Combining phylogeography and landscape genetics of Xenopipo atronitens (Aves: Pipridae), a white sand campina specialist, to understand Pleistocene landscape evolution in Amazonia

Biological Journal of the Linnean Society

Volumn 110, Issue 1, 2013, Pages 60-76

  Capurucho, João Marcos G ^a   Cornelius, Cintia ^b   Borges, Sergio Henrique ^c   Cohn Haft, Mario ^a   Aleixo, Alexandre ^d   Metzger, Jean Paul ^e   Ribas, Camila C ^a  

^a INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA   (Brazil)

^b FEDERAL UNIVERSITY OF AMAZONAS   (Brazil)

^c Fundacao Vitoria Amazonica   (Brazil)

^d MUSEU PARAENSE EMÍLIO GOELDI   (Brazil)

^e UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Birds; Black manakin; Demographic expansion; Gene flow; Last Glacial Maximum; mtDNA; Tepuis

Indexed keywords

AVIFAUNA; DEMOGRAPHY; GENE FLOW; GENETIC STRUCTURE; LANDSCAPE ECOLOGY; LANDSCAPE EVOLUTION; MIOCENE; MITOCHONDRIAL DNA; PALEOCLIMATE; PALEOECOLOGY; PASSERINE; PATCHINESS; PHYLOGEOGRAPHY; PLEISTOCENE; SAND; SPECIALIST; VEGETATION COVER;

AMAZON BASIN; AMAZONIA;

AVES; PIPRIDAE; XENOPIPO; XENOPIPO ATRONITENS;

EID: 84881617080     PISSN: 00244066     EISSN: 10958312     Source Type: Journal    
DOI: 10.1111/bij.12102     Document Type: Article

References (96)

1. Adeney JM. 2009. Remote sensing of fire, flooding, and white sand ecosystems in the Amazon. PhD Thesis, Duke University.
2. Akaike H. 1973. Information theory and an extension of the maximum likelihood principle. In: Petrov BN, Czáki F, eds. International symposium on information theory. Budapest: Akademiai Kiadi, 267-281.
3. Aleixo A. 2004. Historical diversification of a terra-firme forest bird superspecies: a phylogeographic perspective on the role of different hypotheses of Amazonian diversification. Evolution 58: 1303-1317.
4. Aleixo A. 2006. Historical diversification of floodplain forest specialist species in the Amazon: a case study with two species of the avian genus Xyphorhynchus (Aves: Dendrocolaptidae). Biological Journal of the Linnean Society 89: 383-395.
5. Alonso JA, Whitney BM. 2003. New distributional records of birds from white-sand forests of the Northern Peruvian Amazon, with implications for biogeography of Northern South America. The Condor 105: 552-566.
6. Anderson AB. 1981. White-sand vegetation of Brazilian Amazonia. Biotropica 13: 199-210.
7. Anhuf D, Ledru MP, Behling H, Cruz FW Jr, Cordeiro RC, Van der Hammen T, Karmann I, Marengo JA, Oliveira PE, Pessenda L, Siffedine A, Albuquerque AL, Dias PLS. 2006. Paleo-environmental change in Amazonian and African rainforest during the LGM. Palaeogeography Palaeoclimatology and Palaeoecology 239: 510-527.
8. Bates JM, Tello JG, Silva JMC. 2003. Initial assessment of genetic diversity in ten bird species of South American cerrado. Studies on Neotropical Fauna and Environment 38: 87-94.
9. 2 on Amazonian ecosystems since the last glacial maximum. Global Change Biology 12: 1977-1984.
10. Bonaccorso E, Koch I, Peterson AT. 2006. Pleistocene fragmentation of Amazon species' ranges. Diversity and Distributions 12: 157-164.
11. Bonvicino CRB, Gançalves PR, Oliveira JA, Oliveira LFB, Mattevi MS. 2009. Divergence in Zygodontomys (Rodentia: Sigmodontinae) and distribution of Amazonian savannas. Journal of Heredity 100: 322-328.
12. Borges SH. 2004. Species poor but distinct: bird assemblages in white-sand vegetation in Jaú National Park, Brazilian Amazon. Ibis 146: 114-124.
13. Briceño HO, Schubert C. 1990. Geomorphology of the Gran Sabana, Guayana Shield, southeastern Venezuela. Geomorphology 3: 125-141.
14. Briceño HO, Schubert C, Paolini J. 1990. Table-mountain geology and surficial geochemistry: Chimantá massif, Venezuelan Guayana Shield. Journal of South American Earth Sciences 3: 179-194.
15. Burney CW, Brumfield RT. 2009. Ecology predicts levels of genetic differentiation in Neotropical birds. American Naturalist 174: 358-368.
16. Burnham KP, Anderson DR. 2002. Model selection and multimodel inference: a pratical information-theoretic approach. New York, NY: Springer-Verlag.
17. Bush M. 1994. Amazonian speciation: a necessarily complex model. Journal of Biogeography 21: 5-17.
18. Bush M, Oliveira PE. 2006. The rise and fall of the refugial hypothesis of Amazonian speciation: a paleo-ecological perspective. Biota Neotropica 6: bn00106012006.
19. Cadena CD, Pinto NG, Dávila N, Chesser RT. 2011. No population genetic structure in a widespread aquatic songbird from the Neotropics. Molecular Phylogenetics and Evolution 58: 540-545.
20. Carneiro-Filho A, Schwartz D, Tatumi SH, Rosique T. 2002. Amazonian paleodunes provide evidence for drier climate phases during the Late Pleistocene-Holocene. Quaternary Research 58: 205-209.
21. Clement M, Posada D, Crandall KA. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1660.
22. Cohn-Haft M, Naka LN, Fernandes AM. 2007. Padrões de distribuição da Avifauna da várzea dos rios Solimões e Amazonas. In: Albernaz A, ed. Bases científicas para a conservação da várzea: identificação e caracterização de regiões geográficas. Brasília: IBAMA, 287-323.
23. Colinvaux PA, Oliveira PE, Moreno JE, Miller MC, Bush MB. 1996. A long pollen record from lowland Amazonia: forest and colling in glacial times. Science 274: 85-88.
24. Coomes DA, Grubb PJ. 1996. Amazonian caatinga and related communities at La Esmeralda, Venezuela: forest structure, physiognomy and floristics, and control by soils factors. Vegetatio 122: 167-191.
25. Corander J, Marttinen P, Sirén J, Tang J. 2008. Enhanced Bayesian modeling in BAPS software for learning genetic structure of populations. BMC Informatics 9: 539.
26. Corander J, Tang J. 2007. Bayesian analysis of population structure based on linked molecular information. Mathematical Biosciences 205: 19-31.
27. Cowling SA, Maslin MA, Sykes MT. 2001. Paleovegetation simulations of lowland Amazonia and implications for Neotropical allopatry and speciation. Quaternary Research 55: 140-149.
28. Crawley MJ. 2007. The R book. Chichester: John Wiley & Sons, Ltd.
29. Diaz M, Stiles FG, Telleria JL. 1995. La comunidad de Aves en un gran claro permanente de la selva Amazonica: la Sierra de Chiribiquete (Colombia). Ardeola 42: 191-200.
30. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.
31. Drummond AJ, Rambaut A, Shapiro B, Pybus OG. 2005. Bayesian coalescent inference of past populations dynamics from molecular sequences. Molecular Biology and Evolution 22: 1185-1192.
32. ESRI. 2011. ArcGIS desktop, Version 10.1. Redlands, CA: Environmental Systems Research Institute Incorporated.
33. Fouquet A, Noonan BP, Rodrigues MT, Pech N, Guilles A, Gemmell NJ. 2012. Multiple Quaternary refugia in the Eastern Guiana Shield revealed by comparative phylogeography of 12 frog species. Systematic Biology 61: 461-489.
34. Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking, and background selection. Genetics 147: 915-925.
35. Gansser A. 1954. The Guiana Shield (S. America): geological observations. Ecoglae Geologicae Helvetiae 47: 78-112.
36. Givnish TJ, Evans TM, Zjhra ML, Patterson TB, Berry PE, Sytsma KJ. 2000. Molecular evolution, adaptive radiation, and geographic diversification in the amphiatlantic family Rapateacea: evidence from ndhF sequences and morphology. Evolution 54: 1915-1937.
37. Guilherme E, Borges SH. 2011. Ornithological records from a campina/campinarana enclave on the upper Juruá River, Acre, Brazil. The Wilson Journal of Ornithology 123: 24-32.
38. Gustafson EJ, Parker GR. 1994. Using an index of habitat patch proximity for landscape design. Landscape Urban Planing 29: 117-130.
39. Haffer J. 1969. Speciation in Amazonian forest birds. Science 165: 131-137.
40. Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.
41. Hey J, Nielsen R. 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167: 747-760.
42. Hey J, Nielsen R. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences of the United States of America 104: 2785-2790.
43. Horbe AMC, Horbe MA, Suguio K. 2004. Tropical spodosols in northeastern Amazonas State, Brazil. Geoderma 119: 55-68.
44. Huber O. 1988. Guayana highlands versus Guayana lowlands, a reappraisal. Taxon 37: 595-614.
45. Latrubesse EM. 2000. The Late Pleistocene in Amazonia: a palaeoclimatic model. In: Smolka P, Volkheimer W, eds. Southern hemisphere paleo and neoclimates. New York, NY: Springer-Verlag, 209-222.
46. Latrubesse EM. 2002. Evidence of Quaternary palaeohydrological changes in middle Amazonia: the Aripuanã-Roosevelt and Jiparaná 'fans'. Zeitschrift für Geomorphologie 129: 61-72.
47. Latrubesse EM. 2003. The Late-Quaternary palaeohydrology of large South American fluvial systems. In: Gregory KJ, Bemito G, eds. Palaeohydrology: understanding global change. Chichester: John Wiley & Sons, Ltd, 193-212.
48. Latrubesse EM, Franzinelli E. 2005. The late Quaternary evolution of the Negro River, Amazon, Brazil: implications for island and floodplain formation in large anabranching tropical systems. Geomorphology 70: 372-397.
49. Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
50. Lovette IJ. 2004. Mitochondrial dating and mixed support for the '2% rule' in birds. The Auk 121: 1-6.
51. Maguire B. 1970. On the flora of the Guayana Highland. Biotropica 2: 85-100.
52. Marks BD, Hackett SJ, Capparella AP. 2002. Historical relationships among Neotropical lowland forest areas of endemism as determined by mitochondrial DNA sequence variation within the wedge-billed woodcreeper (Aves: Dendrocolaptidae: Glyphorynchus spirurus). Molecular Phylogenetics and Evolution 24: 153-167.
53. Mayle FE, Beerling DJ, Gosling WD, Bush MB. 2004. Responses of Amazonian ecosystems to climatic and atmospheric carbon dioxide changes since the last glacial maximum. Philosophical Transaction of the Royal Society of London Series B, Biological Sciences 359: 499-514.
54. Mayr E, Phelps WH. 1967. The origin of the bird fauna of the south Venezuelan highlands. Bulletin of the American Museum of Natural History 136: 269-328.
55. McGarigal K, Cushman SA, Neel MC, Ene E. 2002. FRAGSTATS v3: spatial pattern analysis program for categorical maps. Available at: http://www.umass.edu/landeco/research/fragstats/fragstats.html
56. McKay BD, Barker FK, Mays HL, Doucet SM, Hill GE. 2010. A molecular phylogenetic hypothesis for the manakins (Aves: Pipridae). Molecular Phylogenetics and Evolution 55: 733-737.
57. Miller MJ, Bermingham E, Klicka J, Escalante P, Amaral FSR, Weir JT, Winker K. 2008. Out of Amazonia again and again: episodic crossing of the Andes promotes diversification in a lowland forest flycatcher. Proceedings of the Royal Society of London Series B, Biological Sciences 275: 1133-1142.
58. Oren DC. 1981. Zoogeographic analysis of the white sand campina avifauna of Amazonia. PhD Thesis, Harvard University.
59. Patel S, Weckstein JD, Patané JSL, Bates JM, Aleixo A. 2011. Temporal and spatial diversification of Pteroglossus araçaris (Aves: Ramphastidae) in the neotropics: constant rate of diversification does not support an increase in radiation during the Pleistocene. Molecular Phylogenetics and Evolution 58: 105-115.
60. Peakall R, Smouse PE. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research - an update. Bioinformatics 28: 2537-2539.
61. Poletto F, Aleixo A. 2005. Implicações biogeográficas de novos registros ornitológicos em um enclave de vegetação de campina no sudoeste da Amazônia brasileira. Revista Brasileira de Zoologia 22: 1196-1200.
62. Posada D, Crandall KA. 2001. Intraspecific gene genealogies: trees grafting into networks. Trends in Ecology and Evolution 16: 37-45.
63. Posada R. 2008. jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25: 1253-1256.
64. Posada R, Crandall KA. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
65. Prum RO. 1990. Phylogenetic analysis of the evolution and display behavior in the Neotropical manakins (Aves: Pipridae). Ethology 231: 202-231.
66. Prum RO. 1992. Syringeal morphology, phylogeny, and evolution of Neotropical manakins (Aves: Pipridae). American Museum Novitates 3043: 1-65.
67. Quijada-Mascareñas JA, Fergunson JE, Pook CE, Salomão MG, Thorpe RS, Wüster W. 2007. Phylogeographic patterns of trans-Amazonian vicariants and Amazonian biogeography: the Neotropical rattlesnake (Crotalus durissus complex) as an example. Journal of Biogeography 34: 1296-1312.
68. R Development Core Team. 2009. R: a language and environment for statistical computing. Austria: R Foundation for Statistical Computing. Available at: http://www.R-project.org/
69. Rambaut A, Drummond AJ. 2007. Tracer, Version 1.5. Available at: http://beast.bio.ed.ac.uk/Tracer
70. Ramos-Onsins SE, Rozas J. 2002. Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution 19: 2092-2100.
71. Rêgo PS, Araripe J, Marceliano MLV, Sampaio I, Schneider H. 2007. Phylogenetic analysis of the genera Pipra, Lepidothrix, and Dixiphia (Pipridae, Passeriformes) using parcial cytochrome b and 16S mtDNA genes. Zoologica Scripta 36: 565-575.
72. Ribas CC, Aleixo A, Nogueira ACR, Miyaki CY, Cracraft J. 2012. A palaeobiogeographic model for biotic diversification within Amazonia over the past three million years. Proceedings of the Royal Society of London Series B, Biological Sciences 279: 681-689.
73. Ridgely RS, Tudor G. 2009. Field guide to the songbirds of South America: the passerines. Austin, TX: University of Texas Press.
74. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 1-4.
75. Rossetti DF, Bertani TC, Zani H, Cremon EH, Hayakawa EH. 2012. Late Quaternary sedimentary dynamics in Western Amazonia: implications for the origin of open vegetation/forest contrasts. Geomorphology 177: 74-92.
76. Rull V. 2005. Biotic diversification in the Guayana Highlands: a proposal. Journal of Biogeography 32: 921-927.
77. Rull V. 2011. Neotropical biodiversity: timing and potential drivers. Trends in Ecology and Evolution 26: 508-513.
78. Salerno PE, Ron SR, Señaris JC, Rojas-Runjaic FJM, Noonan BP, Cannatella DC. 2012. Ancient tepui summits harbor young rather than old lineages of endemic frogs. Evolution 66: 3000-3013.
79. Silva JMC, Rylands AB, Fonseca GAB. 2005. The fate of the Amazonian áreas of endemism. Conservation Biology 19: 689-694.
80. Sorenson MD, Ast JC, Dimcheff DE, Yuri T, Mindell DP. 1999. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Molecular Phylogenetics and Evolution 12: 105-114.
81. Stotz DF, Fitzpatrick JW, Parker TA III, Moscovits D. 1996. Neotropical birds: ecology and conservation. Chicago, IL: University of Chicago Press.
82. Swofford DL. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods). Sunderland, MA: Sinauer Associates.
83. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphim. Genetics 123: 585-595.
84. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731-2739.
85. Teeuw RM, Rhodes EJ. 2004. Aeolian activity in northern Amazonia: optical dating of Late Pleistocene and Holocene palaeodunes. Journal of Quaternary Science 19: 49-54.
86. Tello JG, Moyle RG, Marchese DJ, Cracraft J. 2009. Phylogeny and phylogenetics classification of tyrant flycatchers, contingas, manakins and their allies (Aves: Tyrannides). Cladistics 25: 429-467.
87. Templeton AR. 2006. Population genetics and microevolutionary theory. New York, NY: Wiley & Sons Inc.
88. Toumisto H. 2007. Interpreting the biogeography of South America. Journal of Biogeography 34: 1294-1295.
89. Van der Peer Y. 2002. ZT: a software tool for simple and partial Mantel tests. Journal of Statistical Software 7: 1-12.
90. Van Houtan KS, Pimm SL, Halley JM, Bierregaard JRO, Lovejoy TE. 2007. Dispersal of Amazonian birds in continuous and fragmented forest. Ecology Letters 10: 219-229.
91. Vargas-Ramírez M, Maran J, Fritz U. 2010. Red- and yellow-footed tortoises, Chelonoides carbonaria and C. denticulata (Reptilia: Testudines: Testudinidae), in South America savannahs and forests: do their phylogeographies reflect distinct habitats? Organisms, Diversity, and Evolution 10: 161-172.
92. Vicentini A. 2004. A vegetação ao longo de um gradiente edáfico no Parque Nacional do Jaú. In: Borges SH, Iwanaga S, Durigan CC, Pinheiro MR, eds. Janelas para a Biodiversidade no Parque Nacional do Jaú: uma estratégia para o estudo da biodiversidade na Amazônia. Manaus: Fundação Vitória Amazônica, 105-131.
93. Weir JT, Price M. 2011. Andean uplift promotes lowland speciation through vicariance and dispersal in Dendrocincla woodcreepers. Molecular Ecology 20: 4550-4563.
94. Weir JT, Schluter D. 2008. Calibrating the avian molecular clock. Molecular Ecology 17: 2321-2328.
95. Werneck FP. 2011. The diversification of eastern South American open vegetation biomes: historical biogeography and perspectives. Quaternary Science Reviews 30: 1630-1648.
96. Wüster W, Fergunson JE, Quijada-Mascareñas A, Pook CE, Salomão MG, Thorpe RS. 2005. Tracing an invasion: landbridges, refugia, and phylogeography of the Neotropical rattlesnake (Serpentes: Viperidae: Crotalus durissus). Molecular Ecology 14: 1095-1108.