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Mountain- and brown hare genetic polymorphisms to survey local adaptations and conservation status of the heath hare (Lepus timidus sylvaticus, Nilsson 1831)

  • Angerbjörn, A. & Flux, J. E. C. Lepus timidus. Mamm. Species 1–11, https://doi.org/10.2307/3504302 (1995).

  • Bergengren, A. On genetics, evolution and history of distribution of the heath-hare, a distinct population of the Arctic hare, Lepus timidus Lin. Swed. Wildl. (Viltrevy) 6, 381–460 (1969).

    Google Scholar 

  • Thulin, C.-G. The distribution of mountain hares Lepus timidus in Europe: a challenge from brown hares L. europaeus? Mamm. Rev. 33, 29–42 (2003).

    Article 

    Google Scholar 

  • Mills, L. S. et al. Camouflage mismatch in seasonal coat color due to decreased snow duration. Proc. Nat.Acad. Sci. 110, 7360–7365 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zimova, M. et al. Lack of phenological shift leads to increased camouflage mismatch in mountain hares. Proc.Royal Soc. B: Biol. Sci. 287, 20201786 (2020).

    Article 

    Google Scholar 

  • Levänen, R., Kunnasranta, M. & Pohjoismäki, J. Mitochondrial DNA introgression at the northern edge of the brown hare (Lepus europaeus) range. Ann Zool Fennici 55, 15–24 (2018).

    Article 

    Google Scholar 

  • Thulin, C.-G., Winiger, A., Tallian, A. G. & Kindberg, J. Hunting harvest data in Sweden indicate precipitous decline in the native mountain hare subspecies Lepus timidus sylvaticus (heath hare). J. Nat. Conserv. 64, 126069 (2021).

    Article 

    Google Scholar 

  • Thulin, C.-G., Jaarola, M. & Tegelström, H. The occurrence of mountain hare mitochondrial DNA in wild brown hares. Mol. Ecol. 6, 463–467 (1997).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Pohjoismäki, J. L. O., Michell, C., Levänen, R. & Smith, S. Hybridization with mountain hares increases the functional allelic repertoire in brown hares. Sci. Rep. 11, 15771 (2021).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hoekstra, H. E. Genetics, development and evolution of adaptive pigmentation in vertebrates. Heredity (Edinb) 97, 222–234 (2006).

    Article 
    CAS 

    Google Scholar 

  • Hamill, R. M., Doyle, D. & Duke, E. J. Spatial patterns of genetic diversity across European subspecies of the mountain hare, Lepus timidus L. Heredity (Edinb) 97, 355–365 (2006).

    Article 
    CAS 

    Google Scholar 

  • Leach, K., Montgomery, W. I. & Reid, N. Biogeography, macroecology and species’ traits mediate competitive interactions in the order Lagomorpha. Mamm. Rev. 45, 88–102 (2015).

    Article 

    Google Scholar 

  • Marques, J. P. et al. Data Descriptor: Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares. Sci. Data 4, 1–11 (2017).

    Article 

    Google Scholar 

  • NCBI Sequence Read Archive https://identifiers.org/insdc.sra:SRP358660 (2022).

  • Andrews, S. FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics. Preprint at http://www.bioinformatics.babraham.ac.uk/projects/fastqc (2010).

  • Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12 (2011).

    Article 

    Google Scholar 

  • Marques, J. P. et al. An annotated draft genome of the mountain hare (Lepus timidus). Genome Biol. Evol. 12, 3656–3662 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Broad Institute. Picard toolkit. Broad Institute, GitHub repository. Preprint at https://broadinstitute.github.io/picard/ (2019).

  • Garrison, E. & Marth, G. Haplotype-based variant detection from short-read sequencing. arXiv 1207.3907 (2012).

  • Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Browning, S. R. & Browning, B. L. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81, 1084–1097 (2007).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Michell, C. T., Pohjoismäki, J. L. O., Spong, G. & Thulin, C.-G. Mountain- and brown hare genetic polymorphisms to survey local adaptations and conservation status of the heath hare (Lepus timidus sylvaticus, Nilsson 1831), Dryad, https://doi.org/10.5061/dryad.3bk3j9kmp (2022).

  • Khan, A. & Mathelier, A. Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. BMC Bioinformatics 18, 287 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/.

  • Jombart, T. & Ahmed, I. adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27, 3070–3071 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jombart, T. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Dierckxsens, N., Mardulyn, P. & Smits, G. NOVOPlasty: De novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45 (2017).

  • Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 30 (2013).

  • Trifinopoulos, J., Nguyen, L. T., von Haeseler, A. & Minh, B. Q. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 44 (2016).

  • Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Stamatakis, A. RaxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Ewels, P., Magnusson, M., Lundin, S. & Käller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047–3048 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kamvar, Z. N., Tabima, J. F. & Grünwald, N. J. Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2, e281 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H. Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Levänen, R., Thulin, C.-G., Spong, G. & Pohjoismäki, J. L. O. Widespread introgression of mountain hare genes into Fennoscandian brown hare populations. PloS One 13, e0191790 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Giska, I. et al. The evolutionary pathways for local adaptation in mountain hares. Mol. Ecol. 31, 1487–1503 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Thulin, C.-G., Isaksson, M. & Tegelström, H. The origin of Scandinavian mountain hares (Lepus timidus). Gibier Faune Savage/Game and Wildlife 14, 463–475 (1997).

    Google Scholar 

  • Ferreira, M. S. et al. The legacy of recurrent introgression during the radiation of hares. Syst. Biol. 70, 593–607 (2021).

    Article 
    PubMed 

    Google Scholar 


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