Abstract
Background Muskellunge (Esox masquinongy) is the largest and most prized game fish for anglers in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used whole genome sequence from 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from Saint-Lawrence river in Canada to study the genetic differences between populations, analyze signatures of selection that might shed light on environmental adaptations, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available for Muskellunge, reads were aligned to the genome of Pike (Esox lucius), a closely-related species.Results Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. The Ti/Tv values were 1.09 and 1.29 for samples from Iowa and Canada, respectively. PCA and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Moreover, PCA showed clustering by sex in the Iowan population although widow-based Fst did not find outlier regions. Window-based pooled heterozygosity found 6 highly heterozygous windows containing 244 genes in the Iowa population and Fst comparing the Iowa and Canadian populations found 14 windows with Fst values larger than 0.9 containing 641 genes. One enriched GO term (sensory perception of pain) was found through pooled heterozygosity analyzes. Although not significant, several enriched GO terms associated to growth and development were found through Fst analyses.Inbreeding calculated as Froh was 0.03 on average for the Iowa population and 0.32 on average for the Canadian samples. The Canadian inbreeding rate appears to be higher, presumably due to isolation of subpopulations, than the inbreeding rate of the Iowa population.Conclusions This study was the first to document that brood stock Muskellunge from Iowa showed marked genetic differences with the Canadian population. Additionally, despite genetic differentiation based on sex has been observed, no major locus has been detected. Inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, but apparent isolation of subpopulations has caused levels of homozygosity to increase in the Canadian Muskellunge population. Finally, these results prove the validity of using genomes of closely related species to perform genomic analyses when no reference genome assembly is available.
Signatures of selection in loci governing major colour patterns in Heliconius butterflies and related species
