Molecular evidence that phoronids are a subtaxon of brachiopods (Brachiopoda: Phoronata) and that genetic divergence of metazoan phyla began long before the early Cambrian

Concatenated SSU (18S) and partial LSU (28S) sequences (~2 kb) from 12 ingroup taxa, comprising 2 phoronids, 2 members of each of the craniid, discinid, and lingulid inarticulate brachiopod lineages, and 4 rhynchonellate, articulate brachiopods (2 rhynchonellides, 1 terebratulide and 1 terebratellide) were aligned with homologous sequences from 6 protostome, deuterostome and sponge outgroups (3964 sites). Regions of potentially ambiguous alignment were removed, and the resulting data (3275 sites, of which 377 were parsimony-informative and 635 variable) were analysed by parsimony, and by maximum and Bayesian likelihood using objectively selected models. There was no base composition heterogeneity. Relative rate tests led to the exclusion (from most analyses) of the more distant outgroups, with retention of the closer pectinid and polyplacophoran (chiton). Parsimony and likelihood bootstrap and Bayesian clade support values were generally high, but only likelihood analyses recovered all brachiopod indicator clades designated a priori. All analyses confirmed the monophyly of (brachiopods+phoronids) and identified phoronids as the sister-group of the three inarticulate brachiopod lineages. Consequently, a revised Linnean classification is proposed in which the subphylum Linguliformea comprises three classes: Lingulata, ‘Phoronata’ (the phoronids), and ‘Craniata’ (the current subphylum Craniiformea). Divergence times of all nodes were estimated by regression from node depths in non-parametrically rate-smoothed and other chronograms, calibrated against palaeontological data, with probable errors not less than 50 My. Only three predicted brachiopod divergence times disagree with palaeontological ages by more than the probable error, and a reasonable explanation exists for at least two. Pruning long-branched ingroups made scant difference to predicted divergence time estimates. The palaeontological age calibration and the existence of Lower Cambrian fossils of both main brachiopod clades together indicate that initial genetic divergence between brachiopod and molluscan (chiton) lineages occurred well before the Lower Cambrian, suggesting that much divergence between metazoan phyla took place in the Proterozoic

Microsatellite markers for the Arctic copepod Calanus glacialis and cross-amplification with C. finmarchicus

Calanus glacialis is a major component of Arctic zooplankton and a keystone species in Arctic marine ecosystems. Due to the observed climate warming, its numbers are being reduced to the advantage of a sibling Atlantic species Calanus finmarchicus. We developed and characterized the first set of microsatellite markers in this species to investigate its population genetic structure and dispersal capabilities. Nine polymorphic loci displayed an average of 7.3 alleles (range between 2 and 13) and the levels of expected heterozygosity ranged from 0.039 to 0.806. These provide a valuable tool to understand present connectivity patterns across Arctic regions, look for signatures of past climate effects and predict the response to future climate-driven environmental changes. Additionally, due to the cross-amplification with C. finmarchicus, the markers can be used to discriminate between these sibling species.National Science Centre, Poland [2011/03/B/NZ8/02876]; FCT, Portugal [PTDC/MAR/72630/2006]; EU FP7 Project ATP [226248]; European Community (ASSEMBLE-MARINE) [227799]info:eu-repo/semantics/publishedVersio

Postglacial expansion of the arctic keystone copepod calanus glacialis

Calanus glacialis, a major contributor to zooplankton biomass in the Arctic shelf seas, is a key link between primary production and higher trophic levels that may be sensitive to climate warming. The aim of this study was to explore genetic variation in contemporary populations of this species to infer possible changes during the Quaternary period, and to assess its population structure in both space and time. Calanus glacialis was sampled in the fjords of Spitsbergen (Hornsund and Kongsfjorden) in 2003, 2004, 2006, 2009 and 2012. The sequence of a mitochondrial marker, belonging to the ND5 gene, selected for the study was 1249 base pairs long and distinguished 75 unique haplotypes among 140 individuals that formed three main clades. There was no detectable pattern in the distribution of haplotypes by geographic distance or over time. Interestingly, a Bayesian skyline plot suggested that a 1000-fold increase in population size occurred approximately 10,000 years before present, suggesting a species expansion after the Last Glacial Maximum.GAME from the National Science Centre, the Polish Ministry of Science and Higher Education Iuventus Plus [IP2014 050573]; FCT-PT [CCMAR/Multi/04326/2013]; [2011/03/B/NZ8/02876

A transcriptome resource for the copepod Calanus glacialis across a range of culture temperatures

The copepod Calanus glacialis plays a key role in the Arctic pelagic ecosystem. Despite its ecological importance and ongoing climate changes, limited knowledge at the genomic level has hindered the understanding of the molecular processes underlying environmental stress responses and ecological adaptation. Transcriptome data was generated from an experiment with C glacialis copepodite (CV) subjected to five different temperatures. We obtained a total of 512,352 high-quality 454 pyrosequencing reads, which were assembled into 55,562 contigs distributed in 128 KEGG pathways. Functional analysis revealed numerous genes related to diverse biological functions and processes, including members of all major conserved signaling pathways. Comparative analysis of acclimated individuals to experimental temperatures has provided information about gene variations observed in several pathways (e.g. genes involved in energy, lipid and amino acid metabolism were shown to be down-regulated with increasing temperatures). These mRNA sequence resources will facilitate further studies on genomics and physiology-driven molecular processes in C glacialis and related species. (C) 2015 Elsevier B.V. All rights reserved.European Commission [FP7-ENV-2008-1-226248]; Polish National Science Centre [2011/03/B/NZ8/02876]; Portuguese Science and Technology Foundation (FCT) [FCT PTDC/MAR/72630]; FCT [SFRH/BPD/64174/2009]info:eu-repo/semantics/publishedVersio

Mitochondrial genomes of the key zooplankton copepods Arctic Calanus glacialis and North Atlantic Calanus finmarchicus with the longest crustacean non-coding regions

We determined the nearly complete mitochondrial genomes of the Arctic Calanus glacialis and its North Atlantic sibling Calanus finmarchicus, which are key zooplankton components in marine ecosystems. The sequenced part of C. glacialis mitogenome is 27,342 bp long and consists of two contigs, while for C. finmarchicus it is 29,462 bp and six contigs, what makes them the longest reported copepod mitogenomes. The typical set of metazoan mitochondrial genes is present in these mitogenomes, although the non-coding regions (NCRs) are unusually long and complex. The mitogenomes of the closest species C. glacialis and C. finmarchicus, followed by the North Pacific C. sinicus, are structurally similar and differ from the much more typical of deep-water, Arctic C. hyperboreus. This evolutionary trend for the expansion of NCRs within the Calanus mitogenomes increases mitochondrial DNA density, what resulted in its similar density to the nuclear genome. Given large differences in the length and structure of C. glacialis and C. finmarchicus mitogenomes, we conclude that the species are genetically distinct and thus cannot hybridize. The molecular resources presented here: the mitogenomic and rDNA sequences, and the database of repetitive elements should facilitate the development of genetic markers suitable in pursuing evolutionary research in copepods.Polish Ministry of Science and Higher Education [Iuventus Plus] [IP2014 050573]; FCT-CCMAR Portugal [Multi/04326/2013

Responses in Arctic marine carbon cycle processes: conceptual scenarios & implications for ecosystem.

The Arctic Ocean is one of the fastest changing oceans, plays an important role in global carbon cycling and yet is a particularly challenging ocean to study. Hence, observations tend to be relatively sparse in both space and time. How the Arctic functions, geophysically, but also ecologically, can have significant consequences for the internal cycling of carbon, and subsequently influence carbon export, atmospheric CO2 uptake and food chain productivity. Here we assess the major carbon pools and associated processes, specifically summarizing the current knowledge of each of these processes in terms of data availability and ranges of rates and values for four geophysical Arctic Ocean domains originally described by Carmack & Wassmann (2006): inflow shelves, which are Pacific-influenced and Atlantic-influenced; interior, river-influenced shelves; and central basins. We attempt to bring together knowledge of the carbon cycle with the ecosystem within each of these different geophysical settings, in order to provide specialist information in a holistic context. We assess the current state of models and how they can be improved and/or used to provide assessments of the current and future functioning when observational data are limited or sparse. In doing so, we highlight potential links in the physical oceanographic regime, primary production and the flow of carbon within the ecosystem that will change in the future. Finally, we are able to highlight priority areas for research, taking a holistic pan-Arctic approach

Toward a global reference database of COI barcodes for marine zooplankton

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bucklin, A., Peijnenburg, K. T. C. A., Kosobokova, K. N., O'Brien, T. D., Blanco-Bercial, L., Cornils, A., Falkenhaug, T., Hopcroft, R. R., Hosia, A., Laakmann, S., Li, C., Martell, L., Questel, J. M., Wall-Palmer, D., Wang, M., Wiebe, P. H., & Weydmann-Zwolicka, A. Toward a global reference database of COI barcodes for marine zooplankton. Marine Biology, 168(6), (2021): 78, https://doi.org/10.1007/s00227-021-03887-y.Characterization of species diversity of zooplankton is key to understanding, assessing, and predicting the function and future of pelagic ecosystems throughout the global ocean. The marine zooplankton assemblage, including only metazoans, is highly diverse and taxonomically complex, with an estimated ~28,000 species of 41 major taxonomic groups. This review provides a comprehensive summary of DNA sequences for the barcode region of mitochondrial cytochrome oxidase I (COI) for identified specimens. The foundation of this summary is the MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data and metadata portal that is linked to NCBI GenBank and BOLD data repositories. The MZGdb provides enhanced quality control and tools for assembling COI reference sequence databases that are specific to selected taxonomic groups and/or ocean regions, with associated metadata (e.g., collection georeferencing, verification of species identification, molecular protocols), and tools for statistical analysis, mapping, and visualization. To date, over 150,000 COI sequences for ~ 5600 described species of marine metazoan plankton (including holo- and meroplankton) are available via the MZGdb portal. This review uses the MZGdb as a resource for summaries of COI barcode data and metadata for important taxonomic groups of marine zooplankton and selected regions, including the North Atlantic, Arctic, North Pacific, and Southern Oceans. The MZGdb is designed to provide a foundation for analysis of species diversity of marine zooplankton based on DNA barcoding and metabarcoding for assessment of marine ecosystems and rapid detection of the impacts of climate change.Funding sources for authors of the review paper are described here: Scientific Committee on Oceanic Research (SCOR), and a grant to SCOR from the U.S. National Science Foundation (OCE-1840868). Netherlands Organization for Scientific Research (NWO) Vidi Grant/Award Number: 016.161.351 to K.T.C.A.P. European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 746186 (POSEIDoN) to D.W.P. The work of K.N.K. was performed in the framework of the state assignment of IO RAS (Theme No. 0128-2021-0007) and partially supported by Russian Foundation for Basic Research grants No. 18-05-60158 and No. 19-04-00955. The work of A.W.Z. was supported by a grant from HIDEA—Hidden diversity of the Arctic Ocean (No. 2017/27/B/NZ8/01056) from the National Science Centre, Poland, and a Fulbright Senior Award. The Norwegian Taxonomy Initiative of the Norwegian Biodiversity Information Centre provided funding for A.H. and L.M. (Project Nos. 70184233/HYPNO and 70184240/NORHYDRO), and for T.F. (Project Nos. 70184233/COPCLAD and 70184241/HYPCOP). The work of R.R.H. and J.M.Q. was supported by Census of Marine Life and NOAA Ocean Exploration and Research (NA05OAR4601079 and NA15OAR0110209). The work of S.L. was conducted at the Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB). HIFMB is a collaboration between the Alfred-Wegener-Institute, Helmholtz-Center for Polar and Marine Research, and the Carl-von-Ossietzky University Oldenburg, initially funded by the Ministry for Science and Culture of Lower Saxony and the Volkswagen Foundation through the Niedersächsisches Vorab’ grant program (Grant No. ZN3285)

Ocean acidification reduces demersal zooplankton that reside in tropical coral reefs

The in situ effects of ocean acidification on zooplankton communities remain largely unexplored. Using natural volcanic CO2 seep sites around tropical coral communities, we show a threefold reduction in the biomass of demersal zooplankton in high-CO2 sites compared with sites with ambient CO2. Differences were consistent across two reefs and three expeditions. Abundances were reduced in most taxonomic groups. There were no regime shifts in zooplankton community composition and no differences in fatty acid composition between CO2 levels, suggesting that ocean acidification affects the food quantity but not the quality for nocturnal plankton feeders. Emergence trap data show that the observed reduction in demersal plankton may be partly attributable to altered habitat. Ocean acidification changes coral community composition from branching to massive bouldering coral species, and our data suggest that bouldering corals represent inferior daytime shelter for demersal zooplankton. Since zooplankton represent a major source of nutrients for corals, fish and other planktivores, this ecological feedback may represent an additional mechanism of how coral reefs will be affected by ocean acidification

Population genomics of marine zooplankton

Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here for personal use, not for redistribution. The definitive version was published in Bucklin, Ann et al. "Population Genomics of Marine Zooplankton." Population Genomics: Marine Organisms. Ed. Om P. Rajora and Marjorie Oleksiak. Springer, 2018. doi:10.1007/13836_2017_9.The exceptionally large population size and cosmopolitan biogeographic distribution that distinguish many – but not all – marine zooplankton species generate similarly exceptional patterns of population genetic and genomic diversity and structure. The phylogenetic diversity of zooplankton has slowed the application of population genomic approaches, due to lack of genomic resources for closelyrelated species and diversity of genomic architecture, including highly-replicated genomes of many crustaceans. Use of numerous genomic markers, especially single nucleotide polymorphisms (SNPs), is transforming our ability to analyze population genetics and connectivity of marine zooplankton, and providing new understanding and different answers than earlier analyses, which typically used mitochondrial DNA and microsatellite markers. Population genomic approaches have confirmed that, despite high dispersal potential, many zooplankton species exhibit genetic structuring among geographic populations, especially at large ocean-basin scales, and have revealed patterns and pathways of population connectivity that do not always track ocean circulation. Genomic and transcriptomic resources are critically needed to allow further examination of micro-evolution and local adaptation, including identification of genes that show evidence of selection. These new tools will also enable further examination of the significance of small-scale genetic heterogeneity of marine zooplankton, to discriminate genetic “noise” in large and patchy populations from local adaptation to environmental conditions and change.Support was provided by the US National Science Foundation to AB and RJO (PLR-1044982) and to RJO (MCB-1613856); support to IS and MC was provided by Nord University (Norway)