Home » Different waves of postglacial recolonisation and genomic structure of bank vole populations in NE Poland – Heredity

Different waves of postglacial recolonisation and genomic structure of bank vole populations in NE Poland – Heredity

  • Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19(9):1655–1664

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Björck S (1995) A review of the history of the Baltic Sea, 13.0-8.0 ka BP. Quat Int 27:19–40

    Article 

    Google Scholar
     

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Catchen J, Amores A, Hohenlohe P, Cresko W, Postlethwait J (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genet 1:171–182

    Article 
    CAS 

    Google Scholar
     

  • Catchen J, Hohenlohe P, Bassham S, Amores A, Cresko W (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 11:3124–3140

    Article 

    Google Scholar
     

  • Cingolani P, Patel VM, Coon M, Nguyen T, Land SJ, Ruden DM et al. (2012) Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a New Program, SnpSift. Front Genet 3:35–35

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Clark PU, Dyke AS, Shakun JD, Carlson AE, Clark J, Wohlfarth B et al. (2009) The Last Glacial Maximum. Science 325:710–714

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4:1

    Article 

    Google Scholar
     

  • Corander J, Sirén J, Arjas E (2008) Bayesian spatial modeling of genetic population structure. Computational Stat 23(1):111–129

    Article 

    Google Scholar
     

  • Cox MP, Peterson DA, Biggs PJ (2010) SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinforma 11:485

    Article 

    Google Scholar
     

  • Czarnomska SD, Jędrzejewska B, Borowik T, Niedziałkowska M, Stronen AV, Nowak S et al. (2013) Concordant mitochondrial and microsatellite DNA structuring between Polish lowland and Carpathian Mountain wolves. Conserv Genet 14(3):573–588

    Article 

    Google Scholar
     

  • Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA et al. (2011) The variant call format and VCFtools. Bioinformatics 27(15):2156–2158

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Deffontaine VLR, Kotlik P, Sommer R, Nieberding C, Paradis E, Searle JB et al. (2005) Beyond the Mediterranean peninsulas: evidence for central European glacial refugia for a temperate mammal species, the bank vole (Clethrionomys glareolus). Mol Ecol 14:1727–1739

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Doan K, Niedziałkowska M, Stefaniak K, Sykut M, Jędrzejewska B, Ratajczak-Skrzatek U et al. (2022) Phylogenetics and phylogeography of red deer mtDNA lineages during the last 50 000 years in Eurasia. Zool J Linn Soc 194(2):431–456

    Article 

    Google Scholar
     

  • ESRI (Environmental Systems Resource Institute) (2012) ArcGIS 10.2. [computer program]. ESRI, Redlands

  • Ellison CK, Burton RS (2006) Disruption of mitochondrial function in interpopulation hybrids of Tigriopus californicus. Evolution 60:1382–1391

    CAS 
    PubMed 

    Google Scholar
     

  • Etter PD, Bassham S, Hohenlohe PA, Johnson EA, Cresko WA (2011) SNP discovery and genotyping for evolutionary genetics using RAD sequencing. In: Orgogozo V, Rockman MV editors. Molecular methods for evolutionary genetics. Springer, New York, p 157–78

  • Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10(3):564–567

    Article 
    PubMed 

    Google Scholar
     

  • Fløjgaard C, Normand S, Skov F, Svenning J-C (2009) Ice age distributions of European small mammals: insights from species distribution modelling. J Biogeogr 36(6):1152–1163

    Article 

    Google Scholar
     

  • Gonen S, Lowe NR, Cezard T, Gharbi K, Bishop SC, Houston RD (2014) Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing. BMC Genom 15(1):1

    Article 

    Google Scholar
     

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hirschfeld M, Kirschning CJ, Schwandner R, Wesche H, Weis JH, Wooten RM et al. (1999) Cutting edge: inflammatory signaling by Borrelia burgdorferi lipoproteins is mediated by toll-like receptor 2. J Immunol 163:2382–2386

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Horníková M, Markova S, Lanier H, Searle J, Kotlík P (2021) A dynamic history of admixture from Mediterranean and Carpathian glacial refugia drives genomic diversity in the bank vole. Ecol Evolution 11:8215–8225

    Article 

    Google Scholar
     

  • Hutterer R, Kryštufek B, Yigit N, Mitsainas G, Palomo L, Henttonen H et al. (2021) Myodes glareolus (amended version of 2016 assessment). IUCN Red List Threatened Species 2021:e.T4973A197520967. https://doi.org/10.2305/IUCN.UK.20211.RLTS.T4973A197520967.en. Downloaded on 15 October 2021

    Article 

    Google Scholar
     

  • Konczal M, Babik W, Radwan J, Sadowska ET, Koteja P (2015) Initial molecular-level response to artificial selection for increased aerobic metabolism occurs primarily through changes in gene expression. Mol Biol Evol 32(6):1461–1473

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kondracki J (1994) Geografia Polski. Mezoregiony fizycznogeograficzne. Państwowe Wydawnictwo Naukowe, Warszawa


    Google Scholar
     

  • Kotlík P, Deffontaine V, Mascheretti S, Zima J, Michaux JR, Searle JB (2006) A northern Glacial refugium for bank voles (Clethrionomys glareolus). Proc Natl Acad Sci USA 103:14860–14864

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kotlík P, Marková S, Vojtek L, Stratil A, Šlechta V, Hyršl P et al. (2014) Adaptive phylogeography: functional divergence between haemoglobins derived from different glacial refugia in the bank vole. Proc R Soc B: Biol Sci 281:20140021

    Article 

    Google Scholar
     

  • Kotlík P, Marková S, Konczal M, Babik W, Searle JB (2018) Genomics of end-Pleistocene population replacement in a small mammal. Proc R Soc B: Biol Sci 285:20172624

    Article 

    Google Scholar
     

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 33:1870–1874

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lane N (2009) On the origin of bar codes. Nature 462(7271):272–274

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lee HY, Chou JY, Cheong L, Chang NH, Yang SY, Leu JY (2008) Incompatibility of nuclear and mitochondrial genomes causes hybrid sterility between two yeast species. Cell 135:1065–1073

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li H, Durbin R (2010) Fast and accurate long-read alignment with burrows–wheeler transform. Bioinformatics 26(5):589–595

    Article 
    PubMed 

    Google Scholar
     

  • Lima TG, Burton RS, Willett CS (2019) Genomic scans reveal multiple mito-nuclear incompatibilities in population crosses of the copepod Tigriopus californicus. Evolution 73:609–620

    Article 
    PubMed 

    Google Scholar
     

  • Marková S, Horníková M, Lanier HC, Henttonen H, Searle JB, Weider LJ et al. (2020) High genomic diversity in the bank vole at the northern apex of a range expansion: The role of multiple colonisations and end-glacial refugia. Mol Ecol 29:1730–1744

    Article 
    PubMed 

    Google Scholar
     

  • Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. 2011 17(1):10–12


    Google Scholar
     

  • McDevitt AD, Zub K, Kawałko A, Oliver MK, Herman JS, Wójcik JM (2012) Climate and refugial origin influence the mitochondrial lineage distribution of weasels (Mustela nivalis) in a phylogeographic suture zone. Biol J Linn Soc 106(1):57–69

    Article 

    Google Scholar
     

  • Niedziałkowska M, Kończak J, Czarnomska S, Jędrzejewska B (2010) Species diversity and abundance of small mammals in relation to forest productivity in northeast Poland. Écoscience 17(1):109–119

    Article 

    Google Scholar
     

  • Niedziałkowska M, Hundertmark KJ, Jędrzejewska B, Niedziałkowski K, Sidorovich VE, Górny M et al. (2014) Spatial structure in European moose (Alces alces): genetic data reveal a complex population history. J Biogeogr 41:2173–2184

    Article 

    Google Scholar
     

  • Niedziałkowska M, Hundertmark KJ, Jędrzejewska B, Sidorovich VE, Zalewska H, Veeroja R et al. (2016) The contemporary genetic pattern of European moose is shaped by postglacial recolonization, bottlenecks, and the geographical barrier of the Baltic Sea. Biol J Linn Soc 117:879–894

    Article 

    Google Scholar
     

  • Niedziałkowska M, Tarnowska E, Ligmanowska J, Jędrzejewska B, Podgórski T, Radziszewska A et al. (2021a) Clear phylogeographic pattern and genetic structure of wild boar Sus scrofa population in Central and Eastern Europe. Sci Rep. 11:9680

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Niedziałkowska M, Doan K, Górny M, Sykut M, Stefaniak K, Piotrowska N et al. (2021b) Winter temperature and forest cover have shaped red deer distribution in Europe and the Ural Mountains since the Late Pleistocene. J Biogeogr 48(1):147–159

    Article 

    Google Scholar
     

  • Plis K, Niedziałkowska M, Borowik T, Lang J, Heddergott M, Tiainen J et al. (2022) Pan-European phylogeography of the European roe deer (Capreolus capreolus). Ecol Evol 12(5):e8931

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81:559–575

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Queirós J, Acevedo P, Santos JPV, Barasona J, Beltran-Beck B, González-Barrio D et al. (2019) Red deer in Iberia: Molecular ecological studies in a southern refugium and inferences on European postglacial colonisation history. PLOS ONE 14(1):e0210282

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • R Development Core Team (2015) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, http://www.R-project.org

  • Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG et al. (2016) The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxf) 2016:ID baw100

    Article 

    Google Scholar
     

  • Searle JB, Kotlík P, Rambau RV, Marková S, Herman JS, McDevitt AD (2009) The Celtic fringe of Britain: insights from small mammal phylogeography. Proc R Soc B: Biol Sci 276(1677):4287–4294

    Article 
    CAS 

    Google Scholar
     

  • Singhal S, Moritz C (2012) Strong selection against hybrids maintains a narrow contact zone between morphologically cryptic lineages in a reinforest lizard. Evolution 66:1474–1489

    Article 
    PubMed 

    Google Scholar
     

  • Sommer RS, Nadachowski A (2006) Glacial refugia of mammals in Europe: evidence from fossil records. Mammal Rev 36:251–265

    Article 

    Google Scholar
     

  • Stojak J, McDevitt AD, Herman JS, Kryštufek B, Uhlíková J, Purger JJ et al. (2016) Between the Balkans and the Baltic: Phylogeography of a common vole mitochondrial DNA lineage limited to Central Europe. PLOS ONE 11:e0168621

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stojak J, Tarnowska E (2019) Polish suture zone as the goblet of truth in post-glacial history of mammals in Europe. Mammal Res 64:463–475

    Article 

    Google Scholar
     

  • Stuglik MT, Babik W, Prokop Z, Radwan J (2014) Alternative reproductive tactics and sex-biased gene expression: the study of the bulb mite transcriptome. Ecol Evol 4:623–632

    Article 

    Google Scholar
     

  • Stojak J, Borowik T, Górny M, McDevitt AD, Wójcik JM (2019) Climatic influences on the genetic structure and distribution of the common vole and field vole in Europe. Mammal Res 64(1):19–29

    Article 

    Google Scholar
     

  • Sunnucks P, Morales HE, Lamb AM, Pavlova A, Greening C (2017) Integrative approaches for studying mitochondrial and nuclear genome co-evolution in oxidative phosphorylation. Front Genet 8:25

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF (1998) Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol 7(4):453–464

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tarnowska E, Niedziałkowska M, Gerc J, Korbut Z, Górny M, Jędrzejewska B (2016) Spatial distribution of the Carpathian and Eastern mtDNA lineages of the bank vole in their contact zone relates to environmental conditions. Biol J Linn Soc 119(3):732–744

    Article 

    Google Scholar
     

  • Tarnowska E, Niedziałkowska M, Jędrzejewska B (2019) Genetic structure of bank vole populations in the contact zone of two lineages in north-eastern Poland. Mamm Biol 96:93–101

    Article 

    Google Scholar
     

  • Tarnowska E, Niedziałkowska M, Stojak J, Jędrzejewska B (2020) Polymorphism of TLR2 in bank vole populations in North Eastern Poland is not associated with Borrelia afzelii infection prevalence. Mammal Res 65(4):779–791

    Article 

    Google Scholar
     

  • Toews DPL, Brelsford A (2012) The biogeography of mitochondrial and nuclear discordance in animals. Mol Ecol 21:3907–3930

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tschirren B, Andersson M, Scherman K, Westerdahl H, Mittl PRE, Råberg L (2013) Polymorphisms at the innate immune receptor (TLR2) are associated with Borrelia infection in a wild rodent population. Proc R Soc B: Biol Sci 280:20130364

    Article 

    Google Scholar
     

  • Wallis GP, Cameron-Christie SR, Kennedy HL, Palmer G, Sanders TR, Winter DJ (2017) Interspecific hybridization causes long-term phylogenetic discordance between nuclear and mitochondrial genomes in freshwater fishes. Mol Ecol 26:3116–3127

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wójcik JM, Kawałko A, Markova S, Searle JB, Kotlik P (2010) Phylogeographic signatures of northward post-glacial colonization from high-latitude refugia: a case study of bank voles using museum specimens. J Zool 281:249–262

    Article 

    Google Scholar
     

  • Veličković N, Ferreira E, Djan M, Ernst M, Obreht Vidaković D, Monaco A et al. (2016) Demographic history, current expansion and future management challenges of wild boar populations in the Balkans and Europe. Heredity 117:348–357

    Article 
    PubMed 
    PubMed Central 

    Google Scholar