Data from: 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 mounta...
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ftzenodo:oai:zenodo.org:5815656 2023-06-06T11:53:33+02:00 Data from: The evolutionary pathways for local adaptation in mountain hares 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 2022-01-05 https://zenodo.org/record/5815656 https://doi.org/10.5061/dryad.fqz612jtt unknown https://zenodo.org/communities/dryad https://zenodo.org/record/5815656 https://doi.org/10.5061/dryad.fqz612jtt oai:zenodo.org:5815656 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode info:eu-repo/semantics/other dataset 2022 ftzenodo https://doi.org/10.5061/dryad.fqz612jtt 2023-04-13T23:02:08Z 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. Mitochondrial DNA alignment of 59 mountain hare individuals from Ireland, Alps and Fennoscandia. Funding provided by: Fundação para a Ciência e a TecnologiaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001871Award Number: PTDC/BIA-EVL/28124/2017Funding provided by: Fundação para a Ciência e a TecnologiaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001871Award Number: CEECIND/00372/2018 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). Dataset Fennoscandia Lepus timidus mountain hare Zenodo Bia ENVELOPE(22.891,22.891,70.317,70.317) Ferreira ENVELOPE(-62.050,-62.050,-64.600,-64.600) Jackman ENVELOPE(163.250,163.250,-72.400,-72.400) |
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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. Mitochondrial DNA alignment of 59 mountain hare individuals from Ireland, Alps and Fennoscandia. Funding provided by: Fundação para a Ciência e a TecnologiaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001871Award Number: PTDC/BIA-EVL/28124/2017Funding provided by: Fundação para a Ciência e a TecnologiaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001871Award Number: CEECIND/00372/2018 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). |
format |
Dataset |
author |
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 |
spellingShingle |
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 Data from: The evolutionary pathways for local adaptation in mountain hares |
author_facet |
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 |
author_sort |
Giska, Iwona |
title |
Data from: The evolutionary pathways for local adaptation in mountain hares |
title_short |
Data from: The evolutionary pathways for local adaptation in mountain hares |
title_full |
Data from: The evolutionary pathways for local adaptation in mountain hares |
title_fullStr |
Data from: The evolutionary pathways for local adaptation in mountain hares |
title_full_unstemmed |
Data from: The evolutionary pathways for local adaptation in mountain hares |
title_sort |
data from: the evolutionary pathways for local adaptation in mountain hares |
publishDate |
2022 |
url |
https://zenodo.org/record/5815656 https://doi.org/10.5061/dryad.fqz612jtt |
long_lat |
ENVELOPE(22.891,22.891,70.317,70.317) ENVELOPE(-62.050,-62.050,-64.600,-64.600) ENVELOPE(163.250,163.250,-72.400,-72.400) |
geographic |
Bia Ferreira Jackman |
geographic_facet |
Bia Ferreira Jackman |
genre |
Fennoscandia Lepus timidus mountain hare |
genre_facet |
Fennoscandia Lepus timidus mountain hare |
op_relation |
https://zenodo.org/communities/dryad https://zenodo.org/record/5815656 https://doi.org/10.5061/dryad.fqz612jtt oai:zenodo.org:5815656 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.fqz612jtt |
_version_ |
1767959748414537728 |