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            <gco:CharacterString>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]</gco:CharacterString>
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        <gco:CharacterString>Database summarizing independent studies of nekton taxa associated with oyster reefs Dataset Description:  Methods and Sampling: &amp;lt;p&amp;gt;&amp;lt;strong&amp;gt;Literature review&amp;lt;/strong&amp;gt;:&amp;lt;br /&amp;gt;
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 (&amp;amp;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.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;&amp;lt;strong&amp;gt;Data Extraction&amp;lt;/strong&amp;gt;:&amp;lt;br /&amp;gt;
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 &amp;amp;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&amp;amp;nbsp;Davenport et al. 2021).&amp;lt;/p&amp;gt;</gco:CharacterString>
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        <gmx:Anchor xlink:href="http://lod.bco-dmo.org/id/award/709941.rdf" xlink:title="OCE-1652320" xlink:actuate="onRequest">Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1652320 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1652320</gmx:Anchor>
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            http://lod.bco-dmo.org/id/dataset-parameter/846388.rdf
	Name: line_no
	Units: NA
	Description: &lt;p&gt;number assigned to each line (row) in the dataset&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846389.rdf
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http://lod.bco-dmo.org/id/dataset-parameter/846390.rdf
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http://lod.bco-dmo.org/id/dataset-parameter/846391.rdf
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	Units: NA
	Description: &lt;p&gt;shorthand name of the study; e.g. Smith et al. 2000&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846392.rdf
	Name: study
	Units: NA
	Description: &lt;p&gt;separate number assigned to each study, in the order they were entered in the dataset&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846393.rdf
	Name: exp_no
	Units: NA
	Description: &lt;p&gt;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.&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846394.rdf
	Name: rep_no
	Units: NA
	Description: &lt;p&gt;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.&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846395.rdf
	Name: rep_id
	Units: NA
	Description: &lt;p&gt;Unique identifier for each replicate that is a concatenation of study, exp.no and rep.no.&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846396.rdf
	Name: taxon
	Units: NA
	Description: &lt;p&gt;A common name for the nekton family.&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846397.rdf
	Name: LH_cat
	Units: NA
	Description: &lt;p&gt;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.&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846398.rdf
	Name: family
	Units: NA
	Description: &lt;p&gt;scientific family name&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846399.rdf
	Name: scientific_name
	Units: NA
	Description: &lt;p&gt;scientific species name&lt;/p&gt; 
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: &lt;p&gt;density or relative abundance of fish species at oyster habitat&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846401.rdf
	Name: se_oys_fish
	Units: 1 standard error of the mean
	Description: &lt;p&gt;spread of fish density or relative abundance at oyster habitats&lt;/p&gt; 
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: &lt;p&gt;density or relative abundance  of fish species at control (mud or sand) habitat&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846403.rdf
	Name: se_con_fish
	Units: 1 standard error of the mean
	Description: &lt;p&gt;spread of fish density or relative abundance at control habitats&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846404.rdf
	Name: SI
	Units: NA
	Description: &lt;p&gt;subtidal or intertidal designation. S = oyster habitat is subtidal; I = oyster habitat is intertidal&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846405.rdf
	Name: Con
	Units: NA
	Description: &lt;p&gt;restored or natural oyster habitat designation. Y = oyster habitat is constructed (restored); N = oyster habitat is natural&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846406.rdf
	Name: Reef_size_m2
	Units: meters squared
	Description: &lt;p&gt;reported area of oyster habitat&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846407.rdf
	Name: Height_m
	Units: meters
	Description: &lt;p&gt;maximum height of oyster habitat off of the seafloor&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846408.rdf
	Name: Reef_age_yr
	Units: year
	Description: &lt;p&gt;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.&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846409.rdf
	Name: tidal_elev_m_MLW
	Units: meters
	Description: &lt;p&gt;tidal elevation relative to mean low water (positive values are above MLW; negative values below MLW)&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846410.rdf
	Name: LRR
	Units: NA
	Description: &lt;p&gt;Log Response Ratio of nekton density in oyster vs control habitat&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846411.rdf
	Name: n_oys_ind
	Units: NA
	Description: &lt;p&gt;number of independent replicates in space used to construct the LRR&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846412.rdf
	Name: n_time_ind
	Units: NA
	Description: &lt;p&gt;number of independent replicates in time used to construct the LRR&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846413.rdf
	Name: n_rep_ind
	Units: NA
	Description: &lt;p&gt;total number of independent replicates at oyster habitat (product of n.oys.ind and n.time.ind). Used to weight experiment by sample size&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846414.rdf
	Name: sample_yr
	Units: year
	Description: &lt;p&gt;year samples taken at both oyster and control&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846415.rdf
	Name: con_yr
	Units: year
	Description: &lt;p&gt;year the oyster habitat (e.. Reef) was constructed&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846416.rdf
	Name: ocean
	Units: NA
	Description: &lt;p&gt;ocean basin, ATL = Atlantic. GOM = Gulf of Mexico&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846417.rdf
	Name: lat_dd
	Units: decimal degrees
	Description: &lt;p&gt;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 (&amp;gt;500m^2) oyster reef&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846418.rdf
	Name: long_dd
	Units: decimal degrees
	Description: &lt;p&gt;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 (&amp;gt;500m^2) oyster reef&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846419.rdf
	Name: state
	Units: NA
	Description: &lt;p&gt;US state (in state abbreviations) the samples were taken&lt;/p&gt; 
http://lod.bco-dmo.org/id/dataset-parameter/846420.rdf
	Name: embayment
	Units: NA
	Description: &lt;p&gt;name of embayment inside which sampling is completed. If control is elsewhere, embayment refers to where the oyster treatment is located&lt;/p&gt; 
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                <gco:CharacterString>&amp;lt;p&amp;gt;&amp;lt;strong&amp;gt;Literature review&amp;lt;/strong&amp;gt;:&amp;lt;br /&amp;gt;
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 (&amp;amp;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.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;&amp;lt;strong&amp;gt;Data Extraction&amp;lt;/strong&amp;gt;:&amp;lt;br /&amp;gt;
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 &amp;amp;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&amp;amp;nbsp;Davenport et al. 2021).&amp;lt;/p&amp;gt;</gco:CharacterString>
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                <gco:CharacterString>&amp;lt;p&amp;gt;&amp;lt;strong&amp;gt;Analyses&amp;lt;/strong&amp;gt;:&amp;lt;br /&amp;gt;
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&amp;amp;nbsp;Davenport et al. 2021). An LRR with CIs &amp;amp;gt; 0 implies that nekton recruitment was enhanced by oyster reefs, an LRR with CIs &amp;amp;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&amp;amp;nbsp;Davenport et al. 2021) and data availability with mosaic and violin plots (Appendix S4 of&amp;amp;nbsp;Davenport et al. 2021).&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;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&amp;amp;nbsp;Davenport et al. 2021). Furthermore, the reef characteristics in our database differed across tidal zones (Appendix S4: Fig. S1-S12 of&amp;amp;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 (&amp;quot;NA&amp;quot; on Fig. 2 of&amp;amp;nbsp;Davenport et al. 2021). Results of randomization and resampling in support of these criteria are presented in Appendix S5 of&amp;amp;nbsp;Davenport et al. (2021).&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;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; &amp;quot;insufficient data&amp;quot; in Figs. 3-8 of&amp;amp;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)&amp;amp;nbsp;for methods and Appendix S5&amp;amp;nbsp;of&amp;amp;nbsp;Davenport et al. 2021&amp;amp;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&amp;amp;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.&amp;lt;/p&amp;gt;

&amp;lt;p&amp;gt;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).&amp;lt;/p&amp;gt;

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