I provide my personal perspective of the application of genetics to conservation. I began graduate school shortly after the first description of genetic variation in natural populations. The use of allozymes uncovered an unexpected amount of genetic variation in a wide variety of species. During this same period, Motoo Kimura proposed The Neutral Theory of Evolution. Understanding the adaptive significance of allozyme variation became the major focus of population genetics. The utility of population genetic data for conservation and management was questioned because if the observed patterns were determined primarily by selection, then they could not be used to estimate gene flow or genetic drift. The study of mitochondrial DNA next provided a different view of genetic variation by allowing the overlaying of genealogical information on the locations of sampled individuals (phylogeography). The introduction of microsatellites allowed the study of a large number of nuclear markers. The many loci and large number of alleles at microsatellites were valuable for detecting bottlenecks and identifying relationships of individuals. The use of single nucleotide polymorphisms next opened the door to genomic analysis that allowed sampling a mapped genome to detect forces affecting particular genomic regions instead of using a representative sample of loci. For example, using runs of homozygosity has revolutionized our understanding of the effects of inbreeding and the detection of inbreeding depression. Current techniques provide unprecedented power to study genetic variation in natural populations. Nevertheless, application of this information requires sound understanding of population genetics theory.

The sympatric existence of genetically distinct populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves only certain parts of the genome. We return to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (lactate dehydrogenase, LDH-A1) in brown trout in the small Lakes Bunnersjöarna, central Sweden. We use DNA from samples collected in the 1970s and a 96 SNP fluidigm array to verify the existence of the coexisting demes. We then apply whole-genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; strong genetic divergence is observed with genome-wide FST=0.13. Nucleotide diversity is estimated to 0.0013 in Deme I but only 0.0005 in Deme II. Individual whole-genome resequencing of two individuals per deme suggests considerably higher inbreeding in Deme II vs. Deme I. Comparing with similar data from other lakes we find that the genome-wide divergence between the demes is similar to that between reproductively isolated populations. We located two genes for LDH-A and found divergence between the demes in a regulatory section of one of the genes, but we could not find a perfect fit between allozyme and sequence data. Our data demonstrate genome-wide divergence governed by genetic drift and diversifying selection, confirming reproductive isolation between the sympatric demes.