Speciation in an avian complex endemic to the mountains of Middle America (Ergaticus, Aves: Parulidae)

Molecular Phylogenetics and Evolution

Volumn 62, Issue 3, 2012, Pages 907-920

  Barrera Guzmán, Alfredo O ^a   Milá, Borja ^b   Sánchez González, Luis A ^a,c   Navarro Sigüenza, Adolfo G ^a  

^a UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

^b MUSEO NACIONAL DE CIENCIAS NATURALES   (Spain)

^c UNIVERSITY OF KANSAS   (United States)

Author keywords

Ergaticus; Genetic structure; Middle America; Montane forests; Phylogeography; Species limits

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; GENETIC VARIABILITY; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; PHYLOGEOGRAPHY; SONGBIRD; WESTERN HEMISPHERE;

AMERICAS; ANIMALS; BIODIVERSITY; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETIC VARIATION; PASSERIFORMES; PHYLOGENY; PHYLOGEOGRAPHY;

AVES; EMBERIZINAE; ERGATICUS; ERGATICUS RUBER;

EID: 84856258763     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.11.020     Document Type: Article

References (113)

1. Acosta S. Afinidades de la flora genérica de algunos bosques mesófilos de montaña del Nordeste, Centro y Sur de México: un enfoque fenético. An. Inst. Biol. Univ. Nac. Auton. Mex. Ser. Bot. 2004, 75:61-72.
2. Arbeláez-Cortés E., Nyári A.S., Navarro-Sigüenza A.G. The differential effect of lowlands on the phylogeographic pattern of a Mesoamerican montane species (Lepidocolaptes affinis, Aves: Furnariidae). Mol. Phylogenet. Evol. 2010, 57:658-668.
3. Arbogast B.S., Edwards S.V., Wakeley J., Beerli P., Slowinski J.B. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Ann. Rev. Ecol. Evol. Syst. 2002, 33:707-740.
4. Arbogast B.S., Drovetski S.V., Curry R.L., Boag P.T., Seutin G., Grant P.T., Grant B.R., Anderson D.J. The origin and diversification of Galapagos Mockingbirds. Evolution 2006, 60:370-382.
5. Arellano E., González-Cozátl F.X., Rogers D.S. Molecular systematics of Middle American harvest mice Reithrodontomys (Muridae), estimated from mitochondrial cytochrome b gene sequences. Mol. Phylogenet. Evol. 2005, 37:529-540.
6. Avise J.C., Walker D. Pleistocene phylogeographic effects on avian populations and the speciation process. Proc. Roy. Soc. Lond. B 1998, 265:457-463.
7. Avise J.C. Phylogeography: The History and Formation of Species 2000, Harvard University Press, Cambridge, MA.
8. Bandelt H.J., Forster P., Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 1999, 16:37-48.
9. Barber B.R., Klicka J. Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna. Proc. Roy. Soc. Lond. B 2010, 277:2675-2681.
10. Barraclough T.G., Vogler A.P. Detecting the geographical pattern of speciation from species-level phylogenies. Am. Nat. 2000, 155:419-434.
11. Barrowclough G.F., Zink R.M. Funds enough, and time: mtDNA, nuDNA and the discovery of divergence. Mol. Ecol. 2009, 18:2934-2936.
12. Beheregaray L.B. Twenty years of phylogeography: the state of the field and the challenges for the Southern Hemisphere. Mol. Ecol. 2008, 17:3754-3774.
13. Beheregaray L.B., Caccone A. Cryptic biodiversity in a changing world. J. Biol. 2007, 6:9.
14. Binford L.C. A distributional survey of the birds of the Mexican state of Oaxaca. Ornithol. Monogr. 1989, 43:1-405.
15. Bonaccorso E. Historical biogeography and speciation in the Neotropical highlands: molecular phylogenetics of the jay genus Cyanolyca. Mol. Phylogenet. Evol. 2009, 50:618-632.
16. Bonaccorso E., Navarro-Sigüenza A.G., Sánchez-González L.A., Peterson A.T., García-Moreno J. Genetic differentiation of the Chlorospingus ophthalmicus complex in Mexico and Central America. J. Avian Biol. 2008, 39:311-321.
17. Bye R. Prominence of the Sierra Madre Occidental in the biological diversity of Mexico. Biodiversity and Management of the Madrean Archipelago: The Sky Islands of the Southwestern United States and Northwestern Mexico 1995, 19-27. USDA Forest Service Rocky Mountain Forest and Range Experiment Station, Colorado. L. DeBano, G.J. Gottfried, R.H. Hamre, C.B. Edminster, P. Ffolliott, A. Ortega-Rubio (Eds.).
18. Cadena C.D., Klicka J., Ricklefs R.E. Evolutionary differentiation in the Neotropical montane region: molecular phylogenetics and phylogeography of Buarremon brush-finches (Aves, Emberizidae). Mol. Phylogenet. Evol. 2007, 44:993-1016.
19. Cadena C.D., Cheviron Z.A., Funk W.C. Testing the molecular and evolutionary causes of a 'leapfrog' pattern of geographical variation in coloration. J. Evol. Biol. 2010, 24:402-414.
20. Castoe T.A., Daza J.M., Smith E.N., Sasa M.M., Kuch U., Campbell J.A., Chippindale P.T., Parkinson C.L. Comparative phylogeography of pitvipers suggests a consensus of ancient Middle American highland biogeography. J. Biogeogr. 2009, 36:88-103.
21. Cortés-Rodríguez N., Hernández-Baños B.E., Navarro-Sigüenza A.G., Peterson A.T., García-Moreno J. Phylogeography and population genetics of the amethyst-throated hummingbird (Lampornis amethystinus). Mol. Phylogenet. Evol. 2008, 48:1-11.
22. Coyne J.A., Orr H.A. Speciation 2004, Sinauer Associates, Sunderland, MA.
23. Colbeck G.J., Gibbs H.L., Marra P.P., Hobson K., Webster M.S. Phylogeography of a widespread North American migratory songbird (Setophaga ruticilla). J. Hered. 2008, 99:453-463.
24. Curson J., Quinn D., Beadle D. New World Warblers 1995, Christopher Helm, London.
25. De Queiroz K. The general lineage concept of species, species criteria, and the process of speciation: a conceptual unification and terminological recommendations. Endless Forms: Species and Speciation 1998, 57-75. Oxford University Press, Oxford. D.J. Howard, S.H. Berlocher (Eds.).
26. Curson J. New world warblers. Handbook of the Birds of the World. Weavers to New World Warblers 2010, vol. 15:660-800. Lynx Edicions, Barcelona.
27. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4:699-710.
28. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
29. Edwards S.V., Beerli P. Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 2000, 54:1839-1854.
30. Edwards S., Bensch S. Looking forwards or looking backwards in avian phylogeography? A comment on Zink and Barrowclough 2008. Mol. Ecol. 2009, 18:2930-2933.
31. Edwards S.V., Kingan S.B., Calkins J.D., Balakrishnan C.N., Jennings W.B., Swanson W.J., Sorenson M.D. Speciation in birds: genes, geography, and sexual selection. Proc. Natl. Acad. Sci. USA 2005, 102:6550-6557.
32. Elliott B.G. Life history of the red warbler. Wilson Bull. 1969, 81:184-195.
33. Escalante-Pliego P., Navarro-Sigüenza A.G., Peterson A.T. Un análisis geográfico, ecológico e histórico de la diversidad de aves terrestres de México. Diversidad Biológica de México: Orígenes y Distribución 1998, 279-304. UNAM, Ciudad de México. T.P. Ramamoorthy, R. Bye, A. Lot, J. Fa (Eds.).
34. Excoffier L., Laval G., Schneider S. Arlequin (version 3.0.): an integrated software package for population genetics data analysis. Evol. Bioinform. Online 2005, 1:47-50.
35. Excoffier L., Smouse P.E., Quattro J.M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 1992, 131:479-491.
36. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 1981, 17:368-376.
37. Ferrusquía-Villafranca V.I. Geología de México: Una sinopsis. Diversidad Biológica de México: Orígenes y Distribución 1998, 3-108. UNAM, Ciudad de México. T.P. Ramamoorthy, R. Bye, A. Lot, J. Fa (Eds.).
38. Fu Y.X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 1997, 147:915-925.
39. Funk D.J., Omland K.E. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Ann. Rev. Ecol. Evol. Syst. 2003, 34:397-423.
40. García-Moreno J., Navarro-Sigüenza A.G., Peterson A.T., Sánchez-González L.A. Genetic variation coincides with geographic structure in the common bush-tanager (Chlorospingus ophthalmicus) complex from Mexico. Mol. Phylogenet. Evol. 2004, 33:186-196.
41. González C., Ornelas J.F., Gutiérrez-Rodríguez C. Selection and geographic isolation influence hummingbird speciation: genetic, acoustic and morphological divergence in the wedge-tailed sabrewing (Campylopterus curvipennis). BMC Evol. Biol. 2011, 11:38.
42. Graves G.R. Elevational correlates of speciation and intraspecific geographic variation in plumage in Andean forest birds. Auk 1985, 102:556-579.
43. Graves G.R. Linearity of geographic range and its possible effect on the population structure of Andean birds. Auk 1988, 105:47-52.
44. Hackett S.J. Molecular phylogenetics and biogeography of tanagers in the genus Ramphocelus (Aves). Mol. Phylogenet. Evol. 1996, 5:368-382.
45. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. 1999, 41:95-98.
46. Helbig A.J., Knox A.G., Parkin D.T., Sangster G., Collinson M. Guidelines for assigning species rank. Ibis 2002, 144:518-525.
47. Hernández-Baños B.E., Peterson A.T., Navarro-Sigüenza A.G., Escalante-Pliego B.P. Bird faunas of the humid montane forests of Mesoamerica: biogeographic patterns and priorities for conservation. Bird Conserv. Int. 1995, 5:251-277.
48. Hewitt G.M. Some genetic consequences of ice ages, and their role, in divergence and speciation. Biol. J. Linn. Soc. 1996, 58:247-276.
49. Hillis D.M., Bull J.J. An empirical test of bootstraping as a method for assessing confidence in phylogenetic analyses. Syst. Biol. 1993, 42:182-192.
50. Ho S.Y.W. Calibrating molecular estimates of substitution rates and divergence times in birds. J. Avian Biol. 2007, 38:409-414.
51. Ho S.Y.W., Phillips M.J. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst. Biol. 2009, 58:367-380.
52. Ho S.Y.W., Saarma U., Barnett R., Haile J., Shapiro B. The effect of inappropriate calibration: three case studies in molecular ecology. PloS One 2008, 3:e1615.
53. Huelsenbeck J.P., Ronquist F. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
54. Johansson U.S., Irestedt M., Parsons T.J., Ericson P.G.P. Basal phylogeny of the Tyrannoidea based on comparisons of cytochrome b and exons of nuclear c-myc and RAG-1 genes. Auk 2002, 119:984-995.
55. Johnson N.K., Cicero C. New mitochondrial DNA data affirm the importance of Pleistocene speciation in North American birds. Evolution 2004, 58:1122-1130.
56. Johnson K.P., Sorenson M.D. Comparing molecular evolution in two mitochondrial protein coding genes (cytochrome b and ND2) in the dabbling ducks (Tribe Anatini). Mol. Phylogenet. Evol. 1998, 10:82-94.
57. Kapelle M. Neotropical montane oak forests: overview and outlook. Ecology and Conservation of Neotropical Montane Oak Forests. Ecological Studies 185 2006, 447-467. Springer, Heidelberg. M. Kapelle (Ed.).
58. Kerhoulas N.J., Arbogast B.S. Molecular systematics and Pleistocene biogeography of Mesoamerican flying squirrels. J. Mammal. 2010, 91:654-667.
59. Klicka J., Zink R.M. The importance of recent ice ages in speciation: a failed paradigm. Science 1997, 277:1666-1669.
60. Kocher T.D., Thomas W.K., Meyer A., Edwards S.V., Pääbo S., Villablanca F.X., Wilson A.C. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA 1989, 86:6196-6200.
61. Larget B., Simon D.L. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 1999, 16:750-759.
62. León-Paniagua L., Navarro-Sigüenza A.G., Hernández-Baños B.E., Morales J.C. Diversification of the arboreal mice of the genus Habromys (Rodentia: Cricetidae: Neotominae) in the Mesoamerican highlands. Mol. Phylogenet. Evol. 2007, 42:653-664.
63. Librado P., Rozas J. DnasSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25:1451-1452.
64. Lovette I.J. Molecular phylogeny and plumage signal evolution in a trans Andean and circum Amazonian avian species complex. Mol. Phylogenet. Evol. 2004, 32:512-523.
65. Lovette I.J., Bermingham E. What is a wood-warbler? Molecular characterization of a monophyletic Parulidae. Auk 2002, 119:695-714.
66. Lovette I.J., Pérez-Emán J.L., Sullivan J.P., Banks R.C., Fiorentino I., Córdoba-Córdoba S., Echeverry-Galvis M., Barker F.K., Burns K.J., Klicka J., Lanyon S.M., Bermingham E. A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Aves). Mol. Phylogenet. Evol. 2010, 57:753-770.
67. Luna-Vega I., Alcántara-Ayala O., Espinosa-Organista D., Morrone J.J. Historical relationships of the Mexican cloud forests: a preliminary vicariance model applying Parsimony Analysis of Endemicity to vascular plant taxa. J. Biogeogr. 1999, 26:1299-1305.
68. Manthey J.D., Klicka J., Spellman G.M. Cryptic diversity in a widespread North American songbird: phylogeography of the brown creeper (Certhia americana). Mol. Phylogenet. Evol. 2011, 58:502-512.
69. Marshall J.S. The geomorphology and physiographic provinces of Central America. Central America: Geology, Resources and Hazards 2007, 75-122. Balkema, Leiden, The Netherlands. J. Bundschuh, G. Alvarado (Eds.).
70. Marshall C.J., Liebherr J.K. Cladistic biogeography of the Mexican transition zone. J. Biogeogr. 2000, 27:203-216.
71. McCormack J.E., Heled J., Delaney K.S., Peterson A.T., Knowles L.L. Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays. Evolution 2010, 65:184-202.
72. McCormack J.E., Peterson A.T., Bonaccorso E., Smith T.B. Speciation in the highlands of Mexico: genetic and phenotypic divergence in the Mexican jay (Aphelocoma ultramarina). Mol. Ecol. 2008, 17:2505-2521.
73. McKay B.D., Zink R.M. The causes of mitochondrial DNA gene tree paraphyly in birds. Mol. Phylogenet. Evol. 2010, 54:647-650.
74. Medina-Macías M.N., González-Bernal M.A., Navarro-Sigüenza A.G. Distribución altitudinal de las aves en una zona prioritaria en Sinaloa y Durango, Mexico. Rev. Mex. Biodivers. 2010, 81:487-503.
75. Milá B., Smith T.B., Wayne R.K. Postglacial population expansion drives the evolution of long-distance migration in a songbird. Evolution 2006, 60:2403-2409.
76. Milá B., Smith T.B., Wayne R.K. Speciation and rapid phenotypic differentiation in the yellow-rumped warbler Dendroica coronata complex. Mol. Ecol. 2007, 16:159-173.
77. Milá B., McCormack J.E., Castañeda G., Wayne R.K., Smith T.B. Recent post glacial range expansion drives the rapid diversification of a songbird lineage in the genus Junco. Proc. Roy. Soc. Lond. B 2007, 274:2653-2660.
78. Minin V.N., Bloomquist E.W., Suchard M.A. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol. Biol. Evol. 2008, 25:1459-1471.
79. Myers N., Mittermeier R.A., Mittermeier C.G., Da Fonseca G.A.B., Kent J. Biodiversity hotspots for conservation priorities. Nature 2000, 403:853-858.
80. Navarro-Sigüenza A.G., Peterson A.T. An alternative species taxonomy of the birds of México. Biota Neotrop. 2004, 4:1-32.
81. Navarro-Sigüenza A.G., Peterson A.T., Nyari A., García-Deras G.M., García-Moreno J. Phylogeography of the Buarremon brush-finch complex (Aves, Emberizidae) in Mesoamerica. Mol. Phylogenet. Evol. 2008, 47:21-35.
82. Nei M., Li W. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 1979, 76:5269-5273.
83. Nylander J.A.A., Ronquist F., Huelsenbeck J.P., Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 2004, 53:47-67.
84. Nylander J.A.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 2008, 24:581-583.
85. Parra-Olea G., Garcia-Paris M., Papenfuss T.J., Wake D.B. Systematics of the Pseudoeurycea bellii (Caudata: Plethodontidae) species complex. Herpetologica 2005, 61:145-158.
86. Pérez-Emán J.L. Molecular phylogenetics and biogeography of the Neotropical redstarts (Myioborus; Aves, Parulinae). Mol. Phylogenet. Evol. 2005, 37:511-528.
87. Pérez-Emán J.L., Mumme R.L., Jabłoński P.G. Phylogeography and adaptative plumage evolution in Central American subspecies of the slate-throated redstarts (Myioborus miniatus). Ornithol. Monogr. 2010, 67:90-102.
88. Peterson A.T., Navarro-Sigüenza A.G. Alternate species concepts as bases of determining priority conservation areas. Conserv. Biol. 1999, 13:427-431.
89. Posada D. J Modeltest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
90. Price T. Speciation in Birds 2008, Roberts and Company Publishers, Colorado.
91. Puebla-Olivares F., Bonaccorso E., Espinosa de los Monteros A., Omland K.E., Llorente-Bousquets J.E., Peterson A.T., Navarro-Sigüenza A.G. Speciation in the emerald toucanet (Aulacorhynchus prasinus) complex. Auk 2008, 125:39-50.
92. Ramos-Onsins S.E., Rozas J. Statistical properties of new neutrality tests against population growth. Mol. Biol. Evol. 2002, 19:2092-2100.
93. Rodgers A.R., Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 1992, 9:552-569.
94. Rojas-Soto O.R., Navarro-Sigüenza A.G., Espinosa de los Monteros A. Systematics and bird conservation policies: the importance of species limits. Bird Conserv. Int. 2010, 20:176-185.
95. Rzedowski J. Vegetación de México 1986, Limusa, DF. second ed.
96. Sánchez-González L.A., Navarro-Sigüenza A.G. History meets ecology: a geographical analysis of ecological restriction in the Neotropical humid montane forests avifaunas. Divers. Distrib. 2009, 15:1-11.
97. Sánchez-González L.A., Morrone J.J., Navarro-Sigüenza A.G. Distributional patterns of the Neotropical humid montane forest avifaunas. Biol. J. Linn. Soc. 2008, 94:175-194.
98. Shaffer H.B., McKnight M.L. The polytypic species revisited: genetic differentiation and molecular phylogenetics of the tiger salamander Ambystoma tigrinum (Amphibia: Caudata) complex. Evolution 1996, 50:417-433.
99. Sibley C.G., Monroe B.L. Distribution and Taxonomy of the Birds of the World 1990, Yale University Press, New Haven.
100. Sorenson M.D., Ast J.C., Dimcheff D.E., Yuri T., Mindell D.P. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol. Phylogenet. Evol. 1999, 12:105-114.
101. Sullivan J., Arellano E., Rogers D.S. Comparative phylogeography of Mesoamerican highland rodents: concerted versus independent response to past climatic fluctuations. Am. Nat. 2000, 155:755-768.
102. Sullivan J., Markert J.A., Kilpatrick C.W. Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood. Syst. Biol. 1997, 46:426-440.
103. -and Other Methods). Ver. 4.0b4a 2002, Sinauer Associates, Sunderland, MA.
104. Warshall P. The Madrean sky island archipelago: a planetary overview. Biodiversity and Management of the Madrean Archipelago: The Sky Islands of the Southwestern United States and Northwestern Mexico 1995, 6-18. USDA Forest Service Rocky Mountain Forest and Range Experiment Station, Colorado. L. DeBano, G.J. Gottfried, R.H. Hamre, C.B. Edminster, P. Ffolliott, A. Ortega-Rubio (Eds.).
105. Weir J.T. Divergent timing and patterns of species accumulation in lowland and highland Neotropical birds. Evolution 2006, 60:842-855.
106. Weir J.T. Implications of genetic differentiation in Neotropical montane forest birds. Ann. Missouri Bot. Gard. 2009, 96:410-433.
107. Weir J.T., Bermingham E., Miller M.J., Klicka J., González M.A. Phylogeography of a morphologically diverse Neotropical montane species, the common bush-tanager (Chlorospingus ophthalmicus). Mol. Phylogenet. Evol. 2008, 47:650-664.
108. Weir J.T., Schluter D. Ice sheets promote speciation in boreal birds. Proc. Roy. Soc. Lond. B 2004, 271:1881-1887.
109. Weir J.T., Schluter D. Calibrating the avian molecular clock. Mol. Ecol. 2008, 17:2321-2328.
110. Wilson J., Will T. The current status of the pink-headed warbler Ergaticus versicolor in Chiapas, Mexico. Cotinga 1997, 8:34-38.
111. Zink R.M., Barrowclough G.F. Mitochondrial DNA under siege in avian phylogeography. Mol. Ecol. 2008, 17:2107-2121.
112. Zink R.M., Klicka J. The tempo of avian diversification: a comment on Johnson and Cicero. Evolution 2006, 60:411-412.
113. Zwickl, D.J., 2006. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion. Ph.D. Dissertation, University of Texas, Austin.