BCO-DMO ERDDAP
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Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String Refer to the following publication for complete methodology details:\n \nGoetze, E.,\\u00a0Andrews, K., Peijnenburg, K. T. C. A., Portner, E., Norton,\nE. L. (2015) Temporal Stability of Genetic Structure in a Mesopelagic\nCopepod.\\u00a0\\u00a0PLoS One\\u00a010(8):\ne0136087.\\u00a0[doi:10.1371/journal.pone.0136087](\\\\\"http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0136087\\\\\")\n \nIn summary (excerpted from above):\n \nFor\\u00a0H.\\u00a0longicornis species 1, deviations from Hardy-Weinberg\nequilibrium (HWE) and linkage disequilibrium were examined using ARLEQUIN\nv3.5.1.3 and GENEPOP v4.2 for all microsatellite loci [36\\u201338]. We tested\nfor the presence of null alleles in microsatellite data using MICROCHECKER\nv2.2.3 [39], and estimated null allele frequencies and calculated population\npairwise\\u00a0FST\\u00a0values with correction for null alleles in FreeNA [40].\nMicrosatellite genetic diversity indices of observed and expected\nheterozygosity, average alleles per locus, and allele richness were calculated\nin GENETIX v4.05 and FSTAT [35,41]. Pairwise\\u00a0FST\\u00a0values were\ncalculated among all sample sites using both microsatellite and mtCOII data,\nas a measure of population subdivision across samples (ARLEQUIN v3.5.1.3,\n[38]). Significance was assessed following correction for multiple comparisons\nusing the false discovery rate (FDR, [42,43]). Pairwise \\u03a6ST\\u00a0values\nalso were calculated for the mtCOII data. We identified the nucleotide\nsubstitution model that best fit our mtCOII data using the Akaike Information\nCriterion, as implemented in jModelTest v2.1.4 [44], and the K81 or three-\nparameter model was selected as the best model (TPM3uf+G). The Tamura and Nei\nsubstitution model, which was the closest available model in Arlequin, was\nused to calculate pairwise and global \\u03a6ST\\u00a0values, and to estimate\ngenetic diversity at each site. Hierarchical Analyses of Molecular Variance\n(AMOVA) based on\\u00a0FST\\u00a0were carried out to partition the genetic\nvariance across both space (ocean gyres) and time (sampling years), for both\nmarker types. In these analyses, we tested for population structure under the\nfollowing groupings: with samples stratified by (1) northern and southern\nsubtropical gyres (2 gyres), and (2) across two sampling years (2010, 2012).\nGlobal\\u00a0FST\\u00a0values were estimated using non-hierarchical AMOVAs among\nall samples, as well as among subsets of the data across ocean gyres and\nsampling years. Significance was tested with 10,000 permutations of genotypes\nor haplotypes among populations. Principal coordinate analysis (PCA) plots of\nlinearized pairwise\\u00a0FST\\u00a0values based on both mtCOII and\nmicrosatellite data were used to visualize spatial and temporal genetic\ndifferentiation among samples. Population structure was further examined using\na Bayesian clustering method implemented in STRUCTURE [45,46] for\nmicrosatellite loci. We used admixture and correlated allele frequency models,\nwith a burn-in of 105\\u00a0steps followed by 106\\u00a0steps, with and without\nusing sampling location as a prior. We ran these analyses for each of the 2010\nand 2012 datasets using\\u00a0K\\u00a0= 1 to\\u00a0K\\u00a0= 10, and for the\ndataset of combined years using\\u00a0K\\u00a0= 1 to\\u00a0K\\u00a0= 20. We ran\nthree separate replicates for each K to investigate consistency of Pr(X|K).\nThe true\\u00a0K\\u00a0was evaluated by visual inspection of barplots and\ncomparing Pr(X|K) across\\u00a0K\\u00a0values.
attribute NC_GLOBAL awards_0_award_nid String 537990
attribute NC_GLOBAL awards_0_award_number String OCE-1338959
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1338959 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL awards_1_award_nid String 539716
attribute NC_GLOBAL awards_1_award_number String OCE-1029478
attribute NC_GLOBAL awards_1_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1029478 (external link)
attribute NC_GLOBAL awards_1_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_1_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_1_funding_source_nid String 355
attribute NC_GLOBAL awards_1_program_manager String David L. Garrison
attribute NC_GLOBAL awards_1_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Haloptilus longicorns population structure \n  Erica Goetze, PI \n  Version 20 March 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 creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3  19 Dec 2019
attribute NC_GLOBAL date_created String 2017-05-04T17:20:16Z
attribute NC_GLOBAL date_modified String 2019-03-28T19:36:57Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.699458.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/699458 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Thermal Cycler
attribute NC_GLOBAL instruments_0_dataset_instrument_description String PCR products were genotyped
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 699475
attribute NC_GLOBAL instruments_0_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.\n\n(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
attribute NC_GLOBAL instruments_0_instrument_name String PCR Thermal Cycler
attribute NC_GLOBAL instruments_0_instrument_nid String 471582
attribute NC_GLOBAL instruments_0_supplied_name String ABI3730 Genetic Analyzer
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, chemical, data, dataset, diploid, diploidGenotype1_HALOM264, diploidGenotype1_HALOMS175, diploidGenotype1_HALOMS27, diploidGenotype1_HALOMS32, diploidGenotype1_HALOMS86, diploidGenotype1_HALOMS91, diploidGenotype1_HALOMX66, diploidGenotype2_HALOM264, diploidGenotype2_HALOMS175, diploidGenotype2_HALOMS27, diploidGenotype2_HALOMS32, diploidGenotype2_HALOMS86, diploidGenotype2_HALOMS91, diploidGenotype2_HALOMX66, dmo, erddap, genotype1, genotype2, halom264, haloms175, haloms27, haloms32, haloms86, haloms91, halomx66, management, oceanography, office, preliminary, sample, sample_id, station
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/699458/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/699458 (external link)
attribute NC_GLOBAL param_mapping String {'699458': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/699458/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of Hawaii at Manoa
attribute NC_GLOBAL people_0_affiliation_acronym String SOEST
attribute NC_GLOBAL people_0_person_name String Erica Goetze
attribute NC_GLOBAL people_0_person_nid String 473048
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_1_person_name String Hannah Ake
attribute NC_GLOBAL people_1_person_nid String 650173
attribute NC_GLOBAL people_1_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL project String Plankton Population Genetics,Plankton_PopStructure
attribute NC_GLOBAL projects_0_acronym String Plankton Population Genetics
attribute NC_GLOBAL projects_0_description String Description from NSF award abstract:\nMarine 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.\nNote: 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).\nOnline science outreach blog at: https://atlanticplankton.wordpress.com
attribute NC_GLOBAL projects_0_end_date String 2015-11
attribute NC_GLOBAL projects_0_geolocation String Atlantic Ocean, 46 N - 46 S
attribute NC_GLOBAL projects_0_name String Basin-scale genetics of marine zooplankton
attribute NC_GLOBAL projects_0_project_nid String 537991
attribute NC_GLOBAL projects_0_start_date String 2013-12
attribute NC_GLOBAL projects_1_acronym String Plankton_PopStructure
attribute NC_GLOBAL projects_1_description String Description from NSF award abstract:\nThis 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:\n1) Develop novel nuclear markers that can be used to resolve genetic structure and estimate gene flow among copepod populations,\n2) 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\n3) 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.\nDrawing 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.\nPublications produced with support from this award include:\nBurridge, A., Goetze, E., Raes, N., Huisman, J., Peijnenburg, K. T. C. A.  (in revision)  Global biogeography and evolution of Cuvierina pteropods.   BMC Evolutionary Biology.\nAndrews, 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.\nHalbert , 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\nNorton , E. L., Goetze, E. (2013) Equatorial dispersal barriers and limited connectivity among oceans in a planktonic copepod.  Limnology and Oceanography 58: 1581-1596.\nPeijnenburg, 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).\nFernandez-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\nBron, 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.\nGoetze, E. (2011) Population differentiation in the open sea: Insights from the pelagic copepod Pleuromamma xiphias.  Integrative and Comparative Biology 51: 580-597.  \nMaster’s theses supported under this award include:\nEmily L. Norton. Empirical and biophysical modeling studies of dispersal barriers for marine plankton. (2013).  University of Hawaii at Manoa.\nK. 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_1_end_date String 2014-07
attribute NC_GLOBAL projects_1_geolocation String Global Ocean
attribute NC_GLOBAL projects_1_name String Does habitat specialization drive population genetic structure of oceanic zooplankton?
attribute NC_GLOBAL projects_1_project_nid String 539717
attribute NC_GLOBAL projects_1_start_date String 2010-08
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String Haloptilus longicornis population structure (Atlantic Ocean) - Microsatellite data.
attribute NC_GLOBAL title String [H. longicornis Population Structure] - Haloptilus longicornis population structure (Atlantic Ocean) - Microsatellite data. (Basin-scale genetics of marine zooplankton)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable station String
attribute station bcodmo_name String station
attribute station description String Station number where sampling occurred
attribute station long_name String Station
attribute station units String unitless
variable sample_id String
attribute sample_id bcodmo_name String sample
attribute sample_id description String PI issued sample ID number
attribute sample_id long_name String Sample Id
attribute sample_id nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute sample_id units String unitless
variable diploidGenotype1_HALOMS175 byte
attribute diploidGenotype1_HALOMS175 _FillValue byte 127
attribute diploidGenotype1_HALOMS175 actual_range byte 93, 113
attribute diploidGenotype1_HALOMS175 bcodmo_name String count
attribute diploidGenotype1_HALOMS175 description String Diploid genotypes reported for each locus and individual
attribute diploidGenotype1_HALOMS175 long_name String Diploid Genotype1 HALOMS175
attribute diploidGenotype1_HALOMS175 units String count
variable diploidGenotype2_HALOMS175 byte
attribute diploidGenotype2_HALOMS175 _FillValue byte 127
attribute diploidGenotype2_HALOMS175 actual_range byte 93, 119
attribute diploidGenotype2_HALOMS175 bcodmo_name String count
attribute diploidGenotype2_HALOMS175 description String Diploid genotypes reported for each locus and individual
attribute diploidGenotype2_HALOMS175 long_name String Diploid Genotype2 HALOMS175
attribute diploidGenotype2_HALOMS175 units String count
variable diploidGenotype1_HALOMS27 short
attribute diploidGenotype1_HALOMS27 _FillValue short 32767
attribute diploidGenotype1_HALOMS27 actual_range short 214, 258
attribute diploidGenotype1_HALOMS27 bcodmo_name String count
attribute diploidGenotype1_HALOMS27 description String Diploid genotypes reported for each locus and individual
attribute diploidGenotype1_HALOMS27 long_name String Diploid Genotype1 HALOMS27
attribute diploidGenotype1_HALOMS27 units String count
variable diploidGenotype2_HALOMS27 short
attribute diploidGenotype2_HALOMS27 _FillValue short 32767
attribute diploidGenotype2_HALOMS27 actual_range short 220, 258
attribute diploidGenotype2_HALOMS27 bcodmo_name String count
attribute diploidGenotype2_HALOMS27 description String Diploid genotypes reported for each locus and individual
attribute diploidGenotype2_HALOMS27 long_name String Diploid Genotype2 HALOMS27
attribute diploidGenotype2_HALOMS27 units String count
variable diploidGenotype1_HALOMS32 short
attribute diploidGenotype1_HALOMS32 _FillValue short 32767
attribute diploidGenotype1_HALOMS32 actual_range short 126, 150
attribute diploidGenotype1_HALOMS32 bcodmo_name String count
attribute diploidGenotype1_HALOMS32 description String Diploid genotypes reported for each locus and individual
attribute diploidGenotype1_HALOMS32 long_name String Diploid Genotype1 HALOMS32
attribute diploidGenotype1_HALOMS32 units String count
variable diploidGenotype2_HALOMS32 short
attribute diploidGenotype2_HALOMS32 _FillValue short 32767
attribute diploidGenotype2_HALOMS32 actual_range short 126, 159
attribute diploidGenotype2_HALOMS32 bcodmo_name String count
attribute diploidGenotype2_HALOMS32 description String Diploid genotypes reported for each locus and individual
attribute diploidGenotype2_HALOMS32 long_name String Diploid Genotype2 HALOMS32
attribute diploidGenotype2_HALOMS32 units String count
variable diploidGenotype1_HALOMS86 short
attribute diploidGenotype1_HALOMS86 _FillValue short 32767
attribute diploidGenotype1_HALOMS86 actual_range short 136, 181
attribute diploidGenotype1_HALOMS86 bcodmo_name String count
attribute diploidGenotype1_HALOMS86 description String Diploid genotypes reported for each locus and individual
attribute diploidGenotype1_HALOMS86 long_name String Diploid Genotype1 HALOMS86
attribute diploidGenotype1_HALOMS86 units String count
variable diploidGenotype2_HALOMS86 short
attribute diploidGenotype2_HALOMS86 _FillValue short 32767
attribute diploidGenotype2_HALOMS86 actual_range short 136, 181
attribute diploidGenotype2_HALOMS86 bcodmo_name String count
attribute diploidGenotype2_HALOMS86 description String Diploid genotypes reported for each locus and individual
attribute diploidGenotype2_HALOMS86 long_name String Diploid Genotype2 HALOMS86
attribute diploidGenotype2_HALOMS86 units String count
variable diploidGenotype1_HALOM264 short
attribute diploidGenotype1_HALOM264 _FillValue short 32767
attribute diploidGenotype1_HALOM264 actual_range short 151, 172
attribute diploidGenotype1_HALOM264 bcodmo_name String count
attribute diploidGenotype1_HALOM264 description String Diploid genotypes reported for each locus and individual
attribute diploidGenotype1_HALOM264 long_name String Diploid Genotype1 HALOM264
attribute diploidGenotype1_HALOM264 units String count
variable diploidGenotype2_HALOM264 short
attribute diploidGenotype2_HALOM264 _FillValue short 32767
attribute diploidGenotype2_HALOM264 actual_range short 163, 177
attribute diploidGenotype2_HALOM264 bcodmo_name String count
attribute diploidGenotype2_HALOM264 description String Diploid genotypes reported for each locus and individual
attribute diploidGenotype2_HALOM264 long_name String Diploid Genotype2 HALOM264
attribute diploidGenotype2_HALOM264 units String count
variable diploidGenotype1_HALOMS91 short
attribute diploidGenotype1_HALOMS91 _FillValue short 32767
attribute diploidGenotype1_HALOMS91 actual_range short 190, 212
attribute diploidGenotype1_HALOMS91 bcodmo_name String count
attribute diploidGenotype1_HALOMS91 description String Diploid genotypes reported for each locus and individual
attribute diploidGenotype1_HALOMS91 long_name String Diploid Genotype1 HALOMS91
attribute diploidGenotype1_HALOMS91 units String count
variable diploidGenotype2_HALOMS91 short
attribute diploidGenotype2_HALOMS91 _FillValue short 32767
attribute diploidGenotype2_HALOMS91 actual_range short 194, 218
attribute diploidGenotype2_HALOMS91 bcodmo_name String count
attribute diploidGenotype2_HALOMS91 description String Diploid genotypes reported for each locus and individual
attribute diploidGenotype2_HALOMS91 long_name String Diploid Genotype2 HALOMS91
attribute diploidGenotype2_HALOMS91 units String count
variable diploidGenotype1_HALOMX66 short
attribute diploidGenotype1_HALOMX66 _FillValue short 32767
attribute diploidGenotype1_HALOMX66 actual_range short 178, 193
attribute diploidGenotype1_HALOMX66 bcodmo_name String count
attribute diploidGenotype1_HALOMX66 description String Diploid genotypes reported for each locus and individual
attribute diploidGenotype1_HALOMX66 long_name String Diploid Genotype1 HALOMX66
attribute diploidGenotype1_HALOMX66 units String count
variable diploidGenotype2_HALOMX66 short
attribute diploidGenotype2_HALOMX66 _FillValue short 32767
attribute diploidGenotype2_HALOMX66 actual_range short 181, 196
attribute diploidGenotype2_HALOMX66 bcodmo_name String count
attribute diploidGenotype2_HALOMX66 description String Diploid genotypes reported for each locus and individual
attribute diploidGenotype2_HALOMX66 long_name String Diploid Genotype2 HALOMX66
attribute diploidGenotype2_HALOMX66 units String count

 
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