Abstract
Populations in upstream versus downstream river locations can be exposed to vastly different environmental and ecological conditions and can thus harbor different genetic resources due to selection and neutral processes. An interesting question is how upstream–downstream directionality in rivers affects the evolution of immune response genes. We used next‐generation amplicon sequencing to identify eight alleles of the major histocompatibility complex (MHC) class II β exon 2 in the cyprinid longnose dace (Rhinichthys cataractae) from three rivers in Alberta, upstream and downstream of municipal and agricultural areas along contaminant gradients. We used these data to test for directional and balancing selection on the MHC. We also genotyped microsatellite loci to examine neutral population processes in this system. We found evidence for balancing selection on the MHC in the form of increased nonsynonymous variation relative to neutral expectations, and selection occurred at more amino acid residues upstream than downstream in two rivers. We found this pattern despite no population structure or isolation by distance, based on microsatellite data, at these sites. Overall, our results suggest that MHC evolution is driven by upstream–downstream directionality in fish inhabiting this system.
Highlights
Upstream versus downstream river habitats have been shown to harbor divergent biological resources
We considered an amino acid site to be under diversifying selection if the posterior probability of ω being greater than expected under neutrality was 0.95 or greater in both runs, when rounding to the nearest 100th of a decimal place
We found evidence of balancing selection at several amino acid residues in the major histocompatibility complex (MHC) II β in longnose dace
Summary
Upstream versus downstream river habitats have been shown to harbor divergent biological resources. Downstream areas have been shown to typically harbor increased intraspecific genetic diversity relative to populations upstream in the same rivers (review: Paz-Vinas, Loot, Stevens, & Blanchet, 2015) This pattern was shown to be strong in organisms without overland dispersal, such as fishes, and was not associated with any other particular species traits (Paz-Vinas et al, 2015). We used alleles from this subunit of the MHC, the second exon, because of its known involvement in peptide binding, and primers have already been designed for their amplification in longnose dace (Girard & Angers, 2011) We contrast these patterns of MHC variation with patterns of population structure observed using putatively neutral microsatellite loci. We contrast patterns of diversity between MHC and microsatellite markers to infer a role of selection versus neutral processes in shaping genetic variation
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