Phylogenetic relationships among Synallaxini spinetails (Aves: Furnariidae) reveal a new biogeographic pattern across the Amazon and Paraná river basins

Molecular Phylogenetics and Evolution

Volumn 78, Issue 1, 2014, Pages 223-231

  Claramunt, Santiago ^a  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

Amazon basin; Biogeography; Furnariidae; Paran river; Phylogenetics; Z linked markers

Indexed keywords

ANIMAL; CLASSIFICATION; DNA SEQUENCE; GENETICS; INTRON; PHYLOGENY; PHYLOGEOGRAPHY; RIVER; SONGBIRD; SOUTH AMERICA;

ANIMALS; INTRONS; PASSERIFORMES; PHYLOGENY; PHYLOGEOGRAPHY; RIVERS; SEQUENCE ANALYSIS, DNA; SOUTH AMERICA;

EID: 84902461078     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2014.05.011     Document Type: Article

References (60)

1. Allman E.S., Degnan J.H., Rhode J.A. Species tree inference by the STAR method and its generalizations. J. Comp. Biol. 2013, 20:50-61.
2. Barker F.K., Vandergon A.J., Lanyon S.M. Assessment of species limits among yellow-breasted meadowlarks (Sturnella spp.) using mitochondrial and sex-linked markers. Auk 2008, 125(4):869-879.
3. Bonaccorso E., Peterson T., Navarro-Sigüenza A.G., Fleischer R.C. Molecular systematics and evolution of the Cyanocorax jays. Mol. Phylogenet. Evol. 2010, 54:897-909.
4. Bouckaert, R., Heled, J., Kuhnert, D., Vaughan, T.G., Wu, C.H., Xie, D., Suchard, M.A., Rambaut, A., Drummond, A.J., 2013. BEAST2: a software platform for Bayesian evolutionary analysis. http://beast2.cs.auckland.ac.nz/.
5. Campbell K.E., Frailey C.D., Romero-Pittman L. The Pan-Amazonian Ucayali Peneplain, Late Neogene sedimentation in Amazonia, and the birth of the modern Amazon river system. Palaeogeogr. Palaeoclimatol. Palaeoecol. 2006, 239:166-219.
6. Claramunt S. Discovering exceptional diversifications at continental scales: the case of the endemic families of Neotropical suboscine passerines. Evolution 2010, 64(7):2004-2019. 10.1111/j.1558-5646.2010.00971.x.
7. Claramunt S., Derryberry E.P., Chesser R.T., Aleixo A., Brumfield R.T. Polyphyly of Campylorhamphus, and description of a new genus for C. pucherani (Dendrocolaptinae). Auk 2010, 127(2):430-439. 10.1525/auk.2009.09022.
8. Claramunt S., Derryberry E.P., Brumfield R.T., Remsen J.V. Ecological opportunity and diversification in a continental radiation of birds: climbing adaptations and cladogenesis in the Furnariidae. Am. Naturalist 2012, 179(5):649-666. 10.1086/664998.
9. Claramunt S., Derryberry E.P., Remsen J.V., Brumfield R.T. High dispersal ability inhibits speciation in a continental radiation of passerine birds. Proc. Roy. Soc. B 2012, 279:1567-1574. 10.1098/rspb.2011.1922.
10. Corl A., Ellegren H. Sampling strategies for species trees: the effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal. Mol. Phylogenet. Evol. 2013, 67:358-366.
11. Cory C.B., Hellmayr C.E. Catalogue of birds of the Americas and the adjacent islands, Part IV, Furnariidae-Dendrocolaptidae. Field Mus. Nat. Hist. Zool. Ser. 1925, 13(3):1-390.
12. Cracraft J. Phylogenetic models and classification. Syst. Zool. 1974, 23:71-90.
13. Dávalos L.M., Porzecanski A.L. Accounting for molecular stochasticity in systematic revisions: species limits and phylogeny of Paroaria. Mol. Phylogenet. Evol. 2009, 53:234-248.
14. de Queiroz K., Gauthier J. Phylogenetic taxonomy. Annu. Rev. Ecol. Syst. 1992, 23:449-480.
15. Derryberry E.P., Claramunt S., Chesser R.T., Remsen J.V., Cracraft J., Aleixo A., Brumfield R.T. Lineage diversification and morphological evolution in a large-scale continental radiation: the Neotropical ovenbirds and woodcreepers (Aves: Furnariidae). Evolution 2011, 65:2973-2986.
16. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4:e88.
17. Espurt N., Baby P., Brusset S., Roddaz M., Hermoza W., Barbarand J. The Nazca Ridge and uplift of the Fitzcarrald Arch: implications for regional geology in northern South America. Amazonia: Landscape and Species Evolution: A Look into the Past 2010, 89-100. Blackwell. C. Hoorn, F.P. Wesselingh (Eds.).
18. Fitzpatrick J.W., Bates J.M., Bostwick K.S., Caballero I.C., Clock B., Farnsworth A., Hosner P., Joseph L., Langham G., Lebbin D., Mobley J.A., Robbins M.B., Scholes E., Tello J.G., Walther B., Zimmer K.J. Family Tyrannidae (Tyrant Flycatchers): species accounts. Handbook of the Birds of the World, vol. 9. Cotingas to Pipits and Wagtails 2004, vol. 9:258-462. Lynx Edicions, Barcelona.
19. Fjeldså J., Zuccon D., Irestedt M., Johansson U.S., Ericson P.G. Sapayoa aenigma: a NEW WORLD representative of 'Old World suboscines'. Proc. R. Soc. Lond. B 2003, 270:238-241.
20. Fjeldså J., Irestedt M., Ericson P.G. Molecular data reveal some major adaptational shifts in the early evolution of the most diverse avian family, the Furnariidae. J. Ornithol. 2005, 146:1-13.
21. Han K., Robbins M.B., Braun M.J. A multi-gene estimate of phylogeny in the nightjars and nighthawks (Caprimulgidae). Mol. Phylogenet. Evol. 2010, 55:443-453.
22. Hernández R.M., Jordan T.E., Dalenz Farjat A., Echavarría L., Idleman B.D., Reynolds J.H. Age, distribution, tectonics, and eustatic controls of the Paranense and Caribbean marine transgressions in southern Bolivia and Argentina. J. S. Am. Earth Sci. 2005, 19:495-512.
23. Hillis D.M., Heath T.A., St John K. Analysis and visualization of tree space. Syst. Biol. 2005, 54:471-482.
24. Hoorn C., Wesselingh F.P., Hovikoski J., Guerrero J. The development of the Amazonian mega-wetland (Miocene; Brazil, Colombia, Peru, Bolivia). Amazonia: Landscape and Species Evolution: A Look into the Past 2009, Wiley-Blackwell. C. Hoorn, F.P. Wesselingh (Eds.).
25. Hulka C., Gräfe K.-U., Sames B., Uba C.E., Heubeck C. Depositional setting of the middle to late Miocene Yecua formation of the Chaco foreland basin, Southern Bolivia. J. S. Am. Earth Sci. 2006, 21:135-150.
26. Irestedt M., Fjeldså J., Dalén L., Ericson P.G.P. Convergent evolution, habitat shifts and variable diversification rates in the ovenbird-woodcreeper family (Furnariidae). BMC Evol. Biol. 2009, 9:268.
27. 18O. Geol. Soc. Am. Bull. 2012, 124:335-351.
28. 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.
29. Kimball R.T., Braun E.L., Barker F.K., Bowie R.C., Braun M.J., Chojnowski J.L., Hackett S.J., Han K.L., Harshman J., Heimer-Torres V., Holznagel W., Huddleston C.J., Marks B.D., Miglia K.J., Moore W.S., Reddy S., Sheldon F.H., Smith J.V., Witt C.C., Yuri T. A well-tested set of primers to amplify regions spread across the avian genome. Mol. Phylogenet. Evol. 2009, 50:654-660.
30. Lanyon S.M. Polyphyly of the blackbird genus Agelaius and the importance of assumptions of monophyly in comparative studies. Evolution 1994, 48:679-693.
31. Latrubesse E.M., Cozzuol M., da Silva-Caminha S.A.F., Risgby C.A., Absy M.L., Jaramillo C. The Late Miocene paleogeography of the Amazon Basin and the evolution of the Amazon River system. Earth Sci. Rev. 2010, 99:99-124.
32. Liu L., Yu L., Kubatko L., Pearl D.K., Edwards S.V. Coalescent methods for estimating phylogenetic trees. Mol. Phylogenet. Evol. 2009, 53:320-328.
33. Liu L., Yu L., Pearl D.K., Edwards S.V. Estimating species phylogenies using coalescence times among sequences. Syst. Biol. 2009, 58:468-477.
34. Lundberg J.G., Marshall L.G., Guerrero J., Horton B., Malabarba M.C.S.L., Wesselingh F. The stage for Neotropical fish diversification: a history of tropical South American rivers. Phylogeny and Classification of Neotropical Fishes 1998, 13-48. Edipucrs, Porto Alegre. L.R. Malabarba, R.E. Reis, R.P. Vari, Z.M. Lucena, C.A.S. Lucena (Eds.).
35. Maddison W.P. Gene trees in species trees. Syst. Biol. 1997, 46:523-536.
36. Moyle R.G., Chesser R.T., Brumfield R.T., Tello J.G., Marchese D.J., Cracraft J. Phylogeny and phylogenetic classification of the antbirds, ovenbirds, woodcreepers, and allies (Aves: Passeriformes: infraorder Furnariides). Cladistics 2009, 25:1-20.
37. Nelson G.J. Phylogenetic relationship and classification. Syst. Zool. 1972, 21:227-231.
38. Ohlson J.I., Irestedt M., Ericson P.G.P., Fjeldså J. Phylogeny and classification of the New World suboscines (Aves, Passeriformes). Zootaxa 2013, 3613:1-35.
39. Peters J.L., Mccracken K.G., Zhuravlev Y.N., Lu Y., Wilson R.E., Johnson K.P., Omland K.E. Phylogenetics of wigeons and allies (Anatidae: Anas): the importance of sampling multiple loci and multiple individuals. Mol. Phylogenet. Evol. 2005, 35:209-224.
40. Powell A.F.L.A., Barker F.K., Lanyon S.M. Empirical evaluation of partitioning schemes for phylogenetic analyses of mitogenomic data: an avian case study. Mol. Phylogenet. Evol. 2013, 66:69-79.
41. Räsänen M.E., Linna A.M., Santos J.C.R., Negri F.R. Late Miocenen tidal deposits in the Amazonian foreland basin. Science 1995, 269:386-390.
42. Remsen J.V. Family furnariidae (ovenbirds). Handbook of the Birds of the World, vol. 8, Broadbills to Tapaculos 2003, 162-357. Lynx Edicions, Barcelona. J. del Hoyo, A. Elliott, D.A. Christie (Eds.).
43. Remsen J.V., Parker T.A. Contribution of river-created habitats to bird species richness in Amazonia. Biotropica 1983, 15:223-231.
44. Rheindt F.E., Christidis L., Norman J.A. Habitat shifts in the evolutionary history of a Neotropical flycatcher lineage from forest and open landscapes. BMC Evol. Biol. 2008, 8:1193.
45. Ribas C.C., Miyaki C.Y., Cracraft J.L. Phylogenetic relationships, diversification and biogeography in Neotropical Brotogeris parakeets. J. Biogeogr. 2009, 36:1712-1729.
46. Ridgely R.S., Tudor G. The Birds of South America, vol. 2. The Suboscines Passerines 1994, University of Texas Press, Austin.
47. Rosenberg G.H. Habitat specialization and foraging behavior by birds of Amazonian river islands in northeastern Peru. Condor 1990, 92:427-443.
48. Schliep K.P. Phangorn: phylogenetic analysis in R. Bioinformatics 2011, 27:592-593.
49. Seo T. Calculating bootstrap probabilities of phylogeny using multilocus sequence data. Mol. Biol. Evol. 2008, 25:960-971.
50. Shaw T., Ruan Z., Glenn T., Liu L. STRAW: a web server for species tree analysis. Nucleic Acids Res. 2013, 41(W1):W238-W241. 10.1093/nar/gkt377.
51. Stamatakis A., Ludwig T., Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 2005, 21:456-463.
52. Stamatakis A., Hoover P., Rougemont J. A rapid bootstrap algorithm for the RAxML web-servers. Syst. Biol. 2008, 75:758-771.
53. Steel M.A., Penny P. Distributions of tree comparison metrics: some new results. Syst. Biol. 1993, 42:126-141.
54. Sullivan J., Joyce P. Model selection in phylogenetics. Annu. Rev. Ecol. Evol. Syst. 2005, 36:445-466.
55. Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
56. Vaurie C. Taxonomy and geographical distribution of the Furnariidae (Aves, Passeriformes). Bull. Am. Mus. Nat. Hist. 1980, 166:1-357.
57. Venables W.N., Ripley B.D. Modern Applied Statistics with S 2002, Springer. fourth ed.
58. Weir J.T., Schluter D. Calibrating the avian molecular clock. Mol. Ecol. 2008, 17:2321-2328.
59. Wilkinson M.J., Marshall L.G., Lundberg J.G. River behavior on megafans and potential influences on diversification and distribution of aquatic organisms. J. S. Am. Earth Sci. 2006, 21:151-172.
60. Zyskowski K., Prum R.O. Phylogenetic analysis of the nest architecture of Neotropical ovenbirds (Furnariidae). Auk 1999, 116(4):891-911.