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.