Accessing BCO-DMO data
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|data||files||public||Data from: Iacchei, M., E. Butcher, E. Portner, Goetze, E. (in press) It\u2019s about time: |
Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices.
|Row Type||Variable Name||Attribute Name||Data Type||Value|
|attribute||NC_GLOBAL||acquisition_description||String||Collection:\u00a0Bulk zooplankton were collected at an open ocean time series
site in the North Pacific Subtropical Gyre (station ALOHA, 22.45N, 158W)
during 11 of the routine Hawai'i Ocean Time-series (HOT) research cruises at
approximately monthly intervals from September of 2012 to October of 2013
(HOT-246 to HOT-256). Mesozooplankton were collected using a 1 m2, 200 um-mesh
ring net towed obliquely from a mean maximum depth of 155 m (SD = 31 m) to the
sea surface. Zooplankton for this study were collected from three nighttime
tows completed between the hours of 2200-0200 on consecutive nights for each
sampling period so that all collections for a single cruise were collected
within three days of one another. Following net retrieval, bulk plankton were
quantitatively split using a Folsom plankton splitter, and 1/4 of the material
was preserved in 95% non-denatured ethyl alcohol (EtOH) and stored at -20C.
From these bulk collections, 50 Haloptilus longicornis and 50 Pleuromamma
xiphias individuals were sorted from each net tow for use in this study.
mtDNA Sequence Generation:\u00a0For both H. longicornis and P. xiphias, DNA
was extracted using the Qiagen DNeasy Blood and Tissue Kit (Qiagen, Inc.,
Valencia, CA). For H. longicornis, a 546 base-pair fragment of the
mitochondrial cytochrome c oxidase subunit II (mtCOII) gene was amplified by
polymerase chain reaction (PCR) with species-specific primers COII_F6 and
COII_R9. For P. xiphias, a 551 base-pair fragment of the mitochondrial
cytochrome c oxidase subunit I (mtCOI) was amplified by PCR using species-
specific primers PLXI_VH and PLXI_VL. Specific information on primer
sequences, PCR reaction mixes, thermal cycler conditions, and PCR purification
is provided in the manuscript associated with this submission. Purified PCR
products were sequenced on an ABI 3730XL capillary sequencer (Applied
Biosystems, Foster City, CA). Sequences were aligned, edited and trimmed using
Geneious 7.0.6 (Biomatters, Ltd., Auckland, New Zealand). Unique haplotypes
were identified using the Haplotype Collapser and Converter in FaBox 1.35
birc.au.dk/biopv/php/fabox/\\")), and deposited with their respective protein
translations in GenBank under accession numbers: KY560470 - KY560565. An mtDNA
sequence for each individual specimen is deposited in this BCO-DMO submission
as part of one of two fasta files. Each fasta file contains the mtDNA sequence
fragments from all individuals from a single species aligned together.
Methodology is further described in the paper itself:
Iacchei, M., E. Butcher, E. Portner, Goetze, E. (in press) It\u2019s about
time: Insights into temporal genetic patterns in oceanic zooplankton from
biodiversity indices.\u00a0 Limnology and Oceanography
|attribute||NC_GLOBAL||awards_0_funder_name||String||NSF Division of Ocean Sciences|
|attribute||NC_GLOBAL||awards_0_program_manager||String||David L. Garrison|
|attribute||NC_GLOBAL||awards_1_funder_name||String||NSF Division of Ocean Sciences|
|attribute||NC_GLOBAL||awards_1_program_manager||String||David L. Garrison|
|attribute||NC_GLOBAL||awards_2_funder_name||String||NSF Division of Ocean Sciences|
|attribute||NC_GLOBAL||awards_2_program_manager||String||David L. Garrison|
|attribute||NC_GLOBAL||awards_3_funder_name||String||NSF Division of Ocean Sciences|
|attribute||NC_GLOBAL||awards_3_program_manager||String||Elizabeth L. Rom|
|attribute||NC_GLOBAL||comment||String||Temporal genetic patterns in P. xiphias and H. longicornis - Mitochondrial data, station ALOHA
Data files associated with Iacchei et al. (L&O)
PI: Erica Goetze (University of Hawaii)
Version: 10 Feb 2017
|attribute||NC_GLOBAL||Conventions||String||COARDS, CF-1.6, ACDD-1.3|
|attribute||NC_GLOBAL||creator_email||String||info at bco-dmo.org|
|attribute||NC_GLOBAL||data_source||String||extract_data_as_tsv version 2.3 19 Dec 2019|
|attribute||NC_GLOBAL||instruments_0_dataset_instrument_description||String||Mesozooplankton were collected using a 1 m2, 200 um-mesh ring net towed obliquely from a mean maximum depth of 155 m (SD = 31 m) to the sea surface.|
|attribute||NC_GLOBAL||instruments_0_description||String||A Ring Net is a generic plankton net, made by attaching a net of any mesh size to a metal ring of any diameter. There are 1 meter, .75 meter, .25 meter and .5 meter nets that are used regularly. The most common zooplankton ring net is 1 meter in diameter and of mesh size .333mm, also known as a 'meter net' (see Meter Net).|
|attribute||NC_GLOBAL||instruments_0_supplied_name||String||mesh ring net|
|attribute||NC_GLOBAL||instruments_1_dataset_instrument_description||String||Specific information on primer sequences, PCR reaction mixes, thermal cycler conditions, and PCR purification is provided in the manuscript associated with this submission.|
|attribute||NC_GLOBAL||instruments_1_description||String||General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
|attribute||NC_GLOBAL||instruments_1_instrument_name||String||PCR Thermal Cycler|
|attribute||NC_GLOBAL||instruments_2_dataset_instrument_description||String||Following net retrieval, bulk plankton were quantitatively split using a Folsom plankton splitter.|
|attribute||NC_GLOBAL||instruments_2_description||String||A Folsom Plankton Splitter is used for sub-sampling of plankton and ichthyoplankton samples.|
|attribute||NC_GLOBAL||instruments_2_instrument_name||String||Folsom Plankton Splitter|
|attribute||NC_GLOBAL||instruments_2_supplied_name||String||Folsom Plankton Splitter|
|attribute||NC_GLOBAL||keywords||String||bco, bco-dmo, biological, chemical, data, dataset, description, dmo, erddap, file, file_link, link, management, oceanography, office, preliminary|
|attribute||NC_GLOBAL||people_0_affiliation||String||University of Hawaii at Manoa|
|attribute||NC_GLOBAL||people_1_affiliation||String||University of Hawaii at Manoa|
|attribute||NC_GLOBAL||people_1_person_name||String||Dr Matthew Iacchei|
|attribute||NC_GLOBAL||people_2_affiliation||String||University of Hawaii at Manoa|
|attribute||NC_GLOBAL||people_3_affiliation||String||Woods Hole Oceanographic Institution|
|attribute||NC_GLOBAL||people_3_role||String||BCO-DMO Data Manager|
|attribute||NC_GLOBAL||project||String||HOT,Plankton Population Genetics,Plankton_PopStructure|
|attribute||NC_GLOBAL||projects_0_description||String||Systematic, long-term observations are essential for evaluating natural variability of Earth’s climate and ecosystems and their responses to anthropogenic disturbances. Since October 1988, the Hawaii Ocean Time-series (HOT) program has investigated temporal dynamics in biology, physics, and chemistry at Stn. ALOHA (22°45' N, 158°W), a deep ocean field site in the oligotrophic North Pacific Subtropical Gyre (NPSG). HOT conducts near monthly ship-based sampling and makes continuous observations from moored instruments to document and study NPSG climate and ecosystem variability over semi-diurnal to decadal time scales. HOT was founded to understand the processes controlling the time-varying fluxes of carbon and associated biogenic elements in the ocean and to document changes in the physical structure of the water column. To achieve these broad objectives, the program has several specific goals:
Quantify time-varying (seasonal to decadal) changes in reservoirs and fluxes of carbon (C) and associated bioelements (nitrogen, oxygen, phosphorus, and silicon).
Identify processes controlling air-sea C exchange, rates of C transformation through the planktonic food web, and fluxes of C into the ocean’s interior.
Develop a climatology of hydrographic and biogeochemical dynamics from which to form a multi-decadal baseline from which to decipher natural and anthropogenic influences on the NPSG ecosystem.
Provide scientific and logistical support to ancillary programs that benefit from the temporal context, interdisciplinary science, and regular access to the open sea afforded by HOT program occupation of Sta. ALOHA, including projects implementing, testing, and validating new methodologies, models, and transformative ocean sampling technologies.
Over the past 24+ years, time-series research at Station ALOHA has provided an unprecedented view of temporal variability in NPSG climate and ecosystem processes. Foremost among HOT accomplishments are an increased understanding of the sensitivity of bioelemental cycling to large scale ocean-climate interactions, improved quantification of reservoirs and time varying fluxes of carbon, identification of the importance of the hydrological cycle and its influence on upper ocean biogeochemistry, and the creation of long-term data sets from which the oceanic response to anthropogenic perturbation of elemental cycles may be gauged.
A defining characteristic of the NPSG is the perennially oligotrophic nature of the upper ocean waters. This biogeochemically reactive layer of the ocean is where air-sea exchange of climate reactive gases occurs, solar radiation fuels rapid biological transformation of nutrient elements, and diverse assemblages of planktonic organisms comprise the majority of living biomass and sustain productivity. The prevailing Ekman convergence and weak seasonality in surface light flux, combined with relatively mild subtropical weather and persistent stratification, result in a nutrient depleted upper ocean habitat. The resulting dearth of bioessential nutrients limits plankton standing stocks and maintains a deep (175 m) euphotic zone. Despite the oligotrophic state of the NPSG, estimates of net organic matter production at Sta. ALOHA are estimated to range ~1.4 and 4.2 mol C m2 yr1. Such respectable rates of productivity have highlighted the need to identify processes supplying growth limiting nutrients to the upper ocean. Over the lifetime of HOT numerous ancillary science projects have leveraged HOT science and infrastructure to examine possible sources of nutrients supporting plankton productivity. Both physical (mixing, upwelling) and biotic (N2 fixation, vertical migration) processes supply nutrients to the upper ocean in this region, and HOT has been instrumental in demonstrating that these processes are sensitive to variability in ocean climate.
Station ALOHA - site selection and infrastructure
Station ALOHA is a deep water (~4800 m) location approximately 100 km north of the Hawaiian Island of Oahu. Thus, the region is far enough from land to be free of coastal ocean dynamics and terrestrial inputs, but close enough to a major port (Honolulu) to make relatively short duration (45 m depth), below depths of detection by Earth-orbiting satellites. The emerging data emphasize the value of in situ measurements for validating remote and autonomous detection of plankton biomass and productivity and demonstrate that detection of potential secular-scale changes in productivity against the backdrop of significant interannual and decadal fluctuations demands a sustained sampling effort.
Careful long-term measurements at Stn. ALOHA also highlight a well-resolved, though relatively weak, seasonal climatology in upper ocean primary productivity. Measurements of 14C-primary production document a ~3-fold increase during the summer months (Karl et al., 2012) that coincides with increases in plankton biomass (Landry et al., 2001; Sheridan and Landry, 2004). Moreover, phytoplankton blooms, often large enough to be detected by ocean color satellites, are a recurrent summertime feature of these waters (White et al., 2007; Dore et al., 2008; Fong et al., 2008). Analyses of ~13-years (1992-2004) of particulate C, N, P, and biogenic Si fluxes collected from bottom-moored deep-ocean (2800 m and 4000 m) sediment traps provide clues to processes underlying these seasonal changes. Unlike the gradual summertime increase in sinking particle flux observed in the upper ocean (150 m) traps, the deep sea particle flux record depicts a sharply defined summer maximum that accounts for ~20% of the annual POC flux to the deep sea, and appears driven by rapidly sinking diatom biomass (Karl et al., 2012). Analyses of the 15N isotopic signatures associated with sinking particles at Sta. ALOHA, together with genetic analyses of N2 fixing microorganisms, implicates upper ocean N2 fixation as a major control on the magnitude and efficiency of the biological carbon pump in this ecosystem (Dore et al., 2002; Church et al., 2009; Karl et al., 2012).
Science results from HOT continue to raise new, important questions about linkages between ocean climate and biogeochemistry that remain at the core of contemporary oceanography. Answers have begun to emerge from the existing suite of core program measurements; however, sustained sampling is needed to improve our understanding of contemporary ecosystem behavior and our ability to make informed projections of future changes to this ecosystem. HOT continues to focus on providing answers to some of the questions below:
How sensitive are rates of primary production and organic matter export to short- and long-term climate variability?
What processes regulate nutrient supply to the upper ocean and how sensitive are these processes to climate forcing?
What processes control the magnitude of air-sea carbon exchange and over what time scales do these processes vary?
Is the strength of the NPSG CO2 sink changing in time?
To what extent does advection (including eddies) contribute to the mixed layer salinity budget over annual to decadal time scales and what are the implications for upper ocean biogeochemistry?
How do variations in plankton community structure influence productivity and material export?
What processes trigger the formation and demise of phytoplankton blooms in a persistently stratified ocean ecosystem?
|attribute||NC_GLOBAL||projects_0_geolocation||String||North Pacific Subtropical Gyre; 22 deg 45 min N, 158 deg W|
|attribute||NC_GLOBAL||projects_0_name||String||Hawaii Ocean Time-series (HOT): Sustaining ocean ecosystem and climate observations in the North Pacific Subtropical Gyre|
|attribute||NC_GLOBAL||projects_1_acronym||String||Plankton Population Genetics|
|attribute||NC_GLOBAL||projects_1_description||String||Description from NSF award abstract:
Marine zooplankton show strong ecological responses to climate change, but little is known about their capacity for evolutionary response. Many authors have assumed that the evolutionary potential of zooplankton is limited. However, recent studies provide circumstantial evidence for the idea that selection is a dominant evolutionary force acting on these species, and that genetic isolation can be achieved at regional spatial scales in pelagic habitats. This RAPID project will take advantage of a unique opportunity for basin-scale transect sampling through participation in the Atlantic Meridional Transect (AMT) cruise in 2014. The cruise will traverse more than 90 degrees of latitude in the Atlantic Ocean and include boreal-temperate, subtropical and tropical waters. Zooplankton samples will be collected along the transect, and mitochondrial and microsatellite markers will be used to identify the geographic location of strong genetic breaks within three copepod species. Bayesian and coalescent analytical techniques will test if these regions act as dispersal barriers. The physiological condition of animals collected in distinct ocean habitats will be assessed by measurements of egg production (at sea) as well as body size (condition index), dry weight, and carbon and nitrogen content. The PI will test the prediction that ocean regions that serve as dispersal barriers for marine holoplankton are areas of poor-quality habitat for the target species, and that this is a dominant mechanism driving population genetic structure in oceanic zooplankton.
Note: This project is funded by an NSF RAPID award. This RAPID grant supported the shiptime costs, and all the sampling reported in the AMT24 zooplankton ecology cruise report (PDF).
Online science outreach blog at: https://atlanticplankton.wordpress.com
|attribute||NC_GLOBAL||projects_1_geolocation||String||Atlantic Ocean, 46 N - 46 S|
|attribute||NC_GLOBAL||projects_1_name||String||Basin-scale genetics of marine zooplankton|
|attribute||NC_GLOBAL||projects_2_description||String||Description from NSF award abstract:
This research will test whether habitat depth specialization is a primary trait driving large-scale population genetic structure in open ocean zooplankton species. Very little is known about population connectivity in marine zooplankton. Although zooplankton were long thought to be high-gene-flow systems with little genetic differentiation among populations, recent observations have challenged this view. In fact, zooplankton species may be genetically subdivided at macrogeographic, regional, or even smaller spatial scales. Recent studies also indicate that subtle, species-specific ecological factors play an important role in controlling gene flow among plankton populations. The investigator hypothesizes that depth-related habitat, including diel vertical migration (DVM) behavior, plays a critical role in controlling dispersal of plankton among ocean regions, through interactions with ocean circulation and bathymetry. This study will compare the population genetic structures of eight planktonic copepods that utilize different depth-related habitats, in order to test key predictions of genetic structure based on the interaction of organismal depth with the oceanographic environment. The objectives of the research are to:
1) Develop novel nuclear markers that can be used to resolve genetic structure and estimate gene flow among copepod populations,
2) Characterize the spatial patterns of gene flow among populations in distinct ocean regions of the Atlantic, Pacific, and Indian Oceans for eight target species using a multilocus approach, and
3) Test the central hypothesis that depth-related habitat will significantly impact the extent of genetic structure both across and within ocean basins, the magnitude and direction of gene flow among populations, and in the timing of major slitting events within species.
Drawing on genomic resources (cDNA libraries) recently developed by the PI, five (or more) polymorphic nuclear markers will be developed for each species. These new markers will be used, in combination with the mitochondrial gene cytochrome oxidase I, to characterize the population genetic structure of each species throughout its global distribution using graph theoretic and coalescent analytical techniques. Gene flow among populations and the timing of major splitting events will be estimated under a coalescent model (IMa), and empirical support for the hypothesis of depth-related trends in population structure will be assessed using graph theoretic congruence tests. Because the depth specialization and diel vertical migration behaviors of the target species are representative of distinct zooplankton species groups, the results of this study will have broad implications for understanding and predicting the genetic structure of these important grazers in pelagic ecosystems.
Publications produced with support from this award include:
Burridge, A., Goetze, E., Raes, N., Huisman, J., Peijnenburg, K. T. C. A. (in revision) Global biogeography and evolution of Cuvierina pteropods. BMC Evolutionary Biology.
Andrews, K. R., Norton, E. L., Fernandez-Silva, I., Portner†, E. Goetze, E. (in press) Multilocus evidence for globally-distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod. Molecular Ecology.
Halbert , K. M. K., Goetze, E., Carlon, D. B. (2013) High cryptic diversity across the global range of the migratory planktonic copepods Pleuromamma piseki and P. gracilis. PLOS One 8(10): e77011. doi:10.1371/journal.pone.0077011
Norton , E. L., Goetze, E. (2013) Equatorial dispersal barriers and limited connectivity among oceans in a planktonic copepod. Limnology and Oceanography 58: 1581-1596.
Peijnenburg, K. T. C. A., Goetze, E. (2013) High evolutionary potential of marine zooplankton. Ecology & Evolution 3(8): 2765-2781. doi: 10.1002/ece3.644 (both authors contributed equally).
Fernandez-Silva, I., Whitney, J., Wainwright, B., Andrews, K. R., Ylitalo-Ward, H., Bowen, B. W., Toonen, R. J., Goetze, E., Karl, S. A. (2013) Microsatellites for Next-Generation Ecologists: A Post-Sequencing Bioinformatics Pipeline. PLOS One 8(2): e55990. doi:10.1371/journal.pone.0055990
Bron, J. E., Frisch, D., Goetze, E., Johnson, S. C., Lee, C. E., Wyngaard, G. A. (2011) Observing Copepods through a Genomic Lens. Frontiers in Zoology 8: 22.
Goetze, E. (2011) Population differentiation in the open sea: Insights from the pelagic copepod Pleuromamma xiphias. Integrative and Comparative Biology 51: 580-597.
Master’s theses supported under this award include:
Emily L. Norton. Empirical and biophysical modeling studies of dispersal barriers for marine plankton. (2013). University of Hawaii at Manoa.
K. M. K. Halbert. Genetic isolation in the open sea: Cryptic diversity in the Pleuromamma piseki - P. gracilis species complex. (2013). University of Hawaii at Manoa.
|attribute||NC_GLOBAL||projects_2_name||String||Does habitat specialization drive population genetic structure of oceanic zooplankton?|
|attribute||NC_GLOBAL||publisher_name||String||Biological and Chemical Oceanographic Data Management Office (BCO-DMO)|
|attribute||NC_GLOBAL||standard_name_vocabulary||String||CF Standard Name Table v55|
|attribute||NC_GLOBAL||summary||String||This dataset\u00a0consists of mitochondrial sequence data and specimen
information for two species of copepods, Haloptilus longicornis and
Pleuromamma xiphias, collected at an open ocean time series site in the North
Pacific Subtropical Gyre (station ALOHA, 22.45N, 158W) during 11 of the
routine Hawai'i Ocean Time-series (HOT) research cruises from September of
2012 to October of 2013 (HOT-246 to HOT-256).\u00a0Data for Haloptilus
longicornis include\u00a0a 546 base-pair fragment of mitochondrial cytochrome
c oxidase subunit II for each of 483 individuals (mean of 44 animals per
cruise). Data for Pleuromamma xiphias include\u00a0a 551 base-pair fragment of
mitochondrial cytochrome c oxidase subunit I for each of 510 individuals (mean
of 46 animals per cruise). Information is also provided on the HOT cruise
number, date, and specific tow from which each individual was collected. Life
stage and sex of each animal are also noted when identifiable
These data are associated with the forthcoming publication:
Iacchei, M., E. Butcher, E. Portner, Goetze, E. (in press) It\u2019s about
time: Insights into temporal genetic patterns in oceanic zooplankton from
biodiversity indices.\u00a0 Limnology and Oceanography \u00a0
The unique haplotypes in these data are also available under NCBI accession
numbers KY560470 - KY560514 [Haloptilus longicornis], KY560515 -
The following files have been included in this dataset (note that the sequence
IDs in these files differ from the NCBI sequence IDs):
HOT-HALO.fasta: A fasta-formatted text file containing sequences for a
portion of the mitochondrial cytochrome c oxidase subunit II gene (COII; 546
bp) for 483 Haloptilus longicornis individuals collected at Station ALOHA.
HOT-PLXI.fasta: A fasta-formatted text file containing sequences for a portion
of the mitochondrial cytochrome c oxidase subunit I gene (COI; 551 bp) for 510
Pleuromamma xiphias individuals collected at Station ALOHA.
HALO.csv and PLXI.csv: Converted to csv from an Excel file consisting of one
worksheet for Haloptilus longicornis and one worksheet for Pleuromamma
xiphias. In each worksheet, column headings designate:
sample_id: the sample ID number associated with the original organism
collected, DNA extraction, and PCR amplification.
sequence_id: the sample ID number associated with sequences analysed for the
genus: Genus of the collected organism.
species: Species of the collected organism.
cruise: The cruise number for the Hawai'i Ocean Time Series (HOT) cruise on
which the specimen was collected.
tow: The net tow number on which the specimen was collected.
collection_date: The date on which the specimen was collected, formatted as
stage_sex: The life stage (Copepodite or Adult) of the individual, and the
sex (Copepodite, Female, Male).
stage: The life stage (Copepodite or Adult) of the individual. Column added
by BCO-DMO\u00a0from the original stage_sex column for ease of use.
sex: The sex (Copepodite, Female, or Male) of the individual.\u00a0Column
added by BCO-DMO\u00a0from the original stage_sex column for ease of use.
mtCO*_sequence: The mtDNA sequence (COII for Haloptilus longicornis; COI for
Pleuromamma xiphias) associated with that individual. This sequence matches
the sequence associated with the Sequence ID number in the respective fasta
|attribute||NC_GLOBAL||title||String||Data from: Iacchei, M., E. Butcher, E. Portner, Goetze, E. (in press) It\u2019s about time: Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices.|
|attribute||file_link||description||String||Link to data file containing sequence information.|
|attribute||description||description||String||Description of data in file.|
The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.