Data from: Subspecies delineation amid phenotypic, geographic, and genetic discordance in a songbird

Understanding the processes that drive divergence within and among species is a long-standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra- and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to evaluate intraspecific variation within the Nelson's (Ammodramus nelsoni) and saltmarsh (A. caudacutus) sparrow complex, a group with populations that span considerable geographic distributions and a habitat gradient. We evaluated genetic structure among and within five putative subspecies of A. nelsoni and A. caudacutus using a reduced-representation sequencing approach to generate a panel of 1,929 SNPs among 69 individuals. Although we detected morphological differences among some groups, individuals sorted along a continuous phenotypic gradient. In contrast, the genetic data identified three distinct clusters corresponding to populations that inhabit coastal salt marsh, interior freshwater marsh, and coastal brackish-water marsh habitats. These patterns support the current species-level recognition but do not match the subspecies-level taxonomy within each species– a finding which may have important conservation implications. We identified loci exhibiting patterns of elevated divergence among and within these species, indicating a role for local selective pressures in driving patterns of differentiation across the complex. We conclude that this evidence for adaptive variation among subspecies warrants the consideration of evolutionary potential and genetic novelty when identifying conservation units for this group.FASTQ file one of fourFASTQ input for Nelson's and Saltmarsh SparrowsSNPfileplaceholder1.fastq.gzFASTQ file two of fourRAD data for Nelson's and Saltmarsh SparrowsSNPfileplaceholder2.fastq.gzFASTQ file three of fourRAD data for Nelson's and Saltmarsh sparrowsSNPfileplaceholder3.fastq.gzFASTQ file four of fourRAD data for Nelson's and Saltmarsh SparrowsSNPfileplaceholder4.fastq.gzStacks output with identified variants in VCF formatVariants identified by Stacksall_loci.vcfMorphometric DataWeight, wing chord, and bill measurements for five subspecies comparisonsMorphometrics.xlsxFunding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DBI 152371