The evolutionary pathways for local adaptation in mountain hares

Understanding the evolution of local adaptations is a central aim of evolutionary biology and key for the identification of unique populations and lineages of conservation relevance. By combining RAD sequencing and whole-genome sequencing, we identify genetic signatures of local adaptation in mountain hares (Lepus timidus) from isolated and distinctive habitats of its wide distribution: Ireland, the Alps and Fennoscandia. We recovered full mitochondrial DNA sequences from whole-genome sequencing data and used it to recontruct the evolutionary relationships among mountain hare haplotypes.

Methods
Complete mitochondrial DNA (mtDNA) genomes were recovered for each mountain hare individual for which the whole genome was sequenced at lower coverage, using the ABySS assembler (Jackman et al., 2017; Simpson et al., 2009). The standard ABySS run was done with k-mer size of 64 bp (k=64), but modified to k=96 and/or randomly subsampling input reads, when it allowed increasing the contig length. For each individual, the nearly full mtDNA sequence was retrieved by inspecting the longest contigs and then aligning with a mountain hare mtDNA reference (GenBank Acc. Nr KJ397605; Melo-Ferreira, Seixas, Cheng, Mills, & Alves, 2014). Final alignments were produced using ClustalW (Thompson, Higgins, & Gibson, 1994), followed by manual corrections in BioEdit (Hall, 1999).