Locally specific genome-wide signatures of adaptation to environmental
variation at high resolution in an alpine plant
Abstract
Microevolutionary processes shape adaptive responses to heterogeneous
environments, where these effects vary both among and within species.
However, it remains largely unknown to which degree signatures of
adaptation to environmental drivers can be detected based on the choice
of spatial scale and genomic marker. We studied signatures of local
adaptation across two levels of spatial extents, investigating
complementary types of genomic variants–single nucleotide polymorphisms
(SNPs) and polymorphic transposable elements (TEs)–in populations of
the alpine model plant species Arabis alpina. We coupled environmental
factors, derived from remote sensing digital elevation models at very
high resolution (0.5m), with whole-genome sequencing data of 304
individuals across four populations. By comparing putatively adaptive
loci detected between each local population versus a regional assessment
including all populations simultaneously, we demonstrate that responses
of A. alpina to similar amounts of abiotic variation are largely
governed by local evolutionary processes. Furthermore, we find minimally
overlapping signatures of local adaptation between SNPs and polymorphic
TEs. Notably, functional annotations of candidate genes for adaptation
revealed several symbiosis-related genes associated with the abiotic
factors studied, which could represent selective pressures from biotic
agents. Our results highlight the importance of considering different
spatial extents and types of genomic polymorphisms when searching for
signatures of adaptation to environmental variation. Such insights
provide key information on microevolutionary processes and could guide
management decisions to mitigate negative impacts of climate change on
alpine plant populations.