133 research outputs found
DNA barcodes unite two problematic taxa: the meiobenthic Boreohydra simplex is a life-cycle stage of Plotocnide borealis (Hydrozoa: Aplanulata)
No full textPyataeva, Sofia V., Hopcroft, Russell R., Lindsay, Dhugal J., Collins, Allen G. (2016): DNA barcodes unite two problematic taxa: the meiobenthic Boreohydra simplex is a life-cycle stage of Plotocnide borealis (Hydrozoa: Aplanulata). Zootaxa 4150 (1): 85-92, DOI: http://doi.org/10.11646/zootaxa.4150.1.
Identification, Discrimination, and Discovery of Species of Marine Planktonic Ostracods Using DNA Barcodes
No full textThe Ostracoda (Crustacea; Class Ostracoda) is a diverse, frequently abundant, and ecologically important component of the marine zooplankton assemblage. There are more than 200 described species of marine planktonic ostracods, many of which (especially conspecific species) can be identified only by microscopic examination and dissection of fragile morphological characters. Given the complexity of species identification and increasing lack of expert taxonomists, DNA barcodes (short DNA sequences for species discrimination and identification) are particularly useful and necessary. Results are reported from analysis of 210 specimens of 78 species of marine planktonic ostracods, including two novel species, and 51 species for which barcodes have not been previously published. Specimens were collected during 2006 to 2008 from the Atlantic, Indian, and Southern Oceans, Greenland Sea and Gulf of Alaska. Samples were collected from surface to 5,000 m using various collection devices. DNA sequence variation was analyzed for a 598 base-pair region of the mitochondrial cytochrome oxidase subunit I (COI) gene. Kimura-2-Parameter (K2P) genetic distances within described species (mean = 0.010 ± 0.017 SD) were significantly smaller than between species (0.260 + 0.080), excluding eight taxa hypothesized to comprise cryptic species due to morphological variation (especially different size forms) and/or collection from different geographic regions. These taxa showed similar K2P distance values within (0.014 + 0.026) and between (0.221 ± 0.068) species. All K2P distances > 0.1 resulted from comparisons between identified or cryptic species, with no overlap between intra- and interspecific genetic distances. A Neighbor Joining tree resolved nearly all described species analyzed, with multiple sequences forming monophyletic clusters with high bootstrap values (typically 99%). Based on taxonomically and geographically extensive sampling and analysis (albeit with small sample sizes), the COI barcode region was shown to be a valuable character for discrimination, recognition, identification, and discovery of species of marine planktonic ostracods
FIGURE 2 in DNA barcodes unite two problematic taxa: the meiobenthic Boreohydra simplex is a life-cycle stage of Plotocnide borealis (Hydrozoa: Aplanulata)
No full textFIGURE 2. The egg of the polyp stage of Plotocnide borealis. A. SEM of the polyp with the egg, marked by (*). B. SEM of the egg, front view. C. Live image of the gastric region of the polyp with the egg. D. Transverse semi-thin section of the polyp stage stained with a mixture of toluidine blue and methylene blue clearly showing the egg. E, F. TEM of the oocyte wall, the invaginations of the outer membrane are marked by arrows.Published as part of Pyataeva, Sofia V., Hopcroft, Russell R., Lindsay, Dhugal J. & Collins, Allen G., 2016, DNA barcodes unite two problematic taxa: the meiobenthic Boreohydra simplex is a life-cycle stage of Plotocnide borealis (Hydrozoa: Aplanulata), pp. 85-92 in Zootaxa 4150 (1) on page 90, DOI: 10.11646/zootaxa.4150.1.5, http://zenodo.org/record/26239
FIGURE 1. A in DNA barcodes unite two problematic taxa: the meiobenthic Boreohydra simplex is a life-cycle stage of Plotocnide borealis (Hydrozoa: Aplanulata)
No full textFIGURE 1. A. ML topology for all publically available 18S sequences (n=519) of Hydroidolina, showing the positions of Plotocnide borealis and Protohydra leuckarti within Aplanulata. SH-like branch support values are shown at the nodes, as well as bootstrap indices if exceeding 60. Uncollapsed topologies are provided as Supplementary Figures at https://dx.doi.org/ 10.6084/m9.figshare.3406654.v3. B. SEM of the polyp stage previously known as Boreohydra simplex, the mouth is marked by (*). C. Live image of the medusa stage of Plotocnide borealis, tentacles contracted.Published as part of Pyataeva, Sofia V., Hopcroft, Russell R., Lindsay, Dhugal J. & Collins, Allen G., 2016, DNA barcodes unite two problematic taxa: the meiobenthic Boreohydra simplex is a life-cycle stage of Plotocnide borealis (Hydrozoa: Aplanulata), pp. 85-92 in Zootaxa 4150 (1) on page 87, DOI: 10.11646/zootaxa.4150.1.5, http://zenodo.org/record/26239
Deep-sea sampling on CMarZ cruises in the Atlantic Ocean – an Introduction
No full textThe deep-sea zooplankton assemblage is hypothesized to have high species diversity, with low abundances of each species. However, even rare species may have huge population sizes and play a critical role in the dynamics of deep-sea environments. The Census of Marine Zooplankton (CMarZ) study sought to accurately assess zooplankton diversity in the mesopelagic and bathypelagic zones of the subtropical/tropical of the northwest and eastern sections of the Atlantic Ocean using integrated morphological and molecular analysis of large-volume samples to depths of 5,000 m. The field surveys in April 2006 and November 2007 included scientists and students associated with the CMarZ. The cruise field work entailed at-sea analysis of samples and identification of specimens by expert taxonomists, with at-sea DNA sequencing to determine a barcode (i.e., a short DNA sequence for species recognition) for selected species. Environmental data and zooplankton samples were collected with 1-m2 and 10-m2 opening/closing MOCNESS (0–1000 m and 1000–5000 m, respectively), and with either a 0.25-m2 MOCNESS or a 0.5-m2 Multi-net above 1000 m. More than 500 species were identified and more than 1000 specimens placed in a queue for barcoding on each cruise; several hundred species were barcoded at sea. For several taxonomic groups, a significant fraction of the region’s known species were collected and identified. For example, in the northwest Atlantic 93 of 140 known ostracod species for the Atlantic Ocean were collected, 6 undescribed species were found, and the first DNA barcode for a planktonic ostracod was obtained. The deployment of trawls with fine-mesh nets to sample large volumes at great depths for small zooplankton confirmed that there is considerable species diversity at depth, with more species yet to be discovered.<br/
Fine-scale spatial patterns of gelatinous zooplankton in the Northern Gulf of Alaska
No full textThesis (M.S.) University of Alaska Fairbanks, 2024The Northern Gulf of Alaska (NGA) is characterized by high variability across spatial and temporal scales. In the NGA, zooplankton are a crucial link between primary production and higher trophic levels. Understanding the mechanisms that structure zooplankton assemblages is important to our overall understanding of ecosystem functioning. Nonetheless, thorough description of zooplankton abundance and distribution patterns is challenging due to the inherent variability and complexity of the marine environment. The study of gelatinous zooplankton is further complicated by the limitations of traditional plankton net sampling methods that are inefficient for the collection of high-resolution spatiotemporal data and often inflict damage on these fragile bodied organisms. In the NGA, and many other ocean systems, this has historically left gelatinous zooplankton under sampled and poorly studied in comparison to cooccurring crustacean zooplankton. To address these challenges, recent advances in imaging technology and computing power were leveraged by deploying an In Situ Ichthyoplankton Imaging System Deep-Focus Particle Imager (ISIIS-DPI) in the NGA from 2022-2023. The ISIIS-DPI is a towed vehicle capable of collecting vast amounts of high-resolution imaging and oceanographic data. An analysis pipeline with convolutional neural network (CNN) architecture was employed to automate the identification of zooplankton images and expedite processing time, allowing for description of fine-scale distributional patterns of gelatinous zooplankton and their associations with surrounding biophysical drivers. Evidence is presented that ctenophore, hydromedusae, and siphonophore aggregations are concentrated around frontal features and track with the surrounding variability in their ocean environment. Several first records in the NGA of previously undetected species are also presented. These novel datasets demonstrate the previously underestimated prominence of gelatinous zooplankton in the NGA and improve our understanding of ctenophore, hydromedusae, and siphonophore abundance and distribution patterns in the context of their oceanographic environment. This work is the first adaptation of in situ imaging and machine learning technologies in the NGA and presents the opportunity to more accurately describe the role of gelatinous zooplankton in marine ecosystem function.NGA LTER (Phase 1: NSF Award OCE-1656070, Phase 2: NSF Award OCE-2322806), M.J. Murdock Charitable Trust, UAF’s Office of the Vice Chancellor of Research, and the Alaska Ocean Observing System (AOOS), NSF, the Exxon Valdez Oil Spill Trustee Council via Gulf Watch Alaska, the North Pacific Research BoardChapter 1: General introduction -- Chapter 2: Fine-scale spatial patterns of gelatinous zooplankton in the Northern Gulf of Alaska -- 2.1 Introduction -- 2.2 Methods -- 2.2.1 Study site -- 2.2.2 Data collection -- 2.2.3 Data processing -- 2.2.4 Zooplankton image identification -- 2.2.5 Statistical analyses -- 2.3 Results -- 2.3.1 Physical environment -- 2.3.2 Zooplankton identification and abundance -- 2.3.3 Zooplankton distributions -- 2.3.4 Zooplankton community composition -- 2.4 Discussion -- 2.4.1 Species abundance estimates derived from in situ imaging vs plankton net collection -- 2.4.2 Dryodora and detection of novel species -- 2.4.3 Community composition and influence of the surrounding ocean environment -- 2.5 Conclusions & future prospects -- 2.6 References -- 2.7 Supplemental figures
Abundance, composition and distribution of predatory gelatinous zooplankton in the northern Gulf of Alaska
No full textThesis (M.S.) University of Alaska Fairbanks, 2020Jellyfish are conspicuous yet under-studied components of marine zooplankton communities. Abundance, biomass, size, and distribution of large-jellyfish were measured during July and September of 2018 and 2019 as part of the Northern Gulf of Alaska Long-Term Ecological Research (NGA-LTER) cruises. Nearly 1000 kg dispersed among ~13,800 jellies were collected using a 5 m² Methot net. Catches were dominated by two macro-jellies, the hydrozoan Aequorea sp. and the scyphozoan Chrysaora sp. During 2018, epipelagic macro-jellies biomass averaged 1.46 ± 0.36 g WW m⁻³ for July and 1.14 ± 0.23 g WW m⁻³ for September, while during 2019 they averaged 0.86 ± 0.19 g WW m⁻³ for July and 0.72 ± 0.21 g WW m⁻³ by September. Despite similar biomass among sampling seasons within the same year, July abundances were fivefold greater than abundances in September, with July catches dominated by juvenile jellyfish over the inner shelf, while during September jellyfish adults were more prominent and most predominant at offshore stations. Comparison to over 20 years of data from standard towed nets allowed determination of the relative magnitude of the three dominant predatory zooplankton components: Scyphozoans, Hydrozoans, and Chaetognaths in the NGA. The biomass of these smaller epipelagic predators (10 mg WW m⁻³ for hydrozoans and 8 mg WW m⁻³ for chaetognaths) is a low percentage of the macro-jellies, despite their much higher numerical abundance. Acknowledging that changes in gelatinous biomass could have profound effects on fisheries, we argue that jellyfish should be quantitatively monitored in ecosystems with high fisheries productivity.Pollock Conservation Cooperative Research CenterGeneral introduction -- Chapter 1. Abundance, composition and distribution of predatory gelatinous zooplankton in the Northern Gulf of Alaska -- General conclusion -- References
Controls on zooplankton assemblages in the northeastern Chukchi Sea
No full textDissertation (Ph.D.) University of Alaska Fairbanks, 2016The Chukchi Sea is a broad and shallow marginal sea of the western Arctic Ocean that lies between the Bering Sea and the deeper Amerasian basin. It plays a pivotal role as the only gateway for transporting heat, carbon, nutrients, and plankton from the North Pacific into the Arctic Ocean. I examined the seasonal and inter-annual variability of the zooplankton communities in the northeastern region of the Chukchi Sea as part of a high-resolution multidisciplinary ecosystem study. Specifically, I examined how the physical onset of each open water season influenced the composition, abundance, and biomass of zooplankton assemblages from the 2008 to 2010 field seasons. Copepods in the genus Pseudocalanus are key members of the Chukchi community, and may be undergoing species-level biogeographic shift in response to climate change. I determined the degree of gene flow and population connectivity in the Chukchi Sea through comparative phylogeographic analysis of the Pseudocalanus species complex to the northern Gulf of Alaska and Beaufort Sea. I then investigated the extent to which biogeochemical factors influence these zooplankton assemblages by relating a portion of the seasonal production to concurrent changes in herbivorous mesozooplankton biomass during 2010 and 2011. This work demonstrates just how complex and variable marine ecosystems of the western Arctic are, where multidisciplinary and analytical approaches will become essential in detecting change, especially with the rate of present-day climate perturbations.Chapter 1: Seasonal and interannual variation in the planktonic communities of the northeastern Chukchi Sea during the summer and early fall -- Chapter 2: Phylogeography and connectivity of the Pseudocalanus (Copepoda: Calanoida) species complex in the eastern North Pacific Ocean and the Pacific Arctic Region -- Chapter 3: Community production in the northeastern Chukchi Sea and its relationship to phytoplankton and mesozooplankton biomass, 2010-2011 -- General Conclusions -- References
Microbes to mammals: metabarcoding of the marine pelagic assemblage
No full textNo abstracts are to be cited without prior reference to the author.Conveners: Ann Bucklin (USA), Rowena Stern (UK), Katja Metfies (Germany).CM 2017/C:447. Inclusion of DNA Sequencing into an Ecosystem Observing Program in the Southern California Bight. Kelly D. Goodwin, Lisa Zeigler Allen, Ariel Rabines, John McCrow, Andrew AllenCM 2017/C:230. The Earth Microbiome Project: lessons from a massive metagenetic survey. Luke R. ThompsonCM 2017/C:449. Assessing Biodiversity in the Florida Keys National Marine Sanctuary Through Environmental DNA Metabarcoding. Natalie Sawaya, Anni Djurhuus, Collin J. Closek, Megan Hepner, Emily Olesin, Lindsey Visser, Chris Kelble, Katherine Hubbard, Mya BreitbartCM 2017/C:441. Multi-gene metabarcoding of plankton tow samples and eDNA: a comparative morphological-molecular analysis of coastal zooplankton diversity. Annette F. Govindarajan, Jennifer M. Questel, Nancy J. Copley, John P. Wares, Ann BucklinCM 2017/C:201. Developing a robust framework for applying metabarcoding analyses to identify pelagic ichthyoplankton in the California Current. Dovi Kacev, David Gillett, Eric Stein, Andrew ThompsonCM 2017/C:160. Metabarcoding analysis of zooplankton biodiversity of the Pacific-Arctic Chukchi Borderlands region. Jennifer M. Questel, Russell R. Hopcroft, Ann BucklinCM 2017/C:75. Diet composition and variability of wild cephalopod paralarvae: a metagenomic approach to identifying dietary preferences. Lorena Olmos-Pérez, Álvaro Roura, Graham J. Pierce, Stéphane Boyer, Ángel F. GonzálezCM 2017/C:183. Metagenetic analysis of the pelagic food web: prey choice and selectivity of the copepod Calanus finmarchicus in the Gulf of Maine (NW Atlantic).. Heidi Yeh, Jennifer Questel, Ann BucklinCM 2017/C:437. DNA barcoding Pan-Arctic copepod assemblages: toward a regional reference DNA sequence database for COI and 18S rRNA. Hayley M. DeHart, Jennifer M. Questel, Russell R. Hopcroft, Ksenia N. Kosobokova, Ann BucklinCM 2017/C:409. Time-series analysis of zooplankton diversity of the NW Atlantic continental shelf based on COI and 18S rRNA metabarcodes. Ann Bucklin, Jennifer M. Questel, Bo Reese, Nancy J. Copley, Peter H. Wiebe</p
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