DOI: 10.5061/dryad.gf1vhhmwp
title: Ecological characteristics explain neutral genetic variation of three coastal sparrow species

description: Eco-phylogeographic approaches to comparative population genetic analyses
 allow for the inclusion of intrinsic influences as drivers of
 intraspecific genetic structure. This insight into microevolutionary
 processes, including changes within a species or lineage, provides better
 mechanistic understanding of species-specific interactions and enables
 predictions of evolutionary responses to environmental change. In this
 study, we used single nucleotide polymorphisms (SNPs) identified from
 reduced representation sequencing to compare neutral population structure,
 isolation by distance (IBD), genetic diversity, and effective population
 size (Ne) across three closely related and co-distributed saltmarsh
 sparrow species differing along a specialization gradient –Nelson’s
 (Ammospiza nelsoni subvirgata), saltmarsh (A.caudacuta), and seaside
 sparrows (A. maritima maritima). Using an eco-phylogeographic lens within
 a conservation management context, we tested predictions about species’
 degree of evolutionary history and ecological specialization to tidal
 marshes, habitat, current distribution, and population status on
 population genetic metrics. Population structure differed among the
 species consistent with their current distribution and habitat factors,
 rather than degree of ecological specialization: seaside sparrows were
 panmictic, saltmarsh sparrows showed hierarchical structure, and Nelson’s
 sparrows were differentiated into multiple, genetically distinct
 populations. Neutral population genetic theory and
 demographic/evolutionary history predicted patterns of genetic diversity
 and Ne rather than degree of ecological specialization. Patterns of
 population variation and evolutionary distinctiveness (Shapely metric)
 suggest different conservation measures for long-term persistence and
 evolutionary potential in each species. Our findings contribute to a
 broader understanding of the complex factors influencing genetic
 variation, beyond specialist-generalist status, and support the role of an
 eco-phylogeographic approach in population and conservation genetics.
description: Data were collected via SNP identificaiton from ddRAD
 Sequencing. 
description: # Eco-phylogeographic approach explains genetic variation of three coastal
 sparrow species ## Description of the Data and file structure Two Excel
 spreadsheets and three structure files, contains 1) metadata for each
 sample used in the study; 2) environmental data for marsh patches used in
 dbRDA - one tab each for saltmarsh, Nelson's and seaside sparrow; and
 3) genotype data for all individuals across the 3 species (final filtered
 SNP datasets used in the analyses in structure file format). Details for
 sample metadata ('SupportingDatafile1') Description: an Excel
 sheet with sample ID, species, location sampled, groupings and filenames
 used for the analysis, collector name, and if the sampled has been
 published previously. Format: Individual birds are in rows, each with a
 unique ID. Associated metadata belonging to that sample are in columns.
 Dimensions: 725 rows x 13 columns Variables: * USGS AL band number for the
 bird in column A * Species_Dataset: species of bird sampled (NESP, SALS,
 or SESP) * Year_Sampled: the year which the sample was collected * State:
 state in which the sample was collected * Site: marsh site name from where
 the sample was collected * Group: the population grouping that the sample
 belongs to that was used in analyses * Negrouping: grouping which sampled
 belongs to and was used to calculated effective population sizes *
 X_Coord: X coordinate of the sampling location * Y_Coord: Y coordinate of
 the sampling location * File_Name: the name of the file used in the
 analysis (this can be matched up to samples in STR files; name is made up
 of species, last 5 digits of band number, and sampling location) *
 Collector: the collector of the sample * In_Analyses: if the sample passed
 the filtering and was in the final dataset analyzed (Y/N) * Publication:
 study listed for which samples were previously published. If no other
 publication exists, listed as "this study" Details for marsh
 environmental data ('SupportingDatafile2') Description: excel
 spread sheet of marsh-level environmental data used in the dbRDA to test
 the effects or landscape/environment on genetic differentiation taken from
 previously published GIS layer (Wiest et al., 2019). This data is filtered
 to exclude sites which did not have environmental data or which did not
 meet the sampling threshold for analysis (more than 3 individuals per
 marsh). Format: Unique mash IDs are in rows and associated environmental
 data are in columns. The excel sheet contains 3 tabs for each species -
 saltmarsh, Nelson's, and seaside sparrow. Dimensions for tab 1
 ('SALS_envData'): 33 rows x 12 columns Dimensions for tab 2
 ('NESP_envData'): 19 rows x 12 columns Dimensions for tab 3
 ('SESP_envData'): 15 rows x 12 columns Variables (same in each
 tab): * Loc: ID of the marsh in column A * X_Coord: X coordinate of the
 sampling location * Y_Coord: Y coordinate of the sampling location *
 Patch_ID: the ID number from the GIS layer from which data was taken
 (Weist et al., 2019) * samplesize: the amount of birds sampled from the
 marsh location * State: state marsh is located in * Marsh_area_ha: the
 area of the marsh patch sampled (in hectares; ha) * high_marsh_prop: the
 proportion of high marsh vegetation of the marsh area (0-1). An area
 considered high marsh is dominated by Spartina patens, Spartina
 alterniflora short form, Juncus gerardii, and/or Distichlis spicata *
 Marsh_150m: proportion of area that is marsh in a 150meter buffer around
 the patch * Marsh_1000m: proportion of area that is marsh in a 1000meter
 buffer around the patch -sea-level_rise_trend: trends (changes) in mean
 sea level (rise or fall) in mm/year * distance_to_coast: the distance of
 the sampling location to the Atlantic coastline, calculated from the patch
 layer using the measuring tool in QGIS Details for filtered SNP datasets
 for each species ('SALS_final_SamplingLoc.str',
 'NESP_final_SamplingLoc.str', &
 'SESP_final_SamplingLoc.str') Description: structure file for
 each species containing genotypes all of individual birds from fully
 filtered SNP dataset used in the final analysis. Format: First row
 contains a list of all the markers (loci) Subsequent rows represent
 individual birds, with the genotype split across 2 consecutive rows for an
 individual. The first column is the bird ID, followed by the sampling
 location, and then locus information. Missing data are coded as
 '0' in these datasets. Dimensions for saltmarsh sparrow
 ('SALS_final_SamplingLoc.str'): 567 rows x 5008 columns
 Dimensions for Nelson's sparrow
 ('NESP_final_SamplingLoc.str'): 343 rows x 5854 columns
 Dimensions for seaside sparrow ('SESP_final_SamplingLoc.str'):
 283 rows x 2846 columns Variables (same for each file): * column A is
 unique bird ID / filename (including species, last 5 digits of the band
 number, and sampling site name) * column 2 is the population or sampling
 location bird was sampled from (numerical: 1 through the total number of
 populations sampled) * column 3-end of file: remaining columns are all the
 loci, including genotype at the locus for each individual