Abstract
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.
Highlights
In light of the worldwide observed and predicted changes in biodiversity, there is an urgent need to measure spatial and temporal variation in biodiversity from local to global scales, to understand what impacts these changes might have on communities and ecosystems, and how biodiversity can be conserved (Costello, 2001; Ash et al, 2009)
Calanoid copepods were collected in the benthopelagic boundary layer (BBL) during RV Meteor cruise M79-1 (Supporting Information 1) (Project DIVA 3) in the South Atlantic Ocean from station 580 (14°58.91’ S, 29°56.48’ W) at a depth of 5139 m using an epibenthic sledge (EBS; Brenke, 2005)
Pre-tests with epipelagic copepods showed no significant differences in proteomic composition using the whole body or only parts of the cephalosome
Summary
In light of the worldwide observed and predicted changes in biodiversity, there is an urgent need to measure spatial and temporal variation in biodiversity from local to global scales, to understand what impacts these changes might have on communities and ecosystems, and how biodiversity can be conserved (Costello, 2001; Ash et al, 2009). Molecular techniques have added a new dimension to the traditional phenotypic approach and allow researchers to overcome taxonomic difficulties in the identification of species with different life history stages They can improve and contribute to estimating species diversity and were successfully applied to understand the diversity of calanoid copepods (e.g., Blanco-Bercial et al, 2014; Bucklin, Hopcroft, et al, 2010; Bucklin, Ortman, et al, 2010; Laakmann et al., 2013), resolve problematic taxa (e.g., Aarbakke et al, 2014; Hill et al, 2001) or reveal cryptic and new species (Caudill & Bucklin, 2004; Chen & Hare, 2011; Goetze, 2003). The aim of our study was to (i) find an adequate unsupervised technique to estimate species richness of a community from proteomic profiles only, (ii) evaluate resolution, accuracy and efficiency of species separation based on proteomic fingerprinting using cross-validation with morphology and COI sequencing, and (iii) provide for the first time data on diversity and composition of benthopelagic abyssal copepods using an integrated morphological, genetic and proteomic approach
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