Accessing BCO-DMO data
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| Dataset Title: | [FL Stegastes Partitus Otolith Summary Data] - Summary of otolith microstructure data from Stegastes partitus collected by SCUBA dives in the Upper Florida Keys, USA from 2003-2008 (FK Fish Recruitment project, FK Population Connectivity project) (Scope and Consequences of Variability in the Early Life History Traits of a Caribbean Coral Reef Fish) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_523365) |
| Information: | Summary
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| FGDC
| ISO 19115
| Metadata
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Attributes {
s {
stage {
String bcodmo_name "stage";
String description "Life stage of fish upon collection. Larva = late stage larva caught in light trap; Juvenile = < 1 month old juvenile collected during visual survey.";
String long_name "Stage";
String units "text";
}
date_collected {
Int32 _FillValue 2147483647;
Int32 actual_range 20010613, 20080812;
String bcodmo_name "date";
String description "Year-month-day of collection written as YYYYMMDD.";
String long_name "Date Collected";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String units "unitless";
}
collection {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 4;
String bcodmo_name "unknown";
String description "For larvae this refers to light trap number fish was collected in. For juveniles this refers to habitat of survey and collection: 1 = reef habitat; 2 = rubble habitat.";
String long_name "Collection";
String units "integer";
}
site_name {
String bcodmo_name "site";
String description "Name of the site.";
String long_name "Site Name";
String units "text";
}
site_code {
String bcodmo_name "Site_ID";
String description "Code that refers to the site of the survey and collection located off of the upper Florida Keys. FR = French Reef; MO = Molasses Reef; PI = Pickles Reef; SI = Sand Island Reef; TR = Triangles; WB = White Banks.";
String long_name "Site Code";
String units "text";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 24.98717, 25.04348;
String axis "Y";
String bcodmo_name "latitude";
String description "Latitude of the site in degrees north.";
String ioos_category "Location";
String long_name "Site Lat";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -80.43787, -80.35;
String axis "X";
String bcodmo_name "longitude";
String description "Longitude of the site in degrees west.";
String ioos_category "Location";
String long_name "Site Lon";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "degrees_east";
}
sample {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 45;
String bcodmo_name "sample";
String description "The sample number of the individual fish in the collection.";
String long_name "Sample";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "integer";
}
std_length {
Float32 _FillValue NaN;
Float32 actual_range 7.750223, 21.5;
String bcodmo_name "fish_len";
String description "Standard length.";
String long_name "Std Length";
String units "millimeters (mm)";
}
monthly_cohort {
String bcodmo_name "unknown";
String description "Month and two digit year of collection.";
String long_name "Monthly Cohort";
String units "mon-yr";
}
site_descrip {
String bcodmo_name "site_descrip";
String description "Description of location of survey and collection sites; offshore = reefs that part of the bank reef tract; inshore = reefs that are inshore patch reefs; only applies to juveniles.";
String long_name "Site Descrip";
String units "text";
}
collect_catch_or_density {
Float64 _FillValue NaN;
Float64 actual_range 0.013333333, 40.0;
String bcodmo_name "unknown";
String description "For larvae this refers to total light trap catch; for juveniles this refers to collection density estimated from 15 5 x 1 m transects and then converted to number of juvenile fish per meter-squared.";
String long_name "Collect Catch Or Density";
String units "numeric";
}
pel_larv_dur {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 19, 38;
String bcodmo_name "unknown";
String description "Pelagic larval duration in days which was estimated from the number of daily larval otolith increments.";
String long_name "Pel Larv Dur";
String units "number of days";
}
juv_age {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 0, 30;
String bcodmo_name "age";
String description "Juvenile age in days, which was estimated from the number of daily juvenile otolith increments.";
String long_name "Juv Age";
String units "days";
}
date_hatched {
Int32 _FillValue 2147483647;
Int32 actual_range 20030208, 20080717;
String bcodmo_name "date";
String description "Date of hatching which was estimated by subtracting PLD and Juv Age from Collect Date. in the format YYYYMMDD";
String long_name "Date Hatched";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String units "unitless";
}
date_spawn {
Int32 _FillValue 2147483647;
Int32 actual_range 20030206, 20080713;
String bcodmo_name "date";
String description "Date of spawning which was estimated by subtracting 4 days from Hatch Date. in the format YYYYMMDD";
String long_name "Date Spawn";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String units "unitless";
}
lunar_day_spawn {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 30;
String bcodmo_name "unknown";
String description "Lunar day of spawning which was assigned based on Spawn Date with day 1 corresponding to the new moon; day 8 corresponding to the 1st quarter; day 15 corresponding to the full moon; and day 23 corresponding to the 3rd quarter";
String long_name "Lunar Day Spawn";
String units "integer";
}
lunar_phase_spawn {
String bcodmo_name "unknown";
String description "Lunar phase of spawning which was assigned based on Lunar Day with 1st quarter moon: days 5-11; 2nd quarter/full moon: days 12-18; 3rd quarter moon: days 19-26; 4th quarter/new moon: days 27-4.";
String long_name "Lunar Phase Spawn";
String units "ordinal";
}
date_settled {
Int32 _FillValue 2147483647;
Int32 actual_range 20030313, 20080810;
String bcodmo_name "date";
String description "Date of settlement which was estimated by subtracting Juv Age from Collect Date. in the format YYYYMMDD";
String long_name "Date Settled";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String units "unitless";
}
lunar_day_settled {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 30;
String bcodmo_name "unknown";
String description "Lunar day of settlement which was assigned based on Settle Date with day 1 corresponding to the new moon; day 8 corresponding to the 1st quarter; day 15 corresponding to the full moon; and day 23 corresponding to the 3rd quarter.";
String long_name "Lunar Day Settled";
String units "integer";
}
lunar_phase_settled {
String bcodmo_name "unknown";
String description "Lunar phase of settlement which was assigned based on Lunar Day with 1st quarter moon: days 5-11; 2nd quarter/full moon: days 12-18; 3rd quarter moon: days 19-26; 4th quarter/new moon: days 27-4.";
String long_name "Lunar Phase Settled";
String units "ordinal";
}
tidal_day_settled {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 30;
String bcodmo_name "unknown";
String description "Tidal amplitude day of settlement which was assigned based Settle Date with day 1 corresponding to the maximum tidal amplitude closest to the new moon.";
String long_name "Tidal Day Settled";
String units "?";
}
larval_radius {
Float64 _FillValue NaN;
Float64 actual_range 146.1600037, 266.9200134;
String bcodmo_name "unknown";
String description "Otolith radius in um at the last daily larval otolith increment.";
String long_name "Larval Radius";
String units "micrometers (um)";
}
settle_radius {
Float64 _FillValue NaN;
Float64 actual_range 146.1600037, 273.0899963;
String bcodmo_name "unknown";
String description "Otolith radius in um at the settlement otolith increment.";
String long_name "Settle Radius";
String units "micrometers (um)";
}
otolith_radius {
Float64 _FillValue NaN;
Float64 actual_range 146.1600037, 377.0;
String bcodmo_name "unknown";
String description "Otolith radius in um to the edge of the otolith.";
String long_name "Otolith Radius";
String units "micrometers (um)";
}
larval_growth_avg {
Float64 _FillValue NaN;
Float64 actual_range 5.986999814, 9.733809238;
String bcodmo_name "growth";
String description "Mean daily larval otolith increment width in um.";
String long_name "Larval Growth Avg";
String units "micrometers (um)";
}
juv_growth_avg {
Float64 _FillValue NaN;
Float64 actual_range 3.328889635, 9.050003052;
String bcodmo_name "growth";
String description "Mean daily juvenile otolith increment width in um.";
String long_name "Juv Growth Avg";
String units "micrometers (um)";
}
juv_growth_1_2_d_avg {
Float64 _FillValue NaN;
Float64 actual_range 3.084999084, 10.36500549;
String bcodmo_name "growth";
String description "Mean daily juvenile otolith increment width over the first 2 days post-settlement in um.";
String long_name "Juv Growth 1 2 D Avg";
String units "micrometers (um)";
}
temp_larval {
Float64 _FillValue NaN;
Float64 actual_range 22.76948052, 30.31876585;
String bcodmo_name "unknown";
String description "Mean water temperature at 21 m depth at Conch Reef in the upper Florida Keys averaged over the larval period of each Monthly Cohort.";
String long_name "Temp Larval";
String units "degrees Celsius (?)";
}
temp_juv {
Float64 _FillValue NaN;
Float64 actual_range 22.86419355, 30.53923611;
String bcodmo_name "unknown";
String description "Mean water temperature at 21 m depth at Conch Reef in the upper Florida Keys averaged over the juvenile period of each Monthly Cohort.";
String long_name "Temp Juv";
String units "degrees Celsius (?)";
}
density_juv {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 0.453333333;
String bcodmo_name "unknown";
String description "Density of juvenile conspecifics (20-30 mm SL) estimated from 15 5 x 1 m transects and then converted to number of fish per meter-squared; only surveyed in 2007 and 2008.";
String long_name "Density Juv";
String units "number of fish per square meter (fish/m^2)";
}
density_int {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 0.64;
String bcodmo_name "unknown";
String description "Density of intermediate conspecifics (30-50 mm SL) estimated from 15 5 x 1 m transects and then converted to number of fish per meter-squared; only surveyed in 2007 and 2008.";
String long_name "Density Int";
String units "number of fish per square meter (fish/m^2)";
}
density_adult {
Float64 _FillValue NaN;
Float64 actual_range 0.026666667, 0.853333333;
String bcodmo_name "unknown";
String description "Density of adult conspecifics ( > 50 mm SL) estimated from 15 5 x 1 m transects and then converted to number of fish per meter-squared; only surveyed in 2007 and 2008.";
String long_name "Density Adult";
String units "number of fish per square meter (fish/m^2)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Collections were made over many small boat SCUBA dives from 2003-2008; cruises
and dives were not numbered.\\u00a0
The otoliths were extracted using standard dissecting techniques and placed in
a drop of medium viscosity immersion oil on a microscope slide to clear for a
minimum of 30 d. Based on ease of reading, only the lapilli were
examined.\\u00a0The clearest lapillus was chosen from each individual and
viewed under 400 magnification through a Leica DMLB microscope equipped with a
polarized filter between the first stage and light source. The image was
captured by a Dage MTI video camera and analyzed using Image Pro Plus 4.5
software (Media Cybernetics). Each otolith was read once blind (i.e., without
sample information available) and saved as a digital file. Every 5th
individual was measured a second time. The images of the remaining 1029 fish
were examined to determine if there was any ambiguity in the placement of the
increments and an additional 161 fish were aged a second time, resulting in a
total of 418 fish aged twice. Otoliths were rejected where the difference
between the first and second reads was > 5%, resulting in six exclusions.
Otolith analysis was utilized to determine the following ELHTs: post-
settlement age (number of concentric increments after the settlement mark),
pelagic larval duration (PLD; number of concentric increments from the
primordium to the settlement mark), larval and juvenile growth rates (widths
between consecutive increments), and size-at-age (otolith radius-at-each age,
including settlement).";
String awards_0_award_nid "521580";
String awards_0_award_number "OCE-9986359";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=9986359";
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 "Phillip R. Taylor";
String awards_0_program_manager_nid "50451";
String awards_1_award_nid "521581";
String awards_1_award_number "OCE-0550732";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0550732";
String awards_1_funder_name "NSF Division of Ocean Sciences";
String awards_1_funding_acronym "NSF OCE";
String awards_1_funding_source_nid "355";
String awards_1_program_manager "David L. Garrison";
String awards_1_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"Otolith Summary Data
Stegastes partitus from the Florida Keys
PI: Su Sponaugle (RSMAS)
Contact: Tauna Rankin (NOAA NMFS)
Version: 15 Aug 2014";
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 "2014-08-15T08:11:00Z";
String date_modified "2019-12-30T20:36:08Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.523365.1";
Float64 Easternmost_Easting -80.35;
Float64 geospatial_lat_max 25.04348;
Float64 geospatial_lat_min 24.98717;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -80.35;
Float64 geospatial_lon_min -80.43787;
String geospatial_lon_units "degrees_east";
String history
"2024-11-21T08:43:05Z (local files)
2024-11-21T08:43:05Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_523365.html";
String infoUrl "https://www.bco-dmo.org/dataset/523365";
String institution "BCO-DMO";
String instruments_0_dataset_instrument_description "The clearest lapillus was chosen from each individual and viewed under 400 magnification through a Leica DMLB microscope equipped with a polarized filter between the first stage and light source. The image was captured by a Dage MTI video camera and analyzed using Image Pro Plus 4.5 software (Media Cybernetics).";
String instruments_0_dataset_instrument_nid "526673";
String instruments_0_description "Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB06/";
String instruments_0_instrument_name "Microscope-Fluorescence";
String instruments_0_instrument_nid "695";
String instruments_0_supplied_name "Leica DMLB microscope";
String keywords "adult, age, average, bco, bco-dmo, biological, catch, chemical, code, cohort, collect, collect_catch_or_density, collected, collection, data, dataset, date, date_collected, date_hatched, date_settled, date_spawn, day, density, density_adult, density_int, density_juv, depth, descrip, dmo, dur, erddap, growth, hatched, int, juv, juv_age, juv_growth_1_2_d_avg, juv_growth_avg, larv, larval, larval_growth_avg, larval_radius, length, lunar, lunar_day_settled, lunar_day_spawn, lunar_phase_settled, lunar_phase_spawn, management, month, monthly, monthly_cohort, name, oceanography, office, otolith, otolith_radius, pel, pel_larv_dur, phase, preliminary, profiler, radius, salinity, salinity-temperature-depth, sample, settle, settle_radius, settled, site, site_code, site_descrip, site_lat, site_lon, site_name, spawn, stage, std, std_length, temp_juv, temp_larval, temperature, tidal, tidal_day_settled";
String license "https://www.bco-dmo.org/dataset/523365/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/523365";
Float64 Northernmost_Northing 25.04348;
String param_mapping "{'523365': {'site_lon': 'flag - longitude', 'site_lat': 'flag - latitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/523365/parameters";
String people_0_affiliation "University of Miami Rosenstiel School of Marine and Atmospheric Science";
String people_0_affiliation_acronym "UM-RSMAS";
String people_0_person_name "Su Sponaugle";
String people_0_person_nid "521582";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "National Marine Fisheries Service";
String people_1_affiliation_acronym "NMFS";
String people_1_person_name "Tauna Rankin";
String people_1_person_nid "521639";
String people_1_role "Contact";
String people_1_role_type "related";
String people_2_affiliation "Woods Hole Oceanographic Institution";
String people_2_affiliation_acronym "WHOI BCO-DMO";
String people_2_person_name "Shannon Rauch";
String people_2_person_nid "51498";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "FK Fish Recruitment,FK Population Connectivity";
String projects_0_acronym "FK Fish Recruitment";
String projects_0_description
"Description from NSF award abstract:
Events occurring during the pelagic larval stage of benthic marine organisms can play an important role in the regulation of open populations. The transition between the pelagic larval stage and the benthic juvenile stage (settlement and metamorphosis) is generally recognized as a critical period in the life of many benthic marine fishes such as coral reef fishes, yet the linkage between these phases had received relatively little attention. Biological traits exhibited during the larval stage can influence not only larval survival, but also the recruitment and survival of subsequent juvenile stages. Patterns of natural variability in early life history (ELH) traits, early juvenile mortality, and trait--related survival are entirely unknown. We currently have no knowledge of which larvae survive to settle successfully, and which of those then survive the early life on the reef, including the energetically expensive process of metamorphosis. While ecological theory concerning the ELH traits that confer higher survival has been developed for larval fishes in temperate systems, rarely has this theory been extended across the transition to juveniles, and very few data are available on the relationship between ELH traits and survival for tropical species such as coral reef fishes.
This field study is designed to investigate patterns of natural variability in the ELH traits of a common Caribbean coral reef fish and the consequences of this variation to the survival of young larvae and juveniles during the transition from the plankton to the reef. Multiple cohorts of newly recruited Thalassoma bifasciatum will be censused and collected from sites in the Florida Keys over several seasons (6 mos.) and hydrographic conditions to identify the relationship between environmental conditions, ELH traits, and recruitment success. Recruits will be collected from replicate sites with high and low densities of resident fishes to examine how variable growth and mortality further influence the distribution of ELH traits of recruits. Examination of the otolith record of late-stage larvae and young juveniles will enable the identification of within--cohort, among-cohort, and among-site differences in ELH traits such as larval growth rates, size-at-age, size and age at settlement, and juvenile growth rates. In addition, cohort-specific condition indices will be measured for late-stage larvae and emerging juveniles (";
String projects_0_end_date "2003-03";
String projects_0_geolocation "Upper Florida Keys, Florida, USA";
String projects_0_name "Scope and Consequences of Variability in the Early Life History Traits of a Caribbean Coral Reef Fish";
String projects_0_project_nid "521586";
String projects_0_project_website "http://yyy.rsmas.miami.edu/groups/reef-fish-ecology/";
String projects_0_start_date "2000-04";
String projects_1_acronym "FK Population Connectivity";
String projects_1_description
"Description from NSF award abstract:
This project deals with the important and timely theme of marine population connectivity. The degree to which populations of benthic marine organisms are connected via the dispersal of larval propagules is a central unanswered ecological and oceanographic question. The complex oceanography of marine systems, and high mortality and diffuse concentrations of larvae make direct measurement of larval sources generally unfeasible, particularly for marine populations distributed along open coastlines. In addition, ecological population connectivity is not only a function of the physical transport of larvae, but also the interaction of factors influencing larval growth, survival, and condition at settlement. For example, oligotrophic open-ocean environments may lead to slower larval growth, longer pelagic larval durations, and lower survivorship of larvae compared to larvae from nutrient-rich nearshore waters. Data indicate that the relative condition of larvae influences their survival on the reef and the degree to which they contribute to the population. Ultimately, as ocean currents, spawning patterns, larval survivorship, settlement, and their interactions are highly variable, the only method for examining ecological population connectivity over multiple time and space scales in oceanographically complex environments will be data-validated three dimensional biophysical models capable of assessing dispersal outcomes over a wide range of temporal and spatial variation.
The overall goal of this study is to quantify the relative contributions of upstream (far-field) versus local (near-field) sources of reef fish larvae to the Florida Keys. The proposed study will integrate a comprehensive, three dimensional hydrodynamic model with a Lagrangian particle tracking model to connect the pathways between observed ichthyoplankton distributions and larval settlement.";
String projects_1_end_date "2011-10";
String projects_1_geolocation "Upper Florida Keys, Florida, USA";
String projects_1_name "Linkages Between Larvae and Recruitment of Coral Reef Fishes Along the Florida Keys Shelf: an Integrated Field and Modeling Analysis of Population Connectivity in a Complex System";
String projects_1_project_nid "521633";
String projects_1_project_website "http://yyy.rsmas.miami.edu/groups/reef-fish-ecology/";
String projects_1_start_date "2006-11";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 24.98717;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Summary of data from analyses of otoliths from Stegastes partitus collected from the Florida Keys.";
String title "[FL Stegastes Partitus Otolith Summary Data] - Summary of otolith microstructure data from Stegastes partitus collected by SCUBA dives in the Upper Florida Keys, USA from 2003-2008 (FK Fish Recruitment project, FK Population Connectivity project) (Scope and Consequences of Variability in the Early Life History Traits of a Caribbean Coral Reef Fish)";
String version "1";
Float64 Westernmost_Easting -80.43787;
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.