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1. COI Metabarcoding of Zooplankton Species Diversity for Time-Series Monitoring of the NW Atlantic Continental Shelf

   https://doi.org/10.3389/fmars.2022.867893  

   Bucklin, Ann; Batta-Lona, Paola G.; Questel, Jennifer M.; Wiebe, Peter H.; Richardson, David E.; Copley, Nancy J.; O’Brien, Todd D. (April 2022, Frontiers in Marine Science)

   Marine zooplankton are rapid-responders and useful indicators of environmental variability and climate change impacts on pelagic ecosystems on time scales ranging from seasons to years to decades. The systematic complexity and taxonomic diversity of the zooplankton assemblage has presented significant challenges for routine morphological (microscopic) identification of species in samples collected during ecosystem monitoring and fisheries management surveys. Metabarcoding using the mitochondrial Cytochrome Oxidase I (COI) gene region has shown promise for detecting and identifying species of some – but not all – taxonomic groups in samples of marine zooplankton. This study examined species diversity of zooplankton on the Northwest Atlantic Continental Shelf using 27 samples collected in 2002-2012 from the Gulf of Maine, Georges Bank, and Mid-Atlantic Bight during Ecosystem Monitoring (EcoMon) Surveys by the NOAA NMFS Northeast Fisheries Science Center. COI metabarcodes were identified using the MetaZooGene Barcode Atlas and Database ( https://metazoogene.org/MZGdb ) specific to the North Atlantic Ocean. A total of 181 species across 23 taxonomic groups were detected, including a number of sibling and cryptic species that were not discriminated by morphological taxonomic analysis of EcoMon samples. In all, 67 species of 15 taxonomic groups had ≥ 50 COI sequences; 23 species had >1,000 COI sequences. Comparative analysis of molecular and morphological data showed significant correlations between COI sequence numbers and microscopic counts for 5 of 6 taxonomic groups and for 5 of 7 species with >1,000 COI sequences for which both types of data were available. Multivariate statistical analysis showed clustering of samples within each region based on both COI sequence numbers and EcoMon counts, although differences among the three regions were not statistically significant. The results demonstrate the power and potential of COI metabarcoding for identification of species of metazoan zooplankton in the context of ecosystem monitoring. 

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2. Pan-Arctic Phylogeography of the Pelagic Chaetognath Eukrohnia hamata

   Passacantando, M; Questel, J; Bucklin, A (February 2018, Ocean Sciences Meeting)

   Chaetognatha are highly-effective predatory components of the marine planktonic assemblages. Many species exhibit disjunct biogeographical distributions throughout the global ocean, and thus serve as sentinel species for examining climate-driven changes in ocean circulation on zooplankton species, communities, and food webs. Of particular interest are ecological changes in the Arctic, a region being drastically affected by climate change. In this study, a 650 base-pair region of the mitochondrial cytochrome oxidase I (mtCOI) gene was sequenced for 131 individuals for the chaetognath Eukrohnia hamata collected from diverse regions throughout the Arctic. DNA sequence analysis was done to characterize population genetic diversity and structure, phylogeography (i.e., geographic distribution of genetic lineages within species), and connectivity among regional populations. High haplotype diversity (Hd) and significant (p <0.02) negative values for Fu’s and Li’s F statistic imply that E. hamata is undergoing population expansion.. Patterns and pathways of population connectivity examined to test several migration hypotheses revealed that pan-Arctic population connectivity followed the primary ocean currents. The reliance of this ecologically important zooplankton species on Arctic Ocean currents has implications for future warming conditions, which have the potential to modify these currents, resulting in altered biogeographical distributions and population connectivity of Arctic zooplankton. 

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3. Pan-Arctic Phylogeography of the Pelagic Chaetognath Eukrohnia hamata.

   Passacantando, M. (February 2018, Ocean Sciences Meeting)

   Chaetognatha are highly-effective predatory components of the marine planktonic assemblages. Many species exhibit disjunct biogeographical distributions throughout the global ocean, and thus serve as sentinel species for examining climate-driven changes in ocean circulation on zooplankton species, communities, and food webs. Of particular interest are ecological changes in the Arctic, a region being drastically affected by climate change. In this study, a 650 base-pair region of the mitochondrial cytochrome oxidase I (mtCOI) gene was sequenced for 131 individuals for the chaetognath Eukrohnia hamata collected from diverse regions throughout the Arctic. DNA sequence analysis was done to characterize population genetic diversity and structure, phylogeography (i.e., geographic distribution of genetic lineages within species), and connectivity among regional populations. High haplotype diversity (Hd) and significant (p <0.02) negative values for Fu’s and Li’s F statistic imply that E. hamata is undergoing population expansion.. Patterns and pathways of population connectivity examined to test several migration hypotheses revealed that pan-Arctic population connectivity followed the primary ocean currents. The reliance of this ecologically important zooplankton species on Arctic Ocean currents has implications for future warming conditions, which have the potential to modify these currents, resulting in altered biogeographical distributions and population connectivity of Arctic zooplankton. 

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4. The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages

   https://doi.org/10.7717/peerj.4409  

   Dudoit, ‘Ale‘alani; Iacchei, Matthew; Coleman, Richard R.; Gaither, Michelle R.; Browne, William E.; Bowen, Brian W.; Toonen, Robert J. (January 2018, PeerJ)

   The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120–253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus , we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range. Phylogenetic analyses reveal that S. hispidus has a Western Atlantic lineage and a widely distributed Indo-Pacific lineage, separated by sequence divergence of 2.1%. Genetic diversity is much higher in the Western Atlantic ( h = 0.929; π  = 0.004) relative to the Indo-Pacific ( h = 0.105; π  < 0.001), and coalescent analyses indicate that the Indo-Pacific population expanded more recently (95% HPD (highest posterior density) = 60,000–400,000 yr) than the Western Atlantic population (95% HPD = 300,000–760,000 yr). Divergence of the Western Atlantic and Pacific lineages is estimated at 710,000–1.8 million years ago, which does not readily align with commonly implicated colonization events between the ocean basins. The estimated age of populations contradicts the prevailing dispersal route for tropical marine biodiversity (Indo-Pacific to Atlantic) with the oldest and most diverse population in the Atlantic, and a recent population expansion with a single common haplotype shared throughout the vast Indian and Pacific oceans. In contrast to the circumtropical fishes, this diminutive reef shrimp challenges our understanding of conventional dispersal capabilities of marine species. 

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5. Toward a global reference database of COI barcodes for marine zooplankton

   https://doi.org/10.1007/s00227-021-03887-y  

   Bucklin, Ann; Peijnenburg, Katja T. C. A.; Kosobokova, Ksenia N.; O’Brien, Todd D.; Blanco-Bercial, Leocadio; Cornils, Astrid; Falkenhaug, Tone; Hopcroft, Russell R.; Hosia, Aino; Laakmann, Silke; et al (May 2021, Marine Biology)

   Abstract 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. 

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