Detecting Local Adaptation between North and South European Atlantic Salmon Populations

Abstract

Pollution and other anthropogenic effects have driven a decrease in Atlantic salmon (Salmo salar) in the Iberian Peninsula. The restocking effort carried out in the 1980s, with salmon from northern latitudes with the aim of mitigating the decline of native populations, failed, probably due to the deficiency in adaptation of foreign salmon from northern Europe to the warm waters of the Iberian Peninsula. This result would imply that the Iberian populations of Atlantic salmon have experienced local adaptation in their past evolutionary history, as has been described for other populations of this species and other salmonids. Local adaptation can occur by divergent selections between environments, favoring the fixation of alleles that increase the fitness of a population in the environment it inhabits relative to other alleles favored in another population. In this work, we compared the genomes of different populations from the Iberian Peninsula (Atlantic and Cantabric basins) and Scotland in order to provide tentative evidence of candidate SNPs responsible for the adaptive differences between populations, which may explain the failures of restocking carried out during the 1980s. For this purpose, the samples were genotyped with a 220,000 high-density SNP array (Affymetrix) specific to Atlantic salmon. Our results revealed potential evidence of local adaptation for North Spanish and Scottish populations. As expected, most differences concerned the comparison of the Iberian Peninsula with Scotland, although there were also differences between Atlantic and Cantabric populations. A high proportion of the genes identified are related to development and cellular metabolism, DNA transcription and anatomical structure. A particular SNP was identified within the NADP-dependent malic enzyme-2 (mMEP-2*), previously reported by independent studies as a candidate for local adaptation in salmon from the Iberian Peninsula. Interestingly, the corresponding SNP within the mMEP-2* region was consistent with a genomic pattern of divergent selection.

Loci associated with maturation, migration and appetite control are linked with signals of fine-scale local selection in a large Atlantic salmon population

“…This block (hereafter "six6 block") included the six6 gene that encodes an evolutionarily conserved transcription factor and is expressed in the developing eyes, nose, brain, gill, and testis of salmon (Kurko et al, 2020;Moustakas-Verho et al, 2020). It is involved in fine-and broad-scale local adaptation and/or spatial differentiation within and among multiple lineages of Atlantic salmon (Gabián, Morán, Saura, & Carvajal-Rodríguez, 2022;Pritchard et al, 2018;Zueva et al, 2021), as well as Pacific salmonids (Andrews et al, 2023;Tigano & Russello, 2022), and is thus a strong candidate for being the selective target in the genomic region in this study.…”

iHDSel software: The Price equation and the population stability index to detect genomic patterns compatible with selective sweeps. An example with SARS-CoV-2.

“…In previous works, studying the distribution of alleles around a candidate site in both samples P and Q , has been performed comparing in several ways the HAC variances of the partitions that have the reference allele or not in the different samples (Carvajal-Rodríguez 2017; Gabián et al 2022). There are some problems with this type of approach as the unknown distribution of the defined statistics or a loss of power when using homogeneity variance tests.…”

“…The same simulated data as in (Carvajal-Rodríguez 2017; Gabián et al 2022) were used. Two populations of 1000 facultative hermaphrodites were simulated under divergent selection and different conditions about mutation, recombination, migration and selection.…”