Data from: A latitudinal cline in the taxonomic structure of eelgrass epifaunal communities is associated with plant genetic diversity
Data files
Sep 26, 2024 version files 195.01 KB
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Code_and_data.zip
185.31 KB
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README.md
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Abstract
Biogenic structural complexity increases mobile animal diversity and abundance at local, regional, and global scales. Yet taxa vary in their response to complexity, and when these taxa functionally differ, variation in structure created by foundation species may affect ecosystem function. We characterized global patterns of epifaunal mesograzers in eelgrass beds that varied in structural and genetic composition across 30° latitude. Total mesograzer richness decreased with latitude, but this was accompanied by a taxonomic shift from peracarid to gastropod dominance. Greater eelgrass genetic diversity was strongly correlated with both richness and abundance of peracarids, but less so for gastropods. These two taxa exhibited complementary functional traits, creating an association between genetic diversity and animal functional traits at the site level across the eelgrass range. Our results add to a growing body of literature that suggests genetic variation in plant traits influences the structure and function of faunal assemblages across broad spatial scales.
README: Data from: A latitudinal cline in the taxonomic structure of eelgrass epifaunal communities is associated with plant genetic diversity
Description of the data and file structure
Environmental, species abundance and trait data were collected from 50 sites in the Zostera Experimental Network (ZEN) in 2014.
This dataset consists of 5 data files:
- Bug_traits.csv, created February 21, 2023.
Trait data for peracarid crustaceans found in epifaunal community samples.
* eat.microalgae, eat.macroalgae, eat.seagrass, eat.seagrass.detritus, suspension.feeder, detritivore.deposit.feeder, carnivore.parasite.scavenger: Binary feeding traits. Does the animal eat the specified food source or feed in the specified way?
- broadcast.spawner.brooder.lays.egg.case: Parental care traits. Is the animal a broadcast spawner, brooder, or does it create an egg case?
- lecithotrophic.planktotrophic.direct.development: Developmental mode. Does the animal have lecithotrophic or planktotrophic larvae, or is it a direct developer?
- mode.obs.size: Mode body size, as measured by sieving epifauna through a series of 9 sieves with pore sizes of 0.5, 0.71, 1, 1.4, 2, 2.8, 4, 5.6, 8 mm
- max.obs.size: Maximum body size, measured as described above
- mean.obs.size: Mean body size, measured as described above
- max.lit.size.mm: Maximum body size in mm as described in the literature.
- max.lat: Maximum absolute latitude, from filtered point occurrences collected from GBIF and OBIS.
- min.lat: Minimum absolute latitude, from filtered point occurrences collected from GBIF and OBIS.
- lat.range: Absolute latitudinal range, from filtered point occurrences collected from GBIF and OBIS.
- lat.mean: Mean absolute latitude, from filtered point occurrences collected from GBIF and OBIS
- marine, brackish, freshwater: Binary salinity traits. Does the animal occur in the specified habitat?
- Snail_traits.csv, created February 21, 2023. Trait data for gastropod mollusks found in epifaunal community samples. Traits are as described above.
- plot_data.csv, created August 19, 2016.
Count and taxonomic data for each species found in each of 20 samples (one per plot) from each site. Each species was size-sorted into a series of 9 sieves of different mesh sizes.
- Site.Code: Two-letter code for each broader site containing two paired subsites.
- Site: One of two paired subsites within each region, with site code.
- Subsite: One of two paired subsites within each region.
- Site.Code.Sampling.Time: Which of the two sampling times the site was sampled.
- Plot.ID: Which plot (of 20) was sampled in each subsite.
- Unique.ID: Unique combination of site, subsite, plot, and sampling time for each plot.
- Old.Species.Name: Original name as identified in 2014.
- Sieve.8, Sieve.5.6, Sieve.4, Sieve.2.8, Sieve.2, Sieve.1.4, Sieve.1, Sieve.0.71, Sieve.0.5: Number of individuals collected in each sieve (mesh size in mm)
- Unknown.Size: Number of individuals of unknown size
- Bodies: Number of headless bodies
- Heads: Number of bodiless heads
- Total.Abundance.Whole: Total abundance of whole animals across all sieves
- Total.Abundance.Partials: Total abundance of whole and partial animals across all sieves
- Molts: Number of molts
- Species.Revised: Species name from WoRMS, 2016
- Group.Revised: Broader taxonomic group
- Subspecies, Species, Subgenus, Genus, Tribe, Subfamily, Family, Superfamily, Subsection, Section, Parvorder, Infraorder, Suborder, Order, Superorder, Infraclass, Subclass, Class, Superclass, Subphylum, Phylum: Taxonomic ranks from WoRMS, 2016
- Finest.Taxonomic.Resolution: The name for the finest taxonomic level of the animal from WoRMS, 2016
- Finest.Taxonomic.Resolution.Level: The rank of the finest taxonomic level of the animal from WoRMS, 2016
- grass_plots.csv, created April 17, 2023.
Eelgrass morphological measurements were collected from each of the 20 plots in each site.
- Site.Code: As described above
- Site: As described above
- Sampling.Time: As described above
- Unique.ID: As described above
- Plot.ID: As described above
- Shoots.Zmarina.per.m2: Number of shoots in a standard 20-cm diameter wire sampling ring, standardized to square meters.
- Mean.Sheath.Width.cm.: Mean width of eelgrass shoots measured at the end of the leaf sheath (where leaves emerge), averaged over 5 random shoots
- Mean.Sheath.Length.cm.: Mean length of eelgrass leaf sheaths, averaged over 5 random shoots
- Mean.Longest.Leaf.Length.cm.: Mean length of the longest leaf on an eelgrass shoot, averaged over 5 random shoots
- Mean.Above.Zmarina.g: Total aboveground biomass of eelgrass averaged across two 20-cm diameter cores.
- site_data.csv, created August 20, 2017.
Site-level summary data on eelgrass habitat structure, in-situ abiotic environmental data, predation intensity, and abiotic environmental data collected from the Bio-Oracle dataset.
- Site.Code: As described above
- Site: As described above
- Subsite: As described above
- Subsite.Name: The name of the subsite
- Ocean: Was the site in the Atlantic or Pacific?
- Coast: Combination of ocean and basin value for each site
- Basin: Was the site on the eastern or western margin of the ocean?
- Latitude: Subsite latitude
- Longitude: Subsite longitude
- Sampling.Time: Which of the two sampling times the site was sampled
- Month: Month corresponding to the sampling time
- Date.Collected: Date the subsite was sampled
- Temperature.C: In-situ temperature (ºC)
- Salinity.ppt: In-situ salinity (ppt)
- GenotypicRichness: Effective number of distinct genotypes
- AllelicRichness: Average number of alleles per locus, normalized to 7 genets
- Mean.Shoots.Zmarina.per.m2: Average shoot density across 20 plots per subsite.
- Mean.Site.Std.Periphyton: Mean epiphyte load (g cm-2 eelgrass)
- Mean.Site.Std.TotalEpibiota: Mean total epibiont load (g cm-2 eelgrass)
- Mean.Macroalgae.g.m2: Mean plot-level macroalgal biomass
- Sheath.Width.cm.: Average eelgrass sheath width across 20 plots per subsite
- Sheath.Length.cm.: Average eelgrass sheath length across 20 plots per subsite
- Longest.Leaf.Length.cm.: Average length of the longest eelgrass leaf across 20 plots per subsite
- Above.Zmarina.g TOTAL.Seagrass.Biomass: Total aboveground eelgrass biomass
- Total.Seagrass.Biomass.Above: Total aboveground seagrass biomass (eelgrass and others, if present)
- Mean.Leaf.PercN: Mean % Nitrogen of measured eelgrass leaves.
- Mean.Leaf.PercC: Mean % Carbon of measured eelgrass leaves.
- Mean.Pred.Amphipod, Mean.Pred.Gastropod, Mean.Pred.Lettuce, Mean.Pred.Squid: Predation on tethered animals or kale, averaged across 20 prey tethering units per subsite.
- Mean.Epifaunal.Richness: Average observed epifaunal richness across 20 plots per subsite
- Mean.Total.Abund: Average epifaunal abundance across 20 plots per subsite
- Mean.Std.Total.Abund: Average epifaunal abundance across 20 plots per subsite, standardized by macrophyte biomass
- Omega: Site-level aragonite saturation state.
- calcite: Site-level calcite concentration (mmol m-3)
- chlomax, chlomean, chlomin, chlorange: Site-level maximum, mean, minimum, and range of chlorophyll a (mg m-3)
- cloudmax,cloudmean, cloudmin: Site-level maximum, mean, and minimum % cloud cover
- damax, damean, damin: Site-level maximum, mean, and minimum diffuse attenuation coefficient (m-1)
- dissox: Site-level dissolved oxygen concentration (mmol m-3)
- nitrate: Site-level nitrate concentration (mmol m-3)
- parmax, parmean: Site-level maximum and mean photosynthetically active radiation (E m-2 year-1)
- ph: Site-level pH
- phos: Site-level phosphorus concentration (mmol m-3)
- phosphate: Site-level phosphate concentration (mmol m-3)
- salinity: Annual mean site-level salinity (ppt)
- silicate: Site-level silicate concentration (mmol m-3)
- sstmax, sstmean, sstmin, sstrange: Annual maximum, mean, minimum, and range of sea surface temperature (ºC)
Sharing/Access information
- Data was derived from the following sources: Species abundance and environmental parameters were collected according to protocols described in Gross et. al 2024 (doi: 10.1111/geb.13918), Duffy et al. 2022 (doi: 10.1073/pnas.2121425119), Gross et al. 2022 (doi: 0.1098/rspb.2021.1762), and Reynolds et al. 2018 (doi: 10.1002/ecy.2064), the World Ocean Database and Bio-ORACLE. Trait data was compiled from literature, measured individuals, and the Ocean Biogeographic Information System and the Global Biodiversity Information Facility records as described in the Methods section and supplementary materials of Gross et al. 2024.
Code/Software
Most_Analyses.R is a script covering data curation and most analyses recorded in the manuscript, including:
- Modeling latitudinal gradients in richness and species composition in epifaunal communities
- Modeling the relationships between the richness and abundance of peracarids and gastropods and the genetic diversity and structural complexity of eelgrass.
- Examining the relationship between the relative abundance of peracarids vs. gastropods in a site and the similarity of site-level community-weighted mean functional traits.
RF_model_selection.R is a script that runs a random forest analysis on predictor traits from site_data.csv to select candidate predictors that are then compared by AICc scores and subject to model selection.
GEB_figures.R is a script that creates all of the figures in the main text and supplementary material.