Phylogeography of Xiphorhynchus fuscus (Passeriformes, Dendrocolaptidae): Vicariance and recent demographic expansion in southern Atlantic forest

Biological Journal of the Linnean Society

Volumn 91, Issue 1, 2007, Pages 73-84

  Cabanne, Gustavo Sebastián ^a   Santos, Fabrício R ^b   Miyaki, Cristina Yumi ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

Author keywords

Coalescence simulations; Forest refuges; Isolation by distance; Mitochondrial control region; Multiple regression; Neotropics; Pleistocene; Riverine barriers; Valley of the Para ba do Sul river

Indexed keywords

DEMOGRAPHIC HISTORY; FOREST DYNAMICS; GENETIC STRUCTURE; GENETIC VARIATION; HOLOCENE; INTRASPECIFIC VARIATION; MITOCHONDRION; PHYLOGENETICS; PHYLOGENY; PHYLOGEOGRAPHY; PLEISTOCENE; SONGBIRD; VICARIANCE;

ARGENTINA; ATLANTIC FOREST; BAHIA; BRAZIL; MINAS GERAIS; MISIONES [ARGENTINA]; PARAIBA DO SUL VALLEY; PARANA; RIO DE JANEIRO [BRAZIL]; RIO PARAIBA DO SUL; SANTA CATARINA; SAO PAULO [BRAZIL]; SOUTH AMERICA;

AVES; DENDROCOLAPTIDAE; PASSERI; PASSERIFORMES; XIPHORHYNCHUS FUSCUS;

EID: 34247332662     PISSN: 00244066     EISSN: 10958312     Source Type: Journal    
DOI: 10.1111/j.1095-8312.2007.00775.x     Document Type: Article

References (72)

1. Albuquerque JLB. 1996. Padrões de variação geográfica em algumas espécies de aves da floresta atlântica brasileira: o papel de barreiras e eventos vicariantes. Unpublished DPhil Thesis, Universidade Federal do Rio Grande do Sul.
2. Aleixo A. 2004. Historical diversification of a terra-firme forest bird superspecies: a phylogeographic perspective on the role of different hypothesis of amazonian diversification. Evolution 58 : 1303 1317.
3. Baker AJ, Marshall HD. 1997. Mitochondrial control region sequences as tools for understanding evolution. In : Mindell DP, ed. Avian molecular evolution and systematics. New York, NY : Academic Press, 51 82.
4. Bates JM. 2000. Allozyme genetic structure and natural habitat fragmentation: data for five species of Amazonian forest birds. Condor 102 : 770 783.
5. Bates JM. 2002. The genetic effects of forest fragmentation on five species of Amazonian birds. Journal of Avian Biology 33 : 276 294.
6. Behling H. 1998. Late Quaternary vegetational and climatic changes in Brazil. Review of Palaeobotany and Palynology 99 : 143 156.
7. Behling H. 2002. South and southeast Brazilian grasslands during Late Quaternay times: a synthesis. Palaeogeography, Palaeclimatology, Palaeoecology 177 : 19 27.
8. Behling H, Negrelle RRB. 2001. Tropical rain forest and climate dynamics of the atlantic lowland, southern Brazil, during the Late Quaternary. Quaternary Research 56 : 383 389.
9. Brown KS, Ab'Saber AN. 1979. Ice-age forest refuges and evolution in Neotropics: correlation of paleoclimatoligical, geomorphological and pedological data with biological endemism. Paleoclimas 5 : 1 30.
10. Bruford MW, Hanotte O, Brookfield JFY, Burke T. 1992. Single-locus and multilocus DNA fingerprinting. In : Hoelzel AR, ed. Molecular genetic analysis of populations - a practical approach. New York, NY : IRL Press, 287 336.
11. Cheviron ZA, Hackett SJ, Caparella AP. 2005. Complex evolutionary history of a Neotropical lowland fores bird (Lepidothrix coronata) and its implications for historical hypothesis of the origin of Neotropical diversity. Molecular Phylogenetics and Evolution 36 : 338 357.
12. Clapperton C. 1993. Quaternary geology and geomorphology of South America. New York, NY : Elsevier, 143 162.
13. Clement M, Posada D, Crandall KA. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9 : 1657 1659.
14. Costa LP, Leite YL, Fonseca GAB, Fonseca MT. 2000. Biogeography of South American forest mammals: endemism and diversity in the atlantic forest. Biotropica 32 : 872 881.
15. Crandall KA, Templeton RR. 1996. Applications of intraspecific phylogenetics. In : Harvey PH, Leigh AJ, Brown X, Smith JM, Nee S, eds. New uses for new phylogenies. New York, NY : Oxford University Press, 81 99.
16. Excoffier L, Smouse P, Quattro J. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human DNA restriction data. Genetics 131 : 479 491.
17. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using bootstrap. Evolution 39 : 783 791.
18. Fu YX. 1997. Statistical test of neutrality against population growth, hitchhiking and background selection. Genetics 147 : 915 925.
19. Geise L, Smith MF, Patton JL. 2001. Diversification in the Genus Akodon (Rodentia: Sigmodontinae) in southeastern South America: mitochondrial DNA sequence analysis. Journal of Mammalogy 82 : 92 101.
20. Giovanni NM. 2005. Taxonomy of southern populations in the Scytalopus speluncae group, with description of a new species and remarks on the systematics and biogeography of the complez (Passeriformes: Rhinocryptidae). Ararajuba 13 : 5 26.
21. Goudet J. 2002. Fstat, Version 2.9.3.2 Lausanne : Institute of Ecology, UNIL.
22. Guindon S, Gascuel. O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52 : 696 704.
23. Guindon S, Lethiec F, Duroux P, Gascuel O. 2005. PHYML Online - a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Research 33 : W557 W559.
24. Gusmão Câmara I. 2003. Brief history of conservation in the Atlantic forest. In : Galindo-Leal C, Gusmão Câmara I, eds. The state of the hotspots: the Atlantic forest. Washington, DC : Island Press, 31 42.
25. Haffer J. 1969. Speciation in Amazonian birds. Science 165 : 131 131.
26. Haffer J, Prance GT. 2001. Climatic forcing in Amazonia during the Cenozoic: on the refuge theory of biotic differentiation. Amazoniana 16 : 579 607.
27. Hasegawa M, Kishino H, Yano T-A. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22 : 160 174.
28. Hewit G. 2000. The genetic legacy of the Quaternary ice ages. Nature 405 : 907 913.
29. Klicka J, Zink RM. 1999. Pleistocene effects on North American songbird evolution. Proceedings of the Royal Society of London Series B, Biological Sciences 266 : 695 700.
30. Knowles LL. 2001. Did the Pleistocene glaciations promote divergence? Test of explicit refugial models in montane grasshopprers. Molecular Ecology 10 : 691 701.
31. Kumar S, Tamura K, Nei M. 2004. MEGA 3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics 5 : 150 163.
32. Kvist L, Ruokonem M, Lumme J, Orell M. 1999a. Different population structure in northern and southern populations of the European blue tit (Parus caeruleus). Journal of Evolutionary Biology 12 : 798 805.
33. Kvist L, Ruokonem M, Lumme J, Orell M. 1999b. The colonization history and present-day population structure of the Europeian great tit (Parus major major). Heredity 82 : 495 502.
34. Kvist L, Ruokonen M, Thessing A, Lumme J, Orell M. 1998. Mitochondrial control region polymorphism reveal high amount of gene flow in Fennoscandian willow tits (Parus montanus borealis). Hereditas 128 : 133 143.
35. Ledru MP, Salgado-Labouriau ML, Lorscheitter ML. 1998. Vegetational dynamics in southern and central Brazil during the last 10 000 yr B. P. Review of Palaeobotany and Palynology 99 : 131 142.
36. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25 : 955 964.
37. Maddison WP, Maddison DR. 2004. Mesquite, a modular system for evolutionary analysis, Version 1.02. Available at http://mesquiteproject.org.
38. Marantz CA, Aleixo A, Bevier LR, Patten MA. 2003. Family Dendrocolaptidae (Woodcreepes). In : del Hoyo J, Elliot A, Christie D, eds. Handbook of the birds of the world, Vol. 8. Broadbills to tapaculos. Barcelona : Lynx Edicions, 358 447.
39. Merilä J, Björklund M, Baker AJ. 1997. Historical demography and present day population structure of the greenfinch (Carduelis chloris): an analysis of mtDNA control region sequences. Evolution 51 : 946 956.
40. Milot E, Gibbs HL, Hobson KA. 2000. Phylogeography and genetic structure of northern populations of the yellow warbler (Dendroica petechia). Molecular Ecology 9 : 667 681.
41. Mindell DP, Sorenson MD, Dimcheff DE. 1998. Multiple independent origins of mitochondrial gene order in birds. Proceedings of the National Academy of Science of the United States of America 95 : 10693 10697.
42. Moritz C. 2002. Strategies to protect biological diversity and the evolutionary process that sustain it. Systematic Biology 51 : 238 254.
43. Moritz C, Patton JL, Schneider JC, Smith JB. 2000. Diversification of rainforest faunas: an integrated molecular approach. Annual Review in Ecology and Systematics 21 : 533 563.
44. Mustrangi MA, Patton JL. 1997. Phylogeography and systematics of the slender mouse opossum Marmosops (Marsupialia: Didelphidae). Zoology, Vol. 130. Berkeley, CA : University of California Press.
45. Nei M, Kumar S. 2000. Molecular evolution and phylogentics. New York, NY : Oxford University Press.
46. Pellegrino KCM, Rodrigues MT, Waite AN, Morando M, Yassuda YY, Sites JW. 2005. Phylogeography and species limits in the Gymnodactylus darwinii complex (Gekkonidae, Squamata): genetic structure coincides with river system in the Brazilian Atlantic Forest. Biological Journal of the Linnean Society 85 : 13 26.
47. Pereira SL, Baker AJ. 2004. Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics. BMC Evolutionary Biology 4 : 1 8.
48. Petri S, Fulfaro VJ. 1983. Geologia do Brasil - Fanerozoico. São Paulo : Editora da Universidade de São Paulo.
49. Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14 : 817 818.
50. Quinn PQ, Keough MJ. 2002. Experimental design and data analysis for biologists. Cambridge : Cambridge University Press.
51. Ramos-Onsins S, Rozas J. 2002. Statistical properties of new neutrality test against population growth. Molecular Biology and Evolution 19 : 2092 2100.
52. Riccomini C, Peloggia AUG, Salón JCL, Kohner MW, Figueira RM. 1989. Neotectonic activity in the Serra do Mar rift system (southeastern Brazil). Journal of South American Earth Science 2 : 191 197.
53. Rogers AR, Harpending H. 1992. Population growths makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9 : 552 569.
54. Rozas J, Sánchez-Del Barrio JC. 2003. DnaSP, DNA polymorphism analysis by the coalescent and other methods. Bioinformatics 19 : 2496 2497.
55. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4 : 406 425.
56. Schneider S, Roessli D, Excoffier L. 2000. Arlequin vers 2000: a software for population genetics data analysis. Geneva : University of Geneva, Genetics and Biometrics Laboratory.
57. Silva JMC, Stotz DF. 1992. Geographic variation in the Sharp-billed Treehunter Heliobletus contaminatus. Bulletin of the British Ornithologists Club 112 : 98 101.
58. Silva JMC, Straube FC. 1996. Systematics and biogeography of Scaled Woodcreepers (Aves: Dendrocolpatidae). Studies in Neotropical Fauna and Environments 31 : 3 10.
59. Slatkin M, Maddison WP. 1989. A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123 : 603 613.
60. Smouse PE, Long JC, Sokal RR. 1986. Multiple regression and correlation extension of the Mantel test of matrix correspondence. Systematic Zoology 35 : 627 632.
61. Sorenson MD, Ast JC, Dimcheff DE, Yuri T, Mindell DP. 1999. Primers for a PCR-base approach to mitochondrial genome sequencing in birds and other vertebrates. Molecular Phylogenetics and Evolution 12 : 105 114.
62. Swofford D. 2001. PAUP*: phylogenetic analysis using parsimony (* and other methods), Beta Version 4.0.B10. Sunderland, MA : Sinauer Associates Inc.
63. Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in human and chimpanzees. Molecular Biology and Evolution 10 : 512 526.
64. Templeton AR, Crandall KA, Sing CF. 1992. A cladistic analysis of phenotypic association with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132 : 619 633.
65. Templeton AR, Routman E, Phillips C. 1995. Separating population structure from population history: a cladistic analysis of the geographical distribution of mtDNA haplotypes in the Tiger Salamander, Ambystoma tigrinum. Genetics 140 : 767 782.
66. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The Clustal-windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 24 : 4876 4882.
67. Uimaniemi L, Orell M, Kvist L, Jokimäki J, Lumme J. 2003. Genetic variation of the Siberian tit Parus cinctus population at the regional level: a mitochondrial sequence analysis. Ecogeography 26 : 98 106.
68. Vanzolini PE, Williams EE. 1970. South american anoles: the geographic differentiation and evolution of the Anolis chrysolepis species group (Sauria: Iguanidae). Arquivos de Zoologia 19 : 1 298.
69. Veloso HP. 1991. Classificação da vegetação Brasileira, adaptada a um sistema universal. Rio de Janeiro : Fundação Instituto Brasileiro de Geografia e Estatística.
70. Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theoretical Population Biology 7 : 256 276.
71. Wilson AC, Cann RL, Carr SM, George M, Gylensten UB, Helm-Bychowski KM, Higuchi RG, Palumbi SR, Prager EM, Stoneking M. 1985. Mitochondrial DNA and two perspectives on evolutionary genetics. Biological Journal of the Linnean Society 26 : 375 400.
72. Zimmer JT. 1947. New birds from Pernambuco, Brazil. Proceedings of the Biology Society of Washington 60 : 99 106.