Data from: Whole-genome resequencing reveals polygenic signatures of directional and balancing selection on alternative migratory life histories

Migration in animals and associated adaptations to contrasting
environments are underpinned by complex genetic
architecture. Here, we explore the genomic basis of facultative
anadromy in brown trout (Salmo trutta), wherein some individuals migrate
to sea while others remain resident in natal rivers, to better
understand how alternative migratory tactics (AMTs) are
maintained evolutionarily. To identify genomic variants
associated with AMTs, we sequenced whole genomes for 194 individual trout
from five anadromous–resident population pairs, situated above
and below waterfalls, in five different Irish rivers. These waterfalls
act as natural barriers to upstream migration and hence we
predicted that loci underpinning AMTs should be under similar
divergent selection across these replicate pairs. A sliding
windows based analysis revealed a highly polygenic adaptive divergence
between anadromous and resident populations, encompassing 329
differentiated genomic regions. These regions were associated with
292 genes involved in various processes crucial for AMTs,
including energy homeostasis, reproduction, osmoregulation,
immunity, circadian rhythm and neural function. Furthermore,
examining patterns of diversity we were able to link specific genes and
biological processes to putative AMT trait classes:
migratory-propensity, migratory-lifestyle and residency.
Importantly, AMT outlier regions possessed higher genetic
diversity than the background genome, particularly in the anadromous
group, suggesting balancing selection may play a role in
maintaining genetic variation. Overall, the results from this study
provide important insights into the genetic architecture of
migration and the evolutionary mechanisms shaping genomic diversity within
and across populations.