is redescribed based on topotypic material. However, uncertainty in the identity of P. massiliensis due to the original brief description and the absence of type and topotypic material prevents the unequivocal assignment to the lineage assumed in this and previous studies. The remaining five lineages are represented by only a few small specimens with morphological features poorly preserved and were therefore not described in this study. ZooBank: urn:lsid:zoobank.org:pub:50079615-85E5-447E-BDD7-21E81C2A6F4D

Ecological and morphological differentiation among COI haplotype groups in the plant parasitic nematode species Mesocriconema xenoplax

DNA barcoding with the mitochondrial COI gene reveals distinct haplotype subgroups within the monophyletic and parthenogenetic nematode species, Mesocriconema xenoplax. Biological attributes of these haplotype groups (HG) have not been explored. An analysis of M. xenoplax from 40 North American sites representing both native plant communities and agroecosystems was conducted to identify possible subgroup associations with ecological, physiological, or geographic factors. A dataset of 132 M. xenoplax specimens was used to generate sequences of a 712 bp region of the cytochrome oxidase subunit I gene. Maximum-likelihood and Bayesian phylogenies recognized seven COI HG (≥99/0.99 posterior probability/bootstrap value). Species delimitation metrics largely supported the genetic integrity of the HG. Discriminant function analysis of HG morphological traits identified stylet length, total body length, and stylet knob width as the strongest distinguishing features among the seven groups, with stylet length as the strongest single distinguishing morphological feature. Multivariate analysis identified land cover, ecoregion, and maximum temperature as predictors of 53.6% of the total variation (P = 0.001). Within land cover, HG categorized under “herbaceous,” “woody wetlands,” and “deciduous forest” were distinct in DAPC and RDA analyses and were significantly different (analysis of molecular variance P = 0.001). These results provide empirical evidence for molecular, morphological, and ecological differentiation associated with HG within the monophyletic clade that represents the species Mesocriconema xenoplax.

Cryptic Diversity in Cladosporium cladosporioides Resulting from Sequence-Based Species Delimitation Analyses

Cladosporium cladosporioides is an extremely widespread fungus involved in associations ranging from mutualistic to pathogenic and is the most frequently represented Cladosporium species in sequence databases, such as Genbank. The taxonomy of Cladosporium species, currently based on the integration of molecular data with morphological and cultural characters, is in frequent need of revision. Hence, the recently developed species delimitation methods can be helpful to explore cryptic diversity in this genus. Considering a previous study that reported several hypothetical species within C. cladosporioides, we tested four methods of species delimitation using the combined DNA barcodes internal transcribed spacers, translation elongation factor 1-α and actin 1. The analyses involved 105 isolates, revealing that currently available sequences of C. cladosporioides in GenBank actually represent more than one species. Moreover, we found that eight isolates from this set should be ascribed to Cladosporium anthropophilum. Our results revealed a certain degree of discordance among species delimitation methods, which can be efficiently treated using conservative approaches in order to minimize the risk of considering false positives.

DNA barcoding of the mesic adapted striped mouse, Rhabdomys dilectus in the Eastern Cape and KwaZulu-Natal provinces of South Africa

Abstract

South African small mammals are under-represented in DNA barcoding efforts, particularly from the eastern forested regions of the country. This study reports DNA barcoding of Rhabdomys taxa from previously unsampled parts of the Eastern Cape and KwaZulu-Natal provinces of South Africa. The complete mitochondrial DNA cytochrome oxidase I (COI) gene was sequenced for 101 Rhabdomys sp. individuals from 16 localities from all three main forest groups (coastal, mistbelt, and scarp forests). Molecular data were supplemented with external morphological measurements, including those deemed potential taxonomically diagnostic characters. Findings indicate the area to be inhabited solely by Rhabdomys dilectus chakae. Haplotypes distributed across the three forest groups were separated by shallow sequence divergences ranging from 0.001–0.015 (Kimura 2-parameter model) and displayed very little population genetic structure (FST= 0.071787). Morphological data revealed some regional metric differences in external morphology, but all the head-and-body to tail (HB: tail) ratios match that of R. d. chakae, and consequently, molecular and morphological data are congruent. These data confirm a range extension of R. d. chakae, supporting the utility of COI barcodes in the identification of small mammalian species.

Looking at the Nudibranch Family Myrrhinidae (Gastropoda, Heterobranchia) from a Mitochondrial '2D Folding Structure' Point of View

Integrative taxonomy is an evolving field of multidisciplinary studies often utilised to elucidate phylogenetic reconstructions that were poorly understood in the past. The systematics of many taxa have been resolved by combining data from different research approaches, i.e., molecular, ecological, behavioural, morphological and chemical. Regarding molecular analysis, there is currently a search for new genetic markers that could be diagnostic at different taxonomic levels and that can be added to the canonical ones. In marine Heterobranchia, the most widely used mitochondrial markers, COI and 16S, are usually analysed by comparing the primary sequence. The 16S rRNA molecule can be folded into a 2D secondary structure that has been poorly exploited in the past study of heterobranchs, despite 2D molecular analyses being sources of possible diagnostic characters. Comparison of the results from the phylogenetic analyses of a concatenated (the nuclear H3 and the mitochondrial COI and 16S markers) dataset (including 30 species belonging to eight accepted genera) and from the 2D folding structure analyses of the 16S rRNA from the type species of the genera investigated demonstrated the diagnostic power of this RNA molecule to reveal the systematics of four genera belonging to the family Myrrhinidae (Gastropoda, Heterobranchia). The "molecular morphological" approach to the 16S rRNA revealed to be a powerful tool to delimit at both species and genus taxonomic levels and to be a useful way of recovering information that is usually lost in phylogenetic analyses. While the validity of the genera Godiva, Hermissenda and Phyllodesmium are confirmed, a new genus is necessary and introduced for Dondice banyulensis, Nemesis gen. nov. and the monospecific genus Nanuca is here synonymised with Dondice, with Nanuca sebastiani transferred into Dondice as Dondice sebastiani comb. nov.

Unexpectedly high levels of lineage diversity in Sundaland puddle frogs (Dicroglossidae: Occidozyga Kuhl and van Hasselt, 1822)

One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world's so-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ~ 2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high level of genetic diversity within Occidozyga, based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages, defined by the > 5% uncorrected p-distance criterion for the 16S rRNA gene, suggesting that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads to the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar, indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace's Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether observed diversity of Puddle frog lineages warrants taxonomic recognition.

Remarkable Cryptic Diversity of Paratylenchus spp. (Nematoda: Tylenchulidae) in Spain

In previous studies, fifteen species of Paratylenchus, commonly known as pin nematodes, have been reported in Spain. These plant-parasitic nematodes are ectoparasites with a wide host range and global distribution. In this research, 27 populations from twelve Paratylenchus species from 18 municipalities in Spain were studied using morphological, morphometrical and molecular data. This integrative taxonomic approach allowed the identification of twelve species, four of them were considered new undescribed species and eight were already known described. The new species described here are P. caravaquenus sp. nov., P. indalus sp. nov., P. pedrami sp. nov. and P. zurgenerus sp. nov. As for the already known described species, five were considered as first reports for the country, specifically P.enigmaticus, P. hamatus, P. holdemani, P. israelensis, and P. veruculatus, while P. baldaccii, P. goodeyi and P. tenuicaudatus had already been recorded in Spain. This study provides detail morphological and molecular data, including the D2-D3 expansion segments of 28S rRNA, ITS rRNA, and partial mitochondrial COI regions for the identification of different Paratylenchus species found in Spain. These results confirm the extraordinary cryptic diversity in Spain and with examples of morphostatic speciation within the genus Paratylenchus.

Colonization of macroalgal deposits by estuarine nematodes through air and potential for rafting inside algal structures

Dispersal is an important life-history trait. In marine meiofauna, and particularly in nematodes, dispersal is generally considered to be mainly passive, i.e. through transport with water currents and bedload transport. Because nematodes have no larval dispersal stage and have a poor swimming ability, their per capita dispersal capacity is expected to be limited. Nevertheless, many marine nematode genera and even species have near-cosmopolitan distributions, and at much smaller spatial scales, can rapidly colonise new habitat patches. Here we demonstrate that certain marine nematodes, like the morphospecies Litoditis marina, can live inside macroalgal structures such as receptacula and-to a lesser extent-floating bladders, which may allow them to raft over large distances with drifting macroalgae. We also demonstrate for the first time that these nematodes can colonize new habitat patches, such as newly deposited macroalgal wrack in the intertidal, not only through seawater but also through air. Our experimental set-up demonstrates that this aerial transport is probably the result of hitchhiking on vectors such as insects, which visit, and move between, the patches of deposited algae. Transport by wind, which has been observed for terrestrial nematodes and freshwater zooplankton, could not be demonstrated. These results can be important for our understanding of both large-scale geographic distribution patterns and of the small-scale colonization dynamics of habitat patches by marine nematodes.

Redescription of Emplectonema viride - a ubiquitous intertidal hoplonemertean found along the West Coast of North America

Emplectonema viride Stimpson, 1857, a barnacle predator, is one of the most common and conspicuous intertidal nemerteans found along the West Coast of North America from Alaska to California, but it is currently referred to by the wrong name. Briefly described without designation of type material or illustrations, the species was synonymized with the Atlantic look-alike, Emplectonema gracile (Johnston, 1837) by Coe. Here we present morphological and molecular evidence that E. viride is distinct from E. gracile. The two species exhibit differences in color of live specimens and egg size and are clearly differentiated with species delimitation analyses based on sequences of the partial regions of the 16S rRNA and cytochrome c oxidase subunit I genes. In order to improve nomenclatural stability, we re-describe E. viride based on specimens from the southern coast of Oregon and discuss which species should be the type species of the genus. Emplectonema viride was one of the two species originally included in the genus Emplectonema Stimpson, 1857, but subsequent synonymization of E. viride with E. gracile resulted in acceptance of the Atlantic species, E. gracile, as the type species of the genus. We resurrect E. viride Stimpson, 1857 and following Corrêa's designation, this should be the type species of the genus Emplectonema.

Integrative Taxonomy and Molecular Phylogeny of the Plant-Parasitic Nematode Genus Paratylenchus (Nematoda: Paratylenchinae): Linking Species with Molecular Barcodes

Pin nematodes of the genus Paratylenchus are obligate ectoparasites of a wide variety of plants that are distributed worldwide. In this study, individual morphologically vouchered nematode specimens of fourteen Paratylenchus species, including P. aculentus, P. elachistus, P. goodeyi, P. holdemani, P. idalimus, P. microdorus, P. nanus, P. neoamblycephalus, P. straeleni and P. veruculatus, are unequivocally linked to the D2-D3 of 28S, ITS, 18S rRNA and COI gene sequences. Combined with scanning electron microscopy and a molecular analysis of an additional nine known and thirteen unknown species originating from diverse geographic regions, a total of 92 D2-D3 of 28S, 41 ITS, 57 18S rRNA and 111 COI new gene sequences are presented. Paratylenchus elachistus, P. holdemani and P. neoamblycephalus are recorded for the first time in Belgium and P. idalimus for the first time in Europe. Paratylenchus is an excellent example of an incredibly diverse yet morphologically minimalistic plant-parasitic genus, and this study provides an integrated analysis of all available data, including coalescence-based molecular species delimitation, resulting in an updated Paratylenchus phylogeny and the corrective reassignment of 18 D2-D3 of 28S, 3 ITS, 3 18S rRNA and 25 COI gene sequences that were previously unidentified or incorrectly classified.

Interstitial Annelida

Members of the following marine annelid families are found almost exclusively in the interstitial environment and are highly adapted to move between sand grains, relying mostly on ciliary locomotion: Apharyngtidae n. fam., Dinophilidae, Diurodrilidae, Nerillidae, Lobatocerebridae, Parergodrilidae, Polygordiidae, Protodrilidae, Protodriloididae, Psammodrilidae and Saccocirridae. This article provides a review of the evolution, systematics, and diversity of these families, with the exception of Parergodrilidae, which was detailed in the review of Orbiniida by Meca, Zhadan, and Struck within this Special Issue. While several of the discussed families have previously only been known by a few described species, recent surveys inclusive of molecular approaches have increased the number of species, showing that all of the aforementioned families exhibit a high degree of cryptic diversity shadowed by a limited number of recognizable morphological traits. This is a challenge for studies of the evolution, taxonomy, and diversity of interstitial families as well as for their identification and incorporation into ecological surveys. By compiling a comprehensive and updated review on these interstitial families, we hope to promote new studies on their intriguing evolutionary histories, adapted life forms and high and hidden diversity.

A Bioinformatics Tutorial for Comparative Development Genomics in Diverse Meiofauna

Miniaturization, which is a common feature in animals, is particularly manifest in meiofauna-animals sharing peculiar phenotypic features that evolved as adaptations to the highly specialized aquatic interstitial habitat. While revealing much about the extreme phyletic diversity of meiofauna, the genome structure of meiofaunal species could also characterize the phenotype of ancestral states as well as explain the origin and evolution of miniaturization. Here, we present a practical bioinformatics tutorial for genome assembly, genome comparison, and characterization of Hox clusters in meiofaunal species.

Bioactive Compounds from Marine Heterobranchs

The natural products of heterobranch molluscs display a huge variability both in structure and in their bioactivity. Despite the considerable lack of information, it can be observed from the recent literature that this group of animals possesses an astonishing arsenal of molecules from different origins that provide the molluscs with potent chemicals that are ecologically and pharmacologically relevant. In this review, we analyze the bioactivity of more than 450 compounds from ca. 400 species of heterobranch molluscs that are useful for the snails to protect themselves in different ways and/or that may be useful to us because of their pharmacological activities. Their ecological activities include predator avoidance, toxicity, antimicrobials, antifouling, trail-following and alarm pheromones, sunscreens and UV protection, tissue regeneration, and others. The most studied ecological activity is predation avoidance, followed by toxicity. Their pharmacological activities consist of cytotoxicity and antitumoral activity; antibiotic, antiparasitic, antiviral, and anti-inflammatory activity; and activity against neurodegenerative diseases and others. The most studied pharmacological activities are cytotoxicity and anticancer activities, followed by antibiotic activity. Overall, it can be observed that heterobranch molluscs are extremely interesting in regard to the study of marine natural products in terms of both chemical ecology and biotechnology studies, providing many leads for further detailed research in these fields in the near future.

Uncovering the shell game with barcodes: diversity of meiofaunal Caecidae snails (Truncatelloidea, Caenogastropoda) from Central America

Caecidae is a species-rich family of microsnails with a worldwide distribution. Typical for many groups of gastropods, caecid taxonomy is largely based on overt shell characters. However, identification of species using shell characteristics is problematic due to their rather uniform, tubular shells, the presence of different growth stages, and a high degree of intraspecific variability. In the present study, a first integrative approach to caecid taxonomy is provided using light-microscopic investigation with microsculptural analyses and multi-marker barcoding, in conjunction with molecular species delineation analyses (ABGD, haplotype networks, GMYC, and bPTP). In total 132 specimens of Caecum and Meioceras collected during several sampling trips to Central America were analyzed and delineated into a minimum of 19 species to discuss putative synonyms, and supplement the original descriptions. Molecular phylogenetic analyses suggest Meiocerasnitidum and M.cubitatum should be reclassified as Caecum, and the genus Meioceras might present a junior synonym of Caecum. Meiofaunal caecids morphologically resembling C.glabrum from the Northeast Atlantic are a complex of cryptic species with independent evolutionary origins, likely associated with multiple habitat shifts to the mesopsammic environment. Caecuminvisibile Egger & Jörger, sp. nov. is formally described based on molecular diagnostic characters. This first integrative approach towards the taxonomy of Caecidae increases the known diversity, reveals the need for a reclassification of the genus Caecum and serves as a starting point for a barcoding library of the family, thereby enabling further reliable identifications of these taxonomically challenging microsnails in future studies.

Effects of widespread human disturbances in the marine environment suggest a new agenda for meiofauna research is needed

The response of an ecological community to a disturbance event, and its capacity to recover, are of major interest to ecologists, especially at a time of increasing frequencies and intensities of environmental change brought about by humans. Meiofauna, a group of small-sized organisms, are an abundant and ubiquitous component of seafloor communities that respond rapidly to environmental change. We summarise the available research on the response of metazoan meiofauna to the most widespread anthropogenic disturbances in the marine environment, including bottom fishing, the introduction of invasive species and anthropogenic climate change. We show that disturbance effects on habitats interact critically with effects on resident meiofauna species. Their responses are consistent with competitive replacement, where disparate disturbance effects on competing species drive shifts in dominance and intra- and interspecific interactions. The widespread replacement of habitat-specific ecological specialists by broadly-adapted ecological generalists and opportunists results in biotic and functional homogenisation of once disparate biotas. Anthropogenic disturbances may facilitate novel interactions among meiofauna species, and between meiofauna and other benthic organisms, but the number and breadth of these interactions is likely to be limited. Knowledge about the dependence of meiofauna species on their environment and on other benthic species has been growing. Future studies will be most meaningful if this knowledge is expanded alongside understanding the potential of locally adapted species to respond to shifts in environmental conditions.

Make every species count: fastachar software for rapid determination of molecular diagnostic characters to describe species

Only a fraction of species found so far has been described, particularly cryptic species uncovered by molecular data. The latter might require the use of molecular data for its diagnosis, but it is important to make use of the diagnostic content of the molecular data itself. The molecular character-based model provides discrete molecular diagnostic characters within DNA sequences that can be used in species descriptions fulfilling the requirement of most codes of nomenclature for a character-based description of species. Here, we introduce fastachar, a software developed to extract molecular diagnostic characters from one or several taxonomically informative DNA markers of a selected taxon compared with those of other taxa in a single step. The input data consist of a single file with aligned sequences in the fasta format, which can be created using alignment software such as mega or geneious. fastachar is an easy-to-use software with a graphical interface. Thus, the software does not require the user to have any knowledge of the underlying programming environment (Python). We hope this software, based on the method proposed by Jörger and Schrödl (Frontiers in Zoology, 10, 59, 2013) to describe cryptic species, will encourage researchers to take the final step in taxonomy: the formal description of species. We propose the use of this method and fastachar also for the inclusion of molecular data in the description of any species. fastachar is released as open-source software under GNU General Public License V3 and is freely available for all major operating systems from https://github.com/smerckel/FastaChar.

Nematode biodiversity assessments need vouchered databases: A BOLD reference library for plant-parasitic nematodes in the superfamily Criconematoidea

Nematodes are frequently cited as underrepresented in faunistic surveys using DNA barcoding with COI. This underrepresentation is generally attributed to a limited presence of nematodes in DNA databases which, in turn, is often ascribed to structural variability and high evolutionary rates in nematode mitochondrial genomes. Empirical evidence, however, indicates that many taxa are readily amplified with primer sets specifically targeted to different nematode families. Here we report the development of a COI reference library of 1726 specimens in the terrestrial plant parasitic nematode superfamily Criconematoidea. Specimens collected during an ecoregion survey of North America were individually photographed, measured, and PCR amplified to produce a 721 bp region of COI for taxonomic analysis. A neighbor-joining tree structured the dataset into 179 haplotype groups that generally conformed to morphospecies in traditional analysis or Barcode Index Numbers (BINs) in the BOLD system, although absent formal BIN membership due to insufficient overlap with the Folmer region of COI. Approximately one-third of the haplotype groups could be associated with previously described species. The geographic distribution of criconematid nematode species suggests a structure influenced by the major habitat types in the United States and Canada. All sequences collected in the ecoregion survey are deposited in BOLD.

Systematic revision of the Indo-West Pacific colourful bubble-snails of the genus Lamprohaminoea Habe, 1952 (Cephalaspidea : Haminoeidae)

The genus Lamprohaminoea includes species of colourful haminoeid snails associated with coral reefs and rocky shores in the tropical Indo-West Pacific. In this work, we revise the diversity and systematics of Lamprohaminoea species based on a phylogenetic hypothesis and on a detailed morphological analysis of specimens. Shells, external features of the animals and anatomical characters from the jaws, radula, gizzard plates, and male reproductive system were studied by optical and scanning electron microscopy. Additionally, a molecular species delimitation analysis based on the Automatic Barcode Gap Discovery method using DNA sequences of the cytochrome c oxidase subunit I was implemented. Five species were recognised, three of them new to science, namely L. cymbalum, L. ovalis, L. vamiziensis sp. nov., L. evelinae sp. nov., and L. mikkelsenae sp. nov. Morphologically, these species can be separated by subtle differences of their external colouration and by features of the male reproductive system. Lamprohaminoea vamiziensis sp. nov. is known only from the western Indian Ocean and L. evelinae sp. nov., from the west Pacific, whereas the other three occur across the Indo-West Pacific realm.

Metabarcoding data allow for reliable biomass estimates in the most abundant animals on earth

Microscopic organisms are the dominant and most diverse organisms on Earth. Nematodes, as part of this microscopic diversity, are by far the most abundant animals and their diversity is equally high. Molecular metabarcoding is often applied to study the diversity of microorganisms, but has yet to become the standard to determine nematode communities. As such, the information metabarcoding provides, such as in terms of species coverage, taxonomic resolution and especially if sequence reads can be linked to the abundance or biomass of nematodes in a sample, has yet to be determined. Here, we applied metabarcoding using three primer sets located within ribosomal rRNA gene regions to target assembled mock-communities consisting of 18 different nematode species that we established in 9 different compositions. We determined abundances and biomass of all species added to examine if relative sequence abundance or biomass can be linked to relative sequence reads. We found that nematode communities are not equally represented by the three different primer sets and we found that relative read abundances almost perfectly correlated positively with relative species biomass for two of the primer sets. This strong biomass-read number correlation suggests that metabarcoding reads can reveal biomass information even amongst more complex nematode communities as present in the environment and possibly can be transferred to better study other groups of organisms. This biomass-read link is of particular importance for more reliably assessing nutrient flow through food-webs, as well as adjusting biogeochemical models through user-friendly and easily obtainable metabarcoding data.

Broad North Atlantic distribution of a meiobenthic annelid - against all odds

DNA barcoding and population genetic studies have revealed an unforeseen hidden diversity of cryptic species among microscopic marine benthos, otherwise exhibiting highly similar and simple morphologies. This has led to a paradigm shift, rejecting cosmopolitism of marine meiofauna until genetically proven and challenging the "Everything is Everywhere, but the environment selects" hypothesis that claims ubiquitous distribution of microscopic organisms. With phylogenetic and species delimitation analyses of worldwide genetic samples of the meiofaunal family Dinophilidae (Annelida) we here resolve three genera within the family and showcase an exceptionally broad, boreal, North Atlantic distribution of a single microscopic marine species with no obvious means of dispersal besides vicariance. With its endobenthic lifestyle, small size, limited migratory powers and lack of pelagic larvae, the broad distribution of Dinophilus vorticoides seems to constitute a "meiofaunal paradox". This species feasts in the biofilm among sand grains, but also on macroalgae and ice within which it can likely survive long-distance rafting dispersal due to its varying lifecycle stages; eggs encapsulated in cocoons and dormant encystment stages. Though often neglected and possibly underestimated among marine microscopic species, dormancy may be a highly significant factor for explaining wide distribution patterns and a key to solving this meiofaunal paradox.

Diet-driven ecological radiation and allopatric speciation result in high species diversity in a temperate-cold water marine genus Dendronotus (Gastropoda: Nudibranchia)

While the majority nudibranch clades are more species rich in the tropics, the genus Dendronotus is mainly represented in Arctic and boreal regions. This distribution pattern remains poorly understood. An integrative approach and novel data provided valuable insights into processes driving Dendronotus radiation and speciation. We propose an evolutionary scenario based on molecular phylogenetics and morphological, ecological, ontogenetic data, combined with data on complex geology and paleoclimatology of this region. Estimated phylogenetic relationships based on four molecular markers (COI, 16S, H3 and 28S) shows strong correlation with radular morphology, diet and biogeographical pattern. Ancestral area reconstruction (AAR) provides evidence for a tropical Pacific origin of the genus. Based on AAR and divergence time estimates we conclude that the evolution of Dendronotus has been shaped by different processes: initial migration out of the tropics, diet-driven adaptive radiation in the North Pacific influenced by Miocene climate change, and subsequent allopatric speciation resulting from successive closings of the Bering strait and cooling of the Arctic Ocean during the Pliocene-Pleistocene. At the same time, contemporary amphiboreal species appear to have dispersed into the Atlantic fairly recently.

The galaxy of the non-Linnaean nomenclature

Contrary to the traditional claim that needs for unambiguous communication about animal and plant species are best served by a single set of names (Linnaean nomenclature) ruled by international Codes, I suggest that a more diversified system is required, especially to cope with problems emerging from aggregation of biodiversity data in large databases. Departures from Linnaean nomenclature are sometimes intentional, but there are also other, less obvious but widespread forms of not Code-compliant grey nomenclature. A first problem is due to the circumstance that the Codes are intended to rule over the way names are applied to species and other taxonomic units, whereas users of taxonomy need names to be applied to specimens. For different reasons, it is often impossible to refer a specimen with certainty to a named species, and in those cases an open nomenclature is employed. Second, molecular taxonomy leads to the discovery of clusters of gene sequence diversity not necessarily equivalent to the species recognized and named by taxonomists. Those clusters are mostly indicated with informal names or formulas that challenge comparison between different publications or databases. In several instances, it is not even clear if a formula refers to an individual voucher specimen, or is a provisional species name. The use of non-Linnaean names and formulas must be revised and strengthened by fixing standard formats for the different kinds of objects or hypotheses and providing permanent association of 'grey names' with standardized source information such as author and year. In the context of a broad-scope revisitation of aims and scope of scientific nomenclature, it may be worth rethinking if natural objects like plant galls and lichens, although other than the 'single-entity' objects traditionally covered by biological classifications, may nevertheless deserve taxonomic names.

Untangling a mess of worms: Species delimitations reveal morphological crypsis and variability in Southeast Asian semi-aquatic earthworms (Almidae, Glyphidrilus)

Semi-aquatic freshwater earthworms in the genus Glyphidrilus from Southeast Asia are characterized by both an extreme morphological crypsis among divergent phylogenetic lineages and a high morphological variability within the same phylogenetic lineages. The present study provides a new taxonomic framework for this problematic genus in SE Asia by integrating DNA sequence and morphological data. When single-locus and multilocus multispecies coalescent-based (MSC) species delimitation methods were applied to DNA sequence data, they usually yielded highly incongruent results compared to morphology-based species identifications. This suggested the presence of several cryptic species and high levels of intraspecific morphological variation. Applying reciprocal monophyly to the cytochrome c oxidase subunit 1 (COI) gene tree allowed us to propose the existence of 33 monophyletic species. Yet, often substantially more molecular operational taxonomic units (MOTUs) were obtained when species delimitation was based on COI and 16S rRNA sequences. In contrast, the ITS1 and ITS2 sequences suggested fewer MOTUs and did not recover most of the monophyletic species from the Mekong basin. However, several of these latter taxa were better supported when MSC species delimitation methods were applied to the combined mtDNA and ITS datasets. The ITS2 secondary structure retrieved one unnamed Mekong basin species that was not uncovered by the other methods when applied to ITS2 sequences. In conclusion, based on an integrative taxonomic workflow, 26 Glyphidrilus candidate species were retained and two remained to be confirmed. As such, this study provides evidence to suggest nine species new to science and to synonymize 12 nominal morphospecies. It also illustrates that the uncritical use of COI as a universal DNA barcode may overestimate species diversity because COI may be unable to distinguish between divergent conspecific lineages and different candidate species.

Echinoderes pterus sp. n. showing a geographically and bathymetrically wide distribution pattern on seamounts and on the deep-sea floor in the Arctic Ocean, Atlantic Ocean, and the Mediterranean Sea (Kinorhyncha, Cyclorhagida)

Kinorhynchs rarely show a wide distribution pattern, due to their putatively low dispersal capabilities and/or limited sampling efforts. In this study, a new kinorhynch species is described, Echinoderespterussp. n., which shows a geographically and bathymetrically wide distribution, occurring on the Karasik Seamount and off the Svalbard Islands (Arctic Ocean), on the Sedlo Seamount (northeast Atlantic Ocean), and on the deep-sea floor off Crete and on the Anaximenes Seamount (Mediterranean Sea), at a depth range of 675–4,403 m. The new species is characterized by a combination of middorsal acicular spines on segments 4–8, laterodorsal tubes on segment 10, lateroventral tubes on segment 5, lateroventral acicular spines on segments 6–9, tufts of long hairs rising from slits in a laterodorsal position on segment 9, truncated tergal extensions on segment 11, and the absence of any type-2 gland cell outlet. The specimens belonging to the populations from the Arctic Ocean, the Sedlo Seamount, and the Mediterranean Sea show morphological variation in the thickness and length of the spines as well as in the presence/absence of ventromedial sensory spots on segment 7. The different populations are regarded as belonging to a single species because of their overlapping variable characters.

Hidden diversity: Phylogeography of genus Ototyphlonemertes Diesing, 1863 (Ototyphlonemertidae: Hoplonemertea) reveals cryptic species and high diversity in Chilean populations

Ototyphlonemertes is a cosmopolitan genus of meiofaunal nemerteans. Their morphological characters are insufficient to reliably identify and delimit species. Consequently, some of the species are considered cosmopolitan despite anticipated low dispersion capability of the adults and a short planktonic larval phase. Indeed, recent studies show that some species actually comprise cryptic species, and populations are connected by stochastic events of long-distance dispersion. Based solely on morphological traits, a Lactea and a Pallida morph of Ototyphlonemertes are recognized here from collections at eight and five locations respectively along the Chilean coast. To assess the phylogeographic patterns of their populations, two mitochondrial markers (COI and COX3) of 162 specimens of Lactea and 25 of Pallida were sequenced. Final sequences are 605bp and 362bp for COI and COX3, respectively. Results from phylogenetic and haplotype network analyses suggest that the Lactea morph comprises up to three independent evolutionary units (one with only COX3 sequences). A COI gene tree including other previously published Ototyphlonemertes sequences groups the Chilean Lactea with other Lactea, while the Chilean Pallida is grouped with other Pallida. Different structuring and gene flow patterns found for the four groups support the hypothesis that these are four independent evolutionary entities with different ecological, dispersal and demographical characteristics.

Systematics of the genus Halgerda Bergh, 1880 (Heterobranchia : Nudibranchia) of Mozambique with descriptions of six new species

The species of the genus Halgerda Bergh, 1880, are restricted to the Indo-Pacific; some being common inhabitants of reefs off the coast of Mozambique. These species have been relatively well studied morphologically, but few molecular data are available. During a seven-year period surveying the reefs of Mozambique, 11 Halgerda spp. were collected, six of which are described here. We provide details on their morphology, anatomy, novel genetic markers and additional information about their colour variation. The new species described herein are Halgerda leopardalis, sp. nov., H. mozambiquensis, sp. nov., H. jennyae, sp. nov., H. meringuecitrea, sp. nov., H. nuarroensis, sp. nov. and H. indotessellata, sp. nov., the last of which was found to be a pseudocryptic species of H. tessellata. Moreover, we identified two species complexes, one composed mainly of specimens from the Western Indian Ocean and another with specimens mostly from the Pacific Ocean and Western Australia.

Species diversity in the marine microturbellarian Astrotorhynchus bifidus sensu lato (Platyhelminthes: Rhabdocoela) from the Northeast Pacific Ocean

Increasing evidence suggests that many widespread species of meiofauna are in fact regional complexes of (pseudo-)cryptic species. This knowledge has challenged the 'Everything is Everywhere' hypothesis and also partly explains the meiofauna paradox of widespread nominal species with limited dispersal abilities. Here, we investigated species diversity within the marine microturbellarian Astrotorhynchus bifidus sensu lato in the Northeast Pacific Ocean. We used a multiple-evidence approach combining multi-gene (18S, 28S, COI) phylogenetic analyses, several single-gene and multi-gene species delimitation methods, haplotype networks and conventional taxonomy to designate Primary Species Hypotheses (PSHs). This included the development of rhabdocoel-specific COI barcode primers, which also have the potential to aid in species identification and delimitation in other rhabdocoels. Secondary Species Hypotheses (SSHs) corresponding to morphospecies and pseudo-cryptic species were then proposed based on the minimum consensus of different PSHs. Our results showed that (a) there are at least five species in the A. bifidus complex in the Northeast Pacific Ocean, four of which can be diagnosed based on stylet morphology, (b) the A. bifidus complex is a mixture of sympatric and allopatric species with regional and/or subglobal distributions, (c) sympatry occurs on local (sample sites), regional (Northeastern Pacific) and subglobal (Northern Atlantic, Arctic, Northeastern Pacific) scales. Mechanisms for this co-occurrence are still poorly understood, but we hypothesize they could include habitat differentiation (spatial and/or seasonal) and life history characteristics such as sexual selection and dispersal abilities. Our results also suggest the need for improved sampling and exploration of molecular markers to accurately map gene flow and broaden our understanding of species diversity and distribution of microturbellarians in particular and meiofauna in general.

A multilocus view on Mediterranean aeolid nudibranchs (Mollusca): Systematics and cryptic diversity of Flabellinidae and Piseinotecidae

Recent molecular studies revealed high level of endemism and numerous cryptic species within opisthobranchs, with Mediterranean taxa clearly understudied. Here we used genetic data from both mitochondrial and nuclear gene fragments as well as morphological data from taxonomically relevant characters to investigate the phylogenetic relationships and systematics of Mediterranean taxa of the Flabellinidae and Piseinotecidae families. Phylogenetic analyses based on Bayesian and Maximum-Likelihood methods indicate that Flabellinidae and Pisenotecidae taxa and species within the genera Flabellina, Calmella and Piseinotecus do not form monophyletic clades. These results are supported by our morphological analyses which allowed the re-evaluation of the triseriate radula condition in Pisenotecidae and Calmella taxa and their inclusion in the genus Flabellina as Flabellina gaditanacomb. nov. (synonym of F. confusa), Flabellina gabiniereicomb. nov. and Flabellina cavolinicomb. nov. Species delimitation and barcoding gap analyses allowed uncovering cryptic species within Flabellina gracilis (Alder and Hancock, 1844), F. trophina (Bergh, 1890), F. verrucosa (M. Sars, 1829) and F. ischitana Hirano and Thompson, 1990, the latter with an Atlantic form which is under description. This study corroborates the relevance of combining molecular and morphological data from multiple populations and species in the assessment of nudibranch diversity and classification.

Estimating the barcoding gap in a global dataset of cox1 sequences for Odonata: close, but no cigar

We evaluated the extent of intraspecific and interspecific genetic distances for two highly diverse infraorders of Odonata: Anisoptera and Zygoptera. All cytochrome c oxidase subunit I sequences (cox1), the region chosen for zoological DNA barcoding, present in GenBank for each infraorder were downloaded and curated. For Anisoptera, the final dataset consisted of 2,961 individual cox1 sequences for 536 species and the equivalent numbers for Zygoptera were 2,477 sequences for 497 species. More than 7 million individual genetic comparisons were made and the results indicated that there is a tendency towards a barcoding gap, but that the size of the gap may not be sufficient to robustly infer identities for some taxa. DNA barcoding may be of less use for some odonate taxa, perhaps pertaining to misidentifications in global databases. However, at local scales or with more confined taxonomical sampling, this tool may yet be beneficial in identifying these charismatic organisms.

Distinct genetic differentiation and species diversification within two marine nematodes with different habitat preference in Antarctic sediments

Background

Dispersal ability, population genetic structure and species divergence in marine nematodes are still poorly understood, especially in remote areas such as the Southern Ocean. We investigated genetic differentiation of species and populations of the free-living endobenthic nematode genera Sabatieria and Desmodora using nuclear 18S rDNA, internal transcribed spacer (ITS) rDNA, and mitochondrial cytochrome oxidase I (COI) gene sequences. Specimens were collected at continental shelf depths (200–500 m) near the Antarctic Peninsula, Scotia Arc and eastern side of the Weddell Sea. The two nematode genera co-occurred at all sampled locations, but with different vertical distribution in the sediment. A combination of phylogenetic (GMYC, Bayesian Inference, Maximum Likelihood) and population genetic (AMOVA) analyses were used for species delimitation and assessment of gene flow between sampling locations.

Results

Sequence analyses resulted in the delimitation of four divergent species lineages in Sabatieria, two of which could not be discriminated morphologically and most likely constitute cryptic species. Two species were recognised in Desmodora, one of which showed large intraspecific morphological variation. Both genera comprised species that were restricted to one side of the Weddell Sea and species that were widely spread across it. Population genetic structuring was highly significant and more pronounced in the deeper sediment-dwelling Sabatieria species, which are generally less prone to resuspension and passive dispersal in the water column than surface Desmodora species.

Conclusions

Our results indicate that gene flow is restricted at large geographic distance in the Southern Ocean, which casts doubt on the efficiency of the Weddell gyre and Antarctic Circumpolar Current in facilitating circum-Antarctic nematode species distributions. We also show that genetic structuring and cryptic speciation can be very different in nematode species isolated from the same geographic area, but with different habitat preferences (surface versus deeper sediment layers).

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0968-1) contains supplementary material, which is available to authorized users.

Species Delimitation and Description of Mesocriconema nebraskense n. sp. (Nematoda: Criconematidae), a Morphologically Cryptic, Parthenogenetic Species from North American Grasslands

Nematode surveys of North American grasslands conducted from 2010 to 2015 frequently recovered a species of criconematid nematode morphologically resembling Mesocriconema curvatum. These specimens were recovered from remnant native prairies in the central tallgrass ecoregion of North America, and not from surrounding agroecosystems. Historical records indicate that M. curvatum is a cosmopolitan species feeding on a wide range of agronomic and native plants. DNA barcoding indicates North American grasslands contain at least 10 phylogenetically distinct lineages of Mesocriconema that resemble, but are not, M. curvatum. Analysis of the two most common lineages reveals two distinctly different population structures. The variation in population structure suggests unique evolutionary histories associated with their diversification. These two major lineages share a sympatric distribution and their slight morphological differences contrast with a high level of genetic separation. Based on their genetic divergence, fixed diagnostic nucleotides, population structure, species delimitation metrics, and a sympatric distribution, we believe that one of these distinct lineages warrants formal nomenclatural recognition. Herein, we provide formal recognition for Mesocriconema nebraskense n. sp. and discuss its relationship to other Mesocriconema lineages discovered in native North American grasslands.

A new phoronid species, Phoronis embryolabi, with a novel type of development, and consideration of phoronid taxonomy and DNA barcoding

The Phoronida, which is one of the smallest phyla of invertebrates, includes only 13 valid species, although ~40 larval forms of phoronids were recently described. This report uses light microscopy and molecular methods to describe a new phoronid species, Phoronis embryolabi Temereva & Chichvarkhin, sp. nov. The morphology of P. embryolabi, which lives commensally in the burrows of Axiidea shrimp Nihonotrypaea japonica in Vostok Bay (the Sea of Japan), is extremely similar to that of Phoronis pallida Silen, 1952; the bodies of both species exhibit specific regionalisation. However, the organisation of the metanephridia differs between P. pallida and P. embryolabi. Moreover, P. embryolabi has a unique type of development, viviparity, in which mothers release fully developed larvae into the environment. In all other phoronid species, the spawning occurs as a release of fertilised eggs or early embryos. Viviparity of completely developed larvae has not been previously described for any phoronid. According to analysis of partial 28S rRNA, P. embryolabi is close to Phoronis pallida. On the other hand, analysis of partial cytochrome c oxidase subunit I indicated a unique position of P. embryolabi among phoronids. These results should be used for revision of phoronid taxonomy (i.e. the type of development should be considered as characteristic of subgenera within the genus Phoronis). This report also establishes the relationship between P. embryolabi and an Actinotrocha sp. that was described in a previous paper.