Phylogeography and environmental diversification of a highly adaptable marine amphipod, Gammarus duebeni

Living with relatives offsets the harm caused by pathogens in natural populations

Living with relatives can be highly beneficial, enhancing reproduction and survival. High relatedness can, however, increase susceptibility to pathogens. Here, we examine whether the benefits of living with relatives offset the harm caused by pathogens, and if this depends on whether species typically live with kin. Using comparative meta-analysis of plants, animals, and a bacterium (nspecies = 56), we show that high within-group relatedness increases mortality when pathogens are present. In contrast, mortality decreased with relatedness when pathogens were rare, particularly in species that live with kin. Furthermore, across groups variation in mortality was lower when relatedness was high, but abundances of pathogens were more variable. The effects of within-group relatedness were only evident when pathogens were experimentally manipulated, suggesting that the harm caused by pathogens is masked by the benefits of living with relatives in nature. These results highlight the importance of kin selection for understanding disease spread in natural populations.

A new species of Nicippe from the Bering Sea (Crustacea, Amphipoda, Pardaliscidae), with a redescription of N. tumida

A new pardaliscid amphipod, Nicippe beringensis, is described from the Bering Sea at depths between 520 and 536 m, and N. tumida Bruzelius, 1859 is redescribed based on specimens from Fredrikshald, Norway, near the species' type locality. Nucleotide sequences of mitochondrial cytochrome c oxidase subunit I (COI) from the holotype and a paratype of N. beringensis sp. nov. are reported. While N. beringensis sp. nov. is similar to N. tumida, it differs from the latter in having an asetose palp article 1 of maxilla 1, a gnathopod 1 coxa with a straight distal edge, and in the posterior margin of the basis of gnathopods 1 and 2, and pereopod 3, being heavily setose in females. A key to species of Nicippe is provided.

A new species of Melita from Japan (Crustacea, Amphipoda, Melitidae)

A new brackish-water species of melitid amphipod,Melitachoshigawaensis, from the Choshigawa River, Mie Prefecture, Japan, is named and described.Melitachoshigawaensissp. n.is distinguished from the most similarM.shimizui(Uéno, 1940) by having an elongate and weakly arched male uropod 3, and a deep and strongly hooked anterior lobe of the coxa on the female’s pereopod 6. Nucleotide sequences of the mitochondrial cytochromecoxidase subunit I (COI) ofM.choshigawaensisandM.shimizuisupport divergence at the species level. A key to the Japanese species ofMelitais provided.

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 new species of the genus Pseudocrangonyx (Crustacea, Amphipoda, Pseudocrangonyctidae) from Korea

A new subterranean species of pseudocrangonyctid amphipod, Pseudocrangonyx daejeonensissp. n. is described from the interstitial waters in Daejeon, Korea. Pseudocrangonyx daejeonensissp. n. is distinguished from three morphologically similar congeners, P. coreanus Uéno, 1966, P. febras Sidorov, 2009, and P. gudariensis Tomikawa & Sato, 2016, by the characteristics of antenna 1, antenna 2, mandible, gnathopod 2, pleopods, uropods 1-2, and telson. Molecular phylogenetic analyses based on nuclear 28S rRNA and histone H3, and mitochondrial cytochrome c oxidase subunit I and 16S rRNA genes revealed that P. daejeonensis is a sister species of the unnamed Pseudocrangonyx sp. 3 inhabiting central Japan.

A new species of the genus Nicippe from Japan (Crustacea, Amphipoda, Pardaliscidae)

A new species of the pardaliscid amphipod, Nicipperecticaudata, from off Cape Toi, Japan, is named and described. This is the first record of Nicippe Bruzelius, 1859 from the western Pacific coast of the Japanese archipelago. Additionally, nucleotide sequences of nuclear 28S ribosomal RNA and histone H3 as well as mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA from the holotype and paratypes were determined. The morphological characteristics and the COI distance values enforced the distinctiveness of N.recticaudatasp. n. among the known Nicippe species. Nicipperecticaudatasp. n. closely resembles N.tumida Bruzelius, 1859 in having a two-dentate posterior margin of usoromite 1. However, the former is distinguished from the latter by the posterior margin of merus of pereopod 4 with 5–6 setae, anterior margin of merus of pereopod 5 with 9–10 setae, and telson with straight inner margin, tapering proximally. A key to the species of Nicippe is provided.

A new subterranean species of Pseudocrangonyx from China with an identification key to all species of the genus (Crustacea, Amphipoda, Pseudocrangonyctidae)

A subterranean species of Pseudocrangonyxelegantulus Hou, sp. n. is described from caves of Wulongdong National Forest Park in Henan Province, China. Pseudocrangonyxelegantulus is characterized by both male and female with calceoli on antenna II; urosomite III dorsal margin without armature; uropod III with peduncle 0.30 times as long as outer ramus and terminal article of the outer ramus a little shorter than adjacent spines; telson cleft 0.27 of its length. Phylogenetic analysis based on 28S and COI sequences supported the species distinctness. A key to the genus Pseudocrangonyx with 22 species and a map of their distributions are provided.

The enigmatic groundwater amphipod Awacaris kawasawai revisited: synonymisation of the genus Sternomoera, with molecular phylogenetic analyses of Awacaris and Sternomoera species (Crustacea : Amphipoda : Pontogeneiidae)

Amphipod crustaceans are dominant in subterranean habitats, and members of eight genera are endemic to groundwater environments in the Japanese Archipelago. The taxonomic status of two of these genera remains unclear, because their original descriptions were incomplete. The descriptions of the enigmatic subterranean monotypic genus Awacaris and its type species, A. kawasawai Uéno, 1971, are revisited here. Awacaris kawasawai was originally described based on specimens from a subterranean stream at Himise Cave, Tokushima Prefecture, Shikoku, Japan. Recently, a new population of A. kawasawai was found at Saruta Cave, Kochi Prefecture, Shikoku. Detailed observation of the newly collected specimens reveals the presence of sternal gills, which is the diagnostic character of the pontogeneiid genus Sternomoera, making the validity of Sternomoera open to question. Phylogenetic analyses using nuclear 28S rRNA and mitochondrial cytochrome c oxidase subunit I markers demonstrate that A. kawasawai forms a well-supported clade with the subterranean S. morinoi Tomikawa and Ishimaru, 2014. In addition, phylogenetic analysis reveals cryptic diversity in epigean species of Sternomoera. Ancestral state reconstruction suggests that catadromous Sternomoera species have evolved from freshwater ancestors. Based on our morphological and phylogenetic analysis of Awacaris and Sternomoera species, it is concluded here that Sternomoera should be treated as a subjective junior synonym of Awacaris.

The Application of DNA Barcodes for the Identification of Marine Crustaceans from the North Sea and Adjacent Regions

During the last years DNA barcoding has become a popular method of choice for molecular specimen identification. Here we present a comprehensive DNA barcode library of various crustacean taxa found in the North Sea, one of the most extensively studied marine regions of the world. Our data set includes 1,332 barcodes covering 205 species, including taxa of the Amphipoda, Copepoda, Decapoda, Isopoda, Thecostraca, and others. This dataset represents the most extensive DNA barcode library of the Crustacea in terms of species number to date. By using the Barcode of Life Data Systems (BOLD), unique BINs were identified for 198 (96.6%) of the analyzed species. Six species were characterized by two BINs (2.9%), and three BINs were found for the amphipod species Gammarus salinus Spooner, 1947 (0.4%). Intraspecific distances with values higher than 2.2% were revealed for 13 species (6.3%). Exceptionally high distances of up to 14.87% between two distinct but monophyletic clusters were found for the parasitic copepod Caligus elongatus Nordmann, 1832, supporting the results of previous studies that indicated the existence of an overlooked sea louse species. In contrast to these high distances, haplotype-sharing was observed for two decapod spider crab species, Macropodia parva Van Noort & Adema, 1985 and Macropodia rostrata (Linnaeus, 1761), underlining the need for a taxonomic revision of both species. Summarizing the results, our study confirms the application of DNA barcodes as highly effective identification system for the analyzed marine crustaceans of the North Sea and represents an important milestone for modern biodiversity assessment studies using barcode sequences.

Genetic structuring across marine biogeographic boundaries in rocky shore invertebrates

Biogeography investigates spatial patterns of species distribution. Discontinuities in species distribution are identified as boundaries between biogeographic areas. Do these boundaries affect genetic connectivity? To address this question, a multifactorial hierarchical sampling design, across three of the major marine biogeographic boundaries in the central Mediterranean Sea (Ligurian-Tyrrhenian, Tyrrhenian-Ionian and Ionian-Adriatic) was carried out. Mitochondrial COI sequence polymorphism of seven species of Mediterranean benthic invertebrates was analysed. Two species showed significant genetic structure across the Tyrrhenian-Ionian boundary, as well as two other species across the Ionian Sea, a previously unknown phylogeographic barrier. The hypothesized barrier in the Ligurian-Tyrrhenian cannot be detected in the genetic structure of the investigated species. Connectivity patterns across species at distances up to 800 km apart confirmed that estimates of pelagic larval dispersal were poor predictors of the genetic structure. The detected genetic discontinuities seem more related to the effect of past historical events, though maintained by present day oceanographic processes. Multivariate statistical tools were used to test the consistency of the patterns across species, providing a conceptual framework for across-species barrier locations and strengths. Additional sequences retrieved from public databases supported our findings. Heterogeneity of phylogeographic patterns shown by the 7 investigated species is relevant to the understanding of the genetic diversity, and carry implications for conservation biology.

Genetic diversity of the feminising microsporidian parasite Dictyocoela: new insights into host-specificity, sex and phylogeography

Microsporidia of the genus Dictyocoela are parasites of gammarid amphipod Crustacea. They typically exhibit low virulence and efficient vertical transmission and at least some strains are capable of feminising their hosts. Sequencing of a region of the 16S rDNA of Dictyocoela spp. from various gammarid host species and localities in Europe and northern Asia indicates that Dictyocoela is genetically diverse and that different strains predominate in different host species. However, the presence of intermediate sequences casts doubt upon previous attempts to describe Dictyocoela spp. on the basis of rDNA divergence alone. Phylogenetic analysis provides little support for coevolution between gammarids and Dictyocoela. Furthermore, observations of heavily infected individuals, together with genetic evidence of recombination, suggest that some strains of Dictyocoela may be horizontally transmitted and are sexually reproducing. These findings suggest that Dictyocoela may be phenotypically, as well as genotypically, diverse, with the potential to exhibit a range of different interactions with its host populations.

Glacial-driven vicariance in the amphipod Gammarus duebeni

We have examined the genetic diversity using mitochondrial COI and ND2 sequence data from 306 specimens of the amphi-Atlantic-distributed amphipod Gammarus duebeni. Marine populations from the Atlantic Ocean, the Baltic and North Sea, as well as freshwater populations from Ireland, Cornwall and Brittany were analysed. G. duebeni is a complex of five allopatric lineages. Freshwater populations result from multiple invasions of marine ancestors, represented by distinct lineages. We interpret the recent distribution of lineages as the outcome of a series of spatio-temporal vicariant events caused by Pleistocene glaciations and sea level changes. The freshwater lineages are therefore regarded as 'glacial relicts'. Furthermore, inter-specific competition with, for example, Gammarus pulex (which is absent in Ireland and western Brittany) may be another important determinant in the distribution of freshwater G. duebeni. In Ireland and Brittany, three freshwater refugia are suggested. The significantly limited gene flow detected among marine populations is more likely due to inter-specific competition than to salinity. The G. duebeni-complex represents a model system for the study of allopatric speciation accompanied by major habitat shifts. The pattern of spatio-temporal origins of the freshwater entities we describe here provides an excellent system for investigating evolutionary adaptations to the freshwater environment. Our data did not confirm the presently used subspecies classification but are only preliminary in the absence of nuclear genetic analyses.