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.

The growing nutritional demand of the world population poses great challenges to sustainable and productive agriculture. Entomopathogenic nematodes (EPNs) are an economically interesting alternative to traditional methods of pest control, despite poorly understood aspects of their biology and genomics. This study provides a comprehensive characterization of the genome of Heterorhabditis bacteriophora and its capacity to resist benzoxazinoids that are sequestered as defense compounds by an important insect pest. We performed a de novo chromosome-scale assembly of the H. bacteriophora genome and compared it with the genomes of other nematodes, highlighting syntenic orthologs and genome organization in EPNs. Co-phylogenetic analyses and genetic structure data of several H. bacteriophora isolates and their Photorhabdus symbionts suggest divergent evolutionary scenarios of these two species groups. Population genomics analyses within H. bacteriophora identified genetic variation distinguishing between strains susceptible and resistant to benzoxazinoids. Genome-wide differentiation (FST) pointed to genomic regions related to deoxyribonucleotide biosynthetic processes, polypeptide N-acetylgalactosaminyltransferase activity and single-stranded DNA endodeoxyribonuclease activity that were shaped by strong selective pressures. Having identified candidate genes associated with insect pathogenicity and benzoxazinoid resistance, our findings provide a foundation for future work on the efficacy and infectivity of EPNs in pest management.

Microevolutionary processes shape adaptive responses to heterogeneous environments, where these effects vary both among and within species. However, the degree to which signatures of adaptation to environmental drivers can be detected based on spatial scale and genomic marker remains largely unknown. We studied signatures of local adaptation across different 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 high-resolution (0.5m) environmental factors, derived from remote sensing digital elevation models, with whole-genome sequenced data of 304 individuals across four populations. We demonstrate that responses of A. alpina to similar amounts of abiotic variation are largely governed by local evolutionary processes and find minimally overlapping signatures of local adaptation between SNPs and polymorphic TEs. Notably, functional annotations of high-impact genomic variants revealed several defence-related genes associated with the abiotic factors studied, which could indicate indirect selective pressure of 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.