Current perspectives in phylogeography and the significance of South European refugia in the creation and maintenance of European biodiversity

Phylogeography of Southern European Refugia: Evolutionary Perspectives on the Origins and Conservation of European Biodiversity

Volumn , Issue , 2007, Pages 341-357

  Weiss, Steven ^a   Ferrand, Nuno ^b  

^a UNIVERSITY OF GRAZ   (Austria)

^b CENTRO DE INVESTIGAÇÃO EM BIODIVERSIDADE E RECURSOS GENÉTICOS   (Portugal)

Author keywords

coalescence; conservation; hybrid zones; landscape genetics; nested clade phylogeographic analysis; statistical phylogeography

Indexed keywords

EID: 84893081817     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/1-4020-4904-8_14     Document Type: Chapter

References (91)

1. Alexandrino J, Arntzen JW, Ferrand N (2002) Nested clade analysis and the genetic evidence for population expansion in the phylogeography of the golden-striped salamander, Chioglossa lusitanica (Amphibia : Urodela). Heredity 88, 66-74.
2. Alsos IG, Engelskjon T, Gielly L, Taberlet P, Brochman C (2005) Impact of ice ages on circumpolar molecular diversity: Insights from an ecological key species. Molecular Ecology 14, 2739-2754.
3. Arbogast BS, Edwards SV, Wakeley J, Beerli P, Slowinski JB (2002) Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annual Review in Ecology and Systematics 33, 707-740.
4. Arnaud JF (2003) Metapopulation genetic structure and migration pathways in the land snail Helix aspersa: Influence of landscape heterogeneity. Landscape Ecology 18, 333-346.
5. Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge.
6. Avise JC, Lansman RA, Shade RO (1979) The use of restriction endonucleases to measure mitochondrial DNA sequence relatedness in natural populations. I. Population structure and evolution of the genus Peromyscus. Genetics 92, 279-295.
7. Ballard JWO, Whitlock M (2004) The incomplete natural history of mitochondria. Molecular Ecology 13, 729-744.
8. Beaumont M (2005) Adaptation and speciation: What can Fst tell us? Trends in Ecology and Evolution 20, 435-440.
9. Beaumont M, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society London, B 263, 1619-1626.
10. Bernatchez L, Glémet H, Wilson C, Danzman RG (1995) Fixation of introgressed mitochondrial genome of arctic charr (Salvelinus alpinus L.) in an allopatric population of brook charr (Salvelinus fontinalis Mitchill). Canadian Journal of Fisheries and Aquatic Sciences 52, 179-185.
11. Carstens BC, Stevenson AL, Degenhardt JD, Sullivan J (2005) Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group. Systematic Biology 53, 781-792.
12. Castelloe J, Templeton AR (1994) Root probabilities for intraspecfic gene trees under neutral coalescent theory. Molecular Evolution and Phylogenetics 3, 102-113.
13. Catania F, Kauer MO, Daborn PJ, Yen JL, Ffrench-Constant RH, Schlötterer C (2004) World-wide survey of an Accord insertion and its association with DDT resistance in Drosophila melanogaster. Molecular Ecology 13, 2491-2504.
14. Coelho M, Luiselli, D, Bertorelle G, Lopes AI, Seixas S, Destro-Bisol G, Rocha J (2005). Microsatellite variation and evolution of human lactase persistence. Human Genetics 117, 329-339.
15. Comps B, Gömöry D, Letouzey J, Thiebaut B, Petit RJ (2001) Diverging trends between heterozygosity and allelic richness during postglacial colonization in the European beech. Genetics 157, 389-397.
16. Currat M, Ray N, Excoffier L (2004) SPLATCHE: A program to simulate genetic diversity taking into account environmental heterogeneity. Molecular Ecology Notes 4, 139-142.
17. Edwards SV, Beerli P (2000) Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54, 1839-1854.
18. Elson JL, Turnbull DM, Howell N (2004) Comparative genomics and the evolution of human mitochondrial DNA: Assessing the effects of selection. American Journal of Human Genetics 74, 229-238.
19. Excoffier L, Slatkin M (1995) Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Molecular Biology and Evolution 12, 921-927.
20. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131, 479-491.
21. Garcia-Marin JL, Utter FM, Pla C (1999) Postglacial colonization of brown trout in Europe based on distribution of allozyme variants. Heredity 82, 46-56.
22. Geffen E, Anderson MJ, Wayne RK (2004) Climate and habitat barriers to dispersal in the highly mobile grey wolf. Molecular Ecology 13, 2481-2490.
23. Geraldes A, Ferrand N (in press) A 7-bp insertion 3' to the HGM box suggests the duplication and concerted evolution of the rabbit SRY gene. Genetics Selection Evolution.
24. Godinho R, Mendonça B, Crespo EG, Ferrand N (2006) Genealogy of the nuclear β-fibrinogen locus in a highly structured lizard species: Comparison with mtDNA and evidence for intragenic recombination in the hybrid zone. Heredity, doi:10.1038/sj.hdy.6800823.
25. Grivet D, Petit RJ (2002) Phylogeography of the common ivy (Hedera sp.) in Europe: genetic differentiation through space and time. Molecular Ecology 11, 1351-1362.
26. Guillot G, Mortier F, Estoup A (2005a) Geneland: A program for landscape genetics. Molecular Ecology Notes 5, 703-711.
27. Guillot G, Estoup A, Mortier F, Cosson JF (2005b) A spatial statistical model for landscape genetics. Genetics 170, 1261-1280.
28. Hampe A, Petit RJ (2005) Conserving biodiversity under climate change: The rear edge matters. Ecology Letters 8, 461-467.
29. Harding RM, McVean G (2004) A structured ancestral population for the evolution of modern humans. Current Opinion in Genetics and Development 14, 667-674.
30. Hare MP (2001) Prospects for nuclear gene phylogeography. Trends in Ecology and Evolution 16, 700-706.
31. Harris DJ, Sá-Sousa P (2002) Molecular Phylogenetics of Iberian Wall lizards (Podarcis): Is Podarcis hispanica a species complex? Molecular Phylogenetics and Evolution 23, 75- 81.
32. Hein J, Schierup MH, Wiuf C (2005) Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory. Oxford University Press, Oxford.
33. Hewitt, GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society 58, 247-276.
34. Hewitt, GM (1999) Post-glacial recolonization of European biota. Biological Journal of the Linnean Society 68, 87-112.
35. Hewitt, GM (2000) The genetic legacy of the Quaternary ice ages. Nature 405, 907-913.
36. Hey J (2005) On the number of New world founders: A population genetic portrait of the peopling of the Americas. PloS Biology 3, 1-11.
37. Hey J, Machado CA (2003) The study of structured populations-new hope for a difficult and divided science. Nature Reviews Genetics 4, 535-543.
38. Hey J, Nielsen R (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence time of Drosophila pseudoobscura and D. persimilis. Genetics 167, 747-760.
39. Hey J, Won Y-J, Sivasundar A, Nielson R, Markert JA (2004) Using nuclear haplotypes with microsatellites to study gene flow between recently separated populations. Molecular Ecology 13, 909-919.
40. Hofreiter M, Serre D, Rohland N, Rabeder G, Nagel D, Conrad N, Münzel S, Pääbo S. (2004) Lack of phylogeography in European mammals before the last glaciation. Proceedings of the National Academy of Sciences, USA 101, 12963-12968.
41. Hudson RR, Turelli M (2003) Stochasticity overrules the 'Three-Times Rule': genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA. Evolution 57, 182-190.
42. Hugall A, Moritz C, Moussalli A, Stanisic J (2002). Reconciling paleodistribution models and comparative phylogeography in the Wet Tropic rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875). Proceedings of the National Academy of Sciences, USA 99, 6112-6117.
43. Kauer M, Zangerl B, Dieringer D, Schlötterer C (2002) Background selection and hitchhiking - An explanation for the contrasting chromosomal patterns of microsatellite variability in African and non- African populations of D. melanogaster. Genetics 160, 247-256.
44. Kauer MO, Dieringer D, Schlötterer C (2003) A microsatellite variability screen for positive selection associated with the 'out of Africa' habitat expansion of Drosophila melanogaster. Genetics 165, 1137-1148.
45. Knowles LL (2001) Genealogical portraits of speciation in montane grasshoppers (genus Melanoplus) from the sky islands of the Rocky Mountains. Proceedings of the Royal Society London, B 268, 1-6.
46. Knowles LL (2004) The burgeoning field of statistical phylogeography. Journal of Evolutionary Biology 17, 1-10.
47. Knowles LL, Maddison WP (2002) Statistical phylogeography. Molecular Ecology 11, 2623- 2635.
48. Maddison WP, Maddison DR (2004) Mesquite: A Modular System for Evolutionary Analysis, version 1.01. available at http://mesquiteproject.org.
49. Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: Combining landscape ecology and population genetics. Trends in Ecology & Evolution 18, 189-197.
50. Masta SE, Laurent NM, Routman EJ (2003) Population genetic structure of the toad Bufo woodhousii: An empirical assessment of the effects of haplotype extinction on nested cladistic analysis. Molecular Ecology 12, 1541-1454.
51. Melo-Ferreira J, Boursot P, Suchentrunk F, Ferrand N, Alves PC (2005) Invasion from the cold past: Extensive introgression of mountain hare (Lepus timidus) mitochondrial DNA into three other hare species in northern Iberia. Molecular Ecology 14, 2459-2464.
52. Mountain JL, Knight A, Jobin M, Gignoux C, Miller A, Lin AA, Underhill PA (2002) SNPSTRs: Empirically derived, rapidly typed, autosomal haplotypes for inference of population history and mutational processes. Genome Research 12, 1766-1772.
53. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Jennifer K (2000) Biodiversity hotspots for conservation priorities. Nature 403, 853-858.
54. Newton CR, Graham A, Heptinsall LE, Powell SJ, Summers C, Kalsheker N, Smith JC, Markham AF (1989) Analysis of any point mutation in DNA: The amplification refractory mutation system (ARMS). Nucleic Acids Research 17, 2503-2516.
55. Palmé AE, Su Q, Rautenberg A, Manni F, Lascoux M (2003) Postglacial recolonization and cpDNA variation of silver birch Betula pendula. Molecular Ecology 12, 201-212.
56. Paulo OS, Jordan WC, Bruford MW, Nichols RA (2002) Using nested clade analysis to assess the history of colonization and the persistence of populations of an Iberian Lizard. Molecular Ecology 11, 809-820.
57. Petit RJ, Grivet D (2002) Optimal randomization strategies when testing the existence of a phylogeographic structure. Genetics 161, 469-471.
58. Petit RJ, Brewer S, Bordács S, Burg K, Cheddadi R, Coart E, Cottrell J, Czaikl UM, van Dam B, Deans JD, Espinel S, Fineschi S, Finkeldey R, Glaz I, Goicoechea PG, Jensen JS, König AO, Lowe AJ, Madsen SF, Mátyás G, Munro RC, Popescu F, Slade D, Tabbener H, deVries SGM, Ziegenhagen B, de Beaulieu J-L, Kremer A (2002a) Identification of refugia and post-glacial colonisation routes of European white oaks based on chloroplast DNA and fossil pollen evidence. Forest Ecology and Management 156, 49-74.
59. Petit RJ, Csaikl UM, Bordács S, Burg K, Coart E, Cottrell J, van Dam B, Deans JD, Dumolin-Lapègue S, Fineschi S, Finkeldey R, Gillies A, Glaz I, Goicoechea PG, Jensen JS, König AO, Lowe AJ, Madsen SF, Mátyás G, Munro RC, Olalde M, Pemonge M, Popescu F, Slade D, Tabbener H, Tauchini D, Vries SGM, Ziegenhagen B, Kremer A (2002b) Chloroplast DNA variation in European white oaks: Phylogeography and patterns of diversity based on data from over 2600 populations. Forest Ecology and Management 156, 5-26.
60. Petit JR, Aguinagalde I, Beaulieu J-L, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M, Mohanty A, Müller-Starck G, Demesure-Musch B, Palme A, Martin JP, Rendell S, Vendramin GG (2003) Glacial refugia: Hotspots but not melting pots of genetic diversity. Science 300, 1563-1565.
61. Pinho C, Ferrand N, Harris DJ (in press) Reexamination of the Iberian and North African Podarcis (Squamata: Lacertidae) phylogeny based on increased mitochondrial DNA sequencing. Molecular Phylogenetics and Evolution.
62. Pons O, Petit RJ (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144, 1237-1245.
63. Posada D and Crandall KA (2001) Intraspecific phylogenetics: Trees grafting into networks. Trends in Ecology and Evolution 16, 37-45.
64. 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). Molecular Biology and Evolution 18, 2169-2178.
65. Ray N, Currat M, Berthier P, Excoffier L (2005) Recovering the geographic origin of early modern humans by realistic and spatially explicit simulations. Genome Research 15, 1161- 1167.
66. Rendell S, Ennos RA (2002) Chloroplast DNA diversity in Calluna vulgaris (heather) populations in Europe. Molecular Ecology 11, 69-78.
67. Rogers J, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9, 552-569.
68. Sequeira F, Alexandrino J, Rocha R, Arntzen JW, Ferrand N (2005) Genetic exchange across a hybrid zone within the Iberian endemic golden-striped salamander, Chioglossa lusitanica. Molecular Ecology 14, 245-254.
69. Slatkin M, Hudson RR (1991) Pairwise comparison for mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129, 555-562.
70. Smouse PE (1998) To tree or not to tree. Molecular Ecology 7, 399-412.
71. Spear SF, Peterson CR, Matocq MD, Storfer A (2005) Landscape genetics of the blotched tiger salamander (Ambystoma tigrinum melanostrictum). Molecular Ecology 14, 2553- 2564.
72. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. American Journal Human Genetics 68, 978-989.
73. Stewart JR, Lister AM (2001) Cryptic northern refugia and the origins of the modern biota. Trends in Ecology and Evolution 16, 608-613.
74. Storz (2005) Using genome scans of DNA polymorphism to infer adaptive population divergence. Molecular Ecology 14, 671-688.
75. Taberlet P, Cheddadi R (2002) Quaternary refugia and persistence of biodiversity. Science 297, 2009-2010.
76. Teixeira J, Arntzen JW (2002) Potential impact of climate warming on the distribution of the Golden-striped salamander, Chioglossa lusitanica, on the Iberian Peninsula. Biodiversity and Conservation 11, 2167-2176.
77. Teixeira J, Ferrand N, Arntzen JW (2001) Biogeography of the golden-striped salamander, Chioglossa lusitanica: A field survey and spatial modelling approach. Ecography 24, 618- 624.
78. Templeton AR (1998) Nested clade analyses of phylogeographic data: Testing hypotheses about gene flow and population history. Molecular Ecology 7, 381-397.
79. Templeton AR (2002a) 'Optimal' randomization strategies when testing the existence of a phylogeographic structure: A reply to Petit and Grivet. Genetics 161, 473-475.
80. Templeton AR (2002b) Out of Africa again and again. Nature 416, 45-51.
81. Templeton AR (2004) Statistical phylogeography: methods of evaluating and minimizing inference errors. Molecular Ecology 13, 789-809.
82. Tishkoff SA, Varkonyi R, Cahinhian N, Abbes S, Argyropoulos G, Destro-Bisol G, Drousioutou A, Danbgerfield B, Lefranc G, Loiselet J, Piro A, Stoneking M, Tagarelli A, Tagarelli G, Touma EH, Williams SM, Clark AG (2001) Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science 293, 455-462.
83. Van Houdt JKJ, Cleyn DE, Perretti A, Volckaert AM (2005) A mitogenic view on the evolutionary history fo the Holarctic freshwater gadoid, burbot (Lota lota). Molecular Ecology 14, 2445-2457.
84. Vitalis R, Dawson K, Boursot P (2001) Interpretation of variation across marker loci as evidence of selection. Genetics 158, 1811-1823.
85. Volckaert FAM, Hänfling B, Hellmans B, Carvalho GR (2002) Timing of the population dynamics of bullhead Cottus gobio (Teleostei: Cottidae) during the Pleistocene. Journal of Evolutionary Biology 15, 930-944.
86. Wakeley J (2004) Inferences about the structure and history of populations: Coalescents and intraspecific phylogeography. In: The Evolution of Population Biology (eds. Singh RS, Uyenoyama MK), pp. 193-215. Cambridge University Press, Cambridge.
87. Weiss S, Antunes A, Schlötterer C, Alexandrino P (2000) Mitochondrial haplotype diversity among Portuguese brown trout Salmo trutta L. populations: relevance to the post-Pleistocene recolonization of northern Europe. Molecular Ecology 9, 691-698.
88. Weiss S, Persat H, Eppe R, Schlötterer C, Ublein F (2002) Complex patterns of colonization and refugia revealed for European grayling Thymallus thymallus, based on complete sequencing of the mtDNA control region. Molecular Ecology 11, 1393-1407.
89. Won Y-J, Sivasundar A, Wang Y, Hey J (2005) On the origin of Lake Malawi cichlids: A population genetic analysis of divergence. Proceedings of the National Academy of Sciences, USA 102, 6581-6586.
90. Yang Z (1997) On the estimation of ancestral population sizes of modern humans. Genetical Research 69, 111-116.
91. Zhang DX, Hewitt GM (2003) Nuclear DNA analysis in genetic studies of populations: Practice, problems and prospects. Molecular Ecology 12, 563-584.