Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species

Abstract

Unlike most anadromous fishes that have evolved strict homing behaviour, Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within-region population genetic heterogeneity coupled with the morphological and behavioural diversity described for the species suggest that adaptive genetic variation underlying fitness traits may be responsible. We employed restriction site-associated DNA sequencing to genotype 4439 quality filtered single nucleotide polymorphism (SNP) loci for 518 individuals collected across a broad geographical area including British Columbia, Washington, Oregon and California. A subset of putatively neutral markers (N = 4068) identified a significant amount of variation among three broad populations: northern British Columbia, Columbia River/southern coast and 'dwarf' adults (F(CT) = 0.02, P ≪ 0.001). Additionally, 162 SNPs were identified as adaptive through outlier tests, and inclusion of these markers revealed a signal of adaptive variation related to geography and life history. The majority of the 162 adaptive SNPs were not independent and formed four groups of linked loci. Analyses with matsam software found that 42 of these outlier SNPs were significantly associated with geography, run timing and dwarf life history, and 27 of these 42 SNPs aligned with known genes or highly conserved genomic regions using the genome browser available for sea lamprey. This study provides both neutral and adaptive context for observed genetic divergence among collections and thus reconciles previous findings of population genetic heterogeneity within a species that displays extensive gene flow.

Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird

“…Outlier analyses can be powerful tools to detect loci that are under selection, especially when levels of background genomic differentiation are low (e.g., Hess et al., 2013; Keller et al., 2013; Milano et al., 2014). However, several factors can limit the power of these methods or confound the interpretation of results (Mita et al., 2013; Edwards et al., 2015; Lotterhos & Whitlock, 2014; Narum & Hess, 2011).…”

“…An exponential increase in the number of genotyped loci and coverage of the genome over previous methods has also increased power to detect loci that deviate from a neutral model of evolution (i.e., outlier loci) and potentially underlie adaptation. Outlier analyses have allowed researchers to detect loci putatively under selection, which were then able to reveal fine differentiation patterns in otherwise homogenous populations and species (Hess, Campbell, Close, Docker, & Narum, 2013; Keller et al., 2013; Milano et al., 2014). …”

Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments

“…(2013) and sequenced on an Illumina ® HiSeq 1500 genetic analyzer (Illumina Inc., San Diego, CA). Two libraries were constructed containing 96 individuals per library and 500 ng DNA per individual.…”

“…2014) and provide insight into life‐history variation within species (Hess et al. 2013; Pujolar et al. 2014).…”

Adaptation in marine invasion: a genetic perspective

“…Evidence for previously-cryptic structure has also been observed in Atlantic cod (Nielsen et al 2009b;Bradbury et al 2010) and Pacific lamprey (Hess et al 2013). While these approaches have, to date, rarely been applied to marine invasive species, they have tremendous potential to revolutionize the field.…”