http://lod.bco-dmo.org/id/dataset/845755
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2021-03-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Database summarizing independent studies of nekton taxa associated with oyster reefs
2021-03-23
publication
2021-03-23
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-03-25
publication
https://doi.org/10.26008/1912/bco-dmo.845755.1
A. Randall Hughes
Northeastern University
principalInvestigator
Theresa Davenport
Northeastern University
principalInvestigator
Jonathan Grabowski
Northeastern University
principalInvestigator
Philine S.E. zu Ermgassen
University of Edinburgh
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Davenport, T., Hughes, A. R., zu Ermgassen, P. S., Grabowski, J. (2021) Database summarizing independent studies of nekton taxa associated with oyster reefs. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-03-23 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.845755.1 [access date]
Database summarizing independent studies of nekton taxa associated with oyster reefs Dataset Description: Methods and Sampling: <p><strong>Literature review</strong>:<br />
First, we determined the variety of reef characteristics reported by studies investigating nekton recruitment enhancement by oyster reefs using citations from the reference list of a recently completed meta-analysis (zu Ermgassen et al. 2016). We identified nekton families that were regularly reported at oyster reef and control habitats, including both resident (i.e., species that feed, breed, and shelter on reefs long after initial recruitment, Coen et al. 1999; Harding and Mann 2000) and transient (i.e., species that recruit to structured habitats but are more widely distributed across multiple habitats after recruitment, Harding and Mann 2001) reef-associated species. We also performed forward searches in Google Scholar on two published syntheses: Peterson et al. (2003) and zu Ermgassen et al. (2016). We retained studies that met the following criteria: 1) authors quantified density or relative abundance of target nekton families at both oyster reefs (or experimental units that contained oyster shell and served as a mimic for reef habitat; e.g., Humphries et al. 2011) and unstructured mud or sand habitats within the same study; 2) restored reefs used oyster shell, including shell piles, cultch, bagged shell, or shell piles from other species (e.g., surf clams) if topped by oyster shell; 3) restored reefs were within the tidal extent of natural reefs (&lt; 10 m deep relative to mean low water [MLW] at the base of the reef; Kennedy and Sanford 1999), 4) fishing gear(s) quantitatively censused juveniles; and 5) authors reported densities or abundances of target nekton by species or family.</p>
<p><strong>Data Extraction</strong>:<br />
We extracted densities or abundances, measures of spread (standard deviation or standard error), and sample sizes of each nekton species from oyster reefs and their paired unstructured control habitat patches. We extracted data for nine nekton families, including reef residents: toadfish (Batrachoididae), blennies (Blenniidae), gobies (Gobiidae), and skilletfish (Gobiesocidae, which were later removed due to limited data availability); and reef transients: grunts (Haemulidae), snappers (Lutjanidae), swimming crabs (Portunidae), drums (Sciaenidae), and porgies (Sparidae; Table 1 of Davenport et al. 2021). We normalized densities to mean individuals m-2, abundances to mean individuals per sample (relative abundances), and measures of spread to one standard error of the mean (Appendix S2 of Davenport et al. 2021). We extracted tidal zone (subtidal or intertidal), reef type (restored or natural), restoration method (reefs restored with or without live oysters), and when available, reef size (standardized to m2), vertical relief (distance from bare sediment to the highest point on the reef, standardized to m), tidal elevation (at the base of the reef, in m relative to MLW), adult oyster density (individuals m-2 &gt; 75 mm in shell height, or specified as adult by the authors), and the year of restored reef construction, from which we calculated reef age (Appendix S1: Table 1; Appendix S2 of&nbsp;Davenport et al. 2021).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1652320 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1652320
completed
A. Randall Hughes
Northeastern University
781-581-7370
430 Nahant Rd.
Nahant
MA
01908
USA
ann.hughes@northeastern.edu
pointOfContact
Theresa Davenport
Northeastern University
430 Nahant Rd.
Nahant
MA
01908
USA
tdavenport@agcenter.lsu.edu
pointOfContact
Jonathan Grabowski
Northeastern University
781-581-7370 x337
430 Nahant Rd.
Nahant
MA
01908
USA
j.grabowski@northeastern.edu
pointOfContact
Philine S.E. zu Ermgassen
University of Edinburgh
philine.zu.ermgassen@ed.ac.uk
pointOfContact
asNeeded
Dataset Version: 1
Unknown
line_no
author
pub_year
study_name
study
exp_no
rep_no
rep_id
taxon
LH_cat
family
scientific_name
oys_fish
se_oys_fish
con_fish
se_con_fish
SI
Con
Reef_size_m2
Height_m
Reef_age_yr
tidal_elev_m_MLW
LRR
n_oys_ind
n_time_ind
n_rep_ind
sample_yr
con_yr
ocean
lat_dd
long_dd
state
embayment
theme
None, User defined
number
author name (publication)
year
document_name
file_name
experiment id
number of replicates
replicate
taxon
No BCO-DMO term
family
species
density
site description
surface_area
height
age
sea surface elevation
ratio
region
latitude
longitude
site
featureType
BCO-DMO Standard Parameters
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
CAREER: Linking genetic diversity, population density, and disease prevalence in seagrass and oyster ecosystems
https://www.bco-dmo.org/project/709942
CAREER: Linking genetic diversity, population density, and disease prevalence in seagrass and oyster ecosystems
<p><em>NSF Award Abstract:</em><br />
Disease outbreaks in the ocean are increasing, causing losses of ecologically important marine species, but the factors contributing to these outbreaks are not well understood. This 5-year CAREER project will study disease prevalence and intensity in two marine foundation species - the seagrass Zostera marina and the Eastern oyster Crassostrea virginica. More specifically, host-disease relationships will be explored to understand how genetic diversity and population density of the host species impacts disease transmission and risk. This work will pair large-scale experimental restorations and smaller-scale field experiments to examine disease-host relationships across multiple spatial scales. Comparisons of patterns and mechanisms across the two coastal systems will provide an important first step towards identifying generalities in the diversity-density-disease relationship. To enhance the broader impacts and utility of this work, the experiments will be conducted in collaboration with restoration practitioners and guided by knowledge ascertained from key stakeholder groups. The project will support the development of an early career female researcher and multiple graduate and undergraduate students. Students will be trained in state-of-the-art molecular techniques to quantify oyster and seagrass parasites. Key findings from the surveys and experimental work will be incorporated into undergraduate courses focused on Conservation Biology, Marine Biology, and Disease Ecology. Finally, students in these courses will help develop social-ecological surveys and mutual learning games to stimulate knowledge transfer with stakeholders through a series of workshops.</p>
<p>The relationship between host genetic diversity and disease dynamics is complex. In some cases, known as a dilution effect, diversity reduces disease transmission and risk. However, the opposite relationship, known as the amplification effect, can also occur when diversity increases the risk of infection. Even if diversity directly reduces disease risk, simultaneous positive effects of diversity on host density could lead to amplification by increasing disease transmission between infected and uninfected individuals. Large-scale field restorations of seagrasses (Zostera marina) and oysters (Crassostrea virginica) will be utilized to test the effects of host genetic diversity on host population density and disease prevalence/intensity. Additional field experiments independently manipulating host genetic diversity and density will examine the mechanisms leading to dilution or amplification. Conducting similar manipulations in two marine foundation species - one a clonal plant and the other a non-clonal animal - will help identify commonalities in the diversity-density-disease relationship. Further, collaborations among project scientists, students, and stakeholders will enhance interdisciplinary training and help facilitate the exchange of information to improve management and restoration efforts. As part of these efforts, targeted surveys will be used to document the perceptions and attitudes of managers and restoration practitioners regarding genetic diversity and its role in ecological resilience and restoration.</p>
Seagrass and Oyster Ecosystems
largerWorkCitation
project
eng; USA
oceans
1958-01-01
2018-12-31
Coastal New England
0
BCO-DMO catalogue of parameters from Database summarizing independent studies of nekton taxa associated with oyster reefs
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/846388.rdf
Name: line_no
Units: NA
Description: number assigned to each line (row) in the dataset
http://lod.bco-dmo.org/id/dataset-parameter/846389.rdf
Name: author
Units: NA
Description: first author's surname
http://lod.bco-dmo.org/id/dataset-parameter/846390.rdf
Name: pub_year
Units: NA
Description: year study was published, or unpublished data were made available to us
http://lod.bco-dmo.org/id/dataset-parameter/846391.rdf
Name: study_name
Units: NA
Description: shorthand name of the study; e.g. Smith et al. 2000
http://lod.bco-dmo.org/id/dataset-parameter/846392.rdf
Name: study
Units: NA
Description: separate number assigned to each study, in the order they were entered in the dataset
http://lod.bco-dmo.org/id/dataset-parameter/846393.rdf
Name: exp_no
Units: NA
Description: Letter representing the experiment within a study (in order it was entered). A = first experiment of the study. B = second experiment of the study, and so on. Experiments include different locations, sampling gear, experimental comparisons within a study.
http://lod.bco-dmo.org/id/dataset-parameter/846394.rdf
Name: rep_no
Units: NA
Description: Number assigned to a replicate within an experiment in the order they were entered into the dataset. 1 = first replicate of the experiment in a study, 2 = second replicate of an experiment within a study, and so on. Replicates represent repeated sampling events such as those repeated by year, season, or month.
http://lod.bco-dmo.org/id/dataset-parameter/846395.rdf
Name: rep_id
Units: NA
Description: Unique identifier for each replicate that is a concatenation of study, exp.no and rep.no.
http://lod.bco-dmo.org/id/dataset-parameter/846396.rdf
Name: taxon
Units: NA
Description: A common name for the nekton family.
http://lod.bco-dmo.org/id/dataset-parameter/846397.rdf
Name: LH_cat
Units: NA
Description: Categorical level of association with the oyster reef habtiat. Resident: species that feed, breed, and shelter on reefs long after initial recruitment, Coen et al. 1999; Harding and Mann 2000). Transient: species that recruit to structured habitats but are more widely distributed across multiple habitats after recruitment, Harding and Mann 2001.
http://lod.bco-dmo.org/id/dataset-parameter/846398.rdf
Name: family
Units: NA
Description: scientific family name
http://lod.bco-dmo.org/id/dataset-parameter/846399.rdf
Name: scientific_name
Units: NA
Description: scientific species name
http://lod.bco-dmo.org/id/dataset-parameter/846400.rdf
Name: oys_fish
Units: density (per meters squared), or relative abundance (e.g. fish per trap)
Description: density or relative abundance of fish species at oyster habitat
http://lod.bco-dmo.org/id/dataset-parameter/846401.rdf
Name: se_oys_fish
Units: 1 standard error of the mean
Description: spread of fish density or relative abundance at oyster habitats
http://lod.bco-dmo.org/id/dataset-parameter/846402.rdf
Name: con_fish
Units: density (per meters squared), or relative abundance (e.g. fish per trap)
Description: density or relative abundance of fish species at control (mud or sand) habitat
http://lod.bco-dmo.org/id/dataset-parameter/846403.rdf
Name: se_con_fish
Units: 1 standard error of the mean
Description: spread of fish density or relative abundance at control habitats
http://lod.bco-dmo.org/id/dataset-parameter/846404.rdf
Name: SI
Units: NA
Description: subtidal or intertidal designation. S = oyster habitat is subtidal; I = oyster habitat is intertidal
http://lod.bco-dmo.org/id/dataset-parameter/846405.rdf
Name: Con
Units: NA
Description: restored or natural oyster habitat designation. Y = oyster habitat is constructed (restored); N = oyster habitat is natural
http://lod.bco-dmo.org/id/dataset-parameter/846406.rdf
Name: Reef_size_m2
Units: meters squared
Description: reported area of oyster habitat
http://lod.bco-dmo.org/id/dataset-parameter/846407.rdf
Name: Height_m
Units: meters
Description: maximum height of oyster habitat off of the seafloor
http://lod.bco-dmo.org/id/dataset-parameter/846408.rdf
Name: Reef_age_yr
Units: year
Description: age of the oyster habitat (e.g. reef) in years when the replicate sample was taken. Calculated from sample.yr - con.yr. Reported as NA if multiple sampling years are pooled in a replicate.
http://lod.bco-dmo.org/id/dataset-parameter/846409.rdf
Name: tidal_elev_m_MLW
Units: meters
Description: tidal elevation relative to mean low water (positive values are above MLW; negative values below MLW)
http://lod.bco-dmo.org/id/dataset-parameter/846410.rdf
Name: LRR
Units: NA
Description: Log Response Ratio of nekton density in oyster vs control habitat
http://lod.bco-dmo.org/id/dataset-parameter/846411.rdf
Name: n_oys_ind
Units: NA
Description: number of independent replicates in space used to construct the LRR
http://lod.bco-dmo.org/id/dataset-parameter/846412.rdf
Name: n_time_ind
Units: NA
Description: number of independent replicates in time used to construct the LRR
http://lod.bco-dmo.org/id/dataset-parameter/846413.rdf
Name: n_rep_ind
Units: NA
Description: total number of independent replicates at oyster habitat (product of n.oys.ind and n.time.ind). Used to weight experiment by sample size
http://lod.bco-dmo.org/id/dataset-parameter/846414.rdf
Name: sample_yr
Units: year
Description: year samples taken at both oyster and control
http://lod.bco-dmo.org/id/dataset-parameter/846415.rdf
Name: con_yr
Units: year
Description: year the oyster habitat (e.. Reef) was constructed
http://lod.bco-dmo.org/id/dataset-parameter/846416.rdf
Name: ocean
Units: NA
Description: ocean basin, ATL = Atlantic. GOM = Gulf of Mexico
http://lod.bco-dmo.org/id/dataset-parameter/846417.rdf
Name: lat_dd
Units: decimal degrees
Description: latitude in decimal degrees of either the most northern patch sampled per row (= individual study, substudy and replicate for a species), or the center in the case of a very large (>500m^2) oyster reef
http://lod.bco-dmo.org/id/dataset-parameter/846418.rdf
Name: long_dd
Units: decimal degrees
Description: longitude in decimal degrees of either the most northern patch sampled per row (= individual study, substudy and replicate for a species), or the center in the case of a very large (>500m^2) oyster reef
http://lod.bco-dmo.org/id/dataset-parameter/846419.rdf
Name: state
Units: NA
Description: US state (in state abbreviations) the samples were taken
http://lod.bco-dmo.org/id/dataset-parameter/846420.rdf
Name: embayment
Units: NA
Description: name of embayment inside which sampling is completed. If control is elsewhere, embayment refers to where the oyster treatment is located
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
306898
https://darchive.mblwhoilibrary.org/bitstream/1912/26868/1/dataset-845755_meta-analysis-oyster-reef-nekton__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.845755.1
download
onLine
dataset
<p><strong>Literature review</strong>:<br />
First, we determined the variety of reef characteristics reported by studies investigating nekton recruitment enhancement by oyster reefs using citations from the reference list of a recently completed meta-analysis (zu Ermgassen et al. 2016). We identified nekton families that were regularly reported at oyster reef and control habitats, including both resident (i.e., species that feed, breed, and shelter on reefs long after initial recruitment, Coen et al. 1999; Harding and Mann 2000) and transient (i.e., species that recruit to structured habitats but are more widely distributed across multiple habitats after recruitment, Harding and Mann 2001) reef-associated species. We also performed forward searches in Google Scholar on two published syntheses: Peterson et al. (2003) and zu Ermgassen et al. (2016). We retained studies that met the following criteria: 1) authors quantified density or relative abundance of target nekton families at both oyster reefs (or experimental units that contained oyster shell and served as a mimic for reef habitat; e.g., Humphries et al. 2011) and unstructured mud or sand habitats within the same study; 2) restored reefs used oyster shell, including shell piles, cultch, bagged shell, or shell piles from other species (e.g., surf clams) if topped by oyster shell; 3) restored reefs were within the tidal extent of natural reefs (&lt; 10 m deep relative to mean low water [MLW] at the base of the reef; Kennedy and Sanford 1999), 4) fishing gear(s) quantitatively censused juveniles; and 5) authors reported densities or abundances of target nekton by species or family.</p>
<p><strong>Data Extraction</strong>:<br />
We extracted densities or abundances, measures of spread (standard deviation or standard error), and sample sizes of each nekton species from oyster reefs and their paired unstructured control habitat patches. We extracted data for nine nekton families, including reef residents: toadfish (Batrachoididae), blennies (Blenniidae), gobies (Gobiidae), and skilletfish (Gobiesocidae, which were later removed due to limited data availability); and reef transients: grunts (Haemulidae), snappers (Lutjanidae), swimming crabs (Portunidae), drums (Sciaenidae), and porgies (Sparidae; Table 1 of Davenport et al. 2021). We normalized densities to mean individuals m-2, abundances to mean individuals per sample (relative abundances), and measures of spread to one standard error of the mean (Appendix S2 of Davenport et al. 2021). We extracted tidal zone (subtidal or intertidal), reef type (restored or natural), restoration method (reefs restored with or without live oysters), and when available, reef size (standardized to m2), vertical relief (distance from bare sediment to the highest point on the reef, standardized to m), tidal elevation (at the base of the reef, in m relative to MLW), adult oyster density (individuals m-2 &gt; 75 mm in shell height, or specified as adult by the authors), and the year of restored reef construction, from which we calculated reef age (Appendix S1: Table 1; Appendix S2 of&nbsp;Davenport et al. 2021).</p>
Specified by the Principal Investigator(s)
<p><strong>Analyses</strong>:<br />
To compare nekton recruitment to oyster reefs versus unstructured control habitat, we calculated log response ratios (LRRs, Hedges et al. 1999) with 95% confidence intervals by family (Appendix S2 of&nbsp;Davenport et al. 2021). An LRR with CIs &gt; 0 implies that nekton recruitment was enhanced by oyster reefs, an LRR with CIs &lt; 0 implies the opposite, and an LRR with CIs that include 0 implies no difference in recruitment between oyster reef and control habitats. For each research question, we assessed data publication bias with funnel plots (Appendix S3 of&nbsp;Davenport et al. 2021) and data availability with mosaic and violin plots (Appendix S4 of&nbsp;Davenport et al. 2021).</p>
<p>To assess whether recruitment enhancement varied as a function of reef type (natural or restored) and nekton family, we conducted linear mixed model analyses separately for intertidal and subtidal reefs that included two categorical factors (reef type and nekton family) and their interaction as fixed effects, with study as a random effect. We conducted mixed model analyses separately by tidal zone since subtidal and intertidal habitats harbor different nekton communities (Lehnert and Allen 2002), and subtidal and intertidal oyster reefs are distributed unevenly in our database: intertidal reefs are more prevalent on the Atlantic coast and subtidal reefs are more common in the Gulf of Mexico (Fig. 1; Appendix S1: Table S1 of&nbsp;Davenport et al. 2021). Furthermore, the reef characteristics in our database differed across tidal zones (Appendix S4: Fig. S1-S12 of&nbsp;Davenport et al. 2021). We removed any family that was represented by fewer than three independent studies and/or fewer than 10 independent LRRs ("NA" on Fig. 2 of&nbsp;Davenport et al. 2021). Results of randomization and resampling in support of these criteria are presented in Appendix S5 of&nbsp;Davenport et al. (2021).</p>
<p>To evaluate the effects of restored reef characteristics (i.e., reef size, vertical relief, and age) on recruitment enhancement, we focused on restored reefs only, and performed linear mixed effect regression models with orthogonal polynomials (first and second order) for the continuous reef characteristics as fixed effects, and study as a random effect. We conducted separate analyses for each reef characteristic, nekton family, and tidal zone. We did not model families represented by fewer than three independent studies and/or 10 independent LRRs covering different values of the reef characteristics (e.g., reef sizes, vertical reliefs, or ages; "insufficient data" in Figs. 3-8 of&nbsp;Davenport et al. 2021), and results are not reported or plotted for models that did not converge. Since not all families were represented at all values of each reef characteristic (e.g., all vertical reliefs or sizes), we performed separate analyses for each family and included all available data (but for combined-family approaches, see Appendix S2 (Davenport et al. 2021)&nbsp;for methods and Appendix S5&nbsp;of&nbsp;Davenport et al. 2021&nbsp;for results ). We also examined the influence of tidal elevation on recruitment enhancement for each family using linear mixed effect regression models with orthogonal polynomials (first and second order) for tidal elevation as a fixed effect and study as a random effect (Appendix S5 of&nbsp;Davenport et al. 2021). Where models indicated that predictor variables are on substantially different scales (i.e. reef size) we rescaled using natural log transformation.</p>
<p>All models were weighted by sample size (Appendix S2 of Davenport et al. 2021). All analyses were conducted in R 3.6.1 (R Core Team, 2019) on the RStudio IDE 1.2.1335 (RStudio Team, 2019).</p>
<p><strong>BCO-DMO processing description:</strong><br />
- Adjusted field/parameter names to comply with BCO-DMO naming conventions;<br />
- Missing data identifier ‘NA’ replaced with 'nd' (BCO-DMO's default missing data identifier);&nbsp;<br />
- Added a conventional header with dataset name, PI names, version date;<br />
- Removed commas from the "embayment" column;<br />
- Rounded&nbsp;oys_fish, con_fish, and LRR to 3 decimal places;<br />
- Replaced "Humphries 2011" with "Humphries et al. 2011" in the study_name column.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact