DOI: 10.5061/dryad.k0p2ngf83
title: Data from: Range-wide population genetic analysis of Seaside Sparrows (Ammospiza maritima) supports at least five distinct population segments that do not align with current subspecies descriptions

description: As an obligate salt marsh species, Seaside Sparrows (Ammospiza maritima)
 are vulnerable to numerous threats including climate change, coastal
 erosion, sea level rise, and both natural and anthropogenic disasters. Of
 the nine recognized subspecies, two are extinct and one is endangered.
 Previous genetic analyses of mitochondrial DNA (mtDNA) and microsatellite
 loci showed that current taxonomy does not accurately reflect underlying
 genetic diversity, with possible consequences for the distribution of
 conservation resources. To further inform Seaside Sparrow management, we
 comprehensively describe genetic structure among 24 range-wide sampling
 locations that include all extant subspecies. We inferred population
 structure from several thousand single-nucleotide polymorphisms collected
 from 272 individuals via restriction-site associated DNA sequencing.
 Principal components, pairwise FST values, and clustering approaches
 suggest that Seaside Sparrows on the Atlantic and Gulf Coasts are
 distinct, and consist of at least five genetic clusters: one in southern
 Texas, one ranging from Aransas Co., Texas to Mississippi, one in western
 Florida, and two or three genetic groups intermixed along a gradient on
 the Atlantic Coast. These genetic clusters are not consistent with current
 subspecies taxonomy and could be used as distinct population segments
 (DPSs) to inform the most efficient allocation of resources to Seaside
 Sparrow conservation. Our results regarding the endangered subspecies, A.
 m. mirabilis, from southern Florida are inconclusive due to low sample
 size, but indicate it is distinct and may represent a sixth DPS. Based on
 our genetic results, we recommend additional song and morphometric
 analyses in western Florida and a closer study of the boundary between the
 breeding distributions of A. m. maritima and A. m. macgillivraii to ensure
 the proper identification of DPSs.
description: Seaside Sparrow sample information required to demultiplex raw
 data and complete downstream
 analyses<br>Davis-et-al-2021-SeasideSp-sample-info.xlsx
 Read 1 sequence data in fastq format for each iTru7
 pool<br>Davis-et-al-2021-SeasideSp-i7_AGTTCGTC.1.fq.gz<br>Davis-et-al-2021-SeasideSp-i7_ATACTCCG.1.fq.gz<br>Davis-et-al-2021-SeasideSp-i7_CGACCATT.1.fq.gz<br>Davis-et-al-2021-SeasideSp-i7_CTGAAGCT.1.fq.gz<br>Davis-et-al-2021-SeasideSp-i7_GATCGAGT.1.fq.gz<br>Davis-et-al-2021-SeasideSp-i7_TAATGCCG.1.fq.gz<br>Davis-et-al-2021-SeasideSp-i7_TTGAGGCA.1.fq.gz Read 2 sequence data in fastq format for each iTru7 pool<br>Davis-et-al-2021-SeasideSp-i7_AGTTCGTC.2.fq.gz<br>Davis-et-al-2021-SeasideSp-i7_ATACTCCG.2.fq.gz<br>Davis-et-al-2021-SeasideSp-i7_CGACCATT.2.fq.gz<br>Davis-et-al-2021-SeasideSp-i7_CTGAAGCT.2.fq.gz<br>Davis-et-al-2021-SeasideSp-i7_GATCGAGT.2.fq.gz<br>Davis-et-al-2021-SeasideSp-i7_TAATGCCG.2.fq.gz<br>Davis-et-al-2021-SeasideSp-i7_TTGAGGCA.2.fq.gz Final SNP datasets used in downstream population genetic analyses<br>Davis-et-al-2021-SeasideSp-full-SNP-dataset.vcf.gz<br>Davis-et-al-2021-SeasideSp-Atlantic-ssp-subset.vcf.gz<br>Davis-et-al-2021-SeasideSp-Gulf-ssp-subset.vcf.gz<br>Davis-et-al-2021-SeasideSp-Atlantic-DAPC-subset.vcf.gz<br>Davis-et-al-2021-SeasideSp-west-FL-DAPC-subset.vcf.gz<br>Davis-et-al-2021-SeasideSp-west-Gulf-DAPC-subset.vcf.gz