Coalescent models reveal the relative roles of ancestral polymorphism, vicariance, and dispersal in shaping phylogeographical structure of an African montane forest robin

Molecular Phylogenetics and Evolution

Volumn 38, Issue 1, 2006, Pages 171-188

  Bowie, Rauri C K ^a   Fjeldså, Jon ^b   Hackett, Shannon J ^c   Bates, John M ^c   Crowe, Timothy M ^d  

^a STELLENBOSCH UNIVERSITY   (South Africa)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c FIELD MUSEUM OF NATURAL HISTORY   (United States)

^d UNIVERSITY OF CAPE TOWN   (South Africa)

Author keywords

Coalescent; Gene flow; Glacial cycles; MDIV; MIGRATE; NCA; Pogonocichla; TMRCA

Indexed keywords

MITOCHONDRIAL DNA;

AFRICA; ANIMAL; ARTICLE; CLASSIFICATION; GENE FLOW; GENETIC POLYMORPHISM; GENETICS; HAPLOTYPE; HISTOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; SONGBIRD;

AFRICA; ANIMALS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENE FLOW; HAPLOTYPES; PHYLOGENY; POLYMORPHISM, GENETIC; SONGBIRDS;

AVES; POGONOCICHLA; POGONOCICHLA STELLATA; STIPHRORNIS ERYTHROTHORAX;

EID: 28844483498     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2005.06.001     Document Type: Article

References (79)

1. J.C. Avise, and D. Walker Pleistocene phylogeographic effects on avian populations and the speciation process Proc. R. Soc. Lond. B 265 1998 457 463
2. J.C. Avise, D. Walker, and G.C. Jones Speciation durations and Pleistocene effects on vertebrate phylogeography Proc. R. Soc. Lond. B 265 1998 1707 1712
3. P. Beerli, and J. Felsenstein Maximum likelihood estimation of a migration matrix and effective population sizes in two populations using a coalescent approach Genetics 152 1999 763 773
4. P. Beerli, and J. Felsenstein Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach Proc. Natl. Acad. Sci. USA 98 2001 4563 4568
5. J.L. Bossart, and D.P. Prowell Genetic estimates of population structure and gene flow: limitation, lessons, and new directions Trends Ecol. Evol. 13 1998 202 206
6. Bowie, R.C.K, 2003. Birds, molecules, and evolutionary patterns among Africa's Islands in the sky. Ph.D. thesis, University of Cape Town, South Africa.
7. R.C.K. Bowie, J. Fjeldså, S.J. Hackett, and T.M. Crowe Systematics and biogeography of Double-collared sunbirds from the Eastern Arc Mountains, Tanzania Auk 121 2004 660 681
8. R.C.K. Bowie, J. Fjeldså, S.J. Hackett, and T.M. Crowe Molecular evolution in space and through time: mtDNA phylogeography of the Olive Sunbird (Nectarinia olivacea/obscura) throughout continental Africa Mol. Phylogenet. Evol. 33 2004 56 74
9. M. Branco, M. Monnerot, N. Ferrand, and A.R. Templeton Postglacial dispersal of the European Rabbit (Oryctolagus cuniculus) on the Iberian Peninsula reconstructed from nested clade and mismatch analyses of mitochondrial DNA genetic variation Evolution 56 2002 792 803
10. N.L. Bulgin, H.L. Gibbs, P. Vickery, and A.J. Baker Ancestral polymorphism in genetic markers obscure detection of evolutionary distinct populations in the endangered Florida grasshopper sparrow (Ammodramus savannarum floridanus) Mol. Ecol. 12 2003 831 844
11. N.D. Burgess, and C.O.F. Mlingwa Evidence for altitudinal migration of forest birds between montane Eastern Arc and lowland forests in East Africa Ostrich 71 2000 180 190
12. R.H. Carcasson A preliminary survey of the zoogeography of African butterflies E. Afr. Wildl. J. 2 1964 122 157
13. P.A. Clancey Miscellaneous taxonomic notes on African Birds No. 34 Durban Mus. Novitates 9 1972 145 162
14. M. Clement, D. Posada, and K.A. Crandall TCS: a computer program to estimate gene genealogies Mol. Ecol. 9 2000 1657 1660
15. K.A. Crandall, and A.R. Templeton Empirical tests of some predictions from coalescent theory with application to intraspecific phylogeny reconstruction Genetics 134 1993 959 969
16. P.B. deMenocal Plio-Pleistocene African climate Science 270 1995 53 59
17. P.B. deMenocal African climate change and faunal evolution during the Pliocene-Pleistocene Earth Planetary Sci. Lett. 220 2004 3 24
18. P. Desjardins, and R. Morais Sequence and gene organisation of the chicken mitochondrial genome. A novel gene order in higher vertebrates J. Mol. Evol. 212 1990 599 634
19. A.W. Diamond, and A.C. Hamilton The distribution of forest passerine birds and Quaternary climatic change in Africa J. Zool. (Lond.) 191 1980 379 402
20. A.W. Diamond, and G.S. Keith Avifaunas of Kenya Forest islands 1- Mt. Kulal. Scopus 4 1980 49 55
21. Dowsett, R.J., 1982. The population dynamics and seasonal dispersal of the Starred Robin (Pogonocichla stellata). MSc Thesis, University of Natal, South Africa.
22. R.J. Dowsett Site-fidelity and survival rates of some montane forest birds in Malawi, south-central Africa Biotropica 17 1985 145 154
23. R.J. Dowsett, and F. Dowsett-Lemaire Breeding and moult cycles of some montane forest birds in south-central Africa Review Ecology (Terre et Vie) 39 1984 89 111
24. F. Dowsett-Lemaire On the breeding behaviour of three montane sunbirds Nectarinia spp. in northern Malawi Scopus 11 1988 79 86
25. F. Dowsett-Lemaire Food plants and the annual cycle in a montane community of sunbirds (Nectarinia spp.) in northern Malawi Tauraco 1 1989 167 185
26. F. Dowsett-Lemaire, and R.J. Dowsett African forest birds: patterns of endemism and species richness W. Weber African Rain Forest Ecology and Conservation: An Interdisciplinary Perspective 2001 Yale University Press New Haven 233 262
27. S.V. Edwards, and P. Beerli Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies Evolution 54 2000 1839 1854
28. J. Felsenstein Confidence limits of phylogenies: an approach using the bootstrap Evolution 39 1985 783 791
29. Friedmann, H., Stager, K.E., 1969. Results of the 1964 Cheney Tanganyikan Expedition Ornithology. Contributions to Science Los Angeles Mus. 84: 1-1 50.
30. García-Moreno, J., Fjeldså, J., 2000. Chronology and mode of speciation in the Andean Avifauna. In: Rheinwald, G. (Ed.), Isolated Vertebrate Communities in the Tropics, Proceedings of the Fourth International Symposium, Bonn. Zool. Monogr. 46, pp. 25-46.
31. Goloboff, P., 1999. NONA ver. 2 Published by the author, Tucumán, Argentina.
32. C.J. Griffiths The geological evolution of East Africa J.C. Lovett S.K. Wasser Biogeography and Ecology of the Rain Forests of Eastern Africa 1993 Cambridge University Press Cambridge, UK 9 21
33. C.E. Griswold Cladistic biogeography of afromontane spiders Aust. Syst. Biol. 4 1991 73 89
34. C.K. Griswold, and A.J. Baker Time to most recent common ancestor and divergence times of populations of common Chaffinches (Fringilla coelebs) in Europe and North Africa: insights into Pleistocene refugia and current levels of migration Evolution 56 2002 143 153
35. J. Haffer Alternative models of vertebrate speciation in Amazonia: an overview Biodiv. Cons. 6 1997 451 476
36. G.M. Hewitt Some genetic consequences of ice ages, and their role in divergence and speciation Biol. J. Linn. Soc. 58 1996 247 276
37. G.M. Hewitt The genetic legacy of the Quaternary ice-ages Nature 405 2000 907 913
38. Huelsenbeck, J.P., Ronquist, F., 2001. Mr Bayes: a program for the Bayesian inference of phylogeny.
39. M.P.S. Irwin The Starred Bush Robin Pogonocichla stellata in eastern Rhodesia and adjacent Mozambique Bull. B.O.C. 91 1971 14 18
40. M.P.S. Irwin, and P.A. Clancey A re-appraisal of the generic relationships of some African forest-dwelling robins (Aves: Turdudae) Arnoldia (Rhodesia) 6 1974 1 19
41. N.K. Johnson, and C. Cicero New mitochondrial DNA data affirm the importance of Pleistocene speciation in North American birds Evolution 58 2004 1122 1130
42. S. Keith, E.K. Urban, and C.H. Fry The Birds of Africa vol. IV 1992 Academic Press London
43. J. Kingdon Island Africa 1989 Princeton University Press New Jersey
44. J. Kingdon The Kingdon Field Guide to African Mammals 1997 Academic Press New York
45. J. Klicka, and R.M. Zink The importance of recent ice ages in speciation: a failed paradigm Science 277 1997 1666 1669
46. J. Klicka, and R.M. Zink Pleistocene effects on North American songbird evolution Proc. R. Soc. Lond. B 166 2000 695 700
47. L.L. Knowles Did the Pleistocene glaciations promote divergence. Tests of explicit refugial models in montane grasshoppers Mol. Ecol. 10 2001 691 701
48. L.L. Knowles, and W.P. Maddison Statistical phylogeography Mol. Ecol. 11 2002 2623 2635
49. E.P. Lessa, J.A. Cook, and J.L. Patton Genetic footprints of demographic expansion in North America, but not Amazonia, during the late Quaternary Proc. Natl. Acad. Sci. USA 100 2003 10331 10334
50. A. Lewis, and D. Pomeroy A Bird Atlas of Kenya 1989 A.A. Balkema Rotterdam pp. 620
51. P.O. Lewis Phylogenetic systematics turns over a new leaf Trends Ecol. Evol. 16 2001 30 37
52. E. Mayr, and R.J. O'Hara The biogeographic evidence supporting the Pleistocene Forest Refuge Hypothesis Evolution 40 1986 55 66
53. R.E. Moreau Geographical variation and plumage sequence in Pogonocichla Ibis 93 1951 383 401
54. R.E. Moreau The Bird Faunas of Africa and its Islands 1966 Academic Press London
55. Nielson, R., 2002. MDIV software. Available from: 〈 http://www.biom.cornell.edu/Homepages/Rasmus_Nielson/files.html 〉.
56. R. Nielson, and J. Wakeley Distinguishing migration from isolation: a Markov Chain Monte Carlo approach Genetics 158 2001 885 896
57. K.C. Nixon The parsimony ratchet, a new method for rapid parsimony analysis Cladistics 15 1999 407 414
58. Nixon, K.C., 1999-2002. WinClada ver. 1.0000 Published by the author, Ithaca, NY, USA.
59. T.B. Oatley The Starred Robin in Natal, Part 2: Annual cycles and feeding ecology Ostrich 53 1982 193 205
60. Oatley, T.B., Arnott, G., 1998. Robins of Africa. Acorn Books, Randberg, South Africa.
61. T.C. Partridge, B.A. Wood, and P.B. deMenocal The influence of global climatic change and regional uplift in large-mammalian evolution in East and Southern Africa E.S. Vrba G.H. Denton T.C. Partridge L.H. Burckle Paleoclimate and Evolution, with Emphasis on Human Origins 1995 Yale University Press New Haven 331 355
62. M. Pfenninger, and D. Posada Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration and secondary contact Evolution 56 2002 1776 1788
63. D. Posada, and K.A. Crandall Intraspecific gene genealogies: tree grafting into cladograms Trends Ecol. Evol. 16 2001 37 45
64. D. Posada, K.A. Crandall, and A.R. Templeton GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes Mol. Ecol. 9 2000 487 488
65. A. Prigogine Disjunctions of montane birds in the Afrotropical region Bonn. Zool. Beitr. 38 1987 195 207
66. D.A. Roff, and P. Bentzen The statistical analysis of mitochondrial DNA polymorphisms: chi-squared and the problem of small sample sizes Mol. Biol. Evol. 6 1989 539 545
67. M.S. Roy, P. Arctander, and J. Fjeldså Speciation and taxonomy of montane greenbuls of the genus Andropadus (Aves: Pycnonotidae) Steenstrupia 24 1998 51 66
68. M.S. Roy, R. Sponer, and J. Fjeldså Molecular systematics and evolutionary history of Akalats (Genus Sheppardia): a pre-Pleistocene radiation in a group of African forest birds Mol. Phylogenet. Evol. 18 2000 74 83
69. P. Taberlet, L. Fumagalli, A.G. Wust-Saucy, and J.F. Cosson Comparative phylogeography and postglacial colonisation routes in Europe Mol. Ecol. 7 1998 453 464
70. A.R. Templeton Out of Africa again and again Nature 416 2002 45 51
71. A.R. Templeton Statistical phylogeography: methods of evaluating and minimizing inference events Mol. Ecol. 13 2004 789 809
72. A.R. Templeton, and C.F. Sing A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination Genetics 134 1993 659 669
73. A.R. Templeton, E. Boerwinkle, and C.F. Sing A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila Genetics 117 1987 343 351
74. A.R. Templeton, K.A. Crandall, and C.F. Sing A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation Genetics 132 1992 619 633
75. G. Voelker Dispersal, vicariance and clocks: historical biogeography and speciation in a cosmopolitan passerine genus (Anthus: Motacillidae) Evolution 53 1999 1536 1552
76. E.S. Vrba African Bovidae: evolutionary events since the Miocene S. Afr. J. Sci. 81 1985 263 266
77. E.S. Vrba Habitat theory in relation to the evolution in African Neogene biota and Hominids T.G. Bromage S. Schrenk African Biogeography, Climate Change and Human Evolution 1999 Oxford University Press Oxford 19 34
78. F. White The vegetation of Africa 1983 UNESCO Paris
79. R.M. Zink, and J.B. Slowinski Evidence from molecular systematics for decreased avian diversification in the Pleistocene Epoch Proc. Natl. Acad. Sci. USA 92 1995 5832 5835