Spatial patterns of genetic diversity across European subspecies of the mountain hare, Lepus timidus L.

Heredity

Volumn 97, Issue 5, 2006, Pages 355-365

  Hamill, R M ^a,b   Doyle, D ^a   Duke, E J ^a  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

^b ASHTOWN FOOD RESEARCH CENTRE   (Ireland)

Author keywords

Arctic boreal; Cluster analysis; Lepus; Microsatellite; Phylogeography; Timidus

Indexed keywords

MICROSATELLITE DNA; MITOCHONDRIAL DNA;

BAYESIAN ANALYSIS; FOSSIL RECORD; GENETIC VARIATION; MAXIMUM LIKELIHOOD ANALYSIS; MITOCHONDRIAL DNA; MOUNTAIN REGION; PHYLOGEOGRAPHY; POPULATION STRUCTURE; SMALL MAMMAL;

ANIMAL; ARTICLE; CLASSIFICATION; CLIMATE; EUROPE; GENETIC VARIABILITY; GENETICS; HARE; IRELAND; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION GENETICS; SPECIES DIFFERENCE; UNITED KINGDOM;

ANIMALS; BASE SEQUENCE; CLIMATE; DNA, MITOCHONDRIAL; EUROPE; GENETICS, POPULATION; HARES; IRELAND; MICROSATELLITE REPEATS; PHYLOGENY; SCOTLAND; SPECIES SPECIFICITY; VARIATION (GENETICS);

EURASIA; EUROPE;

LEPUS; LEPUS TIMIDUS;

EID: 33750420678     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/sj.hdy.6800880     Document Type: Article

References (65)

1. Altuna J (1971). Fauna de maniferos de los Yacinienter prehistoricos de Guipuzcoa. Con catalogo de los muniferos cuaternarios del Cantabrico del Pirineo occidental. Arazandi Ciencias Naturales: San Sebastian.
2. Alves PC, Ferrand N, Suchentrunk F, Harris DJ (2003). Ancient introgression of Lepus timidus mtDNA into L. granatensis and L. europaeus in the Iberian peninsula. Mol Phylogenet Evol 27: 70-80.
3. Andersson AC, Thulin CG, Tegelstrom H (1999). Applicability of rabbit microsatellite primers for studies of hybridisation between an introduced and a native hare species. Hereditas 130: 309-315.
4. Angerbjorn A, Flux JEC (1995). Lepus timidus, L. Mammalian. Species 495: 1-11.
5. Avise JC (2000). Phylogeography: The History and Formation of Species. Harvard University Press.
6. Balloux F, Brunner H, Lugon-Moulin N, Hausser J, Goudet J (2000). Microsatellites can be misleading: an empirical and simulation study. Evolution 54: 1414-1422.
7. Barnes I, Matheus P, Shapiro B, Jensen D, Cooper A (2002). Dynamics of Pleistocene population extinctions in Beringian brown bears. Science 295: 2267-2270.
8. Beebee TJC, Rowe G (2000). Microsatellite analysis of natterjack toad Bufo calamita Laurenti populations: consequences of dispersal from a Pleistocene refugium. Biol J Linnean Soc 69: 367-381.
9. Branco M, Ferrand N, Monnerot M (2000). Phylogeography of the European rabbit (Oryctolagus cuniculus) in the Iberian peninsula inferred from RFLP analysis of the cytochrome b gene. Heredity 85: 307-317.
10. Caizergues A, Bernard-Laurent A, Brenot JF, Ellison L, Rasplus JY (2003). Population genetic structure of rock ptarmigan Lagopus mutus in northern and western Europe. Mol Ecol 12: 2267-2274.
11. Conroy CJ, Demboski JR, Cook JA (1999). Mammalian biogeography of the Alexander Archipelago of Alaska: a north temperate nested fauna. J Biogeogr 26: 343-352.
12. Cornuet JM, Luikart G (1996). Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144: 2001-2014.
13. Davison A (2000). An East-West distribution of divergent mitochondrial haplotypes in British populations of the land snail, Cepaea nemoralis (Pulmonata). Biol J Linnean Soc 70: 697-706.
14. Edmands S (2001). Phylogeography of the intertidal copepod Tigriopus californicus reveals substantially reduced population differentiation at northern latitudes. Mol Ecol 10: 1743-1750.
15. Ellegren H (2004). Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5: 435-445.
16. Excoffier L, Smouse P, Quattro J (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
17. Fedorov VB, Goropashnaya AV, Jaarola M, Cook JA (2003). Phylogeography of lemmings (Lemmus): no evidence for postglacial colonization of the Arctic from the Beringian refugium. Mol Ecol 12: 725-731.
18. Felsenstein J (1989). PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
19. Flagstad O, Roed KH (2003). Refugial origins of reindeer (Rangifer tarandus L.) inferred from mitochondrial DNA sequences inferred from mitochondrial DNA sequences. Evolution 57: 658-670.
20. Garnier-Gere P, Dillmann C (1992). A computer program for testing pairwise linkage disequilibria in subdivided populations. J Hered 83: 239.
21. Garza JC, Williamson EG (2001). Detection of reduction in population size using data from microsatellite loci. Mol Ecol 10: 305-318.
22. Goudet J (2001). FSTAT. A Program to Estimate and Test Gene Diversities and Fixation Indices, Version 2.9.3. Available from http://www.unil.ch/izea/ softwares/fstat.html.
23. Harley E (2001). AGARst. A Programme for Calculating Allele Frequencies, GST and RST From Microsatellite Data, Version 2. University of Cape Town, Cape Town.
24. Hasegawa, M, Kishino H, Yano T (1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174.
25. Heuertz M, Hausman JF, Hardy OJ, Vendramin GG, Frascaria-Lacoste N, Vekemans X (2004). Nuclear microsatellites reveal contrasting patterns of genetic structure between western and southeastern European populations of the common ash (Fraxinus excelsior L.). Evolution 58: 976-988.
26. Hewitt GM (1999). Post-glacial re-colonization of European biota. Biol J Linnean Soc 68: 87-112.
27. Hewitt GM (2004). Genetic consequences of climatic oscillations in the Quaternary. Philos Trans R Soc Lond Ser B-Biol Sci 359: 183-195.
28. Hewson R (1984). Mountain hare (Lepus timidus L.), bags and moor management. J Zool 204: 563-565.
29. Korstanje R, Gillissen GF, Versteeg SA, van Oost BA, Bosma AA, Rogel-Gaillard C et al (2003). Mapping of rabbit microsatellite markers using chromosome-specific libraries. J Hered 94: 161-169.
30. Lambeck K (1996). Glaciation and sea-level change for Ireland and the Irish Sea since late Devensian/Midlandian time. J Geol Soc 153: 853-872.
31. Lambeck K, Purcell AP (2001). Sea-level change in the Irish Sea since the last glacial maximum: constraints from isostatic modelling. J Quat Sci 16: 497-506.
32. Malez M (1972). On the distribution of ice-age animals in the late Pleistocene of south-eastern Europe. Rad Jugos Akad Znanos i Umjet 364: 133-180.
33. Melo-Ferreira J, Boursot P, Suchentrunk F, Ferrand F, Alves P (2005). Invasion from the cold past: extensive introgression of mountain hare (Lepus timidus) mitochondrial DNA into three other hare species in northern Iberia. Mol Ecol 14: 2459-2464.
34. Nei M (1987). Molecular Evolutionary Genetics. Columbia University Press: New York.
35. Petit RJ, Aguinagalde I, de Beaulieu JL, Bittkau C, Brewer S, Cheddadi R et al (2003). Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300: 1563-1565.
36. 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. Molecular Ecology 8: 1805-1817.
37. Piry S, Luikart G, Cornuet JM (1999). BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. J Hered 90: 502-503.
38. Posada D, Crandall KA (1998). Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817-818.
39. Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
40. Queney G, Ferrand N, Weiss S, Mougel F, Monnerot M (2001). Stationary distributions of microsatellite loci between divergent population groups of the European rabbit (Oryctolagus cuniculus). Mol Biol Evol 18: 2169-2178.
41. Raymond M, Rousset F (1995a). GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86: 248-249.
42. Raymond M, Rousset F (1995b). An exact test for population differentiation. Evolution 49: 1280-1283.
43. Reynolds J, Weir BS, Cockerham CC (1983). Estimation of the coancestry coefficient: basis for a short term genetic distance. Genetics 105: 767-779.
44. Rico C, Rico I, Webb N, Smith S, Bell D, Hewitt G (1994). Four polymorphic microsatellite loci for the European wild rabbit, Oryctolagus cuniculus. Anim Genet 25: 367.
45. Rosenberg NA, Nordborg M (2002). Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat Rev Genet 3: 380-390.
46. Rousset F, Raymond M (1995). Testing heterozygote excess and deficiency. Genetics 140: 1413-1419.
47. Rozas J, Rozas R (1997). DnaSP version 2.0: A novel software package for extensive molecular population genetics analysis. Comput Appl Biosci 13: 307-311.
48. Rueness E, Jorde P, Hellborg L, Stenseth NC, Ellegren H, Jakobsen K et al (2003). Cryptic population structure in a large, mobile mammalian predator: the Scandinavian lynx. Mol Ecol 12: 2623-2633.
49. Sacks B, Mitchell B, Williams C, Ernest H (2005). Coyote movements and social structure along a cryptic population genetic subdivision. Mol Ecol 14: 1241-1249.
50. Schneider S, Roessli D, Excoffier L (2000). Arlequin: A Software for Population Genetics Data Analysis, Version 2-001. Genetics and Biometry Lab., Department of Anthropology, University of Geneva.
51. Suchentrunk F, Polster K, Giacometti M, Ratti P, Thulin CG, Ruhle C et al (1999). Spatial partitioning of allozyme variability in European mountain hares (Lepus timidus): gene pool divergence across a disjunct distributional range? Zeitschrift fuer Saugetierkunde 64: 308-318.
52. Swofford DL (1998). PAUP* - Phylogenetic Analysis Using Parsimony, Version 4. Sinauer Associates, Sunderland, MA.
53. Taberlet P, Bouvet J (1994). Mitochondrial DNA polymorphism, phylogeography, and conservation genetics of the brown bear Ursus arctos in Europe. Proc Roy Soc Lond Ser B Biol Sci 255: 195-200.
54. Thompson JD, Higgins DG, Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucl Acids Res 22: 4673-4680.
55. Thulin CG (2002). Biased geographical distribution of mitochondrial DNA that passed the species barrier from mountain hares to brown hares (genus Lepus): an effect of genetic incompatibility and mating behaviour? J Zool 258: 299-306.
56. Thulin CG (2003). The distribution of mountain hares Lepus timidus in Europe: A challenge from brown hares Lepus europaeus? Mammal Review 33: 29-42.
57. Thulin CG, Tegelstrom H, Fredga K (2003). Haplotype-diversity of mountain hare mtDNA among native mountain-hares and introduced brown hares in Scandinavia. Ann Zool Fenn 40: 45-52.
58. van Haeringen WA, den Bieman M, van Zutphen LFM, van Lith HA (1996). Polymorphic microsatellite DNA markers in the rabbit (Oryctolagus cuniculus). J Exp Anim Sci 38: 49-57.
59. Waits L, Taberlet P, Swenson JE, Sandegren F, Franzen R (2000). Nuclear DNA microsatellite analysis of genetic diversity and gene flow in the Scandinavian brown bear (Ursus arctos). Mol Ecol 9: 421-431.
60. Walsh P, Metzger D, Higuchi R (1991). CHELEX-100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10: 506-513.
61. Waltari E, Demboski JR, Klein DR, Cook JA (2004). A molecular perspective on the historical biogeography of the northern high latitudes. J Mammal 85: 591-600.
62. Weir BS, Cockerham CC (1984). Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
63. Wingfield RTR (1995). A model of sea levels in the Irish and Celtic seas during the end Pleistocene to Holocene transition. In: Preece RC (ed) Island Britain: A Quaternary Perspective. Geological Society Special Publication No. 96: London. pp 209-242.
64. Woodman P, McCarthy M, Monaghan N (1997). The Irish Quaternary fauna project. Quat Sci Rev 16: 129-159.
65. Yalden DW (1999). The History of British Mammals. Poyser Natural History: London.