Population genomic data delineate conservation units in mottled ducks (Anas fulvigula)

Abstract Large multi-locus data sets provide an unprecedented opportunity for detecting fine-scale population structure and identifying populations that warrant independent conservation and management. In this study, we used 3161 polymorphic loci obtained from double-digest restriction-site associated DNA sequencing (ddRAD-seq) to examine genetic differentiation between populations of mottled ducks ( Anas fulvigula ) and their close relative, the mallard ( A. platyrhynchos ). Florida (FL) and western gulf coast (WGC) mottled ducks group into discrete populations in ordination analyses and can be assigned unambiguously to their population of origin based on multi-locus genotypes. Moreover, we find limited evidence of recent admixture between populations, and the range gap separating them is a significant barrier to gene flow. We found no evidence of diversifying selection in the sample of loci we analyzed; instead, the genome-wide pattern of differentiation between mottled duck populations is consistent with historical isolation and divergence by neutral genetic drift. Thus, our results indicate that FL and WGC mottled ducks are discrete populations on separate evolutionary pathways and should be managed as independent conservation units, and perhaps recognized as distinct subspecies given observed differences in plumage and morphology. In contrast, the recently established South Atlantic coastal zone population is indistinguishable from the WGC population but shows evidence of a small amount of admixture from FL mottled ducks. Our study demonstrates a quantitative, operational approach for delineating discrete populations for conservation using ddRAD-seq data; multi-locus genotypes allow for a robust test of historical isolation and evolutionary independence on much shorter evolutionary timescales than the overly conservative standard of reciprocal monophyly in mtDNA.