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Dataset Title:  Grazing preferences by herbivorous fishes in The Bahamas in 2011 Subscribe RSS
Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_700177)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
 
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  date {
    String bcodmo_name "date";
    String description "Date of observation; YYYY/MM/DD";
    String long_name "Date";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
    String source_name "date";
    String time_precision "1970-01-01";
    String units "unitless";
  }
  site {
    String bcodmo_name "site";
    String description "Name of study site (reef)";
    String long_name "Site";
    String units "unitless";
  }
  site_treatment {
    String bcodmo_name "treatment";
    String description "Lionfish treatment of site (reef): Low-lionfish-density reef or High-lionfish-density reef";
    String long_name "Site Treatment";
    String units "unitless";
  }
  replicate_number {
    Byte _FillValue 127;
    Byte actual_range 1, 20;
    String bcodmo_name "sample";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "Replicate number; replicates = algal-covered substrata placed in study site";
    String long_name "Replicate Number";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  }
  replicate_pair {
    String bcodmo_name "sample";
    String description "Replicate pairs";
    String long_name "Replicate Pair";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  }
  observation_time {
    Byte _FillValue 127;
    Byte actual_range 20, 60;
    String bcodmo_name "time_elapsed";
    String description "Length of observation";
    String long_name "Observation Time";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/";
    String units "minutes";
  }
  micro_treatment {
    String bcodmo_name "treatment";
    String description "Lionfish treatment of microhabitat where substrate was placed/observed: lionfish were absent or present during observation";
    String long_name "Micro Treatment";
    String units "unitless";
  }
  algae_initial {
    Float32 _FillValue NaN;
    Float32 actual_range 34.8745, 170.427;
    String bcodmo_name "unknown";
    String description "Initial amount of algae covering substrate";
    String long_name "Algae Initial";
    String units "centimeters squared";
  }
  algae_pcntCoverChange {
    Float32 _FillValue NaN;
    Float32 actual_range 9.0e-4, 0.4637;
    String bcodmo_name "cover_pcent";
    String description "Change in percent cover of algae quantified from before vs. after photos of substrate";
    String long_name "Algae Pcnt Cover Change";
    String units "percent";
  }
  family {
    String bcodmo_name "family";
    String description "Family of fish";
    String long_name "Family";
    String units "unitless";
  }
  species {
    String bcodmo_name "species";
    String description "Species of fish: species codes are first two letters of genus and species (see species key)";
    String long_name "Species";
    String units "unitless";
  }
  fish_size {
    Byte _FillValue 127;
    Byte actual_range 2, 45;
    String bcodmo_name "fish_len";
    String description "Total body length of fish";
    String long_name "Fish Size";
    String units "centimeters";
  }
  bite_number {
    Int16 _FillValue 32767;
    Int16 actual_range 1, 242;
    String bcodmo_name "count";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "Number of bites fish took of algae from substrata during observation";
    String long_name "Bite Number";
    String units "count";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Methods from Kindinger and Albins (2016) \\\"Consumptive and non-consumptive
effects of an invasive marine predator on native coral-reef
herbivores\\\"\\u00a0doi:
[10.1007/s10530-016-1268-1](\\\\\"https://link.springer.com/article/10.1007%2Fs10530-016-1268-1\\\\\")
 
To quantify NCEs of invasive lionfish on native herbivores, we observed the
grazing behavior of herbivorous fishes at each of the 10 experimental reefs
over 10 consecutive days in July 2011, observing paired reefs on adjacent
days. Each day, we collected 20 haphazardly selected pieces of algal-covered
coral rubble (0.43\\u20130.94 m2 surface area) from a nonexperimental reef
containing an extensive area of dead Acropora cervicornis coral rubble
inhabited by a high density of three-spot damselfish (Stegastes planifrons).
This territorial fish maintains higher standing stocks of farmed palatable
seaweeds via interspecific aggression in response to intruding herbivores
(Ceccarelli et al. 2001 ).\\u00a0
 
Each piece of algal substratum was carefully placed into a plastic bag filled
with seawater, photographed out of water onboard a boat, returned to its
plastic bag, and transported in a cooler of seawater to a nearby experimental
reef. At high-lionfish-density reefs, we randomly assigned paired substrata to
two similar, but separate microhabitats (e.g., next to a coral head, on a
ledge, etc.) that differed only in the presence (\\\\\\ 0.25 m away) versus
absence ([ 3 m away) of lionfish at the time of observation. At low-lionfish-
density reefs, we placed algal substrata in paired microhabitats that were
similar to those used at high-lionfish-density reefs, except lionfish were
always absent during observation. All replicates were therefore placed in
types of microhabitats frequented by lionfish, regardless of actual lionfish
presence. Overall, we observed grazing of translocated algal-covered substrata
at three levels of lionfish presence: (1) low-lionfish-density reef with
lionfish absent from the observed microhabitat (n = 100); (2) high-lionfish-
density reef with lionfish absent from the microhabitat (n = 50); and (3)
high-lionfish-density reef with lionfish present in the microhabitat (n = 50);
hereafter referred to as low -absent , high -absent , and high -present
treatments, respectively. These treatments were designed to provide insight on
the spatial scale at which lionfish presence affects herbivorous fish behavior
by allowing simultaneous comparisons of grazing behavior between (1) low- and
high-lionfish-densities at the reef-scale while controlling for lionfish
presence at the within-reef scale (i.e., low-absent vs. high-absent
treatments) and (2) lionfish presence-absence at the within-reef scale while
controlling for lionfish density at the reef-scale (i.e., high-absent vs.
high-present treatments).\\u00a0
 
At each experimental reef, we monitored four of the translocated algal
substrata\\u2014one pair in the morning (0900\\u20131200) and one pair in the
afternoon (1400\\u20131600)\\u2014for 60 min each using automated underwater
video cameras placed approximately 3 m away. Meanwhile, we observed the
remaining 16 algal substrata with SCUBA (8 replicates per diver) one at a time
for 20 min each, with observations divided evenly throughout the day (2 pairs
in the morning and 2 pairs in the afternoon per diver). All observations were
therefore performed during the day when the probability of lionfish predation
is greatly reduced (Green et al. 2011 ; Cure et al. 2012 ) and all lionfish
observed were inactive. We identified the species of each fish that visited
these substrata, visually estimated its TL to the nearest cm, and counted the
number of times it took a bite of algae. Each fish was considered to be a
unique individual once it entered the diver\\u2019s field of view
(approximately 2 m surrounding the focal rock), and continuing until the time
it left the field of view and could no longer be visually tracked. At the end
of each observation period, the algal substratum was carefully returned to its
plastic bag full of fresh seawater and kept underwater until all 20 replicates
had been observed. We then rephotographed each replicate onboard the
boat.\\u00a0
 
Grazing behavior observed at each replicate algal substratum was comprised of
the following response variables: (1) visitation rate (number of fish/minute);
(2) percent visitation rate (percent fish/minute); (3) bite rate (number of
bites/minute); and (4) individual bite rate (number of bites per fish/minute).
The percent visitation rate and individual bite rate allowed us to account for
any potential differences in herbivorous fish densities between low- and high-
lionfish-density reefs. Percent visitation rates were calculated by dividing
the total number of fish observed grazing (per substratum) by the total number
of herbivorous fish counted at each reef during the reef fish surveys
conducted just prior (June 2011) to the grazing observations (July 2011). For
all the herbivorous fish that grazed on each experimental substrate, the
number of bites each fish took during individual grazing bouts was averaged to
measure the individual bite rate. We also used the before and after
photographs of each substrate to estimate the percent loss of algal cover from
observed grazing. We quantified percent cover from photographs using the image
processing program, ImageJ.\\u00a0
 
We analyzed the response of all herbivorous fishes that grazed on the
experimental substrate by fish size class (small and large , with large
encompassing the response among fishes[ 10 cm TL, which remained consistent
regardless of further size binning into medium and large size classes).
Parrotfishes accounted for 69.2 % of the herbivorous fishes that we observed
grazing. Therefore, the behavioral response (same variables as above) of this
fish family was also analyzed by fish size class. The remaining fish families
(surgeonfishes, angelfishes, and damselfishes) were not further divided by
size class, because such extensive division of each response variable would
have resulted in highly zero-inflated data. The percent loss of algae from
substrata was not analyzed by fish size class nor by fish family, because
individual contributions of each fish to the overall algal loss could not be
distinguished.\\u00a0
 
We fitted LMMs using a similar procedure as the one described above to account
for the nested design of the fish grazing surveys when comparing grazing
behavior of herbivorous fish among lionfish treatments. Random effects
consisted of paired microhabitats nested within paired reefs. In addition to
lionfish treatment (lowabsent, high-absent, and high-present), all full models
included the initial algal percent cover (algae ) of each replicate
substratumas a fixed factor in order to account for any influence this
parameter could have on grazing behavior, as well as an algae 9 lionfish
interaction. With the exception of the model of percent loss in algal cover,
we log-transformed all rate response variables and allowed variances to differ
among reefs with weighted terms to meet all assumptions of normality,
homogeneity, and independence. When lionfish treatment was significant in the
model based on LRTs, we performed multiple comparisons of the response at
every combination of lionfish treatments using Tukey\\u2019s Honestly
Significant Difference (HSD) method. All statistical analyses of both reef
fish surveys and fish grazing observations were conducted using the
statistical software R (R Core Team 2014 ) with the associated packages, nlme
(Pinheiro et al. 2014 ) and multcomp (Hothorn et al. 2008 ).";
    String awards_0_award_nid "561016";
    String awards_0_award_number "OCE-1233027";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1233027";
    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 
"Grazing Assays 
  M. Hixon and T. Kindinger 
  Version 16 May 2017";
    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 "2017-05-17T23:30:45Z";
    String date_modified "2019-03-28T19:07:11Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.700177.1";
    String history 
"2022-08-08T23:32:50Z (local files)
2022-08-08T23:32:50Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_700177.das";
    String infoUrl "https://www.bco-dmo.org/dataset/700177";
    String institution "BCO-DMO";
    String keywords "algae, algae_initial, algae_pcntCoverChange, bco, bco-dmo, biological, bite, bite_number, change, chemical, cover, data, dataset, date, dmo, erddap, family, fish, fish_size, initial, management, micro, micro_treatment, number, observation, observation_time, oceanography, office, pair, pcnt, preliminary, replicate, replicate_number, replicate_pair, site, site_treatment, size, species, time, treatment";
    String license "https://www.bco-dmo.org/dataset/700177/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/700177";
    String param_mapping "{'700177': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/700177/parameters";
    String people_0_affiliation "University of Hawaii";
    String people_0_person_name "Mark Hixon";
    String people_0_person_nid "51647";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Oregon State University";
    String people_1_affiliation_acronym "OSU";
    String people_1_person_name "Tye L. Kindinger";
    String people_1_person_nid "51707";
    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 "Hannah Ake";
    String people_2_person_nid "650173";
    String people_2_role "BCO-DMO Data Manager";
    String people_2_role_type "related";
    String project "BiodiversityLossEffects_lionfish";
    String projects_0_acronym "BiodiversityLossEffects_lionfish";
    String projects_0_description 
"The Pacific red lionfish (Pterois volitans), a popular aquarium fish, was introduced to the Atlantic Ocean in the vicinity of Florida in the late 20th century. Voraciously consuming small native coral-reef fishes, including the juveniles of fisheries and ecologically important species, the invader has undergone a population explosion that now ranges from the U.S. southeastern seaboard to the Gulf of Mexico and across the greater Caribbean region. The PI's past research determined that invasive lionfish (1) have escaped their natural enemies in the Pacific (lionfish are much less abundant in their native range); (2) are not yet controlled by Atlantic predators, competitors, or parasites; (3) have strong negative effects on populations of native Atlantic fishes; and (4) locally reduce the diversity (number of species) of native fishes. The lionfish invasion has been recognized as one of the major conservation threats worldwide.
The Bahamas support the highest abundances of invasive lionfish globally. This system thus provides an unprecedented opportunity to understand the direct and indirect effects of a major invader on a diverse community, as well as the underlying causative mechanisms. The PI will focus on five related questions: (1) How does long-term predation by lionfish alter the structure of native reef-fish communities? (2) How does lionfish predation destabilize native prey population dynamics, possibly causing local extinctions? (3) Is there a lionfish-herbivore-seaweed trophic cascade on invaded reefs? (4) How do lionfish modify cleaning mutualisms on invaded reefs? (5) Are lionfish reaching densities where natural population limits are evident?";
    String projects_0_end_date "2016-07";
    String projects_0_geolocation "Three Bahamian sites: 24.8318, -076.3299;  23.8562, -076.2250; 23.7727, -076.1071; Caribbean Netherlands: 12.1599, -068.2820";
    String projects_0_name "Mechanisms and Consequences of Fish Biodiversity Loss on Atlantic Coral Reefs Caused by Invasive Pacific Lionfish";
    String projects_0_project_nid "561017";
    String projects_0_project_website "http://hixon.science.oregonstate.edu/content/highlight-lionfish-invasion";
    String projects_0_start_date "2012-08";
    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 summary "Grazing preferences by herbivorous fishes in The Bahamas in 2011";
    String title "Grazing preferences by herbivorous fishes in The Bahamas in 2011";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

 

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

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.


 
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