Population specific bottlenecks inflated differentiation measures of Louisiana black bear and negate subspecific status

Significant debate has revolved around the delimitation of subspecific boundaries relative to conservation policy, and specifically how best to maximize limited resources. The conservation of subspecies captures intraspecific genetic diversity and aids in the long-term preservation of adaptive potential. Here, we evaluate patterns of neutral and adaptive genomic variation across the eastern lineage of the American black bear. We specifically assess the relative impact of phylogeographic history and local adaptation on differentiation of subpopulations in Louisiana, which were federally protected as a subspecies from 1992-2016. Despite high values of genetic differentiation (Fst >0.127) of these focal populations, we show that serial founder events during range expansion into eastern North America and multiple bottlenecks drove patterns of diversity within Louisiana. While we attribute initial population divergence between Louisiana subpopulations to east-west shifts of the Mississippi River between 6.2 - 2.7kya, drift accelerated following bottlenecks that were likely due to indigenous societies cultural and land-use changes and later to impacts of European fur traders. We further show that local adaptation has had a smaller impact (4.6%) than phylogeography (30.1%) on the distribution of genomic variation across this lineage. The strongest drivers of adaptive variation include mean annual temperature and monthly precipitation variation, where northern populations have substantial derived variation. Our genomic assessment, in conjunction with weak phenotypic data, does not support the continued recognition of Ursus americanus luteolus as a subspecies of American black bear. Continued genetic conservation efforts should focus on maintaining or increasing diversity, while supporting ongoing successes of demographic recovery.