Complex evolutionary history of a Neotropical lowland forest bird (Lepidothrix coronata) and its implications for historical hypotheses of the origin of Neotropical avian diversity

Molecular Phylogenetics and Evolution

Volumn 36, Issue 2, 2005, Pages 338-357

  Cheviron, Z A ^a,c   Hackett, Shannon J ^b   Capparella, Angelo P ^a  

^a ILLINOIS STATE UNIVERSITY   (United States)

^b FIELD MUSEUM OF NATURAL HISTORY   (United States)

^c LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

Amazonia; Historical demography; Lepidothrix; Neotropics; Nested clade analysis; Phylogeography; Refugia; Vicariant events

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; BIRD; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SOUTH AMERICA; TIME; TROPIC CLIMATE;

ANIMALS; BAYES THEOREM; BIRDS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GEOGRAPHY; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SOUTH AMERICA; TIME FACTORS; TROPICAL CLIMATE; VARIATION (GENETICS);

AVES; GALLIFORMES; LEPIDOTHRIX;

EID: 18744367198     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2005.01.015     Document Type: Article

References (90)

1. A. Aleixo Molecular systematics and the role of the "và rzea"-"terra-firme" ecotone in the diversification of Xiphorhynchus woodcreepers (Aves: Dendrocolaptidae) Auk 119 2002 621 640
2. A. Aleixo Historical diversification of a terra-firme forest bird superspecies: a phylogeographic perspective on the role of different hypotheses of Amazonian diversification Evolution 58 2004 1303 1317
3. J.C. Avise Phylogeography: The history and formation of species 2000 Harvard University Press Cambridge
4. J.M. Bates, S.J. Hackett, and J. Cracraft Area-relationships in the Neotropical lowlands: a hypothesis based on raw distributions of Passerine birds J. Biogeogr. 25 1998 783 793
5. J.M. Bates, S.J. Hackett, and J.M. Goerck High levels of mitochondrial DNA differentiation in two lineages of Antbirds (Drymophila and Hypocnemis) Auk 116 1999 1039 1106
6. J.M. Bates, J.G. Tello, and J.M.C. da Silva Initial assessment of genetic diversity in ten bird species of South American cerrado Neotrop. Fauna Eviron. 38 2003 94 97
7. L. Bernatchez The evolutionary history of the brown trout (Salmo trutta) inferred from phylogeographic, nested cladistic, and mismatch analyses of mitochondrial DNA variation Evolution 55 2001 351 379
8. D.R. Brooks, and M.G.P. van Veller Critique of parsimony analysis of endemicity as a method of historical biogeography J. Biogeogr. 30 2003 819 825
9. R.T. Brumfield, and A.P. Capparella Historical diversification of birds in northwestern South America: a molecular perspective on the role of vicariant events Evolution 50 1996 1607 1624
10. R.T. Brumfield, R.W. Jernigan, D.B. McDonald, and M.J. Braun Evolutionary implications of divergent clines in an avian (Manacus:Aves) hybrid zone Evolution 55 2001 2070 2087
11. M.B. Bush Amazonian speciation: a necessarily complex model J. Biogeogr. 21 1994 5 17
12. M.B. Bush, P. Colinvaux, M.C. Weimann, D.R. Piperno, and K.-b. Liu Late Pleistocene temperature depression and vegetational change in Ecuadorian Amazonia Quat. Res. 34 1990 330 345
13. A.P. Capparella Genetic variation in neotropical birds: implications for the speciation process Acta XIX Congr. Int. Ornithol. 19 1988 1658 1664
14. A.P. Capparella Neotropical avian diversity and riverine barriers Acta XX Congr. Int. Ornithol. 20 1991 307 316
15. F.M. Chapman The distribution of bird-life in Colombia Bull. Am. Mus. Nat. Hist. 36 1917 1 729
16. F.M. Chapman The distribution of bird-life in Ecuador Bull. Am. Mus. Nat. Hist. 55 1926 1 784
17. R.T. Chesser Molecular phylogenetics of the Rhinochryptid genus Pteroptochos Condor 101 1999 439 445
18. M. Clement, D. Posada, and K.A. Crandall TCS: a computer program to estimate gene genealogies Mol. Ecol. 9 2000 1657 1660
19. P.E. Colinvaux Amazon diversity in light of the paleoecological record Q. Sci. Rev. 6 1987 93 114
20. P.E. Colinvaux Pleistocene biogeography and diversity in tropical forests of South America P. Goldblatt Biological relationships between africa and south america 1993 Yale University Press New Haven 473 499
21. P.E. Colinvaux A new vicariance model for Amazonian endemics Global Ecol. Biogeogr. Lett. 7 1998 95 96
22. P.E. Colinvaux, P. De Oliveira, J.E. Moreno, M.C. Miller, and M.B. Bush A long pollen record from lowland Amazonia: forest and cooling in glacial times Science 274 1996 85 88
23. P.E. Colinvaux, and P. De Oliveira Palaeoecology and climate of the Amazon basin during the last glacial cycle J. Q. Sci. 15 2000 347 356
24. P.A. Colinvaux, De Oliveira, and M.B. Bush Amazonian and neotropical plant communities on glacial time-scales: The failure of the aridity and refuge hypothesis Quat. Sci. Rev. 19 2000 141 169
25. J. Cracraft, and R.O. Prum Patterns and processes of diversification: speciation and historical congruence in some Neotropical birds Evolution 42 1988 603 620
26. R.A. de Brito, M.H. Mafrin, and F.M. Sene Nested cladistic analysis of Brazilian populations of Drosophila serido Mol. Phylogenet. Evol. 22 2002 131 143
27. P. Desjardins, and R. Morais Sequence and gene organization of the chicken mitochondrial genome: a novel gene order in higher vertebrates J. Biol. 212 1990 599 634
28. J.D. Durand, A.R. Templeton, B. Guinand, A. Imsiridou, and Y. Bouvet Nested clade and phylogeographic analysis of the Chub (Teleostei, Cyprinidae), in Greece: implications for Balkan Peninsula biogeography Mol. Phylogenet. Evol. 13 1999 566 580
29. S.V. Edwards Relevance of microevolutionary processes to higher level systematics D.P. Mindell Avian molecular evolution and systematics 1997 Academic Press San Diego, CA 251 278
30. S.V. Edwards, and P. Beerli Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies Evolution 54 2000 1839 1854
31. J.A. Endler Pleistocene forest refuges: fact or fancy G.T. Prance Biological diversification in the tropics 1982 Columbia University Press 641 657
32. R.C. Fleischer, C.E. McIntosh, and C.L. Tarr Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K-Ar based ages of the Hawaiian Islands to estimate molecular evolutionary rates Mol. Ecol. 7 1998 533 545
33. Y.-X. Fu Statistical tests of neutrality against population growth, hitchhiking, and background selection Genetics 147 1997 915 925
34. S.J. Hackett Molecular phylogenetics and biogeography of tanagers in the genus Ramphocelus (Aves) Mol. Phylogenet. Evol. 5 1996 368 382
35. J.P. Hall, and D.J. Harvey The phylogeography of Amazonia revisited: new evidence from Riodinid butterflies Evolution 56 2002 1489 1497
36. J. Haffer Speciation in Amazonian forest birds Science 165 1969 131 137
37. J. Haffer Speciation in some Amazonian forest birds J. Ornithol. 111 1970 285 331
38. J. Haffer Avian speciation in tropical South America 1974 Nuttall Ornithological Club Cambridge
39. J. Haffer Avian species richness in tropical South America Neotrop. Fauna Environ. 25 1990 157 183
40. J. Haffer Alternative models of vertebrate speciation in Amazonia: an overview Biodiv. Cons. 6 1997 451 476
41. H. Harpending Signature of ancient population growth in a low resolution mitochondrial mismatch distribution Hum. Biol. 66 1994 131 137
42. M. Hasegawa, K. Kishino, and T. Yano Dating the human-ape splitting by a molecular clock of mitochondrial DNA J. Mol. Evol. 22 1985 160 174
43. G. Hewitt Some genetic consequences of ice ages, and their role in divergence and speciation Biol. J. Linn. Soc. 58 1996 247 276
44. G. Hewitt The genetic legacy of the Quaternary ice ages Nature 405 2000 907 913
45. E.A. Hoffman, and M.S. Blouin Evolutionary history of the northern Leopard Frog: reconstruction of phylogeny, phylogeography, and historical changes in population demography from mitochondrial DNA Evolution 58 2004 145 159
46. F.G. Hoffman, and R.G. Baker Comparative phylogeography of short-tailed bats (Carollia: Phyllostomidae) Mol. Ecol. 12 2003 3403 3414
47. H. Hooghiemstra, and T. van der Hammen Neogene and Quaternary development of the neotropical rainforest: the forest refugia hypothesis and a literature review Earth Sci. Rev. 44 1998 147 183
48. J.P. Hulsenbeck, and F. Ronquist MRBAYES: Bayesian inference of phylogeny Bioinformatics 17 2001 754 755
49. L. Joseph, T. Wilke, and D. Alpers Reconciling genetic expectations from host specificity with historical population dynamics in an avian brood parasite, Horsfield's Bronze Cuckoo Chalcites basalis of Australia Mol. Ecol. 11 2002 829 837
50. L.L. Knowles, and W.P. Maddison Statistical phylogeography Mol. Ecol. 11 2002 2623 2635
51. T.D. Kocher, W.K. Wilson, A. Meyer, S.V. Edwards, S. Pääbo, F.X. Villablanca, and A.K. Wilson Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers Proc. Natl. Acad. Sci. USA 86 1989 6196 6200
52. 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
53. K.-B. Liu, and P.E. Colinvaux A 5200-year history of the Amazon rain forest J. Biogeogr. 15 1985 231 248
54. B.D. Marks, S.J. Hackett, and A.P. Capparella Historical relationships among Neotropical lowland forest areas of endemism as inferred from mitochondrial DNA sequence variation within the Wedge-billed Woodcreeper (Aves: Dendrocolaptidae: Glyphorynchus spirurus) Mol. Phylogenet. Evol. 24 2002 155 167
55. S.M. Masta, N.M. Laurent, and E.J. Routman Population genetic structure of the toad Bufo woodhousii: an empirical assessment of the effects of haplotype extinction on nested cladistic analyses Mol. Ecol. 12 2003 1541 1554
56. C. Moritz, J.L. Patton, C.J. Schneider, and T.B. Smith Diversification of rainforest faunas: an integrated molecular approach Annu. Rev. Ecol. Syst. 31 2000 533 563
57. M. Nei Molecular evolutionary genetics 1987 Columbia University Press New York
58. C.L. Nesbo, T. Fossheim, L.A. Vøllestad, and K.S. Jackobsen Genetic divergence and phylogeographic relationships reflect glacial refugia and postglacial colonization Mol. Ecol. 8 1999 1387 1404
59. M. Nores An alternative hypothesis for the origin of Amazonian bird diversity J. Biogeogr. 26 1999 475 485
60. D. Paetkau, G.F. Shields, and C. Strobeck Gene flow between insular, coastal and interior populations of brown bears in Alaska Mol. Ecol. 7 1998 1283 1292
61. A. Pavlova, R.M. Zink, S.V. Drovetski, Y. Red'kin, and S. Rohwer Phylogeographic patterns in Motacilla flava and Motacilla citreola: species limits and population history Auk 120 2003 744 758
62. D. Posada, and K.A. Crandall Modeltest: testing the model of DNA substitution Bioinformatics 14 1998 817 818
63. 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
64. R.O. Prum Historical relationships among avian forest areas of endemism in the Neotropics Acta XIX Congr. Int. Ornithol. 19 1988 2562 2572
65. M.E. Rasanen, A.M. Linna, J.C.R. Santos, and F.R. Negri Late Miocene tidal deposits in the Amazonian foreland basin Science 269 1995 386 390
66. R. Ridgley, and G. Tudor The birds of South America volume II: The Suboscine Passerines 1994 University of Texas Press Austin
67. A.R. Rogers Genetic evidence for a Pleistocene population explosion Evolution 4 1995 608 615
68. S.E. Romis-Onsins, and J. Rozas Statistical properties of new neutrality tests against population growth Mol. Biol. Evol. 19 2002 2092 2100
69. J. Rozas, and R. Rozas DnaSp version 3: an integrated program for molecular population genetics and molecular evolution analysis Bioinformatics 15 1999 174 175
70. Schneider, S., Roessli, D., Excoffier, L., 2000. Arlequin, version 2.0: a software for genetic data analysis. Genetics and Biometry Laboratory, Geneva
71. E.A. Sgariglia, and K.J. Burns Phylogeography of the California Thrasher (Toxostoma redivivum) based on nested-clade analysis of mitochondrial-DNA variation Auk 120 2003 346 363
72. Sick, H., 1967. Rios e enchentes na Amazonia como obstaculo para a avifauna. In: H. Lent (Ed.). Atas do simposio sobre a biota amazonica, vol. 5 (Zoologia). Conselho de Pesquisas Rio de Janeiro, pp. 495-520
73. Snow, D., 2004. Family Pipridae (Manakins). In: del Hoyo, J., Elliot, A., Christie, D. (Eds.). Handbook of Birds of the World, vol. 9. Lynx Edicions, Barcelona, pp. 110-169
74. M.D. Sorenson, and T.W. Quinn Numts: a challenge for avian systematics and population biology Auk 115 1998 214 221
75. Swofford, D.L., 1999. PAUP*. Phylogenetic analysis using parsimony (* and other methods). Version 4.0b10. Sinauer Associates, Sunderland, Massachusetts
76. A.R. Templeton Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history Mol. Ecol. 7 1998 381 397
77. A.R. Templeton Statistical phylogeography: methods for evaluating and minimizing inference errors Mol. Ecol. 13 2004 789 809
78. 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
79. A.R. Templeton, and C.F. Sing A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping IV: nested analysis with cladogram uncertainty and recombination Genetics 134 1993 659 669
80. A.R. Templeton, E. Boerwinkle, and C.F. Sing A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping I: Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila Genetics 117 1987 343 351
81. A.R. Templeton, E. Routman, and C. Phillips Separating population structure from population history: a cladistic analysis of the geographical distribution of mtDNA haplotypes in the Tiger Salamander, Ambystoma tigrinum Genetics 140 1995 767 782
82. W.E. Todd Sixteen new birds from Brazil and Guiana Proc. Biol. Soc. Wash. 38 1925 90 99
83. Traylor Jr., M.A., 1979. Checklist of the Birds of the World: A Continuation of the Work of James Peters, vol. VIII. Museum of Comparative Zoology, Cambridge
84. G. Voelker Dispersal, vicariance, and clocks: historical biogeography and speciation in a cosmopolitan passerine genus (Anthus: Motacillidae) Evolution 53 1999 1536 1552
85. A.R. Wallace Travels on the Amazon 1889 Harper and Row New York
86. S.D. Webb Biological implications of the Middle Miocene Amazon seaway Science 269 1995 361 362
87. T. Wilke, and M. Pfenniger Separating historic events from the recurrent processes in cryptic species: phylogeography of mud snails (Hydrobia spp.) Mol. Ecol. 11 2002 1439 1451
88. X. Zheng, B.S. Arbogast, and G.J. Kenagy Historical demography and genetic structure of sister species: deermice (Peromyscus) in the North American temperate rain forest Mol. Ecol. 12 2003 711 724
89. R.M. Zink The role of subspecies in obscuring avian biological diversity and misleading conservation policy Proc. R. Soc. Lond. B 271 2004 561 564
90. R.M. Zink, G.F. Barrowclough, J.L. Atwood, and R.C. Blackwell-Rago Genetics, taxonomy, and conservation of the threatened California Gnatcatcher Cons. Biol. 14 2000 1394 1405