Emerson BC. Evolution of oceanic islands: molecular phylogenetic approaches to understanding patern and process. Mol Ecol. 2002;11(6):951–66.
Article
CAS
PubMed
Google Scholar
Hewitt GM. Hybrid Zones – Natural Laboratories for Evolutionary Studies. TREE. 1988;3(7):158–67.
CAS
PubMed
Google Scholar
Baker AJ, Jenkins PF. Founder effect and cultural evolution of songs in an isolated population of chaffinches, Fringilla coelebs, in the Chatham islands. Anim Behav. 1987;35(6):1793–803.
Fernandez-Garcia JL, Carranza J, Martinez JG, Randi E. Mitochondrial D-loop phylogeny signals two native Iberian red deer (Cervus elaphus) lineages genetically different to Western and eastern European red deer and infers human-mediated translocations. Biodivers Conserv. 2014;23:537–54.
Article
Google Scholar
van Andel TH, Shackleton JC. Late Paleolithic and Mesolithic coastlines of Greece and the Aegean. J Field Archaeol. 1982;9:445–54.
Google Scholar
Sfenthourakis S, Triantis AK. The Aegean archipelago: a natural laboratory of evolution, ecology and civilizations. J of Biol Res-Thessaloniki. 2017;24(4):1–13.
Google Scholar
Barton NH, Hewitt GM. Adaptation, speciation and hybrid zones. Nature. 1989;341:497–503.
Article
CAS
PubMed
Google Scholar
Hewitt GM. The genetic legacy of the quaternary ice ages. Nature. 2000;405:907–13.
Article
CAS
PubMed
Google Scholar
Hewitt GM. Genetic consequences of climatic oscillations in the quaternary. Phil Trans R Soc Lond B. 2004;359:183–95.
Article
CAS
Google Scholar
Wayne KT, Lehman N. Mitochondrial DNA variability of the gray Wolf: genetic consequences of population decline and habitat fragmentation. Conserv Biol. 1992;6(4):559–69.
Article
Google Scholar
Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF. Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol. 1998;7(4):453–64.
Article
CAS
PubMed
Google Scholar
Dubey S, Zaitsev M, Cosson JF, Abdukadier A, Vogel P. Pliocene and Pleistocene diversification and multiple refugia in a Eurasian shrew (Crocidura suaveolens group). Mol Phylogen Evol. 2006;38(3):635–47.
Article
CAS
Google Scholar
Orth A, Auffray AJ, Bonhomme F. Two deeply divergent mitochondrial clades in the wild mouse Mus macedonicus reveal multiple glacial refuges south of Caucasus. Heredity. 2002;89:353–7.
Article
CAS
PubMed
Google Scholar
Burton RS, Ellison CK, Harrison JS. The sorry state of F2 hybrids: consequences of rapid mitochondrial DNA evolution in allopatric populations. Am Nat. 2006;168:14–24.
Article
Google Scholar
Smith S, Turbill C, Suchentrunk F. Introducing mother’s curse: low male fertility associated with an imported mtDNA haplotype in a captive colony of brown hares. Molecular ecology. 2010;19(1):36–43.
Article
CAS
PubMed
Google Scholar
Bilgin R. Back to the suture: the distribution of intraspecific genetic diversity in and around Anatolia. Int J Mol Sci. 2011;12:4080–103.
Article
PubMed
PubMed Central
Google Scholar
Flux JEC. Introduction to taxonomic problems in hares. Acta Zool Fenn. 1983;174:7–10.
Google Scholar
Fraguglione D. Introduction artificielle et tentative d’ acclimatitation due lièvre commun (Lepus europaeus Pallas, 1778) (par le monde). Royal Saint Hubert Club Belgique. 1964:1–16. https://link.springer.com/article/10.1007/s11598-006-9016-7.
Suchentrunk F, Ben Slimen H, Stamatis C, Sert H, Scandura M, Apollonio M, Mamuris Z. Molecular approaches revealing prehistoric, historic, or recent translocations and introductions of hares (genus Lepus) by humans. Hum Evol. 2006;21:151–65.
Article
Google Scholar
Kasapidis P, Suchentrunk F, Magoulas A, Kotoulas G. The shaping of mitochondrial DNA phylogeographic patterns of the brown hare (Lepus europaeus) under the combined influence of Late Pleistocene climatic fluctuations and anthropogenic translocations. Mol Phylogenet Evol. 2005;34:55–66.
Article
CAS
PubMed
Google Scholar
Stamatis C, Suchentrunk F, Moutou AK, Giacometti M, Haerer G, Djan M, Vapa L, Vukovic M, Tvrtkovic N, Sert H, Alves PC, Mamuris Z. Phylogeography of the brown hare (Lepus europaeus) in Europe: a legacy of South-Eastern Mediterranean refugia? J Biogeogr. 2009;36:515–28.
Article
Google Scholar
Antoniou A, Magoulas A, Platis P, Kotoulas G. Assessing the genetic landscape of a contact zone: the case of European hare in northeastern Greece. Genetics. 2013;141:23–40.
Google Scholar
Djan M, Stefanovic M, Velickovic N, Lavadinovic V, Alves PC, Suchentrunk F. Brown hares (Lepus europaeus Pallas, 1778) from the Balkans: a refined phylogeographic model. Hystrix, the Italian Journal of Mammalogy. 2017;28(2):196–3.
Google Scholar
Amoutzias GD, Giannoulis T, Moutou AK, Psarra AMG, Stamatis C, Tsipourlianos A. Mamuris Z.SNP Identification through Transcriptome Analysis of the European Brown Hare (Lepus europaeus): Cellular Energetics and Mother’s Curse. PLoS ONE. 2016;11(7):e0159939.
Article
PubMed
PubMed Central
CAS
Google Scholar
Blier PU, Dufresne F, Burton RS. Natural selection and the evolution of mtDNA-encoded peptides: evidence for intergenomic co-adaptation. TRENDS in Genetics. 2001;17(7):400–6.
Article
CAS
PubMed
Google Scholar
Giannoulis T, Stamatis C, Tsipourlianos A, Mamuris Z. Mitogenomic analysis in European brown hare (Lepus europaeus) proposes genetic and functional differentiation between the distinct lineages. Mitochondrial DNA A DNA Mapp Seq Anal. 2017;27:1–8.
Google Scholar
Gemmell NJ, Metcalf VJ, Allendorf FW. Mother’s curse: the effect of mtDNA on individual fitness and population viability. Trends Ecol Evol. 2004;19(5):238–44.
Article
PubMed
Google Scholar
Frank SA, Hurst LD. Mitochondria and male disease. Nature. 1996;383:224.
Article
CAS
PubMed
Google Scholar
Dowling DK, Larkeson Nowostawski A, Arnqvist G. Effects of cytoplasmic genes on sperm viability and sperm morphology in a seed beetle: implications for sperm competition theory? J Evol Biol. 2007;20:358–65.
Article
CAS
PubMed
Google Scholar
Froman DP, Kirby JD. Sperm mobility: phenotype in roosters (Gallus domesticus) determined by mitochondrial function. Biol Reprod. 2005;72:562–7.
Article
CAS
PubMed
Google Scholar
Ruiz-Pesini E, Mishmar D, Brandon D, Procaccio V, Wallace DC. Effects of purifying and adaptive selection on regional variation in human mtDNA. Science. 2004;303(5655):223–6.
Article
CAS
PubMed
Google Scholar
Holyoake AJ, McHugh P, Wu M, O’Carroll S, Benny P, Sin IL, Sin FYT. High incidence of single nucleotide substitutions in the mitochondrial genome is associated with poor semen parameters in men. Int J Androl. 2001;24:175–82.
Article
CAS
PubMed
Google Scholar
Koutsogiannouli EA, Moutou AK, Sarafidou T, Stamatis C, Spyrou V, Mamuris Z. Major histocompatibility complex variation at class II DQA locus in the brown hare (Lepus europaeus). Mol Ecol. 2009;18(22):4631–49.
Article
CAS
PubMed
Google Scholar
Smith TR, Tang X, Maricic I, Garcia Z, Fanchiang S, et al. Dendritic cells use endocytic pathway for cross-priming class Ib MHC-restricted CD8alphaalpha+TCRalphabeta+ T cells with regulatory properties. J Immunol. 2009;182:6959–68.
Article
CAS
PubMed
Google Scholar
Penn DJ, Potts WK. The Evolution of Mating Preferences and Major Histocompatibility Complex Genes. The American Naturalist. 1998;153(2):145–64.
Piertney SB, Oliver MK. The evolutionary ecology of the major histocompatibility complex. Heredity. 2006;96:7–21.
Article
CAS
PubMed
Google Scholar
Hughes AL, Yeager M, Tel Elshof AET. A new taxonomy of mammalian MHC class I molecules. Immunol Today. 1999;20(1):22–6.
Article
CAS
PubMed
Google Scholar
Yeager M, Hughes AL. Evolution of the mammalian MHC: natural selection, recombination, and convergent evolution. Immunologican reviews. 1999;167(1):45–8.
Article
CAS
Google Scholar
Iacovakis C, Mamuris Z, Moutou AK, Touloudi A, Hammer AS, et al. Polarisation of Major Histocompatibility Complex II host genotype with pathogenesis of European brown hare syndrome virus. PLOS ONE. 2013;8(9):e74360.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hedrick PW. Evolutionary genetics at the major histocompatibility complex. American naturalist. 1994;143:954–64.
Article
Google Scholar
Bernatchez L, Laundry C. MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years? Journal of Evolutionary Biology. 2003;16:363–77.
Article
CAS
PubMed
Google Scholar
Sommer S. The importance of immune gene variability (MHC) in evolutionary ecology and conservation. Front Zool. 2005;2:16.
Article
PubMed
PubMed Central
CAS
Google Scholar
Smith S, Mang T, de Bellock JG, Schaschl H, Zeitlhofer C, Hackländer K, Suchentrunk F. Homozygosity at a class II MHC locus depresses female reproductive ability in European brown hares. Mol Ecol. 2010;18:4131–43.
Article
Google Scholar
Hartl GB, Suchentrunk F, Willing R, Petznek R. Allozyme heterozygosity and fluctuating asymmetry in the brown hare (Lepus europaeus): a test of the developmental homeostasis hypothesis. Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci. 1995;350:313–23.
Article
Google Scholar
Goritz F, Faßbender M, Broich A, et al. Untersuchungen zur reproduktiven Fitness lebender weiblicher Feldhasen aus unterschiedlichen Habitaten. Zeitschrift fur Jagdwissenschaft. 2001;47:92–9.
Google Scholar
Lee KA. Linking immune defenses and life history at the levels of the individual and the species. Integr Comp Biol. 2006;34:1–14.
Google Scholar
Stamatis C, Suchentrunk F, Sert H, Triantaphyllidis C, Mamuris Z. Genetic evidence for survival of released captive-bread brown hares Lepus europaeus during restocking operations in Greece. Oryx. 2007;41(4):548–51.
Article
Google Scholar
Pierpaoli M, Riga F, Trocchi V, Randi E. Species distinction and evolutionary relationships of the Italian hare (Lepus corsicanus) as described by mitochondrial DNA sequencing. Mol Ecol. 1999;8(11):1805–17.
Article
CAS
PubMed
Google Scholar
Payseur BA. Using differential introgression in hybrid zones to identify genomic regions involved in speciation. Mol Ecol Resour. 2010;10(5):806–20.
Article
PubMed
Google Scholar
Wolf JBW, Ellegren H. Making sense of genomic islands of differentiation in light of speciation. Nat Rev Genet. 2017;18:87–100.
Article
CAS
PubMed
Google Scholar
Pfau RS, Van Den Bussche RA, McBee K, Lochmiller RL. Allelic diversity at the Mhc-DQA locus in cotton rats (Simgodon hispidus) and a comparison of DQA sequences within the family muridae (Mammalia:Rodentia). Immunogenetics. 1999;49:886–93.
Article
CAS
PubMed
Google Scholar
De Bellock JG, Delarbre C, Gachelin G, Morand S. Allelic diversity at the Mhc-DQA locus of woodmouse populations (Apodemus sylvaticus) present in the islands and the mainland of the northern Meditteranean. Glob Ecol Biogeogr. 2005;14:115–22.
Article
Google Scholar
Amills M, Ramíres O, Tomàs A, Obexer-Ruff G, Vidal O. Positive selection on mammalian MHC-DQ genes revisited from a multispecies perspective. Genes Immun. 2008;9:651–8.
Article
CAS
PubMed
Google Scholar
Rand DM. The units of selection on mitochondrial DNA. Annu Rev Ecol Syst. 2001;32:415–48.
Article
Google Scholar
Jia S, Chen H, Zhang G, Wang Z, Lei C, Yao R, Han X. Genetic variation of mitochondrial D-loop region and evolution analysis in some Chinese cattle breeds. J. Genet. Genomics. 2007;34(6):510–8.
Article
CAS
PubMed
Google Scholar
Wilkinson SG, Chapman MA. Length and sequence variation in evening bat D-Lool mtDNA. Genetics. 1991;128:607–17.
CAS
PubMed
PubMed Central
Google Scholar
Brown JR, Beckenbach AT, Smith MJ. Mitochondrial DNA length variation and Heteroplasmy in populations of white sturgeon (Acipenser transmontanus). Genetics. 1992;132:221–8.
CAS
PubMed
PubMed Central
Google Scholar
Taanman JW. The mitochondrial genome: structure, transcription, translation and replication. Biochimica et Biophysica acta. 1999;1410:103–23.
Article
CAS
PubMed
Google Scholar
Clayton AD. Transcription and replication of mitochondrial DNA. Hum Reprod. 2000;15:11–7.
Article
PubMed
Google Scholar
Hill J, Chen Z, Xu H. Selective propagation of functional mitochondrial DNA during oogenesis restricts the transmission of a deleterious mitochondrial variant. Nat Genet. 2014;46(4):389–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sert H, Suchentrunk F, Erdogan A. Genetic diversity within Anatolian brown hares (Lepus europaeus Pallas, 1778) and differentiation among Anatolian and European populations. Mamm Biol. 2005;70:171–86.
Article
Google Scholar
Cheylan G. Patterns of Pleistocene turnover, current distribution and speciation among Mediterranean mammals. In: Groves RH, Di Castri F, editors. Biogeography of Meditterenean Invasion. Cambridge: Cambridge University Press. p. 1991, 262–227.
Roberts N, Kuzucuoglu C, Karabiyikoglu M. The Late Quaternary in the eastern Mediterranean region: an introduction. Quat Sci Rev. 1999;18:497–9.
Article
Google Scholar
Hale ML, Burg TM, Steeves TE. Sampling for Microsatellite-Based Population Genetic Studies: 25 to 30 individuals per Population is Enough to Accurately Estimate Allele Frequencies. PLOS ONE. 2012;7(9):e45170.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ellison CD, Burton RS. Interpopulation hybrid breakdown maps to the mitochondrial genome. Evolution. 2008;62(3):631–8.
Article
PubMed
Google Scholar
Ellison CK, Burton RS. Disruption of mitochondrial function in interpopulation hybrids of Tigriopus californicus. Evolution. 2006;60(7):1382–91.
Article
CAS
PubMed
Google Scholar
Hutter P. X-linked small GPTase and OXPHOS genes are candidates for the genetic bases of hybrid inviability in Drosophila. Dev Genes Evol. 2002;212(10):504–12.
Article
PubMed
Google Scholar
Petit R, Excoffier L. Gene flow and species delimitation. Trends Ecol Evol. 2009;24(7):386–93.
Article
PubMed
Google Scholar
Bray Y, Devillard S, Marboutin E, Mauvy B, Peroux R. Natal dispersal of European hare in France. J Zool. 2007;273:426–34.
Article
Google Scholar
Avril A, Leonard Y, Letty J, Peroux R, Guitton JS, Pontier D. Natal dispersal of European hare in a high-density population. Mamm Biol. 2011;76:148–56.
Article
Google Scholar
Fain MA, Zhao T, Kindt T. Improved typing procedure for the polymorphic single-copy RLA-DQA gene of the rabbit reveals a new allele. Tissue Antigens. 2001;57:332–8.
Article
CAS
PubMed
Google Scholar
Rico C, Rico I, Webb N, Smith S, Bell D, Hewitt G. Four polymorphic microsatellite loci for the European wild rabbit, Oryctolagus cuniculus. Animal Genetics. 1994;25(5):367.
Article
CAS
PubMed
Google Scholar
Surridge AK, Bell DJ, Rico C, Hewitt GM. Polymorphic microsatellite loci in the European Rabbit (Oryctolagus cuniculus) are also amplified in the other lagomorph species. Animal genetics. 1997;28(4):302–5.
Article
CAS
PubMed
Google Scholar
Mougel F, Mounolou JC, Monnerot M. Nine polymorphic microsatellite loci in the rabbit, Oryctolagus cuniculus. Animal genetics. 1997;28:58–71.
Article
CAS
PubMed
Google Scholar
Jombart T. Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics. 2008;24:1403–5.
Article
CAS
PubMed
Google Scholar
Jombart T, Ahmed I. Adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. 2011;27:3070–1.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pond SL, Frost SD. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics. 2005;21:2531–3.
Article
CAS
PubMed
Google Scholar
Pond SL, Frost SD. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol. 2005;22:1208–22.
Article
CAS
Google Scholar
Bondinas GP, Moustakas AK, Papadopoulos GK. The spectrum of HLA-DQ and HLA-DR alleles, 2006: a listing correlating sequence and structure with function. Immunogenetics. 2007;59:539–53.
Article
CAS
PubMed
Google Scholar
Leigh JW, Bryant D. PopART: full-feature software for haplotype network construction. Methods Ecol Evol. 2015;6(9):1110–6.
Article
Google Scholar
Matschiner M, Salzburger W. TANDEM: integrating automated allele binding into genetics and genomics workflows. Bioinformatics. 2009;25(15):1982–3.
Article
CAS
PubMed
Google Scholar
Rousset F. Genepop’ 007: a complete re-implementation of the genepop software for windows and Linux. Mol Ecol Resour. 2008;8:103–6.
Article
PubMed
Google Scholar
Rise WR. Analyzing tables of statistical tests. Evolution. 1989;43:223–5.
Article
Google Scholar
Holm S. A simple sequential rejective multiple test procedure. Scand J Stat. 1979;6:65–70.
Google Scholar
Waples RS. Testing for hardy-Weinberg proportions: have we lost the plot? J Hered. 2015;106(1):1–19.
Article
PubMed
Google Scholar
Dieringer D, Schlötterer C. MICROSATELLITE ANALYSER (MSA): a platform independent analysis tool for large microsatellite data sets. Mol Ecol Resour. 2003;3(1):167–9.
Article
CAS
Google Scholar
Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecolar Ecology. 2005;14:2611–20.
Article
CAS
Google Scholar
Porras-Hurtado L, Ruiz Y, Santos C, Phillips C, Carracedo A, Lareu MV. An overview of STRUCTURE: applications, parameter settings and supporting software. Front Genet. 2013;4:98.
Article
PubMed
PubMed Central
CAS
Google Scholar
Jones OR, Wang J. COLONY: a program for parentage and sibship inference from multilocus genotype data. Mol Ecol Resour. 2009;10(3):551–5.