Accessing BCO-DMO data
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| Dataset Title: | [Data from fish genotyped at 14 and 20 loci] - Data from fish genotyped at 14 and 20 loci at different life stages in the Belizean Barrier Reef in 2013. (An Integrative Investigation of Population Connectivity Using a Coral Reef Fish) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_738724) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Subset
| Files
| Make a graph
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Attributes {
s {
individual_id {
String bcodmo_name "sample";
String description "Unique ID assigned to each fish";
String long_name "Individual Id";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
year {
Int16 _FillValue 32767;
Int16 actual_range 2013, 2013;
String bcodmo_name "year";
String description "Year of sampling";
String long_name "Year";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
String units "unitless";
}
loci {
String bcodmo_name "sample_descrip";
String description "The number of loci individuals were genotyped at; 14 loci or 20 loci. Individuals genotyped at 20 loci were used in the final parentage analysis. Each loci have two columns because each individual has two alleles per locus.";
String long_name "Loci";
String units "unitless";
}
life_stage {
String bcodmo_name "stage";
String description "Whether an individual is a potential offspring (O) or parent (P).";
String long_name "Life Stage";
String units "unitless";
}
tetB_25745 {
Int16 _FillValue 32767;
Int16 actual_range 116, 161;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet B 25745";
String units "count";
}
tetB_25745_2 {
Int16 _FillValue 32767;
Int16 actual_range 116, 161;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet B 25745 2";
String units "count";
}
tetB_29109 {
Int16 _FillValue 32767;
Int16 actual_range 229, 336;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet B 29109";
String units "count";
}
tetB_29109_2 {
Int16 _FillValue 32767;
Int16 actual_range 233, 353;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet B 29109 2";
String units "count";
}
triB_1419 {
Int16 _FillValue 32767;
Int16 actual_range 439, 513;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tri B 1419";
String units "count";
}
triB_1419_2 {
Int16 _FillValue 32767;
Int16 actual_range 439, 513;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tri B 1419 2";
String units "count";
}
triG_18144 {
Int16 _FillValue 32767;
Int16 actual_range 227, 256;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tri G 18144";
String units "count";
}
triG_18144_2 {
Int16 _FillValue 32767;
Int16 actual_range 227, 268;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tri G 18144 2";
String units "count";
}
tetG_985 {
Int16 _FillValue 32767;
Int16 actual_range 358, 552;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet G 985";
String units "count";
}
tetG_985_2 {
Int16 _FillValue 32767;
Int16 actual_range 358, 617;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet G 985 2";
String units "count";
}
tetY_6326 {
Int16 _FillValue 32767;
Int16 actual_range 181, 245;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet Y 6326";
String units "count";
}
tetY_6326_2 {
Int16 _FillValue 32767;
Int16 actual_range 181, 264;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet Y 6326 2";
String units "count";
}
tetR_25632 {
Int16 _FillValue 32767;
Int16 actual_range 140, 261;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet R 25632";
String units "count";
}
tetR_25632_2 {
Int16 _FillValue 32767;
Int16 actual_range 140, 306;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet R 25632 2";
String units "count";
}
tetB_6231 {
Int16 _FillValue 32767;
Int16 actual_range 145, 254;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet B 6231";
String units "count";
}
tetB_6231_2 {
Int16 _FillValue 32767;
Int16 actual_range 149, 262;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet B 6231 2";
String units "count";
}
triB_23889 {
Int16 _FillValue 32767;
Int16 actual_range 367, 417;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tri B 23889";
String units "count";
}
triB_23889_2 {
Int16 _FillValue 32767;
Int16 actual_range 375, 436;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tri B 23889 2";
String units "count";
}
triG_25362 {
Int16 _FillValue 32767;
Int16 actual_range 210, 296;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tri G 25362";
String units "count";
}
triG_25362_2 {
Int16 _FillValue 32767;
Int16 actual_range 214, 408;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tri G 25362 2";
String units "count";
}
triG_21378 {
Int16 _FillValue 32767;
Int16 actual_range 384, 560;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tri G 21378";
String units "count";
}
triG_21378_2 {
Int16 _FillValue 32767;
Int16 actual_range 389, 625;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tri G 21378 2";
String units "count";
}
tetY_14528 {
Int16 _FillValue 32767;
Int16 actual_range 250, 321;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet Y 14528";
String units "count";
}
tetY_14528_2 {
Int16 _FillValue 32767;
Int16 actual_range 250, 342;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet Y 14528 2";
String units "count";
}
triY_6266 {
Int16 _FillValue 32767;
Int16 actual_range 432, 472;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tri Y 6266";
String units "count";
}
triY_6266_2 {
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tri Y 6266 2";
String units "count";
}
tetR_23415 {
Int16 _FillValue 32767;
Int16 actual_range 185, 275;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet R 23415";
String units "count";
}
tetR_23415_2 {
Int16 _FillValue 32767;
Int16 actual_range 185, 296;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet R 23415 2";
String units "count";
}
tetB_24561 {
Int16 _FillValue 32767;
Int16 actual_range 125, 165;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet B 24561";
String units "count";
}
tetB_24561_2 {
Int16 _FillValue 32767;
Int16 actual_range 137, 177;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet B 24561 2";
String units "count";
}
tetB_5796 {
Int16 _FillValue 32767;
Int16 actual_range 216, 323;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet B 5796";
String units "count";
}
tetB_5796_2 {
Int16 _FillValue 32767;
Int16 actual_range 216, 351;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet B 5796 2";
String units "count";
}
tetB_1184 {
Int16 _FillValue 32767;
Int16 actual_range 389, 613;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet B 1184";
String units "count";
}
tetB_1184_2 {
Int16 _FillValue 32767;
Int16 actual_range 389, 637;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet B 1184 2";
String units "count";
}
tetG_24777 {
Int16 _FillValue 32767;
Int16 actual_range 114, 140;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet G 24777";
String units "count";
}
tetG_24777_2 {
Int16 _FillValue 32767;
Int16 actual_range 120, 157;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet G 24777 2";
String units "count";
}
tetG_26721 {
Int16 _FillValue 32767;
Int16 actual_range 174, 267;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet G 26721";
String units "count";
}
tetG_26721_2 {
Int16 _FillValue 32767;
Int16 actual_range 174, 267;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet G 26721 2";
String units "count";
}
tetY_25176 {
Int16 _FillValue 32767;
Int16 actual_range 120, 192;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet Y 25176";
String units "count";
}
tetY_25176_2 {
Int16 _FillValue 32767;
Int16 actual_range 130, 238;
String bcodmo_name "count";
String description "The number of reptitive units in the microsatellite allele.";
String long_name "Tet Y 25176 2";
String units "count";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"We surveyed a 41 km-long transect of the Belize Barrier reef, centered at
Carrie Bow Cay, by SCUBA to conduct a genetic parentage study of the reef fish
Elactinus lori. All underwater sampling was conducted using SCUBA at an
average (\\u00b1SD) depth of 16.03 \\u00b1 2.19 m. A waypoint was recorded from
the boat at the beginning and end of every collection dive, with the midpoint
of each dive taken as the location for all individuals sampled on that dive.
To collect settlers, we sampled ~ 100 individuals every kilometer. Individuals
were collected from the outsides of sponges using slurp guns and placed them
in plastic bags. At the surface, settlers were anesthetized with MS-222. For
adults, we collected non-lethal tissue samples at three regions along the
transect (n \\u2248 1,000 per region). Each adult was collected with a slurp
gun and restrained in a net; we took a small tissue sample from the caudal fin
using scissors. All tissue was stored in 95% EtOH. At each adult collection
sponge, we also measured: sponge depth (m, using dive computers), number of
tubes per sponge, and length of largest sponge tube (nearest cm, using a tape
measure).
For genetic analyses, DNA was extracted using a HotSHOT protocol; fragments
were amplified using the Type-It Microsatellite PCR Kit (Qiagen) and screened
on an ABI 3730 automated sequencer.
Otoliths were extracted from the 120 settlers that were assigned to parents.
Otoliths were dissected, cleared of tissue, immersed in oil for 2-7 days, and
rings were counted under a 50\\u00d7 oil immersion lens
Further details on all methods can be found in D\\u2019Aloia et al. (2015),
PNAS.";
String awards_0_award_nid "544434";
String awards_0_award_number "OCE-1260424";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1260424";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "David L. Garrison";
String awards_0_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"Genotypes
P. Buston and C. D'Aloia, PIs
Version 18 June 2018";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2018-06-18T15:48:37Z";
String date_modified "2019-06-07T16:07:11Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.738724.1";
String history
"2024-12-22T12:18:47Z (local files)
2024-12-22T12:18:47Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_738724.html";
String infoUrl "https://www.bco-dmo.org/dataset/738724";
String institution "BCO-DMO";
String instruments_0_dataset_instrument_description "Used to collect GPS data";
String instruments_0_dataset_instrument_nid "738732";
String instruments_0_description "Acquires satellite signals and tracks your location.";
String instruments_0_instrument_name "GPS receiver";
String instruments_0_instrument_nid "706037";
String instruments_0_supplied_name "GPSMAP 76Cx (Garmin)";
String keywords "bco, bco-dmo, biological, chemical, data, dataset, dmo, erddap, individual, individual_id, life, life_stage, loci, management, oceanography, office, preliminary, stage, tet, tetB_1184, tetB_1184_2, tetB_24561, tetB_24561_2, tetB_25745, tetB_25745_2, tetB_29109, tetB_29109_2, tetB_5796, tetB_5796_2, tetB_6231, tetB_6231_2, tetG_24777, tetG_24777_2, tetG_26721, tetG_26721_2, tetG_985, tetG_985_2, tetR_23415, tetR_23415_2, tetR_25632, tetR_25632_2, tetY_14528, tetY_14528_2, tetY_25176, tetY_25176_2, tetY_6326, tetY_6326_2, tri, triB_1419, triB_1419_2, triB_23889, triB_23889_2, triG_18144, triG_18144_2, triG_21378, triG_21378_2, triG_25362, triG_25362_2, triY_6266, triY_6266_2, year";
String license "https://www.bco-dmo.org/dataset/738724/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/738724";
String param_mapping "{'738724': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/738724/parameters";
String people_0_affiliation "Boston University";
String people_0_affiliation_acronym "BU";
String people_0_person_name "Dr Peter Buston";
String people_0_person_nid "544437";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Woods Hole Oceanographic Institution";
String people_1_affiliation_acronym "WHOI";
String people_1_person_name "Dr Cassidy C. D'Aloia";
String people_1_person_nid "704789";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Boston University";
String people_2_affiliation_acronym "BU";
String people_2_person_name "Dr Peter Buston";
String people_2_person_nid "544437";
String people_2_role "Contact";
String people_2_role_type "related";
String people_3_affiliation "Woods Hole Oceanographic Institution";
String people_3_affiliation_acronym "WHOI BCO-DMO";
String people_3_person_name "Hannah Ake";
String people_3_person_nid "650173";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "Elacatinus Dispersal I";
String projects_0_acronym "Elacatinus Dispersal I";
String projects_0_description
"Understanding the patterns, causes and consequences of larval dispersal is a major goal of 21st century marine ecology. Patterns of dispersal determine the rates of larval exchange, or connectivity, between populations. Both physical factors (e.g., water movement) and biological factors (e.g., larval behavior) cause variation in population connectivity. Population connectivity, in turn, has major consequences for all aspects of an organism's biology, from individual behavior to metapopulation dynamics, and from evolution within metapopulations to the origin and extinction of species. Further, understanding population connectivity is critical for the design of effective networks of marine reserves, creation of vital tools in conservation, and the development of sustainable fisheries.
Over the last decade, three methods, each of which tells something slightly different, have emerged as leading contenders to provide the greatest insights into population connectivity. First, coupled biophysical models make assumptions regarding water flow, larval behavior and ecology, to predict population connectivity. Second, indirect genetic methods use spatial distributions of allele frequencies to infer population connectivity. Third, direct genetic methods use parentage analyses, tracing recruits to specific adults, to measure population connectivity. Despite advances, lack of integration means that we do not know the predictive skill of biophysical models, or the extent to which patterns of dispersal predict spatial genetic structure. The overall objective of this proposal is to conduct an integrated investigation of population connectivity, using all three methods in one tractable system: the neon goby, Elacatinus lori, on the Belizean Barrier Reef. There are three motives for this choice of study system: i) fourteen highly polymorphic microsatellite loci have been developed, facilitating the assignment of recruits to parents using parentage analyses and the measurement of dispersal; ii) the physical oceanography of the Belizean Barrier Reef is well-studied, facilitating the development and testing of coupled biophysical models; and, iii) E. lori has a relatively small biogeographic range, facilitating analysis of the spatial distribution of allele frequencies throughout its range.
Broader Impacts. The grant will support one postdoc and two graduate students who will be trained in scientific diving, marine fieldwork, population genetics, biophysical modeling, and mathematical modeling, and will gain collaborative research experience. PIs will incorporate research findings in their courses, which cover all these topics. The grant will also broaden participation of under-represented groups by supporting six undergraduates from groups traditionally underrepresented in STEM fields. In each year of the project there will be an All Participants meeting to reinforce the network of participants. A project website will be developed, in English and Spanish, on the theme of larval dispersal and population connectivity. This will include a resource for K-12 marine science educators developed in collaboration with a marine science educator. All PIs will ensure that results are broadly disseminated to the scientific community and general public via appropriate forms of media.";
String projects_0_end_date "2017-02";
String projects_0_geolocation "Belizean Barrier Reef System (16.803 degrees North 88.096 degrees West)";
String projects_0_name "An Integrative Investigation of Population Connectivity Using a Coral Reef Fish";
String projects_0_project_nid "544435";
String projects_0_project_website "http://people.bu.edu/buston/lab/Welcome.html";
String projects_0_start_date "2013-03";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "year";
String summary "Data from fish genotyped at 14 and 20 loci at different life stages in the Belizean Barrier Reef in 2013.";
String title "[Data from fish genotyped at 14 and 20 loci] - Data from fish genotyped at 14 and 20 loci at different life stages in the Belizean Barrier Reef in 2013. (An Integrative Investigation of Population Connectivity Using a Coral Reef Fish)";
String version "1";
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.