Genomic and environmental influences on resilience in a cold‐water fish near the edge of its range

Small, isolated populations present a challenge for conservation. The
dueling effects of selection and drift in a limited pool of genetic
diversity make the responses of small populations to environmental
perturbations erratic and difficult to predict. This is particularly true
at the edge of a species range, where populations often persist at the
limits of their environmental tolerances. Populations of
cisco, Coregonus artedi, in inland lakes have experienced
numerous extirpations along the southern edge of their range in recent
decades, which are thought to result from environmental degradation and
loss of cold, well-oxygenated habitat as lakes warm. Yet, cisco
extirpations do not show a clear latitudinal pattern, suggesting that
local environmental factors and potentially local adaptation may influence
resilience. Here, we used genomic tools to investigate the nature of this
pattern of resilience. We used restriction site-associated DNA capture
(Rapture) sequencing to survey genomic diversity and differentiation in
southern inland lake cisco populations and compared the frequency of
deleterious mutations that potentially influence fitness across lakes. We
also examined haplotype diversity in a region of the major
histocompatibility complex involved in stress and immune system response.
We correlated these metrics to spatial and environmental factors including
latitude, lake size, and measures of oxythermal habitat and found
significant relationships between genetic metrics and broad and local
factors. High levels of genetic differentiation among populations were
punctuated by a phylogeographic break and residual patterns of
isolation-by-distance. Although the prevalence of deleterious mutations
and inbreeding coefficients was significantly correlated with latitude,
neutral and non-neutral genetic diversity were most strongly correlated
with lake surface area. Notably, differences among lakes in the
availability of estimated oxythermal habitat left no clear population
genomic signature. Our results shed light on the complex dynamics
influencing these isolated populations and provide valuable information
for their conservation.