Do molecular phylogenies unravel the relationships among the evolutionary young “Brafordian” families (Copepoda; Calanoida)?

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.

The crossover from microscopy to genes in marine diversity: from species to assemblages in marine pelagic copepods

An accurate identification of species and communities is a prerequisite for analysing and recording biodiversity and community shifts. In the context of marine biodiversity conservation and management, this review outlines past, present and forward-looking perspectives on identifying and recording planktonic diversity by illustrating the transition from traditional species identification based on morphological diagnostic characters to full molecular genetic identification of marine assemblages. In this process, the article presents the methodological advancements by discussing progress and critical aspects of the crossover from traditional to novel and future molecular genetic identifications and it outlines the advantages of integrative approaches using the strengths of both morphological and molecular techniques to identify species and assemblages. We demonstrate this process of identifying and recording marine biodiversity on pelagic copepods as model taxon. Copepods are known for their high taxonomic and ecological diversity and comprise a huge variety of behaviours, forms and life histories, making them a highly interesting and well-studied group in terms of biodiversity and ecosystem functioning. Furthermore, their short life cycles and rapid responses to changing environments make them good indicators and core research components for ecosystem health and status in the light of environmental change. This article is part of the theme issue 'Integrative research perspectives on marine conservation'.

New genus and species of calanoid copepods (Crustacea) belonging to the group of Bradfordian families collected from the hyperbenthic layers off Japan

A new genus and species of calanoid copepods belonging to the group of Bradfordian families, Pogonura rugosagen. et sp. nov., is described from the deep-sea hyperbenthic layers off Nagannu Island, Okinawa Prefecture, southwestern Japan. Pogonuragen. nov. is similar to another Bradfordian genus Procenognatha in sharing the following characteristics: (1) segmentation of the antennule, fused segments II–IV, X–XI, XXVII–XXVIII in females and II–IV, X–XII, XXVII–XXVIII, right XXII–XXIII in males; (2) retained setae on the ancestral segments I–IV of the antennary exopod; (3) setules on the mandibular gnathobase; (4) 3 sclerotized setae on the maxillary endopod; (5) absence of sensory seta on the maxilliped; (6) large spinules on the posterior surface of the rami of legs 2 and 3; and (7) setation and segmentation of female leg 5. Pogonuragen. nov. is distinctly distinguished from Procenognatha by the following features: (1) reduction of a seta on the ancestral segment IX of the antennary exopod, (2) 8 setae (7 in Procenognatha) on the maxillular exopod, (3) 5 brush-like setae (6 in Procenognatha) on the maxillary endopod, and (4) reduction of right endopod of male leg 5. The systematic position of Pogonuragen. nov. in the Bradfordian families is also discussed. Although this new genus shares synapomorphies with some diaixid genera, an assignment of this genus to any Bradfordian family should be pending until the taxonomy of this family group is clearly settled.

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.