Exploring the diversity of the deep sea—four new species of the amphipod genus Oedicerina described using morphological and molecular methods

Collections of the amphipod genus Oedicerina were obtained during six expeditions devoted to the study of deep-sea environments of the Pacific Ocean. The material revealed four species new to science. Two species (Oedicerina henricisp. nov. and Oedicerina teresae sp. nov.) were found at abyssal depths of the central eastern Pacific in the Clarion-Clipperton Zone; one species (Oedicerina claudei sp. nov.) was recovered in the Sea of Okhotsk (north-west Pacific), and one (Oedicerina lesci sp. nov.) in the abyss adjacent to the Kuril-Kamchatka Trench (KKT). The four new species differ from each other and known species by the shapes of the rostrum, coxae 1 and 4, basis of pereopod 7, armatures of pereonite 7, pleonites and urosomites. An identification key for all known species is provided. The study of the cytochrome c oxidase subunit I gene of the four new species and Oedicerina ingolfi collected in the North Atlantic confirmed their genetic distinction. However, small intraspecific variation within each of the studied species was observed. In the case of the new species occurring across the KKT, the same haplotype was found on both sides of the trench, providing evidence that the trench does not constitute an insurmountable barrier for population connectivity. None of the species have so far been found on both sides of the Pacific.

Proteomic fingerprinting facilitates biodiversity assessments in understudied ecosystems: A case study on integrated taxonomy of deep sea copepods

Accurate and reliable biodiversity estimates of marine zooplankton are a prerequisite to understand how changes in diversity can affect whole ecosystems. Species identification in the deep sea is significantly impeded by high numbers of new species and decreasing numbers of taxonomic experts, hampering any assessment of biodiversity. We used in parallel morphological, genetic, and proteomic characteristics of specimens of calanoid copepods from the abyssal South Atlantic to test if proteomic fingerprinting can accelerate estimating biodiversity. We cross-validated the respective molecular discrimination methods with morphological identifications to establish COI and proteomic reference libraries, as they are a pre-requisite to assign taxonomic information to the identified molecular species clusters. Due to the high number of new species only 37% of the individuals could be assigned to species or genus level morphologically. COI sequencing was successful for 70% of the specimens analysed, while proteomic fingerprinting was successful for all specimens examined. Predicted species richness based on morphological and molecular methods was 42 morphospecies, 56 molecular operational taxonomic units (MOTUs) and 79 proteomic operational taxonomic units (POTUs), respectively. Species diversity was predicted based on proteomic profiles using hierarchical cluster analysis followed by application of the variance ratio criterion for identification of species clusters. It was comparable to species diversity calculated based on COI sequence distances. Less than 7% of specimens were misidentified by proteomic profiles when compared with COI derived MOTUs, indicating that unsupervised machine learning using solely proteomic data could be used for quickly assessing species diversity.

Revealing paraphyly and placement of extinct species within Epischura (Copepoda: Calanoida) using molecular data and quantitative morphometrics

Epischura (Calanoida: Temoridae) is a Holarctic group of copepods serving important ecological roles, but it is difficult to study because of small range sizes of individual species and widespread distribution of the genus. This genus includes Tertiary relicts, some endemic to single, isolated lakes and can play major roles in unique ecosystems like Lakes Baikal and Tahoe. We present the first molecular and morphological analysis of Epischura that reveals their spatio-temporal evolutionary history. Morphological measurements of mandibles and genetics estimated phylogenetic relationships among all species represented in Epischura, including E. massachusettsensis, whose extinction status is of concern. Analyses used three gene regions for six previously unsequenced species to infer highly-resolved and well-supported phylogenies confirming a split between Siberian and North American species. Previously published age estimates and sequence data from broad taxonomic sampling of calanoid copepods estimated divergence times between the two Epischura groups. Divergence time estimates for Epischura were consistent with earlier molecular clock estimates and late-Miocene cooling events. Additionally, we provide the first taxonomically broad estimates of divergence times within Calanoida. The paraphyletic nature of the genus Epischura (and the family Temoridae) is apparent and requires the resurrection of the genus Epischurella (Smirnov, 1936) to describe the Siberian species.