Data from: The evolutionary pathways for local adaptation in mountain hares ...

• Main Authors: Giska, Iwona, Pimenta, João, Farelo, Liliana, Boursot, Pierre, Hackländer, Klaus, Jenny, Hannes, Reid, Neil, Montgomery, W. Ian, Prodöhl, Paulo A., Alves, Paulo C., Melo-Ferreira, José
• Format: Dataset
• Language: English
• Published: Dryad 2021
• Subjects: Ferreira; Jackman; Fennoscandia; Lepus timidus; mountain hare
• Online Access: https://dx.doi.org/10.5061/dryad.fqz612jtt; https://datadryad.org/stash/dataset/doi:10.5061/dryad.fqz612jtt

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. ... : 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). ...