Mitogenomic analysis in European brown hare (Lepus europaeus) proposes genetic and functional differentiation between the distinct lineages

References

• Amoutzias GD, Giannoulis T, Moutou KA, Psarra A-MG, Stamatis C, Tsipourlianos A, Mamuris Z. 2016. SNP identification through transcriptome analysis of the European Brown Hare (Lepus europaeus): cellular energetics and mother’s curse. PLoS One. 11:e0159939.
   PubMed Web of Science ®Google Scholar
• Antoniou A, Magoulas A, Platis P, Kotoulas G. 2013. Assessing the genetic landscape of a contact zone: the case of European hare in northeastern Greece. Genetica. 141:23–40.
   PubMed Web of Science ®Google Scholar
• Avise JC, Walker DE, Johns JC. 1998. Speciation durations and Pleistocene effects on vertebrate phylogeography. Proc Biol Sci. 265:1707–1712.
   PubMed Web of Science ®Google Scholar
• Avril A, Leonard Y, Letty J, Peroux R, Guitton JS, Pontier D. 2011. Natal dispersal of European hare in a high-density population. Mamm Biol. 76:148–156.
   Web of Science ®Google Scholar
• Bilgin R, Karataş A, Çoraman E, Morales JC. 2008. The mitochondrial and nuclear genetic structure of Myotis capaccinii (Chiroptera: Vespertilionidae) in the Eurasian transition, and its taxonomic implications. Zool Scr. 37:253–262.
   Web of Science ®Google Scholar
• Bilgin R. 2011. Back to the Suture: the distribution of intraspecific genetic diversity in and around Anatolia. Int J Mol Sci. 12:4080–4103.
   PubMed Web of Science ®Google Scholar
• Bray Y, Devillard S, Marboutin E, Mauvy B, Peroux R. 2007. Natal dispersal of European hare in France. J Zool. 273:426–434.
   Web of Science ®Google Scholar
• Cooper SJ, Ibrahim KM, Hewitt GM. 1995. Postglacial expansion and genome subdivision in the European grasshopper Chorthippus parallelus. Mol Ecol. 4:49–60.
   PubMed Web of Science ®Google Scholar
• Creevey CJ, McInerney JO. 2002. An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences. Gene. 300:43–51.
   PubMed Web of Science ®Google Scholar
• Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 9:772.
   PubMed Web of Science ®Google Scholar
• Devillard S, Say L, Pontier D. 2004. Molecular and behavioural analyses reveal male-biased dispersal between social groups of domestic cats. Ecoscience. 11:175–180.
   Web of Science ®Google Scholar
• Edgar R. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792–1797.
   PubMed Web of Science ®Google Scholar
• Edmands S, Burton S. 1995. Cytochrome C oxidase activity in interpopulation hybrids of a marine copepod: a test for nuclear-nuclear or nuclear-cytoplasmic coadaptation. Evolution. 53:1972–1978.
   Google Scholar
• Flux JEC. 1983. Introduction to taxonomic problems in hares. Acta Zool Fennica. 174:7–10.
   Google Scholar
• Foote AD, Morin PA, Durban J, Pitman R, Wade P, Willerslev E, Gilbert MTP, daFonseca RR. 2010. Positive selection on the killer whale mitogenome. Biol Lett. 7:116–118.
   PubMed Web of Science ®Google Scholar
• Gemmell N, Metcalf V, Allendorf F. 2004. Mother's curse: the effect of mtDNA on individual fitness and population viability. Trends Ecol Evol (Amst). 19:238–244.
   PubMed Web of Science ®Google Scholar
• Gillis EA, Krebs CJ. 1999. Natal dispersal of snowshoe hares during a cyclic population increase. J Mammal. 80:933–939.
   Web of Science ®Google Scholar
• Goldberg A, Wildman DE, Schmidt TR, Huttemann M, Goodman M, Weiss ML, Grossman LI. 2003. Adaptive evolution of cytochrome c oxidase subunit VIII in anthropoid primates. Proc Natl Acad Sci USA. 100:5873–5878.
   PubMed Web of Science ®Google Scholar
• Guindon S, Gascuel O. 2003. A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Syst Biol. 52:696–704.
   PubMed Web of Science ®Google Scholar
• Hewitt G. 2000. The genetic legacy of the Quaternary ice ages. Nature. 405:907–913.
   PubMed Web of Science ®Google Scholar
• Kasapidis P, Suchentrunk F, Magoulas A, Kotoulas G. 2005. 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. 34:55–66.
   PubMed Web of Science ®Google Scholar
• Koutsogiannouli E, Moutou KA, Stamatis C, Mamuris Z. 2012. Analysis of MC1R genetic variation in Lepus species in Mediterranean refugia. Mamm Biol. 77:428–433.
   Web of Science ®Google Scholar
• Koutsogiannouli EA, Moutou KA, Sarafidou T, Stamatis C, Spyrou V, Mamuris Z. 2009. Major histocompatibility complex variation at class II DQA locus in the brown hare (Lepus europaeus). Mol Ecol. 18:4631–4649.
   PubMed Web of Science ®Google Scholar
• Kunkele J, von Holst D. 1996. Natal dispersal in the European wild rabbit. Anim Behav. 51:1047–1059.
   Web of Science ®Google Scholar
• Macdonald DW, Newman C, Buesching CD, Johnson PJ. 2008. Male-biased movement in a high-density population of the Eurasian badger (Meles meles). J Mammal. 89:1077–1086.
   Web of Science ®Google Scholar
• Mamuris Z, Moutou AK, Stamatis C, Sarafidou T, Suchentrunk F. 2010. Y DNA and mitochondrial lineages in European and Asian populations of the brown hare (Lepus europaeus). Mamm Biol. 75:233–242.
   Web of Science ®Google Scholar
• Martin AP, Palumbi SR. 1993. Body size, metabolic rate, generation time, and the molecular clock. Proc Natl Acad Sci USA. 90:4087–4091.
   PubMed Web of Science ®Google Scholar
• McLellan BN, Hovey FW. 2001. Natal dispersal of grizzly bears. Can J Zool. 79:838–844.
   Web of Science ®Google Scholar
• Michaux J, Libois R, Paradis E, Filippucci M. 2004. Phylogeographic history of the yellow-necked fieldmouse (Apodemus flavicollis) in Europe and in the Near and Middle East. Mol Phylogenet Evol. 32:788–798.
   PubMed Web of Science ®Google Scholar
• Pierpaoli M, Riga F, Trocchi V, Randi E. 1999. Species distinction and evolutionary relationships of the Italian hare (Lepus corsicanus) as described by mitochondrial DNA sequencing. Mol Ecol. 8:1805–1817.
   PubMed Web of Science ®Google Scholar
• Pond SL, Frost SD. 2005a. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics. 21:2531–2533.
   PubMed Web of Science ®Google Scholar
• Pond SL, Frost SD. 2005b. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol. 22:1208–1222.
   PubMed Web of Science ®Google Scholar
• Pond SL, Frost SD. 2005c. A Genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol Biol Evol. 22:478–485.
   PubMed Web of Science ®Google Scholar
• Rand DM. 2001. The units of selection on mitochondrial DNA. Annu Rev Ecol Syst. 32:415–449.
   Google Scholar
• Ruiz-Pesini E, Mishmar D, Brandon M, Procaccio V, Wallace DC. 2004. Effects of purifying and adaptive selection in regional variation in human mtDNA. Science. 303:223–226.
   PubMed Web of Science ®Google Scholar
• Sackton T, Haney R, Rand D. 2003. Cytonuclear coadaptation in Drosophila: Disruption of cytochrome C oxidase activity in backcross genotypes. Evolution. 57:2315–2325.
   PubMed Web of Science ®Google Scholar
• Santucci F, Emerson BC, Hewitt GM. 1998. Mitochondrial DNA phylogeography of European hedgehogs. Mol Ecol. 7:1163–1172.
   PubMed Web of Science ®Google Scholar
• Scheffler K, Martin DP, Seoighe C. 2006. Robust inference of positive selection from recombining coding sequences. Bioinformatics. 22:2493–2499.
   PubMed Web of Science ®Google Scholar
• Sert H, Ben Slimen H, Erdogan A, Suchentrunk F. 2008. Mitochondrial HVI sequence variation in Anatolian hares (Lepus europaeus Pallas, 1778). Mamm Biol. 74:286–297.
   Web of Science ®Google Scholar
• Smeds L, Künstner A. 2011. ConDeTri-a content dependent read trimmer for Illumina data. PloS ONE. 6:e26314.
   PubMed Web of Science ®Google Scholar
• Smith S, Turbill C, Suchentrunk F. 2010. Introducing mother's curse: low male fertility associated with an imported mtDNA haplotype in a captive colony of brown hares. Mol Ecol. 19:36–43.
   PubMed Web of Science ®Google Scholar
• Stamatis C, Suchentrunk F, Moutou KA, Giacometti M, Haerer G, Djan M, Vapa L, Vukovic M, Tvrtkovic N, Sert H, et al. 2009. Phylogeography of the brown hare (Lepus europaeus) in Europe: a legacy of south-eastern Mediterranean refugia? J Biogeogr. 36:515–528.
   Web of Science ®Google Scholar
• Stamatis C, Suchentrunk F, Sert H, Triantaphyllidis C, Mamuris Z. 2007. Genetic evidence for survival of released captive-bred brown hare Lepus europaeus during restocking operations in Greece. Oryx. 41:548–551.
   Web of Science ®Google Scholar
• Stewart JB, Freyer C, Elson JL, Wredenberg A, Cansu Z, Trifunovic A, Larsson NG. 2008. Strong purifying selection in transmission of mammalian mitochondrial DNA. PLoS Biol. 6:e10.
   PubMed Web of Science ®Google Scholar
• Stöck M, Moritz C, Hickerson M, Frynta D, Dujsebayeva T, Eremchenko V, Macey JR, Papenfuss TJ, Wake DB. 2006. Evolution of mitochondrial relationships and biogeography of Palearctic green toads (Bufo viridis subgroup) with insights in their genomic plasticity. Mol Phylogenet Evol. 41:663–689.
   PubMed Web of Science ®Google Scholar
• Sun C, Kong QP, Zhanq YP. 2007. The role of climate in human mitochondrial DNA evolution: a reappraisal. Genomics. 89:338–342.
   PubMed Web of Science ®Google Scholar
• Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 30:2725–2729.
   PubMed Web of Science ®Google Scholar
• Yu L, Li YW, Ryder O, Zhang YP. 2007. Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation. BMC Evol Biol. 7:198.
   PubMed Web of Science ®Google Scholar
• Zhou T, Shen X, Irwin DM, Shen Y, Zhang Y. 2014. Mitogenomic analyses propose positive selection in mitochondrial genes for high-altitude adaptation in galliform birds. Mitochondrion. 18:70–75.
   PubMed Web of Science ®Google Scholar