Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes.

The sympatric existence of genetically distinguishable 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 certain parts of the genome. We returned to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (coding for lactate dehydrogenase A) in brown trout in the small Lakes Bunnersjöarna, Sweden. First, we verified the existence of the two coexisting demes using a 96-SNP fluidigm array. We then applied whole-genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; nucleotide diversity was higher in deme I than in deme II. Strong genetic divergence is observed with genome-wide FST  ≈ 0.2. Compared with data from populations of similar small lakes, this divergence is of similar magnitude as that between reproductively isolated populations. Individual whole-genome resequencing of two individuals per deme suggests higher inbreeding in deme II versus deme I, indicating different degree of isolation. We located two gene-copies for LDH-A and found divergence between demes in a regulatory section of one of these genes. However, we did not find a perfect fit between the sequence data and previous allozyme results, and this will require further research. Our data demonstrates genome-wide divergence governed mostly by genetic drift but also by diversifying selection in coexisting populations. This type of hidden biodiversity needs consideration in conservation management.

EVOLUTION OF ATLANTIC AND PACIFIC COD: LOSS OF GENETIC VARIATION AND GENE EXPRESSION IN PACIFIC COD.

An allozyme investigation of 41 protein-coding loci in two morphologically similar fishes, Atlantic and Pacific cod, indicates that Pacific cod experienced a severe population bottleneck that led to the loss of gene diversity and gene expression. Pacific cod possesses a significantly lesser amount of gene diversity (H = 0.032) than Atlantic cod (H = 0.125) and lacks gene expression for Me-3. Allele-frequency distributions differ between species as predicted by neutral theory: Atlantic cod has a U-shaped distribution, which is expected for populations in drift-mutation equilibrium, whereas Pacific cod has a J-shaped distribution with an excess of low-frequency alleles. This excess may be explained by the appearance of new alleles through mutation which have not yet reached intermediate frequencies through drift. The population bottleneck in Pacific cod was most likely associated with founder populations that dispersed into the Pacific Ocean after the Bering Strait opened. Under the molecular-clock hypothesis a Nei genetic distance of 0.415 (based on 41 loci) suggests that Pacific cod dispersed into the Pacific Ocean soon after the Bering Strait opened in the mid-Pliocene, 3.0 to 3.5 million years ago.