Identifying biases at different spatial and temporal scales of diversification: A case study in the Neotropical parrotlet genus Forpus

Molecular Ecology

Volumn 22, Issue 2, 2013, Pages 483-494

  Smith, Brian Tilston ^a,b   Ribas, Camila C ^c   Whitney, Bret M ^a   Hernández Baños, Blanca E ^d   Klicka, John ^b,e  

^a LOUISIANA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF NEVADA   (United States)

^c INSTITUTO NACIONAL DE PESQUISAS DA AMAZÔNIA   (Brazil)

^d UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

^e UNIVERSITY OF WASHINGTON   (United States)

Author keywords

diversification rate; neotropics; parrot; speciation; species delimitation; species tree

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BIODIVERSITY; BIOLOGICAL MODEL; CELL NUCLEUS; DNA SEQUENCE; GENETICS; PARROT; SPECIES DIFFERENTIATION;

ANIMALS; BIODIVERSITY; CELL NUCLEUS; DNA, MITOCHONDRIAL; GENETIC SPECIATION; MODELS, GENETIC; PARROTS; SEQUENCE ANALYSIS, DNA;

AVES; FORPUS; PSITTACIDAE;

EID: 84872044734     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12118     Document Type: Article

References (69)

1. Bravo GA, Chesser RT, Brumfield RT, (2012) Isleria, a new genus of antwren (Aves: Passeriformes: Thamnophilidae). Zootaxa, 3195, 61-67.
2. Brumfield RT, Capparella AP, (1996) Historical diversification of birds in northwestern South America: a molecular perspective on the role of vicariant events. Evolution, 50, 1607-1624.
3. Brumfield RT, Edwards SV, (2007) Evolution into and out of the Andes: a Bayesian analysis of historical diversification in Thamnophilus antshrikes. Evolution, 61, 346-367.
4. Cabanne GS, d'Horta FM, Meyer D, Silva JMC, Miyaki CY, (2011) Evolution of Dendrocolaptes platyrostris (Aves: Furnariidae) between the South American open vegetation corridor and the Atlantic Forest. Biological Journal of the Linnean Society, 103, 801-820.
5. Cadena CD, Cuervo AM, (2010) Molecules, ecology, morphology and songs in concert: can we know how many species is Arremon torquatus (Aves, Emberizidae)? Biological Journal of the Linnean Society, 99, 152-176.
6. Chaves JA, Weir JT, Smith TB, (2011) Diversification in Adelomyia hummingbirds follows Andean uplift. Molecular Ecology, 20, 4564-4576.
7. Cusimano N, Stadler T, Renner SS, (2012) A new method for handling missing species in diversification analysis applicable to randomly or nonrandomly sampled phylogenies. Systematic Biology, 61, 785-792.
8. Dacosta JM, Klicka J, (2008) The great American interchange in birds: a phylogenetic perspective with the genus Trogon. Molecular Ecology, 17, 1328-1343.
9. Derryberry EP, Claramunt S, Derryberry G, et al,. (2011) Lineage diversification and morphological evolution in a large-scale continental radiation: the Neotropical ovenbirds and woodcreepers (Aves: Furnariidae). Evolution, 65, 2973-2986.
10. Dmitriev DA, Rakitov RA, (2008) Decoding of superimposed traces produced by direct sequencing of heterozygous indels. PLoS Computational Biology, 4, e1000113.
11. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis sampling trees. BMC Evolutionary Biology, 7, 214.
12. Dubey S, Shine R, (2012) Are reptile and amphibian species younger in the Northern Hemisphere than in the Southern Hemisphere? Journal of Evolutionary Biology, 25, 220-226.
13. Ellegren H, (2007) Molecular evolutionary genomics of birds. Cytogenetic and Genome Research, 117, 120-130.
14. Ence DD, Carstens BC, (2011) spedeSTEM: a rapid and accurate method for species delimitation. Molecular Ecology Research, 11, 473-480.
15. Forshaw J, (2010) Parrots of the World. Princeton University, Princeton, NJ.
16. Gregory-Wodzicki KM, (2000) Uplift history of the Central and Northern Andes: a review. Geological Society of America Bulletin, 112, 1091-1105.
17. Gutiérrez-Pinto N, Cuervo AM, Miranda J, Pérez-Emán JL, Brumfield RT, Cadena CD, (2012) Non-monophyly and deep genetic differentiation across low-elevation barriers in a Neotropical montane bird (Basileuterus tristriatus; Aves: Parulidae). Molecular Phylogenetics and Evolution, 64, 156-165.
18. Haffer J, (1969) Speciation in Amazonian forest birds. Science, 165, 131-137.
19. Harvey MG, Winger BM, Seeholzer GF, Cáceres Apaza D, (2011) Avifauna of the Gran Pajonal and southern Cerros del Sira, Peru. The Wilson Journal of Ornithology, 123, 289-315.
20. Heled J, Drummond AJ, (2010) Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution, 27, 570-580.
21. Hill AW, Guralnick RP, (2010) GeoPhylo: an online tool for developing visualizations of phylogenetic trees in geographic space. Ecography, 33, 1-4.
22. d'Horta FM, Cuervo AM, Ribas CC, Brumfield RT, Miyaki CY, (2012) Phylogeny and comparative phylogeography of Sclerurus (Aves: Furnariidae) reveal constant and cryptic diversification in an old radiation of rainforest understorey specialists. Journal of Biogeography, doi: 10.1111/j.1365-2699.2012. 02760.x.
23. Isler ML, Cuervo AM, Bravo GA, Brumfield RT, (2012) An integrative approach to species-level systematics reveals the depth of diversification in an Andean thamnophilid, the Long-tailed Antbird. The Condor, 114, 571-583.
24. Lara CE, Cuervo AM, Valderrama SV, Calderõn-F D, Cadena CD, (2012) A new species of wren (Troglodytidae: Thryophilus) from the dry Cauca River Canyon, northwestern Colombia. The Auk, 129, 537-550.
25. Leaché AD, Fujita MK, (2010) Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proceedings of the Royal Society B: Biological Sciences, 277, 3071-3077.
26. Maldonado-Coelho M, (2011) Climatic oscillations shape the phylogeographic structure of Atlantic Forest fire-eyes (Aves: Thamnophilidae). Biological Journal of the Linnean Society, 105, 900-924.
27. Marshall LG, Webb SD, Sepkoski JJ, Raup DM, (1982) Mammalian evolution and the great American interchange. Science, 215, 1351-1357.
28. Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P, (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics, 26, 2462-2463.
29. Miller MJ, Bermingham E, Klicka J, et al,. (2008) Out of Amazonia again and again: episodic crossing of the Andes promotes diversification in a lowland forest flycatcher. Proceedings of the Royal Society B: Biological Sciences, 275, 1133-1142.
30. Naka LN, Bechtoldt CL, Herniques LMP, Brumfield RT, (2012) The role of physical barriers in the location of avian suture zones in the Guiana Shield, northern Amazonia. The American Naturalist, 179, E115-E132.
31. Nylander J, (2004) MrModeltest v 2.3. Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
32. O'Neill JP, Lane DF, Naka L, (2011) A cryptic new species of thrush (Turdidae: Turdus) from western Amazonia. The Condor, 113, 869-880.
33. 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 a Pleistocene radiation. Molecular Phylogenetics and Evolution, 58, 105-115.
34. Phillimore AB, Price TD, (2008) Density-dependent cladogenesis in birds. PLoS Biology, 6, e71.
35. Rabosky DL, (2006) LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates. Evolutionary Bioinformatics, 2, 257-260.
36. Rabosky DL, (2009) Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions. Ecology Letters, 12, 735-743.
37. Rambaut A, Drummond AJ, (2010) Tracer v. University of Oxford, Oxford.
38. Rannala B, Yang Z, (2003) Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics, 164, 1645-1656.
39. Reid NM, Carstens BC, (2012) Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the General Mixed Yule Coalescent model. BMC Evolutionary Biology, 12, 196.
40. Remsen JV, Jr, Cadena CD, Jaramillo A, et al,. (2011) A classification of the bird species of South America. American Ornithologists' Union.http://www.museum.lsu.edu/~Remsen/SACCBaseline.html. Baton Rouge, LA
41. Renner SS, Cusimano N, (2010) Slowdowns in diversification rates from real phylogenies may not be real. Systematic Biology, 59, 458-464.
42. Ribas CC, Gaban-Lima R, Miyaki CY, Cracraft J, (2005) Historical biogeography and diversification within the Neotropical parrot genus Pionopsitta (Aves: Psittacidae). Journal of Biogeography, 32, 1409-1427.
43. Ribas CC, Joseph L, Miyaki CY, (2006) Molecular systematics and patterns of diversification of the Pyrrhura parakeets (Aves: Psittacidae) with special reference to the P. picta / P. leucotis complex. The Auk, 123, 660-680.
44. Ribas CC, Moyle RG, Miyaki CY, Cracraft J, (2007) The assembly of montane biotas: linking Andean tectonics and climatic oscillations to independent regimes of diversification in Pionus parrots. Proceedings of the Royal Society B: Biological Sciences, 274, 2399-2408.
45. Ribas CC, Miyaki CY, Cracraft J, (2009) Phylogenetic relationships, diversification and biogeography in Neotropical Brotogeris parakeets. Journal of Biogeography., 36, 1712-1729.
46. Ribas CC, Aleixo A, Nogueira CR, Miyaki CY, Cracraft J, (2012a) A palaeobiogeographic model for biotic diversification within Amazonia over the past three million years. Proceedings of the Royal Society B: Biological Sciences, 279, 681-689.
47. Ribas CC, Maldonado MC, Smith BT, Cabanne GS, d'Horta FM, Naka LN, (2012b) Towards an integrated historical biogeography of the Neotropical lowland avifauna: combining diversification analysis and landscape evolution. Ornitología Neotropical, 129, 187-206.
48. Ronquist F, Huelsenbeck JP, (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
49. Rull V, (2008) Speciation timing and neotropical biodiversity: the tertiary-quaternary debate in the light of molecular phylogenetic evidence. Molecular Ecology, 15, 4257-4259.
50. Rull V, (2011) Neotropical biodiversity: timing and potential drivers. Trends in Ecology and Evolution, 26, 508-513.
51. Salisbury CL, Seddon N, Cooney CR, Tobias JA, (2012) The latitudinal gradient in diversification in dispersal constraints: ecological specialization drives diversification tropical birds. Ecology Letters, 15, 847-855.
52. Santos JC, Coloma LA, Summers K, et al,. (2009) Amazonian amphibian diversity is primarily derived from Late Miocene Andean lineages. PLoS Biology, 7, e1000056.
53. Schirtzinger EE, Tavares ES, Gonzales LA, et al,. (2012) Multiple independent origins of mitochondrial control region duplications in the order Psittaciformes. Molecular Phylogenetics and Evolution, 64, 342-356.
54. Seeholzer GF, Winger BM, Harvey MG, Cáceres Apaza D, Weckstein JD, (2012) A new species of barbet (Capitoninae: Capito) from the southern Cerros del Sira, Ucayali, Peru. The Auk, 129, 551-559.
55. Smith BT, Klicka J, (2010) The profound influence of the Late Pliocene Panamanian uplift on the exchange, diversification, and distribution of New World birds. Ecography, 33, 333-342.
56. Smith BT, Escalante P, Hernández-Baños BE, Navarro-Sigüenza AG, Rohwer S, Klicka J, (2011) The role of historical and contemporary processes on the phylogeography of the Northern Cardinal, Cardinalis cardinalis. BMC Evolutionary Biology, 11, 136.
57. Smith BT, Bryson RW, Houston D, Klicka J, (2012a) An asymmetry in niche conservatism contributes to the latitudinal species diversity gradient in New World vertebrates. Ecology Letters, 15, 1318-1325.
58. Smith BT, Amei A, Klicka J, (2012b) Evaluating the role of contracting and expanding rainforest in initiating cycles of speciation across the Isthmus of Panama. Proceedings of the Royal Society B: Biological Sciences, 279, 3520-3526.
59. Stephens M, Smith NJ, Donnelly P, (2001) A new statistical method for haplotype reconstruction from population data. The American Journal of Human Genetics, 68, 978-989.
60. Stotz DF, Fitzpatrick JW, Parker III TA, Moskovits DK, (1996) Neotropical birds: ecology and conservation. The University of Chicago Press, Chicago.
61. Tavares ES, Baker AJ, Pereira SL, Miyaki CY, (2006) Phylogenetic relationships and historical biogeography of Neotropical parrots (Psittaciformes: Psittacidae: Arini) inferred from mitochondrial and nuclear DNA sequences. Systematic Biology, 55, 454-470.
62. Tobias JA, Bates JM, Hackett SJ, Seddon N, (2008) Comment on "the latitudinal gradient in recent speciation and extinction rates of birds and mammals". Science, 319, 901c.
63. Weir JT, (2006) Divergent time and patterns of species accumulation in lowland and highland Neotropical birds. Evolution, 60, 842-855.
64. Weir JT, Schluter D, (2008) Calibrating the avian molecular clock. Molecular Ecology, 17, 2321-2328.
65. Wiens JJ, (2011a) The causes of species richness patterns across space, time, and clades and the role of "ecological limits". Quarterly Review of Biology, 86, 75-96.
66. Wiens JJ, Pyron RA, Moen DS, (2011b) Phylogenetic origins of local-scale diversity patterns and the causes of Amazonian megadiversity. Ecology Letters, 14, 643-652.
67. Wuster W, Ferguson JE, Quijada-Mascarenas A, Pook CE, (2005) Tracing an invasion: landbridges, refugia, and the phylogeography of the Neotropical rattlesnake (Serpentes: Viperidae: Crotalus durissus). Molecular Ecology, 14, 1095-1108.
68. Yang Z, Rannala B, (2010) Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences of the United States of America, 107, 9264-9269.
69. Zhang C, Zhang D-X, Yang Z, (2011) Evaluation of a Bayesian coalescent method of species delimitation. Systematic Biology, 60, 747-761.