Divergence with gene flow and fine-scale phylogeographical structure in the wedge-billed woodcreeper, glyphorynchus spirurus, a neotropical rainforest bird

Molecular Ecology

Volumn 18, Issue 14, 2009, Pages 2979-2995

  MilA B ^a,b   Wayne, R K ^a   Fitze, P ^b   Smith, T B ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b MUSEO NACIONAL DE CIENCIAS NATURALES   (Spain)

Author keywords

Adaptive divergence; AFLP; Altitudinal gradient; Ecomorphology; Gene flow; mtDNA; Phylogeography

Indexed keywords

MITOCHONDRIAL DNA;

ADAPTATION; ALTITUDE; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ANIMAL; ARTICLE; BODY SIZE; DNA SEQUENCE; ECOSYSTEM; ECUADOR; FEMALE; GENE FLOW; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HISTOLOGY; MALE; MOLECULAR EVOLUTION; PHYLOGENY; POPULATION GENETICS; SONGBIRD;

ADAPTATION, BIOLOGICAL; ALTITUDE; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; ANIMALS; BODY SIZE; DNA, MITOCHONDRIAL; ECOSYSTEM; ECUADOR; EVOLUTION, MOLECULAR; FEMALE; GENE FLOW; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; MALE; PASSERIFORMES; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

AVES; BRYOPHYTA; GLYPHORYNCHUS SPIRURUS;

EID: 67649637131     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2009.04251.x     Document Type: Article

References (102)

1. Able KP, Noon BR (1976) Avian community structure along elevational gradients in the northeastern United States. Oecologia (Berlin), 26, 275 294.
2. 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.
3. Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts.
4. Bears H, Drever MC, Martin K (2008) Comparative morphology of dark-eyed juncos Junco hyemalis breeding at two elevations: a common aviary experiment. Journal of Avian Biology, 39, 152 162.
5. Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society of London. Series B, Biological Sciences, 263, 1619 1626.
6. Boag PT, van Noordwijk AJ (1987) Quantitative genetics. In : Avian Genetics: A Population and Ecological Approach (eds Buckley PA, Cooke F pp. 45 78. Academic Press, New York.
7. Bonin A, Bellemain E, Bronken Eidesen P et al. (2004) How to track and assess genotyping erros in population genetics studies. Molecular Ecology, 13, 3261 3273.
8. Bonin A, Taberlet P, Miaud C, Pompanon F (2006) Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria). Molecular Biology and Evolution, 23, 773 783.
9. Brumfield RT (2005) Mitochondrial variation in Bolivian populations of the Variable Antshrike (Thamnophilus caerulescens). Auk, 122, 414 432.
10. Brumfield RT, Jernigan RW, McDonald DB, Braun MJ (2001) Evolutionary implications of divergent clines in an avian (Manacus: Aves) hybrid zone. Evolution, 55, 2070 2087.
11. Buermann W, Saatchi S, Smith TB et al. (2008) Predicting species distrubutions across the Amazonian and Andean regions using remote sensing data. Journal of Biogeography, 35, 1160 1176.
12. Cabanne GS, Santos FR, Miyaki CY (2007) Phylogeography of Xiphorhynchus fuscus (Passeriformes, Dendrocolaptidae): vicariance and recent demographic expansion in southern Atlantic forest. Biological Journal of the Linnean Society, 91, 73 84.
13. Cadena CD, Klicka J, Ricklefs RE (2007) Evolutionary differentiation in the Neotropical montane region: molecular phylogenetics and phylogeography of Buarremon brush-finches (Aves, Emberizidae). Molecular Phylogenetics and Evolution, 44, 993 1016.
14. Chaves JA, Pollinger JP, Smith TB, LeBhun G (2007) The role of geography and ecology in shaping the phylogeography of the speckled hummingbird (Adelomyia melanogenys) in Ecuador. Molecular Phylogenetics and Evolution, 43, 795 807.
15. Cheviron ZA, Capparella AP, Vuilleumier F (2005) Molecular phylogenetic relationships among the Geositta Miners (Furnariidae) and biogeographic implications for avian speciation in Fuego-Patagonia. Auk, 122, 158 174.
16. Coyne JA, Orr HA (2004) Speciation. Sinauer Associates, Inc., Sunderland, Massachusetts.
17. Dingle C, Lovette IJ, Canaday C, Smith TB (2006) Elevational zonation and the phylogenetic relationships of the Henicorhina woodwrens. Auk, 123, 119 134.
18. Endler JA (1977) Geographic Variation, Speciation and Clines. Princeton University Press, Princeton, New Jersey.
19. Endler JA (1982) Problems in distinguishing historical from ecological factors in biogeography. American Zoologist, 22, 441 452.
20. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software Structure: a simulation study. Molecular Ecology, 14, 2611 2620.
21. 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.
22. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47 50.
23. FjeldsÅ J, Lovett JC (1997) Geographical patterns of old and young species in African forest biota: the significance of specific montane areas as evolutionary centres. Biodiversity and Conservation, 6, 325 346.
24. Forster M, Forster P, Watson J (2007) network (version 4.2.0.1): A software for population genetics data analysis. Fluxus Technology Ltd., Clare, Suffolk.
25. Fridolfsson AK, Ellegren H (1999) A simple and universal method for molecular sexing of non-ratite birds. Journal of Avian Biology, 30, 116 121.
26. Fu YX (1997) Statistical neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915 925.
27. García-Moreno J, FjeldsÅ J (2000) Chronology and mode of speciation in the Andean avifauna. Bonner zoologische Monograph, 46, 25 46.
28. García-Moreno J, Navarro-Sigüenza A, Peterson AT, Sánchez-González LA (2004) Genetic variation coincides with geographic structure in the common bush-tanager (Chlorospingus ophthalmicus) complex from Mexico. Molecular Phylogenetics and Evolution, 33, 186 196.
29. Gentry A (1989) Speciation in tropical forests. In : Tropical Forests: Botanical Dynamics, Speciation and Diversity (eds Holm-Nielsen LB, Nielsen IC, Balslev H pp. 1 22. Academic Press, New York.
30. Grant PR (1986) Ecology and Evolution of Darwin's Finches. Princeton University Press, Princeton, New Jersey.
31. Gregory-Wodzicki KM (2000) Uplift history of Central and Northern Andes: a review. Geological Society of America Bulletin, 112, 1091 1105.
32. Haffer J (1969) Speciation in amazonian forest birds. Science, 165, 131 137.
33. Hedrick PW (2006) Genetic polymorphism in heterogeneus environments: the age of genomics. Annual Review of Ecology and Systematics, 37, 67 93.
34. Hoekstra HE (2006) Genetics, development and evolution of adaptive pigmentation in vertebrates. Heredity, 97, 222 234.
35. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science, 294, 2310 2314.
36. Kleindorfer S, Chapman TW, Winkler H, Sulloway FJ (2006) Adaptive divergence in continuous populations of the Darwin's small ground finch (Geospiza fuliginosa). Evolutionary Ecology Research, 8, 357 372.
37. Knowles LL, Richards CL (2005) Importance of genetic drift during Pleistocene divergence as revealed by analyses of genomic variation. Molecular Ecology, 14, 4023 4032.
38. Knox EB, Palmer JD (1995) Chloroplast DNA variation and the recent radiation of giant senecios (Asteraceae) on the tall mountains of Eastern Africa. Proceedings of the National Academy of Sciences of the United States of America, 92, 10349 10353.
39. Leisler B, Winkler H (1985) Ecomorphology. Current Ornithology, 2, 155 186.
40. Lynch M, Milligan BG (1994) Analysis of population genetic structure with RAPD markers. Molecular Ecology, 3, 91 99.
41. 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.
42. Mayr E, O'Hara RJ (1986) The biogeographical evidence supporting the Pleistocene forest refuge hypothesis. Evolution, 40, 55 67.
43. McCormack JE, Smith TB (2008) Niche expansion leads to small-scale adaptive divergence along an elevation gradient in a medium-sized passerine bird. Proceedings of the Royal Society of London B. Series B, Biological Sciences, 275, 2155 2164.
44. McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature, 351, 652 654.
45. Milá B, McCormack JE, Castañeda G, Wayne RK, Smith TB (2008) Recent postglacial range expansion drives the rapid diversification of a songbird lineage in the genus Junco. Proceedings of the Royal Society of London. Series B, Biological Sciences, 274, 2653 2660.
46. Moreno E, Carrascal LM (1993) Leg morphology and feeding posture in four Parus species: an experimental ecomorphological approach. Ecology, 74, 2037 2044.
47. Moritz C, Patton JL, Schneider CJ, Smith TB (2000) Diversification of rainforest faunas: an integrated molecular approach. Annual Review of Ecology and Systematics, 31, 533 563.
48. Niemiller ML, Fitzpatrick BM, Miller BT (2008) Recent divergence-with-gene-flow in Tenessee cave salamanders (Plethodontidae; Gyrinophilus) inferred from gene genealogies. Molecular Ecology, 17, 2258 2275.
49. Norberg UM (1979) Morphology of the wings, legs and tail of three coniferous forest tits, the goldcrest and the treecreeper in relation to locomotor pattern and feeding station selection. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 287, 131 165.
50. Nosil P (2008) Speciation with gene flow could be common. Molecular Ecology, 17, 2103 2106.
51. Nosil P, Egan SP, Funk DJ (2008) Heterogeneous genomic differentiation between walking-stick ecotypes: 'isolation-by-adaptation' and multiple roles for divergent selection. Evolution, 62, 316 336.
52. Nyári AS (2007) Phylogeographic patterns, molecular and vocal differentiation, and species limits in Schiffornis turdina (Aves). Molecular Phylogenetics and Evolution, 44, 154 164.
53. Nylander JAA (2004) mrmodeltest v2. Evolutionary Biology Centre, Uppsala University, Uppsala. Program distributed by the author. Available from http://www.abc.se/∼nylander/.
54. Ogden R, Thorpe RS (2002) Molecular evidence for ecological speciation in tropical habitats. Proceedings of the National Academy of Sciences of the United States of America, 99, 13612 13615.
55. Orr MR, Smith TB (1998) Ecology and speciation. Trends in Ecology and Evolution, 13, 502 506.
56. Peakall R, Smouse PE (2006) genalex 6: genetic analysis in Excel. Population genetic software for research and teaching. Molecular Ecology Notes, 6, 288 295.
57. Pérez-Emán J (2005) Molecular phylogenetics and biogeography of the Neotropical redstarts (Myioborus; Aves, Parulinae). Molecular Phylogenetics and Evolution, 37, 511 528.
58. Petren K, Grant PR, Grant BR, Keller Lf (2005) Comparative landscape genetics and the adaptive radiation of Darwin's finches: the role of peripheral isolation. Molecular Ecology, 14, 2943 2957.
59. Price TD (1991) Morphology and ecology of breeding warblers along an altitudinal gradient in Kashmir, India. Journal of Animal Ecology, 60, 643 664.
60. Pritchard JK, Wen W (2004) Documentation for Structure software: version 2. Available from http://pritch.bsd.uchicago.edu.
61. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945 959.
62. Puebla-Olivares F, Bonaccorso E, Espinosa de los Monteros A et al. (2008) Speciation in the Emerald Toucanet (Aulachorhynchus prasinus) complex. Auk, 125, 39 50.
63. Pyle P (1997) Identification Guide to North American Birds. Part I. Slate Creek Press, Bolinas, California.
64. Rambaut D, Drummond A (2003) Tracer v. 1.3. Available from http://tree.bio.ed.ac.uk/software/tracer.
65. Ramos-Onsins SE, Rozas J (2002) Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution, 19, 2092 2100.
66. Rasner CA, Yeh P, Eggert LS et al. (2004) Genetic and morphological evolution following a founder event in the dark-eyed junco, Junco hyemalis thurberi. Molecular Ecology, 13, 671 681.
67. Raymond M, Rousset F (1995a) An exact test for population differentiation. Evolution, 49, 1280 1283.
68. Raymond M, Rousset F (1995b) genepop (v. 1.2): a population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248 249.
69. Rayner JMV (1988) Form and function in avian flight. Current Ornithology, 5, 1 66.
70. Restall R, Rodner C, Lentino M (2006) Birds of Northern South America: An Identification Guide. Yale University Press, New Haven, Connecticut.
71. Ribera I, Vogler AP (2004) Speciation in Iberian diving beetles in Pleistocene refugia (Coleoptera, Dytiscidae). Molecular Ecology, 13, 179 193.
72. Rice WR, Hostert EE (1993) Laboratory experiments on speciation: what have we learned in 40 years? Evolution, 47, 1637 1653.
73. Ridgely RS, Greenfield PJ (2001) The Birds of Ecuador. Cornell University Press, Ithaca.
74. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics, 145, 1219 1228.
75. Roy MS, Da Silva JMC, Arctander P, Garcia-Moreno J, FjeldsÅ J (1997) The speciation of South American and African birds in montane regions. In : Avian Molecular Evolution and Systematics (ed. Mindell DP pp. 325 343. Academic Press, San Diego, California.
76. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496 2497.
77. Rundle H, Nosil P (2005) Ecological speciation. Ecology Letters, 8, 336 352.
78. Ryan PG, Bloomer P, Moloney CL, Grant TJ, Delport W (2007) Ecological speciation in South Atlantic island finches. Science, 315, 1420 1423.
79. Schluter D (2000) The Ecology of Adaptive Radiation. Oxford University Press, Oxford.
80. Schluter D (2001) Ecology and the origin of species. Trends in Ecology and Evolution, 16, 372 380.
81. Schluter D, Smith JNM (1986) Natural selection on beak and body size in the song sparrow. Evolution, 40, 221 231.
82. Schneider CJ, Moritz C (1999) Rainforest refugia and evolution in Australia's Wet Tropics. Proceedings of the Royal Society of London. Series B, Biological Sciences, 266, 191 196.
83. Schneider CJ, Smith TB, Larison B, Moritz C (1999) A test of alternative models of diversification in tropical rainforests: ecological gradients vs. rainforest refugia. Proceedings of the National Academy of Sciences of the United States of America, 96, 13869 13873.
84. Sehgal RNM, Jones HI, Smith TB (2005) Molecular evidence for host specificity of parasitic nematode microfilariae in some African rainforest birds. Molecular Ecology, 14, 3988 3997.
85. Smith T, Wayne R, Girman D, Bruford M (1997) A role for ecotones in generating rainforest biodiversity. Science, 276, 1855 1857.
86. Smith TB, Schneider CJ, Holder K (2001) Refugial isolation versus ecological gradients: testing alternative mechanisms of evolutionary divergence in four rainforest vertebrates. Genetica, 112-113, 383 398.
87. Smith TB, Calsbeek R, Wayne RK et al. (2005) Testing alternative mechanisms of evolutionary divergence in an African rain forest passerine bird. Journal of Evolutionary Biology, 18, 257 268.
88. Smith TB, Milá B, Grether GF et al. (2008) Evolutionary consequences of human disturbance in a rainforest bird species from Central Africa. Molecular Ecology, 17, 58 71.
89. Sokal RR, Rohlf FJ (1981) Biometry. The Principles and Practice of Statistics in Biological Research, 2nd edn. W. H. Freeman and Co., New York.
90. Soobramoney S, Downs CT, Adams NJ (2005) Morphological variation in the common fiscal (Lanius collaris) along an altitudinal gradient in southern Africa. Ostrich, 76, 130 141.
91. 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.
92. Stotz DF, Fitzpatrick JW, Parker TA III., Moskovits DK (1996) Neotropical Birds: Ecology and Conservation. University of Chicago Press, Chicago, Illinois.
93. Terborgh J (1971) Distribution on environmental gradients: theory and a preliminary interpretation of distrubutional patterns in the avifauna of the Cordillera Vicabamba, Peru. Ecology, 52, 23 40.
94. Vekemans X, Beauwens T, Lemaire M, Roldán-Ruíz I (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Molecular Ecology, 11, 139 151.
95. Vos P, Hogers R, Bleeker M et al. (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research, 23, 4407 4414.
96. Warren BH, Bermingham E, Bowie RCK, Prys-Jones RP, Thébaud C (2003) Molecular phylogeography reveals island colonization history and diversification of western Indian Ocean sunbirds (Nectarinia: Nectariniidae). Molecular Phylogenetics and Evolution, 29, 67 85.
97. Weir JT, Schluter D (2008) Calibrating the avian molecular clock. Molecular Ecology, 17, 2321 2328.
98. Winkler H, Leisler B (1992) On the ecomorphology of migrants. Ibis, 134, 21 28.
99. Zeffer A, Norberg UM (2003) Leg morphology and locomotion in birds: requirements for force and speed during ankle flexion. Journal of Experimental Biology, 206, 1085 1097.
100. Zeffer A, Johansson C, Marmebro A (2003) Functional correlation between habitat use and leg morphology in birds (Aves). Biological Journal of the Linnean Society, 79, 461 484.
101. Zhivotovsky LA (1999) Estimating population structure in diploids with multilocus dominant DNA markers. Molecular Ecology, 8, 907 913.
102. Zink RM, Remsen JVJ (1986) Evolutionary processes and patterns of geographic variation in birds. In : Current Ornithology (ed. Johnston RF pp. 1 69. Plenum Press, New York.