Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca)

DNA barcoding of passerine birds in Iran

Exploring genetic diversity is essential for precise species delimitation, especially within taxonomically complex groups like passerine birds. Traditional morphological methods often fail to resolve species boundaries; however, DNA barcoding, particularly through the mitochondrial cytochrome c oxidase subunit I (COI) gene, provides a powerful complementary method for accurate species identification. This study establishes a comprehensive DNA barcode library for Iranian passerine birds, analyzing 546 COI sequences from 94 species across 23 families and 53 genera. There is a pronounced barcode gap, with average intraspecific divergence at 0.41% and interspecific divergence at 18.6%. Notable intraspecific variation emerged in the Persian nuthatch (Sittatephronota) and the Lesser whitethroat (Currucacurruca), while the European goldfinch (Cardueliscarduelis) and the grey-crowned goldfinch (Cardueliscaniceps) showed limited genetic differentiation despite marked morphological distinctions. Phylogenetic analysis revealed significant east-west genetic splits in C.curruca and S.tephronota, reflecting Iran's geographic and zoogeographic boundaries. These findings demonstrate the effectiveness of DNA barcoding in elucidating biogeographic patterns, emphasizing Iran's key role as an ornithological crossroads for avian biodiversity. Moreover, our results suggest that much of the genetic variation in the COI gene arises from synonymous mutations, highlighting the role of purifying selection in shaping mtDNA diversity across species.

Final stage phyllosoma of Galearctus sp. (Decapoda: Scyllaridae) from the Coral Sea

Larval stages are known for only four out of eight Galearctus Holthuis, 2002 (Crustacea: Scyllaridae) species, a slipper lobster genus widely distributed throughout the Indo-Pacific region. DNA barcoding analyses of phyllosomae collected from the Coral Sea by the Australian Institute of Marine Science suggest the presence of two new genetic clades in the area, for which larvae cannot be discriminated morphologically. The last instar larva of an unknown species of Galearctus is described and illustrated in detail here. It is possible that this larval material may be assigned to G. umbilicatus, the only species of the genus lacking a DNA barcode. Morphological analyses and a literature review allowed the re-evaluation of previous Galearctus larval studies, identifying several misidentifications and inconsistencies. Further morphological and molecular revision of adult Galearctus species is required to confirm larval identities, but the results presented here indicate that the diversity of Galearctus may be underestimated.

Gene Flow Between Populations With Highly Divergent Mitogenomes in the Australian Stingless Bee, Tetragonula hockingsi

Coadaptation of mitochondrial and nuclear genes is essential for proper cellular function. When populations become isolated, theory predicts that they should maintain mito-nuclear coadaptation in each population, even as they diverge in genotype. Mito-nuclear incompatibilities may therefore arise when individuals from populations with divergent co-evolved mito-nuclear gene sets are re-united and hybridise, contributing to selection against inter-population hybrids and, potentially, to speciation. Here, we explored genetic divergence and gene flow between populations of a stingless bee (Tetragonula hockingsi) that have highly divergent mitogenomes. We identified three distinct populations across the species' 2500 km range on the east coast of Queensland (Australia): 'Cape York', 'Northern', and 'Southern'. The mitogenomes of each population showed > 12% pairwise nucleotide divergence from each other, and > 7% pairwise amino acid divergence. Based on nuclear SNPs from reduced representation sequencing, we identified at least two zones of gene flow between populations: a narrow natural zone between Northern and Southern populations (coinciding with a biogeographic barrier, the Burdekin Gap), and an artificial zone at the southern edge of the species' distribution, where Cape York, Northern, and Southern mito-lineages have been brought together in recent decades due to beekeeping. In the artificial hybrid zone, we also confirmed that males of all three mito-lineages were attracted to the mating aggregations of Southern queens, consistent with inter-population hybridisation. Populations of T. hockingsi thus appear to be in the 'grey zone' of the speciation continuum, having strong genetic differentiation but incomplete reproductive isolation. Among the nuclear SNPs most differentiated between Northern and Southern populations, several were associated with genes involved in mitochondrial function, consistent with populations having co-diverged mito-nuclear gene sets. Our observations suggest that coadapted sets of mitochondrial and nuclear genes unique to each population of T. hockingsi may play a role in maintaining population boundaries, though more study is needed to confirm the fitness costs of mito-nuclear incompatibilities in hybrid individuals.

Morphology and molecular evidence reveal hidden diversity among snapping shrimp of the Alpheus obesomanus group (Decapoda: Alpheidae) with the description of a new species from Brazil

The snapping shrimp family Alpheidae Rafinesque, 1815 includes numerous species, most of which present controversial geographical distributions. The disjunct distribution of Alpheus simus Guérin-Méneville, 1856 in the western Atlantic, from Florida to the south of the Caribbean Sea and then from Rio Grande do Norte to Bahia in Brazil, suggests that Brazilian material may belong to an undescribed species. The examination of specimens previously identified as A. simus revealed the distinct morphology of material from Brazil, resulting in the description of a new species based on morphological and molecular evidence. The specimens were collected from fragments of fire coral at the Parque Municipal Marinho do Recife de Fora, Porto Seguro, Bahia, Brazil. Alpheus coralvivo sp. nov. belongs to the A. obesomanus group and is morphologically similar to A. simus (northwestern Atlantic) and A. saxidomus Holthuis, 1980 (eastern Pacific), differing mainly in the stylocerite and scaphocerite lengths and in the large gap between the cephalothorax and pleuron of the first pleonal segment. Molecular analysis using the mitochondrial cytochrome oxidase subunit I gene support the existence of the new species.

Cryptic diversity and phylogeographic patterns of Deto echinata (Isopoda: Detonidae) in southern Africa

Recent phylogeographic studies of poorly-dispersing coastal invertebrates in highly biodiverse regions have led to the discovery of high levels of cryptic diversity and complex phylogeographic patterns that suggest isolation, geological, and ecological processes have shaped their biodiversity. Studies of southern African coastal invertebrates have uncovered cryptic diversity for various taxa and phylogeographic patterns that, although sharing some similarities across taxa, do differ. These findings underscore the need for additional studies to better understand the biodiversity levels, distributional patterns, and processes responsible for producing coastal biodiversity in that region. The coastal isopod Deto echinata is of particular interest, as its complex taxonomic history, poor dispersal capabilities, and broad geographic distribution suggest the potential for cryptic diversity. We use mitochondrial and nuclear sequences to characterize D. echinata individuals from localities ranging from northern Namibia to Glentana, about 2,500 km along the coastline on the south coast of South Africa. These are used to assess whether D. echinata harbors cryptic genetic diversity and whether phylogeographic distributional patterns correlate with those previously documented for other coastal isopods in the region. Analysis of mitochondrial and nuclear sequences revealed two deeply-divergent lineages that exhibit a distributional break in the Cape Peninsula region. These findings suggest D. echinata is a cryptic species complex in need of taxonomic revision and highlight the need for further taxonomic and phylogeographic studies of similarly poorly-dispersing coastal invertebrates in southern Africa.

Taxonomic insights into Panopeuslacustris Desbonne (Crustacea, Decapoda, Brachyura) based on morphological and molecular data

The genus Panopeus belongs to the family Panopeidae and comprises a group of brachyuran crabs native to the American continent (except for P.africanus). However, taxonomic problems related to the presence of cryptic species have made it difficult to recognize the species and advance the biological knowledge of this group. Herein, a detailed description based on morphological and molecular data is provided for the species P.lacustris for the first time. Additionally, new morphological characters are proposed for the discrimination of the species. It is strongly suggested to increase the knowledge of the gene pool of the group, explore new morphological characters, and update the species descriptions to advance the group's knowledge. This proposal will serve as a reference for future studies aimed at clarifying the taxonomic, conservation and ecological status of the species of Panopeus.

A rapid diagnosis and treatment of Ornithonyssus bacoti infection

Mites serve as pathogens, allergens, or microbial containers, which can seriously damage the health of humans and animals. The substantial amount of mite species and their similar morphology make it complicated to identify and classify. Our mouse breeder incidentally noticed papular-type erythema with itching and peeling of the skin in several places, and an investigation revealed that this symptom was caused by an uncommon parasite that appeared on the skin and around the nest of the mice. By morphological observation, DNA extraction, PCR amplification, and DNA sequencing, we roughly identified the category of the parasite as a mite. Then, we designed a specific primer cox1, amplified and sequenced the mitochondrial cox1 gene fragment of the mite, calculated the intraspecific and interspecific differences, and reconstructed the phylogenetic tree for sequence alignment. Finally, this species was identified and named this Ornithonyssus bacoti-KF. According to the ivermectin gradient test, we found that 0.1 mg/mL concentration of ivermectin solution was the most effective for mite removal in the bath, with no recurrence after 6 months of treatment. Ornithonyssus bacoti, diagnosed by microscopic exam and confirmed by PCR amplification sequencing, was treated with ivermectin to control the rodent-borne parasite effectively.

Single-specimen systematics resolves the phylogeny and diversity conundrum of enigmatic crustacean y-larvae

Resolving the evolutionary history of organisms is a major goal in biology. Yet for some taxa the diversity, phylogeny, and even adult stages remain unknown. The enigmatic crustacean "y-larvae" (Facetotecta) is one particularly striking example. Here we use extensive video-imaging and single-specimen molecular sequencing of >200 y-larval specimens to comprehensively explore for the first time their evolutionary history and diversity. This integrative approach revealed five major clades of Facetotecta, four of which encompass a considerable larval diversity. Whereas morphological analyses recognized 35 y-naupliar "morphospecies", molecular species delimitation analyses suggested the existence of between 88 and 127 species. The phenotypic and genetic diversity between the morphospecies suggests that a more elaborate classification than the current one-genus approach is needed. Morphology and molecular data were highly congruent at shallower phylogenetic levels, but no morphological synapomorphies could be unambiguously identified for major clades, which mostly comprise both planktotrophic and lecithotrophic y-nauplii. We argue that lecithotrophy arose several times independently whereas planktotrophic y-nauplii, which are structurally more similar across clades, most likely display the ancestral feeding mode of Facetotecta. We document a remarkably complex and highly diverse phylogenetic backbone for a taxon of marine crustaceans, the full life cycle of which remains a mystery.

Demographic changes and life-history strategies predict the genetic diversity in crabs

Uncovering what predicts genetic diversity (GD) within species can help us access the status of populations and their evolutionary potential. Traits related to effective population size show a proportional association to GD, but evidence supports life-history strategies and habitat as the drivers of GD variation. Instead of investigating highly divergent taxa, focusing on one group could help to elucidate the factors influencing the GD. Additionally, most empirical data is based on vertebrate taxa; therefore, we might be missing novel patterns of GD found in neglected invertebrate groups. Here, we investigated the predictors of the GD in crabs (Brachyura) by compiling the most comprehensive cytochrome c oxidase subunit I (COI) available. Eight predictor variables were analysed across 150 species (16 992 sequences) using linear models (multiple linear regression) and comparative methods (PGLS). Our results indicate that population size fluctuation represents the most critical trait predicting GD, with species that have undergone bottlenecks followed by population expansion showing lower GD. Egg size, pelagic larval duration and habitat might play a role probably because of their association with how species respond to disturbances. Ultimately, K-strategists that have undergone bottlenecks are the species showing lower GD. Some variables do not show an association with GD as expected, most likely due to the taxon-specific role of some predictors, which should be considered in further investigations and generalizations. This work highlights the complexity underlying the predictors of GD and adds results from a marine invertebrate group to the current understanding of this topic.

Three Loxocaudinae species (Ostracoda, Podocopida) from South Korea

For many ostracod groups in Korea, published records are missing or are very limited. Loxocaudinae is one such subfamily, with only one named species, Loxocaudaorientalis Schornikov, 2011 reported from Korea. Having fewer than 50 species, this subfamily can be considered a small ostracod group, with most of the species known only by their shell morphology. The diagnoses of genera are based on the shell characters that are often homoplastic, and soft body appendages that are difficult to observe, such as the mandibular exopodite. Because of this, the validity of the entire subfamily and some of its genera have been questioned. Here three Loxocaudinae species were collected from the marine macrobenthic assemblages from Korea. Two are new and belong to the genus Glacioloxoconcha Hartmann, 1990, previously known only from Antarctica: Glacioloxoconchajeongokensis sp. nov. and Glacioloxoconchajisepoensis sp. nov. Loxocaudaorientalis is briefly redescribed, with some of the populations having unusual morphological features. COI and 18S rRNA sequences of all three species are provided and the latter marker used to assess the position of the subfamily within the family Loxoconchidae and the superfamily Cytheroidea. The resulting tree shows that within the family Loxoconchidae, the genera Glacioloxoconcha and Loxocauda Schornikov, 1969 are the most closely related, with very shallow but well-supported branches. Polyphyletic and paraphyletic natures of several Cytheroidea families are discussed, inferred from the reconstructed phylogeny.

New insights into the evolution of portunoid swimming crabs (Portunoidea, Heterotremata, Brachyura) and the brachyuran axial skeleton

Portunoidea (Heterotremata) is a morphologically disparate taxon of true crabs (Brachyura) best-known for many of its representatives being considered "swimming crabs". The term "swimming crab", however, sometimes refers to a distinct taxon (traditionally to Portunidae within Portunoidea), and sometimes to a certain morphotype in which the 5th pereiopod (P5) has a specific shape that facilitates swimming. We use the term "P5-swimming crab" or "P5-swimmer" herein, not only to restrict it to the morphotype, but also to distinguish the swimming in question from other kinds of swimming in Brachyura. The evolution of P5-swimming crabs has not yet been satisfactorily investigated. In particular, it is not known whether the morphotype evolved several times independently in different lineages of Portunoidea or whether it evolved only once and was lost in several lineages. Ours is the first approach combining molecular with morphological data to result in a new phylogenetic positioning of some members of Portunoidea. For the first time, data from the axial skeleton and extrinsic musculature are used. Morphological examinations reveal that the axial skeleton and extrinsic musculature in P5-swimming crabs are more diverse than previously thought, with the exception of the P5 anterior coxa muscle, which originates at the median plate in all P5-swimmers. Ancestral state reconstructions based on parsimony reveal that the stem species of Portunoidea already showed the morphotype of a P5-swimming crab, but with a long merus which probably resulted in less effective P5-swimming than in extant P5-swimming crab species with a short merus. Several other extant taxa represent a reversal of the P5-swimmer morphotype to varying degrees, with some extant species showing a complete reversal of unambiguous P5-swimming crab character states-one example being the well-known common shore crab Carcinus maenas. The absence of a connection between interosternite 7/8 and the sella turcica (the secondary loss of the "brachyuran sella turcica") in the stem species of Heterotremata, resulting in a junction plate which forms a cavity that offers room and attachment sites for the P5 extrinsic musculature is uncovered as preadaptation to the P5-swimmer morphotype in Heterotremata. This preadaptation is missing in Podotremata and Thoracotremata, the other two traditional main taxa of Brachyura.

Do pseudogenes pose a problem for metabarcoding marine animal communities?

Because DNA metabarcoding typically employs sequence diversity among mitochondrial amplicons to estimate species composition, nuclear mitochondrial pseudogenes (NUMTs) can inflate diversity. This study quantifies the incidence and attributes of NUMTs derived from the 658 bp barcode region of cytochrome c oxidase I (COI) in 156 marine animal genomes. NUMTs were examined to ascertain if they could be recognized by their possession of indels or stop codons. In total, 309 NUMTs ≥ 150 bp were detected, with an average of 1.98 per species (range = 0-33) and a mean length of 391 bp ± 200 bp. Among this total, 75 (24.3 %) lacked indels or stop codons. NUMTs appear to pose the greatest interpretational risk when short (< 313 bp) amplicons are used, such as in eDNA studies, dietary analyses, or processed fish identification. Employing the standard amplicon length (313 bp) for marine metabarcoding, NUMTs could potentially inflate the OTU count by 21% above the true species count while also raising intraspecific variation at COI by 15%. However, when both amplicon length and position are considered, inflation in OTU counts and in barcode variation were just 9% and 10%, respectively, suggesting NUMTs will not seriously distort biodiversity assessments. There was a weak positive correlation between genome size and NUMT count but no variation among phyla or trophic groups. Until bioinformatic advances improve NUMT detection, the best defense involves targeting long amplicons and developing reference databases that include both mitochondrial sequences and their NUMT derivatives.

Checklist of decapod crustaceans from the coast of the São Paulo state (Brazil) supported by integrative molecular and morphological data: V. Dendrobranchiata and Pleocyemata [Achelata, Astacidea, Axiidea, Caridea (Alpheoidea and Processoidea excluded), Gebiidea, Stenopodidea]

This checklist is the fifth and last compilation on the decapod crustaceans reported to São Paulo (Brazil) coastal area, resulting from long-term multidisciplinary projects, which combined morphological analyses and molecular techniques. The current research includes 75 decapod species, herein referred as shrimps/lobsters-like (shrimps, ghost-shrimps, lobsters, and related groups), reported to São Paulo coastal area. These species occur in marine, estuarine, and amphidromous habitats and are classified into 21 families as follow: Aristeidae (2 spp., 2 genera), Atyidae (4 spp., 2 genera), Axianassidae (1 sp., 1 genus), Callianassidae (1 sp., 1 genus), Callichiridae (6 spp., 4 genera), Crangonidae (1 sp., 1 genus), Glyphocrangonidae (1 sp., 1 genus), Luciferidae (2 spp., 2 genera), Nephropidae (4 spp., 2 genera), Palaemonidae (15 spp., 9 genera), Palinuridae (2 spp., 1 genus), Pandalidae (1 sp., 1 genus), Pasiphaeidae (1 sp., 1 genus), Penaeidae (10 spp., 6 genera), Sergestidae (3 spp., 3 genera), Sicyoniidae (4 spp., 1 genus), Scyllaridae (5 spp., 3 genera), Solenoceridae (4 spp., 3 genera), Stenopodidae (2 spp., 1 genus), and Upogebiidae (6 spp., 1 genus). We generated new sequences of cytochrome oxidase subunit I (barcode region) and 16S genes (51 and 54, respectively) of 54 species. Our examination concluded that 75 shrimps/lobsters-like species are reported to the São Paulo coast. We excluded Leander tenuicornis (Palaemonidae), Penaeus setiferus (Penaeidae), Philocheras gorei (Crangonidae), and Rhynchocinetes typus (Rhynchocinetidae) from this list.  

Holothuriophilus trapeziformis Nauck, 1880 (Decapoda: Pinnotheridae) from the Pacific coast of Mexico: taxonomic revision based on integrative taxonomy

BACKGROUND

Holothuriophilus trapeziformis Nauck, 1880 is a holothurian-dweller pinnotherid crab representing one of the two species of the genus distributed along the Pacific coast of Mexico and Chile, respectively. While the parasitic ecological interaction with its host is well established, the morphology of the male remains unknown, and DNA information for the species is not available. Furthermore, the only morphological trait separating both species of the genus is subjective and corresponds to the presence or absence of a gap between the fingers of the chelae. Our goal is to complete and clarify the taxonomic status of H. trapeziformis and describe the male morphology with the use of the integrative taxonomy, providing additional characters to differentiate this species.

METHODS

We collected new biological material in the Pacific coast of Mexico including the topotypes. We also reviewed material from national collections to integrate morphology (based on a complete and detailed description and illustration of the species using light microscopy), ecological data (based on the identification of the host and the place where it was located within the host), and the mtCOI gene information (commonly known as DNA barcode) to differentiate Holothuriophilus trapeziformis from other related crabs.

RESULTS

This species presents marked sexual dimorphism only in the primary sexual characters. For the first time we describe morphological variability of traditionally stable characters. In addition to the gap between the fingers of the chelae, Holothuriophilus trapeziformis differs from H. pacificus (Poeppig, 1836) by their ornamentation, the shape of the male abdomen, and the gonopod. Cytocrome Oxidase 1 gene (COI) distance divergence was >3% between both Holothuriophilus species forming a clear clade. DNA barcoding indicates only one taxon, with a maximum divergence of 2.2%. All the specimens have the same Barcode Index Number (BIN; BOLD: ADE9974). All the hosts for H. trapeziformis were identified as Holothuria (Halodeima) inornata Semper, 1868; the presence of the crab in the host's coelomic cavity was confirmed, and for the first time we found it within the intestine. The geographical distribution is the Pacific coast of Mexico. Based on the data presented here, the taxonomic status of Holothuriophilus trapeziformis is now complete.

Characterization of spiny lobsters from Bangladesh waters using morphology, COI and 16S rRNA sequences

This study aims to taxonomically identify and characterise the phylogenetic relationships of spiny lobsters based on mitochondrial cytochrome c oxidase I (COI) and 16S rRNA genes from Bangladesh waters. A total of 19 barcode sequences (10 partial COI sequences and 9 partial 16S rRNA) were successfully generated from 12 collected spiny lobster samples representing four species belonging to the family Palinuridae. The average genetic distances within and between species were 0.834 ± 0.427 and 17.810 ± 0.830, respectively, in COI and 0.107 ± 0.255 and 8.401 ± 2.547, respectively, in 16S rRNA genes. The successful amplification rate of 16S rRNA was higher than that of the COI marker. In the maximum likelihood (ML) tree, the sequences of the same species were clustered together under a single clade for both COI and 16S rRNA, which supports the efficacy of both marker genes in differentiating lobster species.

A Mysterious World Revealed: Larval-Adult Matching of Deep-Sea Shrimps from the Gulf of Mexico

The identification of deep-sea (>200 m) pelagic larvae is extremely challenging due to the morphological diversity across ontogeny and duration of larval phases. Within Decapoda, developmental stages often differ conspicuously from their adult form, representing a bizarre and mysterious world still left to be discovered. The difficulties with sampling and rearing deep-sea larvae, combined with the lack of taxonomic expertise, argues for the use of molecular methods to aid in identification. Here, we use DNA barcoding combined with morphological methods, to match larval stages with their adult counterpart from the northern Gulf of Mexico and adjacent waters. For DNA barcoding, we targeted the mitochondrial ribosomal large subunit 16S (16S) and the protein coding cytochrome oxidase subunit 1 (COI). These data were combined with previous sequences to generate phylogenetic trees that were used to identify 12 unknown larval and two juvenile species from the infraorder Caridea and the suborder Dendrobranchiata. Once identified, we provide taxonomic descriptions and illustrations alongside the current state of knowledge for all families. For many groups, larval descriptions are missing or non-existent, so this study represents a first step of many to advance deep-sea larval diversity.

Aegla buenoi n. sp. (Decapoda: Anomura): first record of aeglid crab from Cinzas River basin, Brazil

A new species of freshwater anomuran crab, Aegla buenoi n. sp., is described. The new taxon was collected from two streams within the Cinzas River basin, Paran state, Brazil. We used morphological and molecular data (COI mtDNA) to distinguish the new species from its congeners. Aegla buenoi n. sp. is differentiated by morphological diagnostic features of the cephalothorax, chelipeds, second abdominal epimeron, and uropods. Molecular results confirm the separation of A. buenoi n. sp. from closely related species (A. castro Schmitt, 1942, A. lata Bond-Buckup Buckup, 1994, and A. jacutinga Marl Teixeira, 2020). Hence, our study increases the known diversity of aeglids and reports the first species of Aegla from the Cinzas River basin.

Molecular phylogenetic analysis of the Paguristes tortugae Schmitt, 1933 complex and selected other Paguroidea (Crustacea: Decapoda: Anomura)

Morphological characters, as presently applied to describe members of the Paguristes tortugae Schmitt, 1933 species complex, appear to be of limited value in inferring phylogenetic relationships within the genus, and may have similarly misinformed understanding of relationships between members of this complex and those presently assigned to the related genera Areopaguristes Rahayu McLaughlin, 2010 and Pseudopaguristes McLaughlin, 2002. Previously undocumented observations of similarities and differences in color patterns among populations additionally suggest genetic divergences within some species, or alternatively seem to support phylogenetic groupings of some species. In the present study, a Maximum Likelihood (ML) phylogenetic analysis was undertaken based on the H3, 12S mtDNA, and 16S mtDNA sequences of 148 individuals, primarily representatives of paguroid species from the western Atlantic. This molecular analysis supported a polyphyletic Diogenidae Ortmann, 1892, although incomplete taxonomic sampling among the genera of Diogenidae limits the utility of this finding for resolving family level relationships. Several hypotheses regarding the evolutionary relationships among hermit crab genera were refuted by the Kishino-Hasegawa (KH). Shimodaira-Hasegawa (SH) and Approximately Unbiased (AU) tree topology tests, among them the hypothesis that Areopaguristes is monophyletic. A lack of support for the monophyly of Areopaguristes calls into question the phylogenetic validity of gill number for the differentiation of Paguristes, Areopaguristes, and Pseudopaguristes. The study was inconclusive with regard to the relationships among these three genera, but previously unknown diversity within both Paguristes and Areopaguristes was demonstrated. Existence of an undescribed species confounded under the name Paguristes tortugae Schmitt, 1933 was supported by genetics, morphology, and coloration. A second undescribed species with remarkable similarity to Areopaguristes hummi Wass, 1955 was discovered based on genetics and coloration.

A new species of Procambarus (Decapoda, Cambaridae) from the State of Querétaro, Mexico

With a Nearctic distribution, the family Cambaridae harbors a high species richness in Mexico, which is also evident along the Pánuco River catchment. A series of surveys carried on in five populations from the Sierra Gorda Biosphere Reserve in the State of Querétaro resulted in localizing a putative new species for science. A molecular phylogenetic study and species delimitation analyses including all the known Procambarus species from the Pánuco River catchment were conducted based on three mitochondrial genes (16S rDNA, 12S rDNA, and COI; 2,462 bp in total). Phylogeny recovered all species as monophyletic, including the populations under study. All delimitation results based on barcoding, ABGD, GMYC, bPTP, and gonopod differentiation agree in the recognition of a new taxon, to which the name Procambarusxihuisp. nov. is given, and its diagnosis and description are provided. The new species can be distinguished from the remaining species in the genus, among other characters, by a unique configuration of the terminal elements of the first pleopod of form I male, which includes a central projection lamellate, hood-like, forming a concave blade-like structure mesially directed, as well as a caudal process crest-like, mesiodistally directed, forming a lateral side of the concavity.

Evidence of cryptic diversity in freshwater Macrobrachium prawns from Indochinese riverine systems revealed by DNA barcode, species delimitation and phylogenetic approaches

The diversity of Indochinese prawns in genus Macrobrachium is enormous due to the habitat diversification and broad tributary networks of two river basins: the Chao Phraya and the Mekong. Despite long-standing interest in SE-Asian decapod diversity, the subregional Macrobrachium fauna is still not yet comprehensively clarified in terms of taxonomic identification or genetic diversification. In this study, integrative taxonomic approaches including morphological examination, DNA barcoding, and molecular species delimitation were used to emphasize the broad scale systematics of Macrobrachium prawns in Indochina. Twenty-seven nominal species were successfully re-verified by traditional and molecular taxonomy. Barcode gap analysis supported broad overlapping of species boundaries. Taxonomic ambiguity of several deposited samples in the public database is related to inter- and intraspecific genetic divergence as indicated by BOLD discordance. Diagnostic nucleotide positions were found in six Macrobrachium species. Eighteen additional putative lineages are herein assigned using the consensus of species delimitation methods. Genetic divergence indicates the possible existence of cryptic species in four morphologically complex and wide-ranging species: M. lanchesteri, M. niphanae, M. sintangense, and some members of the M. pilimanus group. The geographical distribution of some species supports the connections and barriers attributed to paleo-historical events of SE-Asian rivers and land masses. Results of this study show explicitly the importance of freshwater ecosystems in Indochinese subregions, especially for the Mekong River Basin due to its high genetic diversity and species composition found throughout its tributaries.

Across the benthic and pelagic realms: a species‐level phylogeny of Benthesicymidae (Crustacea:Decapoda)

Benthesicymidae is a monophyletic group of Decapoda adapted to a life on the sea-floor, in the near-bottom layer, in the bathy- and in the mesopelagic, within an impressive depth range from a few hundred metres (Gennadas) to several thousand metres (Benthesicymus). Higher taxa are known to conquer all main oceanic biotopes such as the benthic, benthopelagic, and pelagic and a wide depth range but few family-level groups have clades evolved within all these oceanic realms. Therefore, the global fauna of Benthesicymidae provides a rare opportunity for an insight into phylogenetic processes favouring colonisation of all principal oceanic biotopes. The first comprehensive phylogenetic study of Benthesicymidae (all 37 valid species) is based on six molecular markers and 105 morphological characters (including 72 female and male copulatory characters). Analyses resulted in trees with similar topology and the same set of robust clades. Molecular methods based on 167 sequences (84 new) provided better resolution of deeper nodes and generally higher support of the clades, while morphological methods allowed analyses of all valid species of the global fauna. Phylogenetic analyses support the monophyly and robustness of all currently known genera except Gennadas, which was split into Gennadas Bate, 1881, Amalopenaeus Smith, 1882, and Notogennema gen. nov. We also retrieved two major clades for which we erected two new subfamilies: Benthesicyminae subfam. nov. (presumably benthic, genera Altelatipes, Bathicaris, Benthesicymus, and Benthonectes) and Gennadinae subfam. nov. (presumably pelagic, genera Amalopenaeus, Bentheogennema, Benthoecetes, Boreogennema, Gennadas, Maorrancaris, and Notogennema gen. nov.). We revealed two groups of morphological characters, that are interlinked evolutionarily: (1) petasma and thelycum; (2) body, mouthparts, and pereopods. Morphological traits within benthic and pelagic clades are different, a model explaining the differences is proposed. Along with previous studies, our results confirm the idea that the elaboration of the copulatory structures is a key to successful colonisation of the pelagic realm. These results extend our knowledge about evolution in the largest habitual biotope of our planet and phylogenetic processes favouring colonisation of all principal oceanic biotopes.

Molecular phylogeny and species delimitation of the freshwater prawn Macrobrachium pilimanus species group, with descriptions of three new species from Thailand

Specific status and species boundaries of several freshwater prawns in the Macrobrachium pilimanus species group remain ambiguous, despite the taxonomic re-description of type materials and additional specimens collected to expand the boundaries of some species. In this study, the "pilimanus" species group of Macrobrachium sensu Johnson (1958) was studied using specimens collected from montane streams of Thailand. Molecular phylogenetic analyses based on sequences of three molecular markers (COI, 16S and 18S rRNA) were performed. The phylogenetic results agreed with morphological identifications, and indicated the presence of at least nine putative taxa. Of these, six morphospecies were recognised as M. malayanum, M. forcipatum, M. dienbienphuense, M. hirsutimanus, M. eriocheirum, and M. sirindhorn. Furthermore, three morphologically and genetically distinct linages were detected, and are described herein as M. naiyanetri Siriwut sp. nov. , M. palmopilosum Siriwut sp. nov. and M. puberimanus Siriwut sp. nov. The taxonomic comparison indicated wide morphological variation in several species and suggested additional diagnostic characters that are suitable for use in species diagnoses, such as the shape and orientation of fingers, the rostrum form, and the presence or absence of velvet pubescence hairs and tuberculated spinulation on each telopodite of the second pereiopods. The "pilimanus" species group was portrayed as non-monophyletic in both ML and BI analyses. The genetic structure of different geographical populations in Thailand was detected in some widespread species. The species delimitation based on the four delimitation methods (BIN, ABGD, PTP and GMYC) suggested high genetic diversity of the "pilimanus" species group and placed the candidate members much higher than in previous designations based on traditional morphology. This finding suggests that further investigation of morphological and genetic diversity of Southeast Asian freshwater prawns in the genus Macrobrachium is still required to provide a comprehensive species list to guide efforts in conservation and resource management.

Mitochondrial heteroplasmy and pseudogenes in the freshwater prawn, Macrobrachium amazonicum (Heller, 1862): DNA barcoding and phylogeographic implications

The mitochondrial cytochrome oxidase c subunit 1 (COI) gene has been widely used in phylogenetic studies of crustaceans and analyses in population genetics. As COI studies have become more popular, there has been an increase in the number of reports of the presence of nuclear insertions of mitochondrial DNA (Numts) and mitochondrial heteroplasmy. Here, we provide evidence of both types of event in the COI sequences of Macrobrachium amazonicum, an economically important freshwater prawn, which is widespread in South America. Heteroplasmy and Numts were confirmed by different methods of DNA extraction (genomic, mitochondrial, and nuclear-enriched DNA), cloning, and sequencing, and were observed in 11 of the 14 populations sampled, primarily in the Amazon region. We discuss how the occurrence of these events affects the interpretation of the genetic relationships among the M. amazonicum populations, and we recommend caution when using COI for genetic inferences in prawns of the genus Macrobrachium, and in particular that any analysis should include nuclear markers.

New insights into the genetic diversity of the stone crayfish: taxonomic and conservation implications

Background

Austropotamobius torrentium is a freshwater crayfish species native to central and south-eastern Europe, with an intricate evolutionary history and the highest genetic diversity recorded in the northern-central Dinarides (NCD). Its populations are facing declines, both in number and size across its entire range. By extanding current knowledge on the genetic diversity of this species, we aim to assist conservation programmes. Multigene phylogenetic analyses were performed using different divergence time estimates based on mitochondrial and, for the first time, nuclear DNA markers on the largest data set analysed so far. In order to reassess taxonomic relationships within this species we applied several species delimitation methods and studied the meristic characters with the intention of finding features that would clearly separate stone crayfish belonging to different phylogroups.

Results

Our results confirmed the existence of high genetic diversity within A. torrentium, maintained in divergent phylogroups which have their own evolutionary dynamics. A new phylogroup in the Kordun region belonging to NCD has also been discovered. Due to the incongruence between implemented species delimitation approaches and the lack of any morphological characters conserved within lineages, we are of the opinion that phylogroups recovered on mitochondrial and nuclear DNA are cryptic subspecies and distinct evolutionary significant units.

Conclusions

Geographically and genetically isolated phylogroups represent the evolutionary legacy of A. torrentium and are highly relevant for conservation due to their evolutionary distinctiveness and restricted distribution.

Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae)

Macropodia czernjawskii (Brandt, 1880), described from the Black Sea, was ignored in the regional faunal accounts for more than a century, although it was recognised in the Mediterranean. Instead, M. longirostris (Fabricius, 1775) and M. rostrata (Linnaeus, 1761) were frequently listed for the Black Sea. We selected a lectotype and redescribed the species on the basis of the type series from the Crimean Peninsula and the new material collected in the Black Sea. Historical and new collections, as well as the analysis of publications, indicate that M. czernjawskii is the only Macropodia species occurring in the Black Sea. Molecular barcode (COI gene marker) data show that M. czernjawskii is a species well-diverged from other studied species of the group. Furthermore, M. parva van Noort &amp; Adema, 1985 has very low genetic distances from M. rostrata and M. longipes A. Milne-Edwards &amp; Bouvier, 1899 is indistinguishable from M. tenuirostris (Leach, 1814), using COI sequences. The respective synonimisations, supported by morphological data, are proposed. M. czernjawskii is a Black Sea – Mediterranean endemic occurring also in the neighbouring Atlantic coastal zone of the Iberian Peninsula and occupying shallower depth, compared to other Mediterranean species of Macropodia. As an upper subtidal inshore species, it is particularly specialised in self-decoration and stimulates abundant epibiosis, providing masking and protection. The bulk of epibiosis consists of algae and cyanobacteria. Amongst the 25 autotrophic eukaryote taxa, identified to the lowest possible level, green chlorophytes Cladophora sp. and calcareous rhodophytes Corallinales gen. sp. were most commonly recorded. Non-indigenous red alga Bonnemaisonia hamifera Hariot, first officially recorded at the Caucasian coast of the Black Sea in 2015, was present in the epibiosis of M. czernjawskii in Crimea as early as 2011.

Characterizing coral reef biodiversity: genetic species delimitation in brachyuran crabs of Palmyra Atoll, Central Pacific

Coral reefs are highly threatened ecosystems, yet there are numerous challenges in conducting inventories of their vanishing biodiversity, partly because many taxa remain difficult to detect and describe. Genetic species delimitation methods provide a standardized means for taxonomic classification including of cryptic, rare, or elusive groups, but results can vary by analytical method and genetic marker. In this study, a combination of morphological and genetic identification methods was used to estimate species richness and identify taxonomic units in true crabs (Infraorder Brachyura; n = 200) from coral reefs of Palmyra Atoll, Central Pacific. Genetic identification was based on matches between mitochondrial 16S ribosomal RNA (16S rRNA) and/or cytochrome c oxidase subunit I (COI) sequences to GenBank data, while morphological work relied on the taxonomic literature. Broad agreement in the number of candidate species delimited by genetic distance thresholds and tree-based approaches was found, although the multi-rate Poisson tree process (mPTP) was less appropriate for this dataset. The COI sequence data identified 30-32 provisional species and the 16S data revealed 34-35. The occurrence of 10 families, 20 genera, and 19 species of brachyurans at Palmyra was corroborated by at least two methods. Diversity levels within Chlorodiella laevissima indicated possible undescribed or cryptic species in currently lumped taxa. These results illustrate the efficacy of DNA sequences in identifying organisms and detecting cryptic variation, and underscore the importance of using appropriate genetic markers and multiple species delimitation analyses, with applications for future species descriptions.

Documenting decapod biodiversity in the Caribbean from DNA barcodes generated during field training in taxonomy

DNA barcoding is a useful tool to identify the components of mixed or bulk samples, as well as to determine individuals that lack morphologically diagnostic features. However, the reference database of DNA barcode sequences is particularly sparsely populated for marine invertebrates and for tropical taxa. We used samples collected as part of two field courses, focused on graduate training in taxonomy and systematics, to generate DNA sequences of the barcode fragments of cytochrome c oxidase subunit I (COI) and mitochondrial ribosomal 16S genes for 447 individuals, representing at least 129 morphospecies of decapod crustaceans. COI sequences for 36% (51/140) of the species and 16S sequences for 26% (37/140) of the species were new to GenBank. Automatic Barcode Gap Discovery identified 140 operational taxonomic units (OTUs) which largely coincided with the morphospecies delimitations. Barcode identifications (i.e. matches to identified sequences) were especially useful for OTUs within Synalpheus, a group that is notoriously difficult to identify and rife with cryptic species, a number of which we could not identify to species, based on morphology. Non-concordance between morphospecies and barcode OTUs also occurred in a few cases of suspected cryptic species. As mitochondrial pseudogenes are particularly common in decapods, we investigate the potential for this dataset to include pseudogenes and discuss the utility of these sequences as species identifiers (i.e. barcodes). These results demonstrate that material collected and identified during training activities can provide useful incidental barcode reference samples for under-studied taxa.

A phylogeny-based revision of the shrimp genera Altelatipes, Benthonectes and Benthesicymus (Crustacea: Decapoda: Benthesicymidae)

A phylogenetic study of deep-sea dendrobranchiate genera Altelatipes, Benthesicymus and Benthonectes based on four molecular markers and 91 morphological characters is presented. All currently recognized species of these genera, representatives of all other genera and species groups of Benthesicymidae, and three outgroups were included in the analyses. The molecular and morphological methods retrieved similar results, the molecular methods provided better resolution of deeper nodes and higher clade support. Both types of analyses showed paraphyly of Benthesicymus, which encompass five robust clades, four of which are diagnosed as new genera (type species in parentheses): Benthesicymus s.s. (B. crenatus), Bathicaris gen. nov. (Benthesicymus brasiliensis), Dalicaris gen. nov. (Benthesicymus altus), Trichocaris gen. nov. (Benthesicymus bartletti) and Maorrancaris gen. nov. (Benthesicymus investigatoris). Altelatipes was found to be monophyletic. The evolution of the major clades of Benthesicymidae is shown to be linked to trophic specialization, while further divergence at the genus level is mainly related to sexual evolution seen in the elaboration of the copulatory structures. We provide amended diagnoses of the previously recognized and new genera, key to species of each of these genera and include an updated key to genera of Benthesicymidae.

A hard-earned draw: phylogeny-based revision of the deep-sea shrimp Bentheogennema (Decapoda: Benthesicymidae) transfers two species to other genera and reveals two new species

The phylogenetic study of the deep-sea genus Bentheogennema is based on four molecular markers and 79 morphological characters. All four previously recognized species and two new species of Bentheogennema, representatives of all other genera and species groups of Benthesicymidae, and three outgroups were included in the analyses. We have examined and coded six major groups of morphological characters related to the carapace (three characters), the pleon and the telson (14), the mouthparts (nine), the armature of the pereopods (five), the thelycum (27) and the petasma (21). Results of morphological and molecular analyses were similar. Two species were transferred from Bentheogennema to other genera (for one of them a new genus was erected) and two new species of Bentheogennema were described. Three pelagic genera (Gennadas, Bentheogennema and a new genus) created a robust clade. The divergence of this clade is linked to ‘smoothening’ of the body (reduction of the branchiostegal spine on the carapace, reduction and loss of the dorsolateral spines and the end-piece on the telson) and elaboration of the copulatory structures. We provide amended diagnoses of these three pelagic genera and key to species of Bentheogennema.

A multigene and morphological analysis expands the diversity of the seabod shrimp Xiphopenaeus Smith, 1869 (Decapoda: Penaeidae), with descriptions of two new species

After being stable for nearly a century, the taxonomic history of the genus Xiphopenaeus has been marked by many changes in the last three decades. The taxonomic status of the Atlantic species has a low resolution, and many species are still undefined and grouped as cryptic species. Here we employed an integrative approach to define the species of Xiphopenaeus and the morphological characters needed to differentiate them. We combined the analyses of two molecular markers (COI and 16 S rDNA), scanning electron microscopy and light microscopy. Based on specimens from 17 localities from the Atlantic and Pacific oceans, we detected five divergent genetic groups, three in the Atlantic (A1, A2, A3) and two in the Pacific (P1, P2). Male secondary sexual characters were able to differentiate four out of the five genetic groups. Group A1 corresponds to X. kroyeri, and A2 and A3 correspond to new species. We redescribed the genus and two new species are described and illustrated: Xiphopenaeus dincao nov. sp. (A2) and Xiphopenaeus baueri nov. sp. (A3). Since the holotype of X. riveti was missing and the specimen analysed from group P2 was a female, the status of the species of Xiphopenaeus from the Pacific remains unresolved.

Redescription of Hargeria rapax (Harger, 1879) and description of H. chetumalensis a new species from the Mexican Caribbean (Crustacea, Peracarida, Tanaidacea, Leptocheliidae) based upon morphological and molecular evidence

Until now, Hargeria was considered a monospecific leptocheliid genus, with the species Hargeria rapax considered a taxon with a wide distribution, from the Northwestern Atlantic to the Mexican Caribbean. Herein, after a detailed revision of type and topotype materials and specimens collected from the Mexican Caribbean, a new species H. chetumalensis sp. nov. is described, and the redescription of H. rapax is provided. Also, we found a significant genetic divergence between the two species based on the nucleotide sequences of cytochrome oxidase subunit I, which support the morphological data. The morphological features used to recognize both species are also adequate to link males, females, and juvenile stages, although these species have a high intraspecific polymorphism.

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized for future collaborative programs. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.

A journey on plate tectonics sheds light on European crayfish phylogeography

Crayfish can be used as model organisms in phylogeographic and divergence time studies if reliable calibrations are available. This study presents a comprehensive investigation into the phylogeography of the European stone crayfish (Austropotamobius torrentium) and includes samples from previously unstudied sites. Two mitochondrial markers were used to reveal evolutionary relationships among haplogroups throughout the species' distributional range and to estimate the divergence time by employing both substitution rates and geological calibration methods. Our haplotype network reconstruction and phylogenetic analyses revealed the existence of a previously unknown haplogroup distributed in Romania's Apuseni Mountains. This haplogroup is closely related to others that are endemic in the Dinarides, despite their vast geographical separation (~600 km). The separation is best explained by the well-dated tectonic displacement of the Tisza-Dacia microplate, which started in the Miocene (~16 Ma) and possibly carried part of the A. torrentium population to the current location of the Apuseni Mountains. This population may thus have been isolated from the Dinarides for a period of ca. 11 m.y. by marine and lacustrine phases of the Pannonian Basin. The inclusion of this geological event as a calibration point in divergence time analyses challenges currently accepted crayfish evolutionary time frames for the region, constraining the evolution of this area's crayfish to a much earlier date. We discuss why molecular clock calibrations previously employed to date European crayfish species divergences should therefore be reconsidered.

Molecular Characterization of Hard Ticks by Cytochrome c Oxidase Subunit 1 Sequences

Although widely studied, the natural diversity of the hard tick is not well known. In this study, we collected 194 sequences from 67 species, covering 7 genera of hard tick. The 5′ region of the mitochondrial cytochrome c oxidase subunit 1 region (586 bp) has been used to investigate intra- and inter-species variation and the phylogenetic tree of neighbor joining method has been used for assessment. As a result, by comparing the K2P-distance of intra- and interspecies, 30 samples (15.2%) shown that interspecies distance was larger than the minimum interspecfic distance. From the phylogenetic analysis, 86.8% (49) of the species were identified correctly at the genus level. On deeper analysis on these species suggested the possibility of presence cryptic species. Therefore, further work is required to delineate species boundaries and to develop a more complete understanding of hard tick diversity over larger scale.

Subdividing the Common Intertidal Hermit Crab Pagurus minutus Hess, 1865 (Decapoda: Anomura: Paguridae) Based on Molecular, Morphological and Coloration Analyses

Jibom Jung, Jongwoo Jung, and Won Kim (2018) A phylogenetic study was conducted to investigate whether distinct genetic groups are present within the East Asian Pagurus minutus. In this study, 167 individuals of P. minutus were collected along the coasts of South Korea, east coast of Honshu, west coast of Kyushu, Okinawa Islands of Japan, and Taiwan. The collection of P. minutus was divided into three groups based on the differences in cytochrome c oxidase subunit I (COI) sequences and morphological and color characters: Major Group (MAG), Minor Group (MIG), and Taiwan-Okinawa Group (TOG). MAG commonly inhabits the entire coast of South Korea (except for the northeast coast), east coast of Honshu, and west coast of Kyushu in Japan. MIG predominantly inhabits the northeast coast of South Korea, while a small proportion inhabits the west coast of South Korea and west coast of Kyushu in Japan. TOG is restricted to Taiwan and the Okinawa Islands of Japan. The COI divergence among MAG, MIG, and TOG was larger than the minimum interspecific divergence of the other Pagurus species. Little ingroup COI divergences exist in the MAG and MIG, but distinct ingroup COI divergence is present between the two subgroups of TOG inhabiting Taiwan and Okinawa Islands. MAG, MIG, and TOG show minor differences among morphological characters. Each specimen of these three groups has distinguishing color patterns. These differences in molecular, morphological and color characters suggest that P. minutus are separated into three groups at the species level, and this subdivision of P. minutus shows that additional phylogenetic studies of other hermit crabs and common marine decapod species in East Asia are needed.

Multiple transgressions and slow evolution shape the phylogeographic pattern of the blind cave-dwelling shrimp Typhlocaris

Background

Aquatic subterranean species often exhibit disjunct distributions, with high level of endemism and small range, shaped by vicariance, limited dispersal, and evolutionary rates. We studied the disjunct biogeographic patterns of an endangered blind cave shrimp, Typhlocaris, and identified the geological and evolutionary processes that have shaped its divergence pattern.

Methods

We collected Typlocaris specimens of three species (T. galilea, T. ayyaloni, and T. salentina), originating from subterranean groundwater caves by the Mediterranean Sea, and used three mitochondrial genes (12S, 16S, cytochrome oxygnese subunit 1 (COI)) and four nuclear genes (18S, 28S, internal transcribed spacer, Histon 3) to infer their phylogenetic relationships. Using the radiometric dating of a geological formation (Bira) as a calibration node, we estimated the divergence times of the Typhlocaris species and the molecular evolution rates.

Results

The multi-locus ML/Bayesian trees of the concatenated seven gene sequences showed that T. salentina (Italy) and T. ayyaloni (Israel) are sister species, both sister to T. galilea (Israel). The divergence time of T. ayyaloni and T. salentina from T. galilea was 7.0 Ma based on Bira calibration. The divergence time of T. ayyaloni from T. salentina was 5.7 (4.4-6.9) Ma according to COI, and 5.8 (3.5-7.2) Ma according to 16S. The computed interspecific evolutionary rates were 0.0077 substitutions/Myr for COI, and 0.0046 substitutions/Myr for 16S.

Discussion

Two consecutive vicariant events have shaped the phylogeographic patterns of Typhlocaris species. First, T. galilea was tectonically isolated from its siblings in the Mediterranean Sea by the arching uplift of the central mountain range of Israel ca. seven Ma. Secondly, T. ayyaloni and T. salentina were stranded and separated by a marine transgression ca. six Ma, occurring just before the Messinian Salinity Crisis. Our estimated molecular evolution rates were in one order of magnitude lower than the rates of closely related crustaceans, as well as of other stygobiont species. We suggest that this slow evolution reflects the ecological conditions prevailing in the highly isolated subterranean water bodies inhabited by Typhlocaris.

Species identification and connectivity of marine amphipods in Canada's three oceans

Monitoring the distribution of marine biodiversity is a crucial step to better assess the impacts of global changes. Arctic marine fauna is dominated by amphipods in terms of abundance and biomass. These peracarids are an important marine order of crustaceans but the number of species found in the different Canadian oceans is currently unknown. Furthermore, most species are difficult to identify due to poor taxonomic descriptions and morphological convergence. The aim of this study was to assess the species diversity of marine amphipods in the three Canadian oceans using DNA barcoding. To do so, we produced a database of DNA barcodes of amphipods from the three Canadian Oceans publicly available from the BOLD website to which we added 310 new sequences from the Canadian Arctic Archipelago. We first delimited amphipod species based on barcode gap detection techniques and tree based method (bPTP) and then compared the composition of amphipods among the three oceans in order to assess the influence of past transarctic exchanges on Arctic diversity. Our analysis of 2309 sequences which represent more than 250 provisional species revealed a high connectivity between the Atlantic and Arctic Oceans. Our results also suggest that a single threshold to delimitate species is not suitable for amphipods. This study highlights the challenges involved in species delimitation and the need to obtain complete barcoding inventories in marine invertebrates.

Diversity of marine planktonic ostracods in South China Sea: a DNA taxonomy approach

Ostracods (Crustacea, Ostracoda) are small bivalved crustaceans, contributing over 200 described species to the marine zooplankton community. They are widely distributed and are relatively abundant components of the mesozooplankton, playing an important role in the transport of organic matter to deep layers. However, identification of ostracods based on micro-morphological characters is extremely difficult and time-consuming. Previous fragmentary taxonomic studies of ostracods in the South China Sea (SCA), were based solely on morphology. Here, by analysing the mitochondrial COI gene, we explore the taxa across the SCA using molecular tools for the first time. Our results show that sequence divergence among species varies within a large range, from 12.93% to 35.82%. Sixteen of the taxonomic units recovered by DNA taxonomy agree well with morphology, but Paraconchoecia oblonga, Conchoecia magna and Halocypris brevirostris split into two clades each, each of which contains cryptic species.

The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages

The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120-253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus, we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range. Phylogenetic analyses reveal that S. hispidus has a Western Atlantic lineage and a widely distributed Indo-Pacific lineage, separated by sequence divergence of 2.1%. Genetic diversity is much higher in the Western Atlantic (h = 0.929; π = 0.004) relative to the Indo-Pacific (h = 0.105; π < 0.001), and coalescent analyses indicate that the Indo-Pacific population expanded more recently (95% HPD (highest posterior density) = 60,000-400,000 yr) than the Western Atlantic population (95% HPD = 300,000-760,000 yr). Divergence of the Western Atlantic and Pacific lineages is estimated at 710,000-1.8 million years ago, which does not readily align with commonly implicated colonization events between the ocean basins. The estimated age of populations contradicts the prevailing dispersal route for tropical marine biodiversity (Indo-Pacific to Atlantic) with the oldest and most diverse population in the Atlantic, and a recent population expansion with a single common haplotype shared throughout the vast Indian and Pacific oceans. In contrast to the circumtropical fishes, this diminutive reef shrimp challenges our understanding of conventional dispersal capabilities of marine species.

DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities

Morphology-based profiling of benthic communities has been extensively applied to aquatic ecosystems' health assessment. However, it remains a low-throughput, and sometimes ambiguous, procedure. Despite DNA metabarcoding has been applied to marine benthos, a comprehensive approach providing species-level identifications for estuarine macrobenthos is still lacking. Here we report a combination of experimental and field studies to assess the aptitude of COI metabarcoding to provide robust species-level identifications for high-throughput monitoring of estuarine macrobenthos. To investigate the ability of metabarcoding to detect all species present in bulk DNA extracts, we contrived three phylogenetically diverse communities, and applied four different primer pairs to generate PCR products within the COI barcode region. Between 78-83% of the species in the contrived communities were recovered through HTS. Subsequently, we compared morphology and metabarcoding-based approaches to determine the species composition from four distinct estuarine sites. Our results indicate that species richness would be considerably underestimated if only morphological methods were used: globally 27 species identified through morphology versus 61 detected by metabarcoding. Although further refinement is required to improve efficiency and output of this approach, here we show the great aptitude of COI metabarcoding to provide high quality and auditable species identifications in estuarine macrobenthos monitoring.