Multiple origins of deep-sea Asellota (Crustacea: Isopoda) from shallow waters revealed by molecular data

Colonization of the ocean floor by jawless vertebrates across three mass extinctions

BACKGROUND

The deep (> 200 m) ocean floor is often considered to be a refugium of biodiversity; many benthic marine animals appear to share ancient common ancestry with nearshore and terrestrial relatives. Whether this pattern holds for vertebrates is obscured by a poor understanding of the evolutionary history of the oldest marine vertebrate clades. Hagfishes are jawless vertebrates that are either the living sister to all vertebrates or form a clade with lampreys, the only other surviving jawless fishes.

RESULTS

We use the hagfish fossil record and molecular data for all recognized genera to construct a novel hypothesis for hagfish relationships and diversification. We find that crown hagfishes persisted through three mass extinctions after appearing in the Permian ~ 275 Ma, making them one of the oldest living vertebrate lineages. In contrast to most other deep marine vertebrates, we consistently infer a deep origin of continental slope occupation by hagfishes that dates to the Paleozoic. Yet, we show that hagfishes have experienced marked body size diversification over the last hundred million years, contrasting with a view of this clade as morphologically stagnant.

CONCLUSION

Our results establish hagfishes as ancient members of demersal continental slope faunas and suggest a prolonged accumulation of deep sea jawless vertebrate biodiversity.

A new species of Mexicope Hooker, 1985 (Crustacea, Isopoda) - the first record of Acanthaspidiidae Menzies, 1962 from the Mediterranean Sea

Background

The marine isopod family Acanthaspidiidae Menzies, 1962 (Asellota, Janiroidea) has global distribution from shelf to hadal depth. The majority of species has been recorded from relatively deep waters and the Southern Hemisphere. To date, 36 species have been described in the family belonging to three genera: Ianthopsis Beddard, 1886; Iolanthe Beddard, 1886; and Mexicope Hooker, 1985.

New information

Here, a new species of Mexicope is described from Maltese waters, adding a fourth species to the genus. It is the first member of the family reported from the Mediterranean Sea. The new species can be recognised by the unique combination of the following characters: cephalothorax with pre-ocular spine large and pointed anterolaterally, rostral projection blunt, eyes reduced; pereonal sternites each with one ventral spine; pereonite two lateral margins with single projection; pleotelson posterior apex long, projecting to approximately half of the length of the uropod protopod; pleopods I distolateral lobes projecting beyond distomedial lobes, apices curved and pointed laterally; uropod exopod length approximately 0.5 endopod length. An identification key to the species of Mexicope is presented and the generic diagnoses of Ianthopsis and Mexicope are compared, discussed and revised.

Diversity under a magnifier lens: the case of Typhlotanaidae (Crustacea: Tanaidacea) in the N Atlantic

Research focusing on 'stout-bodied' typhlotanaids collected from several sites around Iceland and adjacent N Atlantic region has resulted in the description of 15 species new to science, as well as the creation of eight new genera. Typhlotanais eximius Hansen, 1913 is redescribed and transferred to a new genus, while Typhlotanais crassus and Peraeospinosus adipatus are transferred to the genus Larsenotanais. The morphological and the molecular data were combined to consolidate and confirm the validity of the results obtained from both approaches. The polyphyletic nature of the Typhlotanaidae and its serious of its taxonomic diversity are emphasized, although molecular analysis reveals that the 'stout-bodied' Typhlotanaidae form monophyletic clade. Depth and temperature are identified as the main environmental parameters determining the distribution of this group of Typhlotanaidae. Several species are clearly associated with the shelf and upper bathyal of Iceland. The Greenland-Iceland-Faroe Ridge is shown to be a distinct zoogeographical barrier for typhlotanaids inhabiting the deeper slope and abyssal regions around Iceland.

Combining morphological and mitochondrial DNA data to describe a new species of Austroniscus Vanhöffen, 1914 (Isopoda, Janiroidea, Nannoniscidae) linking abyssal and hadal depths of the Puerto Rico Trench

Hadal trenches are perceived as a unique deep-sea ecosystem with fundamentally different communities compared to the nearby abyss. So far, however, scarce information exists about how populations are genetically linked within a trench and about mechanisms for species divergence. The present study presents the morphological and molecular-genetic characterization and description of a new nannoniscid species within the genus Austroniscus Vanhöffen, 1914 obtained from abyssal and hadal depths of the Puerto Rico Trench, NW Atlantic. Samples were collected as part of the Vema-TRANSIT expedition onboard RV Sonne in January 2015. Because of the large depth differences between sampling locations (4,552-8,338 m), we expected to find different species within the genus inhabiting abyssal and hadal sites. Initial morphological examination using traditional light microscopy and Confocal Laser Scanning Microscopy was paired with subsequent molecular analysis based on mtDNA (COI and 16S). Contrary to our assumptions, combined morphological and molecular species delimitation analyses (sGMYC, mPTP, ABGD) revealed the presence of only one species spanning the abyssal and hadal seafloor of the Puerto Rico Trench. In addition, comparison with type material could show that this species belongs to a new species, Austroniscus brandtae n. sp., which is described herein. Incongruence between some species delimitation methods suggesting the presence of multiple species is interpreted as strong genetic population structuring within the trench, which is also supported by the analysis of the haplotype networks. The geographic and bathymetric distribution of Austroniscus species is discussed. The species described herein represents the first in the genus Austroniscus from the Atlantic Ocean and the deepest record of the genus to date, and hence significantly expanding previously known limits of its geographic and bathymetric range.

Two New Phyllopodopsyllus Species (Harpacticoida, Tetragonicipitidae) from Korea

Three species of the genus Phyllopodopsyllus T. Scott, 1906 (Copepoda: Harpacticoida: Tetragonicipitidae) were reported from the intertidal sand of Jeju Island and Busan in Korea, Phyllopdopsyllus kitazimai Karanovic, 2017, Phyllopodopsyllus saywakimi sp. nov. and Phyllopodopsyllus similis sp. nov. The latter two were described here. Phyllopodopsyllus saywakimi sp. nov. collected from only Udo, Jeju is similar to a Pacific species from Costa Rica, Phyllopodopsyllus ancylus Mielke, 1992. However, P. saywakimi sp. nov. differs from the Costa Rica species in the body size, the number of armatures on the antenna, the length ratio of endo- and exopod of the mandible, and the chaetotaxy of the fifth female pereiopod and the sixth male pereiopod. The second new species, P. similis sp. nov., found in Busan and several localities of Jeju, significantly resembles the species complex related to Phyllopodopsyllus aegypticus Nicholls, 1944, which is widely distributed in the Indian, Pacific, and Atlantic oceans. P. similis sp. nov. can be distinguished from the P. aegypticus complex by the body size, the shape of the rostrum, the type of armatures, the length ratio of rami and armatures, and the chaetotaxy of the female P5. In addition to the species descriptions, partial fragments of small and large subunit ribosomal RNA genes, cytochrome b, and cytochrome c oxidase subunit I were provided. Using molecular markers, a phylogenetic analysis was also performed to estimate the relationships among the three Korean species of Phyllopodopsyllus for the first time.

Two New Uromunna Species (Isopoda: Asellota: Munnidae) from the Korean Peninsula and Their Phylogenetic Position within Munnoid Groups

Two new Uromunna species, Uromunna mundongensis sp. n. and Uromunna jejuensis sp. n., are described from the Korean Peninsula, representing the first record of the genus in Korean waters. Genetic analyses using two mitochondrial (COI, Cytb) and one ribosomal (18S rRNA) gene allowed us to confirm high pair-wise interspecific differences with the establishment of reliable barcoding gaps of COI (19.9%) and 18S (0.4%) between the new species. Finally, the phylogenetic relationship between the Uromunna species as well as the position of the genus within the munnoid groups are reconstructed using 18S.

Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea

Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-Ser ^AGY with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-Ser ^AGY. No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea.

Mitogenomics provides new insights into the phylogenetic relationships and evolutionary history of deep-sea sea stars (Asteroidea)

The deep sea (> 200 m) is considered as the largest and most remote biome, which characterized by low temperatures, low oxygen level, scarce food, constant darkness, and high hydrostatic pressure. The sea stars (class Asteroidea) are ecologically important and diverse echinoderms in all of the world’s oceans, occurring from the intertidal to the abyssal zone (to about 6000 m). To date, the phylogeny of the sea stars and the relationships of deep-sea and shallow water groups have not yet been fully resolved. Here, we recovered five mitochondrial genomes of deep-sea asteroids. The A+T content of the mtDNA in deep-sea asteroids were significantly higher than that of the shallow-water groups. The gene orders of the five new mitogenomes were identical to that of other asteroids. The phylogenetic analysis showed that the orders Valvatida, Paxillosida, Forcipulatida are paraphyletic. Velatida was the sister order of all the others and then the cladeValvatida-Spinulosida-Paxillosida-Notomyotida versus Forcipulatida-Brisingida. Deep-sea asteroids were nested in different lineages, instead of a well-supported clade. The tropical Western Pacific was suggested as the original area of asteroids, and the temperate water was initially colonized with asteroids by the migration events from the tropical and cold water. The time-calibrated phylogeny showed that Asteroidea originated during Devonian-Carboniferous boundary and the major lineages of Asteroidea originated during Permian–Triassic boundary. The divergence between the deep-sea and shallow-water asteroids coincided approximately with the Triassic-Jurassic extinction. Total 29 positively selected sites were detected in fifteen mitochondrial genes of five deep-sea lineages, implying a link between deep-sea adaption and mitochondrial molecular biology in asteroids.

Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea)

DNA barcoding has become the most popular approach for species identification in recent years. As part of the German Barcode of Life project, the first DNA barcode library for terrestrial and freshwater isopods from Germany is presented. The analyzed barcode library included 38 terrestrial (78% of the documented species of Germany) and five freshwater (63%) species. A total of 513 new barcodes was generated and 518 DNA barcodes were analyzed. This analysis revealed surprisingly high intraspecific genetic distances for numerous species, with a maximum of 29.4% for Platyarthrus hoffmannseggii Brandt, 1833. The number of BINs per species ranged from one (32 species, 68%) to a maximum of six for Trachelipus rathkii (Brandt, 1833). In spite of such high intraspecific variability, interspecific distances with values between 12.6% and 29.8% allowed a valid species assignment of all analyzed isopods. The observed high intraspecific distances presumably result from phylogeographic events, Wolbachia infections, atypical mitochondrial DNAs, heteroplasmy, or various combinations of these factors. Our study represents the first step in generating an extensive reference library of DNA barcodes for terrestrial and freshwater isopods for future molecular biodiversity assessment studies.

Evolution and phylogeny of the deep-sea isopod families Desmosomatidae Sars, 1897 and Nannoniscidae Hansen, 1916 (Isopoda: Asellota)

In the deep sea, the phylogeny and biogeography of only a few taxa have been well studied. Although more than 200 species in 32 genera have been described for the asellote isopod families Desmosomatidae Sars, 1897 and Nannoniscidae Hansen, 1916 from all ocean basins, their phylogenetic relationships are not completely understood. There is little doubt about the close relationship of these families, but the taxonomic position of a number of genera is so far unknown. Based on a combined morphological phylogeny using the Hennigian method with a dataset of 107 described species and a molecular phylogeny based on three markers (COI, 16S, and 18S) with 75 species (most new to science), we could separate Desmosomatidae and Nannoniscidae as separate families. However, we could not support the concept of the subfamilies Eugerdellatinae Hessler, 1970 and Desmosomatinae Hessler, 1970. Most genera of both families were well supported, but several genera appear as para- or even polyphyletic. Within both families, convergent evolution and analogies caused difficulty in defining apomorphies for phylogenetic reconstructions and this is reflected in the results of the concatenated molecular tree. There is no biogeographic pattern in the distribution as the genera occur over the entire Atlantic and Pacific Ocean, showing no specific phylogeographical pattern. Poor resolution at deep desmosomatid nodes may reflect the long evolutionary history of the family and rapid evolutionary radiations.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13127-021-00509-9.

Quinquelaophonte enormis sp. nov., a new interstitial copepod (Harpacticoida: Laophontidae) from Korea

We collected an undescribed laophontid copepod from a coarse sand habitat on the east coast of Korea and named it Quinquelaophonte enormissp. nov. We compared the detailed morphological characteristics of the new species with those of congeneric species. Among them, the new species shows a superficial resemblance to the Californian species Quinquelaophonte longifurcataLang, 1965. However, the two species are easily distinguishable by the setation of the syncoxa on the maxilliped and the fourth swimming leg. The new species has the variable setation on the second to fourth swimming legs. The variations appear among individuals or between the left and right rami of a pair of legs in a single specimen. Although complex chaetotaxical polymorphism occur in this new species, we used myCOI and Cytb to confirm that the new species is not a species complex. Also, partial sequences of 18S and 28S ribosomal RNA genes were used to analyze the position of the new species within the family Laophontidae. The new speciesis the fourteenth Quinquelaophonte species in the world and the second species in Korea.

Macrostylis metallicola spec. nov.-an isopod with geographically clustered genetic variability from a polymetallic-nodule area in the Clarion-Clipperton Fracture Zone

Background

The Clarion-Clipperton Fracture Zone (CCFZ) in the Northeast Central Pacific Ocean is a region of heightened scientific and public interest because of its wealth in manganese nodules. Due to a poor ecological understanding at the abyssal seafloor and limited knowledge of the organisms inhabiting this area, huge efforts in alpha taxonomy are required. To predict and manage potential hazards associated with future mining, taxonomy is an essential first step to grasp fundamental ecosystem traits, such as biogeographic patterns, connectivity, and the potential for post-impact recolonization. Amongst samples from the Global Sea Mineral Resources NV exploration area (EA) in the CCFZ an undescribed species of the isopod crustacean family Macrostylidae was discovered. Previously, it has been reported from two other nearby regions, the Institut Français de Recherche pour l’Exploitation de la Mer and BGR EAs. There it was one of the more widely distributed and abundant species of the benthic macrofauna and exhibited geographically structured populations. It nevertheless remained taxonomically undescribed so far.

Methods

The new species is described by means of integrative taxonomy. Morphologically, macro photography, confocal microscopy, scanning electron microscopy and light microscopy were used to describe the species and to get first insights on its phylogenetic origin. Additionally, mitochondrial DNA markers were used to test the morphological allocation of the two dimorphic sexes and juvenile stages, to analyze geographic patterns of genetic differentiation, and to study intra-and inter-species relationships, also in light of previously published population genetics on this species.

Results

The new species, Macrostylis metallicola spec. nov., is a typical representative of Macrostylidae as recognizable from the fossosoma, prognathous cephalothorax, and styliform uropods. It can be morphologically distinguished from congeners by a combination of character states which include the autapomorphic shape of the first pleopod of the copulatory male. A sexual dimorphism, as expressed by a peculiar sequence of article length-width ratios of the male antennula, indicates a relationship with M. marionaeKniesz, Brandt & Riehl (2018) and M. longipesHansen (1916) amongst other species sharing this dimorphism. Mitochondrial genetic markers point in a similar direction. M. metallicola appears to be amongst the more common and widely distributed components of the benthic macrofauna in this region which may suggest a resilience of this species to future mining activities because of its apparent potential for recolonization of impacted sites from adjacent areas of particular environmental interest. The genetic data, however, show geographic clustering of its genetic variability, pointing towards a limited potential for dispersal. Local extinction of populations could potentially not be compensated quickly and would mean a loss of genetic diversity of this species.

A new Southern Ocean species in the remarkable and rare amphipod family Podosiridae (Crustacea: Amphipoda) questions existing systematic hypotheses

The amphipod family Podosiridae is unusual in that it combines morphological elements of the disparate families Podoceridae and Eusiridae. Here, we describe a new species in the family from specimens collected from the Southern Ocean in the vicinity of the South Orkney Islands and South Shetland Islands. We present mitochondrial (COI and 16S) and nuclear (18S) nucleic acid sequences for this and a congeneric species and use these to investigate the phylogenetic placement of Podosiridae within the Amphipoda. Our results do not provide evidence for a close relationship between Podosiridae and Podoceridae or Eusiridae, suggesting that the superficial similarity between these families is the result of morphological convergence. Instead, it is likely that Podosiridae are more closely related to families within Amphilochidira, such as Stenothoidae. Definitive placement of Podosiridae in the Amphipoda awaits further specimen collection, additional nucleotide data (including sequences from the Hyperiopsidae and the Vitjazianidae) and a more directed analysis of relationships within this portion of the amphipod phylogeny.

Genetic evidence against monophyly of Oniscidea implies a need to revise scenarios for the origin of terrestrial isopods

Among the few crustacean taxa that managed to inhabit terrestrial environments, Oniscidea includes the most successful colonizers in terms of species richness and abundance. However, neither morphological traits nor molecular markers have definitively resolved phylogenetic relationships among major Oniscidea clades or established the monophyly of the taxon. Herein, we employed the highly conserved, nuclear protein-coding genes Sodium-Potassium Pump (NAK) and Phosphoenolpyruvate Carboxykinase (PEPCK), along with the traditionally used 18 s and 28 s ribosomal RNA genes, in an attempt to clarify these questions. Our dataset included sequences representing all major Oniscidea clades and closely related aquatic taxa, as suggested by previous studies. We applied Bayesian Inference and Maximum Likelihood methods and produced a robust and fully resolved phylogenetic tree that offers strong evidence against the monophyly of Oniscidea. The amphibious genus Ligia appears to be more closely related to representatives of marine suborders, while the phylogenetic pattern of the remaining Oniscidea implies a complex history of the transition from the marine environment to land. With the exception of the basal clade, all other established major clades have been recovered as monophyletic, even though relationships within these clades call for a revised interpretation of morphological characters used in terrestrial isopod taxonomy.

Molecular and Histopathological Data on Levisunguis subaequalis Curran, Overstreet, Collins & Benz, 2014 (Pentastomida: Eupentastomida: Porocephalida: Porocephaloidea: Sebekidae: Sebekinae) from Gambusia affinis in Alabama, USA

Levisunguis subaequalis Curran, Overstreet, Collins & Benz, 2014 , was recently described from the lungs of the definitive hosts, softshell turtles, Apalone ferox (Schneider, 1783), and Apalone spinifera aspera (Agassiz, 1857) as well as the viscera of an intermediate host, the western mosquitofish, Gambusia affinis (Baird and Girard, 1853). However, the original account lacked molecular data. Furthermore, histological examination of infected host tissues in the original account of L. subaequalis did not reveal any pathological changes in the intermediate host. The present work provides a robust morphological description of the nymph and novel molecular data from the 18S and 28S ribosomal gene regions and the cytochrome c oxidase subunit 1 (COI) mitochondrial gene. Phylogenetic analyses using Bayesian inference and maximum likelihood analysis with concatenated sequence data from these 3 regions, as well as each region individually, placed the turtle pentastomid L. subaequalis as a sister clade to the crocodilian pentastomids of the genus Sebekia Sambon, 1922. While only concatenated phylogenetic analyses agreed with the currently accepted classification of the Eupentastomida and phylogenetic signal assessment indicated that the concatenated data set yielded the most phylogenetic signal, data from more taxa are still needed for robust phylogenetic inferences to be made. The intensity of infection ranged from 2 to 171 nymphs per fish, compared with the highest previously reported intensity of 6. These high-intensity infections with L. subaequalis were characterized by the nymphs occupying 5-50% of the coelomic cavity of G. affinis. However, despite this heavy parasite infection, fish exhibited minimal pathology. Observed pathology was characterized by compression or effacement of organs adjacent to the nymphs, particularly liver, swim bladder, and intestines, as well as the formation of granulomas around shed pentastomid cuticles. Nonetheless, the morphological and molecular data provided in the present work will bolster future efforts to identify this pentastomid in other hosts where pathology may be present in addition to aiding in the advancement of the field of molecular pentastomid systematics.

The Kingdom of the Blind: Disentangling Fundamental Drivers in the Evolution of Eye Loss

Light is a fundamentally important biological cue used by almost every animal on earth, to maintain daily rhythms, navigate, forage, find mates, or avoid predators. But an enormous number of species live in darkness: in subterranean caves, deep oceans, underground burrows, and within parasitic host bodies, and the loss of eyes appears consistently across these ecosystems. However, the evolutionary mechanisms that lead to the reduction of the visual system remain the subject of great interest and debate more than 150 years after Darwin tackled the issue. Studies of model taxa have discovered significant roles for natural selection, neutral evolution, and pleiotropy, but the interplay between them remains unclear. To nail down unifying concepts surrounding the evolution of eye loss, we must embrace the enormous range of affected animals and habitats. The fine developmental details of model systems such as the Mexican cave tetra Astyanax mexicanus have transformed and enriched the field, but these should be complemented by wider studies to identify truly overarching patterns that apply throughout animals. Here, the major evolutionary drivers are placed within a conceptual cost-benefit framework that incorporates the fundamental constraints and forces that influence evolution in the dark. Major physiological, ecological, and environmental factors are considered within the context of this framework, which appears faithful to observed patterns in deep-sea and cavernicolous animals. To test evolutionary hypotheses, a comparative phylogenetic approach is recommended, with the goal of studying large groups exhibiting repeated reduction, and then comparing these across habitats, taxa, and lifestyles. Currently, developmental and physiological methods cannot feasibly be used on such large scales, but penetrative imaging techniques could provide detailed morphological data non-invasively and economically for large numbers of species. Comprehensive structural datasets can then be contextualized phylogenetically to examine recurrent trends and associations, and to reconstruct character histories through multiple independent transitions into darkness. By assessing these evolutionary trajectories within an energetic cost-benefit framework, the relationships between fundamental influences can be inferred and compared across different biological and physical parameters. However, substantial numbers of biological and environmental factors affect the evolutionary trajectory of loss, and it is critical that researchers make fair and reasonable comparisons between objectively similar groups.

A molecular phylogeny of Porcellionidae (Isopoda, Oniscidea) reveals inconsistencies with present taxonomy

Porcellionidae is one of the richest families of Oniscidea globally distributed but we still lack a comprehensive and robust phylogeny of the taxa that are assigned to it. Employing five genetic markers (two mitochondrial and three nuclear) we inferred phylogenetic relationships among the majority of Porcellionidae genera. Phylogenetic analyses conducted via Maximum Likelihood and Bayesian Inference resulted in similar tree topologies. The mtDNA genes cytochrome oxidase I (COI) and 16s rRNA (16s) were used for clade dating using previously published mutation rates. Our results provide evidence against the monophyly of both Porcellionidae and the largest genus of the family Porcellio. These results are compared to previous published work based on morphological evidence. The genera Leptotrichus and Brevurus are not grouped with the rest of Porcellionidae whereas Agnaridae are grouped with part of Porcellionidae. Armadillidium and Schizidium (Armadillidiidae) occupy a basal position on the phylogenetic tree. Even though the African genera Tura and Uramba (distributed in East Africa) are grouped together there is no general geographical pattern in other sub-clades. Additional taxonomic issues that arise in this work such as the assignment of the recently described genus Levantoniscus, arealso discussed. The status of Porcellionidae should be further revised and morphological characters traditionally used in Oniscidea taxonomy should be reconsidered in view of molecular evidence. The origin of the monophyletic clade within Porcellionidae as indicated in the present work is dated back to the Oligocene (~32 mya).

Cryptic species in a well-known habitat: applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida)

Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.

A Redescription of Serrasentis sagittifer (Rhadinorhynchidae: Serrasentinae) from Rachycentron canadum (Rachycentridae) with Comments on its Biology and its Relationship to Other Species of Serrasentis

Adult and cystacanth forms of the acanthocephalan Serrasentis sagittifer from Australian coastal waters are redescribed and verified as the same species using both molecular and morphological data. This study provides the baseline 18S rDNA, 28S rDNA, and cox1 sequence data to serve as genetic barcode for S. sagittifer. The validity of the currently recognized species of Serrasentis is discussed. The most recently described species are junior synonyms of either Serrasentis nadakali or S. sagittifer, and a number of species are species inquirenda. When using morphological characters to distinguish the species of Serrasentis, consideration needs to be given to the maturity of the specimens, since the trunk elongates and the number and distribution of the ventral combs changes as worms mature, although the proboscis armature itself does not change. A simple key to assist in the identification of species of Serrasentis is provided. Adult S. sagittifer appear to be highly host specific to the cobia, Rachycentron canadum, in northern Australian waters, whereas cystacanths have been reported from a wide range of fish species. The relationship between host length and number of cystacanths shows that most paratenic infections are acquired as young fish, most likely via a crustacean intermediate host.

Cloning and Functional Analysis of Pax6 from the Hydrothermal Vent Tubeworm Ridgeia piscesae

The paired box 6 (Pax6) gene encodes a transcription factor essential for eye development in a wide range of animal lineages. Here we describe the cloning and characterization of Pax6 gene from the blind hydrothermal vent tubeworm Ridgeia piscesae (RpPax6). The deduced RpPax6 protein shares extensive sequence identity with Pax6 proteins from other species and contains both the paired domain and a complete homeodomain. Phylogenetic analysis indicates that it clusters with the corresponding sequence from the closely related species Platynereis dumerilii (P. dumerilii) of Annelida. Luciferase reporter assay indicate that RpPax6 protein suppresses the transcription of sine oculis (so) in D. melanogaster, interfering with the C-terminal of RpPax6. Taking advantage of Drosophila model, we show that RpPax6 expression is not able to rescue small eye phenotype of ey² mutant, only to cause a more severe headless phenotype. In addition, RpPax6 expression induced apoptosis and inhibition of apoptosis can partially rescue RpPax6-induced headless phenotype. We provide evidence RpPax6 plays at least two roles: it blocks the expression of later-acting transcription factors in the eye development cascade, and it promotes cell apoptosis. Our results indicate alternation of the Pax6 function may be one of the possible causes that lead the eye absence in vestimentiferan tubeworms.

The unique deep sea-land connection: interactive 3D visualization and molecular phylogeny of Bathyhedyle boucheti n. sp. (Bathyhedylidae n. fam.)-the first panpulmonate slug from bathyal zones

The deep sea comprises vast unexplored areas and is expected to conceal significant undescribed invertebrate species diversity. Deep waters may act as a refuge for many relictual groups, including elusive and enigmatic higher taxa, but the evolutionary pathways by which colonization of the deep sea has occurred have scarcely been investigated. Sister group relationships between shallow water and deep sea taxa have been documented in several invertebrate groups, but are unknown between amphibious/terrestrial and deep-sea species. Here we describe in full and interactive 3D morphoanatomical detail the new sea slug species Bathyhedyle boucheti n. sp., dredged from the continental slope off Mozambique. Molecular and morphological analyses reveal that it represents a novel heterobranch gastropod lineage which we establish as the new family Bathyhedylidae. The family is robustly supported as sister to the recently discovered panpulmonate acochlidian family Aitengidae, which comprises amphibious species living along the sea shore as well as fully terrestrial species. This is the first marine-epibenthic representative among hedylopsacean Acochlidiida, the first record of an acochlidian from deep waters and the first documented panpulmonate deep-sea slug. Considering a marine mesopsammic ancestor, the external morphological features of Bathyhedyle n. gen. may be interpreted as independent adaptations to a benthic life style in the deep sea, including the large body size, broad foot and propodial tentacles. Alternatively, the common ancestor of Bathyhedylidae and Aitengidae may have been a macroscopic amphibious or even terrestrial species. We hypothesize that oophagy in the common ancestor of Aitengidae and Bathyhedylidae might explain the impressive ecological and evolutionary flexibility in habitat choice in the Acochlidiida.

Genomic characterization of symbiotic mycoplasmas from the stomach of deep-sea isopod bathynomus sp

Deep-sea isopod scavengers such as Bathynomus sp. are able to live in nutrient-poor environments, which is likely attributable to the presence of symbiotic microbes in their stomach. In this study we recovered two draft genomes of mycoplasmas, Bg1 and Bg2, from the metagenomes of the stomach contents and stomach sac of a Bathynomus sp. sample from the South China Sea (depth of 898 m). Phylogenetic trees revealed a considerable genetic distance to other mycoplasma species for Bg1 and Bg2. Compared with terrestrial symbiotic mycoplasmas, the Bg1 and Bg2 genomes were enriched with genes encoding phosphoenolpyruvate-dependent phosphotransferase systems (PTSs) and sodium-driven symporters responsible for the uptake of sugars, amino acids and other carbohydrates. The genome of mycoplasma Bg1 contained sialic acid lyase and transporter genes, potentially enabling the bacteria to attach to the stomach sac and obtain organic carbons from various cell walls. Both of the mycoplasma genomes contained multiple copies of genes related to proteolysis and oligosaccharide degradation, which may help the host survive in low-nutrient conditions. The discovery of the different types of mycoplasma bacteria in the stomach of this deep-sea isopod affords insights into symbiotic model of deep-sea animals and genomic plasticity of mycoplasma bacteria.

The role of ontogeny in physiological tolerance: decreasing hydrostatic pressure tolerance with development in the northern stone crab Lithodes maja

Extant deep-sea invertebrate fauna represent both ancient and recent invasions from shallow-water habitats. Hydrostatic pressure may present a significant physiological challenge to organisms seeking to colonize deeper waters or migrate ontogenetically. Pressure may be a key factor contributing to bottlenecks in the radiation of taxa and potentially drive speciation. Here, we assess shifts in the tolerance of hydrostatic pressure through early ontogeny of the northern stone crab Lithodes maja, which occupies a depth range of 4-790 m in the North Atlantic. The zoea I, megalopa and crab I stages were exposed to hydrostatic pressures up to 30.0 MPa (equivalent of 3000 m depth), and the relative fold change of genes putatively coding for the N-methyl-D-aspartate receptor-regulated protein 1 (narg gene), two heat-shock protein 70 kDa (HSP70) isoforms and mitochondrial Citrate Synthase (CS gene) were measured. This study finds a significant increase in the relative expression of the CS and hsp70a genes with increased hydrostatic pressure in the zoea I stage, and an increase in the relative expression of all genes with increased hydrostatic pressure in the megalopa and crab I stages. Transcriptional responses are corroborated by patterns in respiratory rates in response to hydrostatic pressure in all stages. These results suggest a decrease in the acute high-pressure tolerance limit as ontogeny advances, as reflected by a shift in the hydrostatic pressure at which significant differences are observed.

Joeropsididae Nordenstam, 1933 (Crustacea, Isopoda, Asellota) from the Lizard Island region of the Great Barrier Reef, Queensland, Australia

The marine isopod family Joeropsididae (Asellota) is documented for the Lizard Island region of the Great Barrier Reef, Australia. Fifteen species of Joeropsis are recorded, including ten new species; descriptive notes are provided for five species that lacked adequate material for description. A revised family and genus diagnosis is presented together with comments on the most useful characters for species identification and a key to Joeropsis of the Lizard Island region.

Temperature impacts on deep-sea biodiversity

Temperature is considered to be a fundamental factor controlling biodiversity in marine ecosystems, but precisely what role temperature plays in modulating diversity is still not clear. The deep ocean, lacking light and in situ photosynthetic primary production, is an ideal model system to test the effects of temperature changes on biodiversity. Here we synthesize current knowledge on temperature-diversity relationships in the deep sea. Our results from both present and past deep-sea assemblages suggest that, when a wide range of deep-sea bottom-water temperatures is considered, a unimodal relationship exists between temperature and diversity (that may be right skewed). It is possible that temperature is important only when at relatively high and low levels but does not play a major role in the intermediate temperature range. Possible mechanisms explaining the temperature-biodiversity relationship include the physiological-tolerance hypothesis, the metabolic hypothesis, island biogeography theory, or some combination of these. The possible unimodal relationship discussed here may allow us to identify tipping points at which on-going global change and deep-water warming may increase or decrease deep-sea biodiversity. Predicted changes in deep-sea temperatures due to human-induced climate change may have more adverse consequences than expected considering the sensitivity of deep-sea ecosystems to temperature changes.

Evolutionary dynamics of a common sub-Antarctic octocoral family

Sequence data were obtained for five different loci, both mitochondrial (cox1, mtMutS, 16S) and nuclear (18S, 28S rDNA), from 64 species representing 25 genera of the common deep-sea octocoral family Primnoidae. We tested the hypothesis that Primnoidae have an Antarctic origin, as this is where they currently have high species richness, using Maximum likelihood and Bayesian inference methods of phylogenetic analysis. Using a time-calibrated molecular phylogeny we also investigated the time of species radiation in sub-Antarctic Primnoidae. Our relatively wide taxon sampling and phylogenetic analysis supported Primnoidae as a monophyletic family. The base of the well-supported phylogeny was Pacific in origin, indicating Primnoidae sub-Antarctic diversity is a secondary species radiation. There is also evidence for a subsequent range extension of sub-Antarctic lineages into deep-water areas of the Indian and Pacific Oceans. Conservative and speculative fossil-calibration analyses resulted in two differing estimations of sub-Antarctic species divergence times. Conservative analysis suggested a sub-Antarctic species radiation occurred ∼52MYA (95% HPD: 36-73MYA), potentially before the opening of the Drake Passage and Antarctic Circumpolar Current (ACC) formation (41-37MYA). Speculative analysis pushed this radiation back into the late Jurassic, 157MYA (95% HPD: 118-204MYA). Genus-level groupings were broadly supported in this analysis with some notable polyphyletic exceptions: Callogorgia, Fanellia, Primnoella, Plumarella, Thouarella. Molecular and morphological evidence supports the placement of Tauroprimnoa austasensis within Dasystenella and Fannyella kuekenthali within Metafannyella.

Explaining bathymetric diversity patterns in marine benthic invertebrates and demersal fishes: physiological contributions to adaptation of life at depth

Bathymetric biodiversity patterns of marine benthic invertebrates and demersal fishes have been identified in the extant fauna of the deep continental margins. Depth zonation is widespread and evident through a transition between shelf and slope fauna from the shelf break to 1000 m, and a transition between slope and abyssal fauna from 2000 to 3000 m; these transitions are characterised by high species turnover. A unimodal pattern of diversity with depth peaks between 1000 and 3000 m, despite the relatively low area represented by these depths. Zonation is thought to result from the colonisation of the deep sea by shallow-water organisms following multiple mass extinction events throughout the Phanerozoic. The effects of low temperature and high pressure act across hierarchical levels of biological organisation and appear sufficient to limit the distributions of such shallow-water species. Hydrostatic pressures of bathyal depths have consistently been identified experimentally as the maximum tolerated by shallow-water and upper bathyal benthic invertebrates at in situ temperatures, and adaptation appears required for passage to deeper water in both benthic invertebrates and demersal fishes. Together, this suggests that a hyperbaric and thermal physiological bottleneck at bathyal depths contributes to bathymetric zonation. The peak of the unimodal diversity-depth pattern typically occurs at these depths even though the area represented by these depths is relatively low. Although it is recognised that, over long evolutionary time scales, shallow-water diversity patterns are driven by speciation, little consideration has been given to the potential implications for species distribution patterns with depth. Molecular and morphological evidence indicates that cool bathyal waters are the primary site of adaptive radiation in the deep sea, and we hypothesise that bathymetric variation in speciation rates could drive the unimodal diversity-depth pattern over time. Thermal effects on metabolic-rate-dependent mutation and on generation times have been proposed to drive differences in speciation rates, which result in modern latitudinal biodiversity patterns over time. Clearly, this thermal mechanism alone cannot explain bathymetric patterns since temperature generally decreases with depth. We hypothesise that demonstrated physiological effects of high hydrostatic pressure and low temperature at bathyal depths, acting on shallow-water taxa invading the deep sea, may invoke a stress-evolution mechanism by increasing mutagenic activity in germ cells, by inactivating canalisation during embryonic or larval development, by releasing hidden variation or mutagenic activity, or by activating or releasing transposable elements in larvae or adults. In this scenario, increased variation at a physiological bottleneck at bathyal depths results in elevated speciation rate. Adaptation that increases tolerance to high hydrostatic pressure and low temperature allows colonisation of abyssal depths and reduces the stress-evolution response, consequently returning speciation of deeper taxa to the background rate. Over time this mechanism could contribute to the unimodal diversity-depth pattern.

Shallow-water northern hemisphere Jaera (Crustacea, Isopoda, Janiridae) found on whale bones in the southern ocean deep sea: ecology and description of Jaera tyleri sp. nov

The skeleton of a natural whale fall discovered in the Southern Ocean at 1,445 m was densely covered by one small, janirid isopod. Jaera tyleri sp. nov. is the first of its genus found in the southern hemisphere and in the deep sea and is described herein. Morphological and molecular investigations revealed the systematic position of this species new to science. Phylogenetic analysis of the 18S locus confirms that this species falls in a strongly supported monophyletic clade of Jaera species. The whale bone habitat of J. tyleri sp. nov. is quite different from those of other species of the genus Jaera. The analysis of bathymetric and distribution patterns of the Janiridae in general and Jaera specifically confirm the unusualness of the habitat for this isopod species. The abundance of J. tyleri sp. nov. on the whale bones and its absence from other nearby habitats suggests it to be a whale-fall specialist. The analysis of the size-frequency distributions of J. tyleri sp. nov. suggests multimodal population structure with continuous breeding activity throughout the year. The fecundity of the species is low but in line with reduced fecundity observed in polar and small-sized isopods.

Comparison of molecular species identification for North Sea calanoid copepods (Crustacea) using proteome fingerprints and DNA sequences

Calanoid copepods play an important role in the pelagic ecosystem making them subject to various taxonomic and ecological studies, as well as indicators for detecting changes in the marine habitat. For all these investigations, valid identification, mainly of sibling and cryptic species as well as early life history stages, represents a central issue. In this study, we compare species identification methods for pelagic calanoid copepod species from the North Sea and adjacent regions in a total of 333 specimens. Morphologically identified specimens were analysed on the basis of nucleotide sequences (i.e. partial mitochondrial cytochrome c oxidase subunit I (COI) and complete 18S rDNA) and on proteome fingerprints using the technology of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). On all three molecular approaches, all specimens were classified to species level indicated by low intraspecific and high interspecific variability. Sequence divergences in both markers revealed a second Pseudocalanus species for the southern North Sea identified as Pseudocalanus moultoni by COI sequence comparisons to GenBank. Proteome fingerprints were valid for species clusters irrespective of high intraspecific variability, including significant differences between early developmental stages and adults. There was no effect of sampling region or time; thus, trophic effect, when analysing the whole organisms, was observed in species-specific protein mass spectra, underlining the power of this tool in the application on metazoan species identification. Because of less sample preparation steps, we recommend proteomic fingerprinting using the MALDI-TOF MS as an alternative or supplementary approach for rapid, cost-effective species identification.

Cenozoic climate change and diversification on the continental shelf and slope: evolution of gastropod diversity in the family Solariellidae (Trochoidea)

Recent expeditions have revealed high levels of biodiversity in the tropical deep-sea, yet little is known about the age or origin of this biodiversity, and large-scale molecular studies are still few in number. In this study, we had access to the largest number of solariellid gastropods ever collected for molecular studies, including many rare and unusual taxa. We used a Bayesian chronogram of these deep-sea gastropods (1) to test the hypothesis that deep-water communities arose onshore, (2) to determine whether Antarctica acted as a source of diversity for deep-water communities elsewhere and (3) to determine how factors like global climate change have affected evolution on the continental slope. We show that although fossil data suggest that solariellid gastropods likely arose in a shallow, tropical environment, interpretation of the molecular data is equivocal with respect to the origin of the group. On the other hand, the molecular data clearly show that Antarctic species sampled represent a recent invasion, rather than a relictual ancestral lineage. We also show that an abrupt period of global warming during the Palaeocene Eocene Thermal Maximum (PETM) leaves no molecular record of change in diversification rate in solariellids and that the group radiated before the PETM. Conversely, there is a substantial, although not significant increase in the rate of diversification of a major clade approximately 33.7 Mya, coinciding with a period of global cooling at the Eocene-Oligocene transition. Increased nutrients made available by contemporaneous changes to erosion, ocean circulation, tectonic events and upwelling may explain increased diversification, suggesting that food availability may have been a factor limiting exploitation of deep-sea habitats. Tectonic events that shaped diversification in reef-associated taxa and deep-water squat lobsters in central Indo-West Pacific were also probably important in the evolution of solariellids during the Oligo-Miocene.

The secret to successful deep-sea invasion: does low temperature hold the key?

There is a general consensus that today’s deep-sea biodiversity has largely resulted from recurrent invasions and speciations occurring through homogenous waters during periods of the Phanerozoic eon. Migrations likely continue today, primarily via isothermal water columns, such as those typical of Polar Regions, but the necessary ecological and physiological adaptations behind them are poorly understood. In an evolutionary context, understanding the adaptations, which allow for colonisation to high-pressure environments, may enable us to predict future events. In this investigation, we examine pressure tolerance during development, in the shallow-water neogastropod Buccinum undatum using thermally acclimated egg masses from temperate and sub-polar regions across the species range. Fossil records indicate neogastropods to have a deep-water origin, suggesting shallow-water species may be likely candidates for re-emergence into the deep sea. Our results show population level differences in physiological thresholds, which indicate low temperature acclimation to increase pressure tolerance. These findings imply this species is capable of deep-sea penetration through isothermal water columns prevailing at high latitudes. This study gives new insight into the fundamentals behind past and future colonisation events. Such knowledge is instrumental to understand better how changes in climate envelopes affect the distribution and radiation of species along latitudinal as well as bathymetric temperature gradients.

Conquered from the deep sea? A new deep-sea isopod species from the Antarctic shelf shows pattern of recent colonization

The Amundsen Sea, Antarctica, is amongst the most rapidly changing environments of the world. Its benthic inhabitants are barely known and the BIOPEARL 2 project was one of the first to biologically explore this region. Collected during this expedition, Macrostylis roaldi sp. nov. is described as the first isopod discovered on the Amundsen-Sea shelf. Amongst many characteristic features, the most obvious characters unique for M. roaldi are the rather short pleotelson and short operculum as well as the trapezoid shape of the pleotelson in adult males. We used DNA barcodes (COI) and additional mitochondrial markers (12S, 16S) to reciprocally illuminate morphological results and nucleotide variability. In contrast to many other deep-sea isopods, this species is common and shows a wide distribution. Its range spreads from Pine Island Bay at inner shelf right to the shelf break and across 1,000 m bathymetrically. Its gene pool is homogenized across space and depth. This is indicative for a genetic bottleneck or a recent colonization history. Our results suggest further that migratory or dispersal capabilities of some species of brooding macrobenthos have been underestimated. This might be relevant for the species' potential to cope with effects of climate change. To determine where this species could have survived the last glacial period, alternative refuge possibilities are discussed.

Evidence for Permo-Triassic colonization of the deep sea by isopods

The deep sea is one of the largest ecosystems on Earth and is home to a highly diverse fauna, with polychaetes, molluscs and peracarid crustaceans as dominant groups. A number of studies have proposed that this fauna did not survive the anoxic events that occurred during the Mesozoic Era. Accordingly, the modern fauna is thought to be relatively young, perhaps having colonized the deep sea after the Eocene/Oligocene boundary. To test this hypothesis, we performed phylogenetic analyses of nuclear ribosomal 18S and 28S and mitochondrial cytochrome oxidase I and 16S sequences from isopod crustaceans. Using a molecular clock calibrated with multiple isopod fossils, we estimated the timing of deep-sea colonization events by isopods. Our results show that some groups have an ancient origin in the deep sea, with the earliest estimated dates spanning 232-314 Myr ago. Therefore, anoxic events at the Permian-Triassic boundary and during the Mesozoic did not cause the extinction of all the deep-sea fauna; some species may have gone extinct while others survived and proliferated. The monophyly of the 'munnopsid radiation' within the isopods suggests that the ancestors of this group evolved in the deep sea and did not move to shallow-water refugia during anoxic events.

Respiratory response of the deep-sea amphipod Stephonyx biscayensis indicates bathymetric range limitation by temperature and hydrostatic pressure

Depth zonation of fauna on continental margins is well documented. Whilst increasing hydrostatic pressure with depth has long been considered a factor contributing significantly to this pattern, discussion of the relative significance of decreasing temperature with depth has continued. This study investigates the physiological tolerances of fed and starved specimens of the bathyal lysianassoid amphipod Stephonyx biscayensis at varying temperature to acute pressure exposure by measuring the rate of oxygen consumption. Acclimation to atmospheric pressure is shown to have no significant interaction with temperature and/or pressure effects. Similarly, starvation is shown to have no significant effect on the interaction of temperature and pressure. Subsequently, the effect of pressure on respiration rate is revealed to be dependent on temperature: pressure equivalent to 2000 m depth was tolerated at 1 and 3°C; pressure equivalent to 2500 m depth was tolerated at 5.5°C; at 10°C pressure equivalent to 3000 m depth was tolerated. The variation in tolerance is consistent with the natural distribution range reported for this species. There are clear implications for hypotheses relating to the observed phenomenon of a biodiversity bottleneck between 2000 and 3000 metres, and for the potential for bathymetric range shifts in response to global climate change.

Pressure tolerance of the shallow-water caridean shrimp Palaemonetes varians across its thermal tolerance window

To date, no published study has assessed the full physiological scope of a marine invertebrate species with respect to both temperature and hydrostatic pressure. In this study, adult specimens of the shallow-water shrimp species Palaemonetes varians were subjected to a temperature/pressure regime from 5 to 30°C and from 0.1 to 30 MPa. The rate of oxygen consumption and behaviour in response to varying temperature/pressure combinations were assessed. Rates of oxygen consumption were primarily affected by temperature. Low rates of oxygen consumption were observed at 5 and 10°C across all pressures and were not statistically distinct (P=0.639). From 10 to 30°C, the rate of oxygen consumption increased with temperature; this increase was statistically significant (P<0.001). Palaemonetes varians showed an increasing sensitivity to pressure with decreasing temperature; however, shrimp were capable of tolerating hydrostatic pressures found outside their normal bathymetric distribution at all temperatures. ‘Loss of equilibrium’ (LOE) in ≥50% of individuals was observed at 11 MPa at 5°C, 15 MPa at 10°C, 20 MPa at 20°C and 21 MPa at 30°C. From 5 to 20°C, mean levels of LOE decreased with temperature; this was significant (P<0.001). Low mean levels of LOE were observed at 20 and 30°C and were not distinct (P=0.985). The physiological capability of P. varians to tolerate a wide range of temperatures and significant hydrostatic pressure is discussed.