Relative abundance of a dominant estuarine fish and spatial extent of structured habitats in Middle Marsh, North Carolina, USA
Data files
Oct 14, 2024 version files 282.66 KB
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Pinfish_abundance_NC_USA_restored_reefs_controls_1997_1998_1999.csv
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README.md
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Structured_habitats_NC_USA_restored_reefs_controls_2024.cpg
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Structured_habitats_NC_USA_restored_reefs_controls_2024.dbf
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Structured_habitats_NC_USA_restored_reefs_controls_2024.prj
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Structured_habitats_NC_USA_restored_reefs_controls_2024.sbn
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Structured_habitats_NC_USA_restored_reefs_controls_2024.sbx
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Structured_habitats_NC_USA_restored_reefs_controls_2024.shp
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Structured_habitats_NC_USA_restored_reefs_controls_2024.shp.xml
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Structured_habitats_NC_USA_restored_reefs_controls_2024.shx
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XY_locations_NC_USA_restored_reefs_controls_1997.csv
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Abstract
Structured biogenic habitats in estuarine and coastal landscapes (or seascapes) augment nekton species’ production; yet, landscape setting may make restored habitats functionally redundant to co-occurring habitats for some species. Few relationships between recruitment enhancement and continuous landscape metrics have been quantified, limiting our ability to incorporate functional redundancy into restoration practice.
To address this gap, we quantified two landscape metrics, percent structure of proximal habitat and near distance to co-occurring structured habitats, for experimentally restored oyster reefs in an intertidal landscape in Middle Marsh, North Carolina, USA. We then examined the relationships between each landscape metric and recruitment enhancement of juvenile pinfish (Lagodon rhomboides), a species that uses multiple biogenic habitats and has high site fidelity as juveniles.
We estimated that reefs with < 33% proximal structured habitat within 15 m and < 59% within 50 m contributed to recruitment enhancement, as defined by greater juvenile pinfish abundances at reefs than controls and no overlap in 95% confidence intervals.
Additionally, functional redundancy, assigned according to percent structure of proximal habitat within 15 or 50 m of restored reefs, reduced estimates of nekton recruitment enhancement in this experimental landscape by 58.3% or 33.3 %, respectively. Estimates of nekton production augmented by restoration may be inflated if they have not been adjusted to account for habitat redundancy.
Synthesis and applications: Landscape metrics offer some predictive capacity to help restoration practitioners avoid habitat redundancy for recruitment enhancement and extend beyond considering individual habitats toward integrating landscape scale processes into predictions and restoration practice. We demonstrated a straightforward process to identify where habitats may be redundant and incorporate the landscape into restoration siting decisions: delineate co-occurring structured habitat with publicly accessible orthoimagery and model juvenile nekton relationships with proximal percent structure and near distance to other structured habitats.
https://doi.org/10.5061/dryad.bvq83bkjm
Description of the data and file structure
Data quantifying pinfish (Lagodon rhomboides) use of restored oyster reefs and control plots in Middle Marsh, Rachel Carson Estuarine Research Reserve, North Carolina, USA were collected from 1997 - 1999 for a prior publication: Grabowski, J. H., Hughes, A. R., Kimbro, D. L., & Dolan, M. A. (2005). How habitat setting influences restored oyster reef communities. Ecology, 86(7), 1926–1935. https://doi.org/10.1890/04-0690 (hereafter Grabowski et al. 2005). The data were used to compare relative pinfish abundances at restored oyster reefs and control plots within three habitat settings: 1) mud flats, 2) adjacent to salt marsh (emergent vegetation), and 3) between salt marsh and submerged aquatic vegetation (SAV).
For the current study (Davenport et al., 2024), the relative abundances of Pinfish from Grabowski et al., (2005) were modeled as a function of landscape characteristics derived from publicly available orthoimagery surrounding the restored oyster reefs and control plots. Thus, in lieu of comparing pinfish abundances among "habitat settings", this study quantified two landscape characteristics surrounding each reef and control plot: percent of structured vegetation (at two spatial scales), and nearest neighbor distance to another structured habitat.
Files and variables
File: Pinfish_abundance_NC_USA_restored_reefs_controls_1997_1998_1999.csv
Description: This dataset contains pinfish (Lagodon rhomboides) abundance on restored oyster reefs and control plots in Middle Marsh, Rachel Carson Estuarine Research Reserve, North Carolina, USA collected from 1997 - 1999 for a prior publication: Grabowski, J. H., Hughes, A. R., Kimbro, D. L., & Dolan, M. A. (2005). How habitat setting influences restored oyster reef communities. Ecology, 86(7), 1926–1935. https://doi.org/10.1890/04-0690 (hereafter Grabowski et al., 2005). Fish data retained by the current study (Davenport et al., 2024) were collected via trap sampling using minnow traps (44.5 cm long x 24.3 cm diameter with 5-mm mesh screen and ~2,5 cm openings on two opposing sides) and modified Morton fish traps (0.7 m long x 0.6 m wide x 0.25 m high, with steel rebar frames and 5-mm nylon mesh walls containing two opposing 7 cm diameter tunnel openings) that were unbaited and set monthly from August through November 1997 and April through November 1998 and1999 during the day. Additional species were captured by this sampling effort, but only L. rhomboides was retained for use in the current study.
Missing data are indicated as NA.
Variables
- year: The year (YYYY) pinfish abundance was collected.
- month: Categorical variable for the pinfish abundance was collected. Note that months are numbered as 1-8, with 1 representing April, and 8 representing November. For clarity, month and year are also offered in mmm-yy format.
- mmm-yy: Month and year (mmm-yy) format for when the pinfish abundance was collected.
- time_of_day: Categorical variable indicating when pinfish traps were set and pulled. Options are day and night; this dataset only contains traps set and pulled during the day.
- block: Categorical variable indicating the experimental block to which the plot (reef or control) belongs. Options are 1, 2, 3, or 4.
- reef_con: Categorical variable indicating whether the plot at which pinfish were sampled is a restored oyster reef or a control; i.e., non-vegetated bottom with no structure present. Options are reef (restored oyster reef) or control (no structured habitat present in the plot).
- treatment: Categorical variable indicating to which habitat setting (per Grabowski et al. 2005) the experimental plot belongs. Options are SM (salt marsh; i.e., plot is situated adjacent to emergent vegetation), SG (i.e., plot is situated between seagrass and salt marsh), and MF (plot is situated on a mud flat without structured or vegetated habitat).
- pinfish: Continuous numeric variable indicating the abundance (number) of pinfish, Lagodon rhomboides, captured in traps.
- label_G2005: Categorical variable indicating a unique label assigned to each experimental block, treatment, and plot, matching labels in the study that collected them (Grabowski et al., 2005). These can be used to connect samples taken at the same location. Options are listed as a concatenation of block and treatment only to indicate reefs, or ending with (C) to indicate control plots. E.g., 1_SM(C) indicates a control plot in the salt marsh habitat setting in experimental block 1.; 2_MF indicates a reef plot in the mud flat habitat setting in experimental block 2.
File: XY_locations_NC_USA_restored_reefs_controls_1997.csv
Description: This dataset contains X,Y locations for experimental plots (including restored oyster reefs and controls without vegetation or structured habitat) in Middle Marsh, Rachel Carson Estuarine Research Reserve, North Carolina, USA created and/or assigned within a prior publication: Grabowski, J. H., Hughes, A. R., Kimbro, D. L., & Dolan, M. A. (2005). How habitat setting influences restored oyster reef communities. Ecology, 86(7), 1926–1935. https://doi.org/10.1890/04-0690 (hereafter Grabowski et al., 2005). Missing data are indicated as NA.
Variables
- lat_dd: Continuous variable indicating the latitude of the centroid of the experimental plot in decimal degrees.
- long_dd: Continuous variable indicating the longitude of the centroid of the experimental plot in decimal degrees.
- label_G2005: Categorical variable indicating a unique label assigned to each experimental block, treatment, and plot, matching labels in the study that collected them (Grabowski et al., 2005). These can be used to connect samples taken at the same location. Options are listed as a concatenation of block and treatment only to indicate reefs, or ending with (C) to indicate control plots. E.g., 1_SM(C) indicates a control plot in the salt marsh habitat setting in experimental block 1.; 2_MF indicates a reef plot in the mud flat habitat setting in experimental block 2.
- block: Categorical variable indicating the experimental block to which the plot (reef or control) belongs. Options are 1, 2, 3, or 4.
- treatment: Categorical variable indicating to which habitat setting (per Grabowski et al. 2005) the experimental plot belongs. Options are SM (salt marsh; i.e., plot is situated adjacent to emergent vegetation), SG (i.e., plot is situated between seagrass and salt marsh), and MF (plot is situated on a mud flat without structured or vegetated habitat).
- reef_con: Categorical variable indicating whether the plot at which pinfish were sampled is a restored oyster reef or a control; i.e., non-vegetated bottom with no structure present. Options are reef (restored oyster reef) or control (no structured habitat present in the plot).
File: Structured_habitats_NC_USA_restored_reefs_controls_2024.shp
Description: This is a shapefile (.shp) of polygons of structured habitats in Middle Marsh, Rachel Carson National Estuarine Research Reserve, North Carolina, USA. Spatial data outlining the locations of structured habitats in the system were manually outlined as polygons from orthoimagery of detailed intertidal and subtidal habitats in Middle Marsh from April 11, 2010, March 05, 2012, and January 30, 2016 (NC OneMap 2019). The earliest available imagery (nearest the dates of fish sampling as possible) that clearly showed the habitats and was closest to the maximum extent of seagrass was used. Mulitple years of imagery were referenced during this process given differential visibility based on solar glare and water levels. The map scale was set to 1:300 and the spatial extent of each each structured habitat (oyster reef – C. virginica, salt marsh – Spartina alterniflora, and seagrass - Halodule wrightii and Zostera marina mixed beds) in the study site was visually delineated by tracing along habitat edges and saved as a shapefile of polygons using ArcGIS Desktop Advanced version 10.4. To check for accuracy, these delineations were then compared to a subset of the study site for which habiats were delineated from aerial imagery (for seagrass, marsh edges, sand flat, and deeper channels), or mapped in summer and fall of 2011 with a Trimble Real-time Kinematic GPS (for oyster reef habitat; Fodrie, F. J., Yeager, L. A., Grabowski, J. H., Layman, C. A., Sherwood, G. D., & Kenworthy, M. D. (2015). Measuring individuality in habitat use across complex landscapes: Approaches, constraints, and implications for assessing resource specialization. Oecologia, 178(1), 75–87. https://doi.org/10.1007/s00442-014-3212-3). Missing data are indicated as NA.
The extent of this shapefile (decimal degrees) is: West -76.624391; East -76.605099; North 34.696919; South 34.682137.
Projected and geographic coordinate system information:
- Projected Coordinate System: NAD_1983_2011_StatePlane_North_Carolina_FIPS_3200_Ft_US
- Projection: Lambert_Conformal_Conic
- False_Easting: 2000000.00000000
- False_Northing: 0.00000000
- Central_Meridian: -79.00000000
- Standard_Parallel_1: 34.33333333
- Standard_Parallel_2: 36.16666667
- Latitude_Of_Origin: 33.75000000
- Linear Unit: Foot_US
- Geographic Coordinate System: GCS_NAD_1983_2011
- Datum: D_NAD_1983_2011
- Prime Meridian: Greenwich
- Angular Unit: Degree
The attribute table contains the following information:
- FID: Categorical variable indicating a unique identifier for each polygon making up the spatial dataset.
- Shape: Categorical variable indicating the geometry type of each element in the dataset. Options are point, line, or polygon; all entries are polygon in this dataset.
- Area: Continuous variable indicating the area (in US square feet) of the polygon.
- Perimeter: Continuous variable indicating the perimeter length (in US feet) of the polygon.
- Habitat: Categorical variable indicating to which habitat setting (per Grabowski et al., 2005) the experimental plot belongs. Options are SM (salt marsh; i.e., plot is situated adjacent to emergent vegetation), SG (i.e., plot is situated between seagrass and salt marsh), and MF (plot is situated on a mud flat without structured or vegetated habitat). NOTE: this is called "treatment" in the other two datasets.
- lat_dd: Continuous variable indicating the latitude of the centroid of the polygon in decimal degrees.
- long_dd: Continuous variable indicating the longitude of the centroid of the polygon in decimal degrees.
Code/software
NA
Access information
Other publicly accessible locations of the data:
- n/a
Data was derived from the following sources:
- n/a
Data quantifying pinfish (Lagodon rhomboides) use of restored oyster reefs and control plots in Middle Marsh, Rachel Carson Estuarine Research Reserve, North Carolina, USA were collected from 1997 - 1999 for a prior publication: Grabowski, J. H., Hughes, A. R., Kimbro, D. L., & Dolan, M. A. (2005). How habitat setting influences restored oyster reef communities. Ecology, 86(7), 1926–1935. https://doi.org/10.1890/04-0690 (hereafter Grabowski et al. 2005). Fish data retained by the current study (Davenport et al., 2024) were collected via trap sampling using minnow traps (44.5 cm long x 24.3 cm diameter with 5-mm mesh screen and ~2,5 cm openings on two opposing sides) and modified Morton fish traps (0.7 m long x 0.6 m wide x 0.25 m high, with steel rebar frames and 5-mm nylon mesh walls containing two opposing 7 cm diameter tunnel openings) that were unbaited and set monthly from August through November 1997 and April through November 1998 and1999 during the day. Additional species were captured by this sampling effort, but only L. rhomboides was retained for use in the current study.
Spatial data outlining the locations of structured habitats in the system were manually outlines as polygons from orthoimagery of detailed intertidal and subtidal habitats in Middle Marsh from April 11, 2010, March 05, 2012, and January 30, 2016 (NC OneMap, 2019). The earliest available imagery (nearest the dates of fish sampling as possible) that clearly showed the habitats and was closest to the maximum extent of seagrass was used. Mulitple years of imagery were referenced during this process given differential visibility based on solar glare and water levels. The map scale was set to 1:300 and the spatial extent of each each structured habitat (oyster reef – C. virginica, salt marsh – Spartina alterniflora, and seagrass - Halodule wrightii and Zostera marina mixed beds) in the study site was visually delineated by tracing along habitat edges and saved as a shapefile of polygons using ArcGIS Desktop Advanced version 10.4. To check for accuracy, these delineations were then compared to a subset of the study site for which habiats were delineated from aerial imagery (for seagrass, marsh edges, sand flat, and deeper channels), or mapped in summer and fall of 2011 with a Trimble Real-time Kinematic GPS (for oyster reef habitat; Fodrie, F. J., Yeager, L. A., Grabowski, J. H., Layman, C. A., Sherwood, G. D., & Kenworthy, M. D. (2015). Measuring individuality in habitat use across complex landscapes: Approaches, constraints, and implications for assessing resource specialization. Oecologia, 178(1), 75–87. https://doi.org/10.1007/s00442-014-3212-3). Reef and control plot centroids were mapped (from XY coordinates collected by Grabowski et al., 2005), and the reefs and controls drawn as 3 m x 5 m rectangular polygons to best represent their original form at the time of construction (Grabowski et al., 2005), and aligned with poles demarcating the corners of each plot that were visible on the orthoimagery.