Calibrating divergence times on species trees versus gene trees: Implications for speciation history of Aphelocoma jays

Evolution

Volumn 65, Issue 1, 2011, Pages 184-202

  McCormack, John E ^a   Heled, Joseph ^b   Delaney, Kathleen S ^c   Peterson, A Townsend ^d   Knowles, L Lacey ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF KANSAS   (United States)

Author keywords

Aphelocoma; BEAST; Divergence times; Fossil calibration; Gene tree; Glaciations; Mountain uplift; Pleistocene; Species tree

Indexed keywords

MITOCHONDRIAL DNA;

CALIBRATION; FOSSIL RECORD; GLACIATION; MIOCENE; PASSERINE; PLEISTOCENE; SPECIATION (BIOLOGY); STOCHASTICITY;

ANIMAL; ARTICLE; CELL NUCLEUS; CENTRAL AMERICA; CLASSIFICATION; DNA SEQUENCE; EVOLUTION; FOSSIL; GENE FLOW; GENETIC VARIABILITY; GENETICS; GEOGRAPHIC AND GEOLOGICAL PHENOMENA; MEXICO; PHYLOGENY; SEQUENCE ALIGNMENT; SONGBIRD; SPECIES DIFFERENTIATION; UNITED STATES;

ANIMALS; BIOLOGICAL EVOLUTION; CELL NUCLEUS; CENTRAL AMERICA; DNA, MITOCHONDRIAL; FOSSILS; GENE FLOW; GENETIC SPECIATION; GENETIC VARIATION; GEOLOGICAL PROCESSES; MEXICO; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SONGBIRDS; UNITED STATES;

APHELOCOMA; AVES; CORVIDAE;

EID: 78650931246     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2010.01097.x     Document Type: Article

References (110)

1. American Ornithologists' Union. 1998. Check-list of North American birds. American Ornithologists' Union, Washington, D.C .
2. Arbogast, B. S., S. V. Edwards, J. Wakeley, P. Beerli, and J. B. Slowinski 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Ann. Rev. Ecol. Syst. 33:707-740.
3. Avise, J. C., and D. Walker 1998. Pleistocene phylogeographic effects on avian populations and the speciation process. Proc. R. Soc. Lond. B. 265:457-463.
4. Axelrod, D. 1979. Age and origin of Sonoran desert vegetation. Occas. Pap. Calif. Acad. Sci. 132:1-74.
5. Badgley, C. 2010. Tectonics, topography, and mammalian diversity. Ecography 33:220-231.
6. Bensch, S., A. J. Helbig, M. Salomon, and I. Seibold 2002. Amplified fragment length polymorphism analysis identifies hybrids between two subspecies of warblers. Mol. Ecol. 11:473-481.
7. Bhagabati, N. K., J. L. Brown, and B. S. Bowen 2004. Geographic variation in Mexican jays (Aphelocoma ultramarina): local differentiation, polyphyly or hybridization? Mol. Ecol. 13:2721-2734.
8. BirdLife International. 2009. Species factsheet: Aphelocoma unicolor. Available at Accessed June 8, 2009.
9. Bonaccorso, E., and A. T. Peterson 2007. A multilocus phylogeny of the New World jay genera. Mol. Phylo. Evol. 42:467-476.
10. Bouckaert, R. R. 2010. DensiTree: making sense of sets of phylogenetic trees. Bioinformatics 26:1372-1373.
11. Brodkorb, P. 1972. Neogene fossil jays from the Great Plains. Condor 74:347-349.
12. Brown, J. L., and S.-H. Li 1995. Phylogeny of social behavior in Aphelocoma jays: a role for hybridization? Auk 112:464-472.
13. Brown, J. W., J. S. Rest, J. García-Moreno, M. D. Sorenson, and D. P. Mindell 2008. Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. BMC Biology 6:6.
14. Brown, J. W., and M. van Tuinen Evolving perceptions on the antiquity of the modern avian tree. in G. Dyke and G. Kaiser, eds. The evolutionary history of modern birds. Univ. of California Press, Berkeley, California In press .
15. Brumfield, R. T., R. W. Jernigan, D. B. McDonald, and M. J. Braun 2001. Evolutionary implications of divergent clines in an avian (Manacus: Aves) hybrid zone. Evolution 55:2070-2087.
16. Brumfield, R. T., L. Liu, D. E. Lum, and S. V. Edwards 2008. Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae, Manacus) from multilocus sequence data. Syst. Biol. 57:719-731.
17. Burt, D. B., and A. T. Peterson 1993. Biology of the cooperatively breeding Scrub Jays (Aphelocoma coerulescens) of Oaxaca, Mexico. Auk 110:207-214.
18. Carling, M. D., and R. T. Brumfield 2008. Haldane's rule in an avian system: using cline theory and divergence population genetics to test for differential introgression of mitochondrial, autosomal, and sex-linked loci across the Passerina bunting hybrid zone. Evolution 62:2600-2615.
19. Carstens, B. C., and L. L. Knowles 2007a. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Syst. Biol. 56:400-411.
20. Carstens, B. C., and L. L. Knowles 2007b. Shifting distributions and speciation: species divergence during rapid climate change. Mol. Ecol. 6:619-627.
21. Cianchi, R., A. Ungaro, M. Marini, and L. Bullini 2003. Differential patterns of hybridization and introgression between the swallowtails Papilo machaon and P. hospiton from Sardinia and Corsica islands (Lepidoptera, Papilionidae). Mol. Ecol. 12:1461-1471.
22. Cicero, C., and N. K. Johnson 2006. The tempo of avian diversification: reply. Evolution 60:413-414.
23. Cranston, K., B. Hurwitz, D. Ware, L. Stein, and R. Wing 2009. Species trees from highly incongruent gene trees in rice. Syst. Biol. 58:489-500.
24. Curry, R. L., A. T. Peterson, and T. A. Langen 2002. Western Scrub-Jay (Aphelocoma californica). in A. Poole, ed. The Birds of North America online. Cornell Laboratory of Ornithology, Ithaca, New York Available at .
25. Dasmahapatra, K. K., M. J. Blum, A. Aiello, S. Hackwell, N. Davies, E. Bermingham, and J. Mallet 2002. Inferences from a rapidly moving hybrid zone. Evolution 56:741-753.
26. Degnan, J. H., and N. A. Rosenberg 2009. Gene tree discordance, phylogenetic inference, and the multispecies coalescent. Trends Ecol. Evol. 24:332-340.
27. Delaney, K. S., S. Zafar, and R. K. Wayne 2008. Genetic divergence and differentiation within Western Scrub-Jays (Aphelocoma californica). Auk 125:839-849.
28. Dmitriev, D. A., and R. A. Rakitov 2008. Decoding of superimposed traces produced by direct sequencing of heterozygous indels. PLoS Comput. Biol. 4:e1000113.
29. Drummond, A. J., S. Y. W. Ho, M. J. Phillips, and A. Rambaut 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4:e88.
30. Drummond, A. J., and A. Rambaut 2006. BEAST v1.4, Available at .
31. Drummond, A. J., and A. Rambaut 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
32. Eckert, A. J., and B. C. Carstens 2008. Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. Mol. Phylogenet. Evol. 49:832-842.
33. Edwards, S. V., and P. Beerli 2000. Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54:1839-1854.
34. Edwards, S. V., L. Liu, and D. K. Pearl 2007. High-resolution species trees without concatentation. Proc. Natl. Acad. Sci. USA 104:5936-5941.
35. Emslie, S. 2007. Fossil passerines from the early Pliocene of Kansas and the evolution of Songbirds in North America. Auk 124:85-95.
36. Emslie, S. D. 1996. A fossil Scrub-Jay supports a recent systematic decision. Condor 98:675-680.
37. Grauer, D., and W. Martin 2004. Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genetics 20:80-86.
38. Haldane, J. B. S. 1922. Sex ratio and unisex sterility in hybrid animals. J. Genetics 12:101-109.
39. Harrigan, R. J., M. E. Mazza, and M. D. Sorenson 2008. Computation versus cloning: evaluation of two methods for haplotype determination. Mol. Ecol. Res. 8:1239-1248.
40. Heled, J., and A. Drummond 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27:570-580.
41. Hewitt, G. 1996. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol. J. Linn. Soc. 58:247-276.
42. Hewitt, G. M. 2004. Genetic consequences of climatic oscillations in the Quaternary. Phil. Trans. R. Soc. Lond. B 359:183-195.
43. Hey, J., and R. Nielsen 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.
44. Ho, S. Y. M. 2007. Calibrating molecular estimates of substitution rates and divergence times in birds. J. Avian Biol. 38:409-414.
45. Ho, S. Y. W. 2005. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol. Biol. Evol. 22:1561-1568.
46. Jaeger, J. R., B. R. Riddle, and D. F. Bradford 2005. Cryptic Neogene vicariance and Quaternary dispersal of the red-spotted toad (Bufo punctatus): insights on the evolution of North American warm desert biotas. Mol. Ecol. 14:3033-3048.
47. Kimball, R. T., E. L. Braun, F. K. Barker, R. C. K. Bowie, M. J. Braun, J. L. Chojnowskia, S. J. Hackett, K.-L. Han, J. Harshman, V. Heimer-Torres, et al. 2009. A well-tested set of primers to amplify regions spread across the avian genome. Mol. Phylogenet. Evol. 50:654-660.
48. Kingman, J. F. C. 1982. The coalescent. Stoch. Process. Appl. 13:235-248.
49. Klicka, J., and R. M. Zink 1997. The importance of recent ice ages in speciation: a failed paradigm. Science 277:1666-1669.
50. Klicka, J., and R. M. Zink 1999. Pleistocene effects on North American songbird evolution. Proc. R. Soc. Lond. B. 266:695-700.
51. Knowles, L. 2009. Species tree estimation: methods of phylogenetic analysis when there is incongruence across genes. Syst. Biol. 58:463-467.
52. Knowles, L., B. Carstens, and M. Keat 2007. Coupling genetic and ecological-niche models to examine how past population distributions contribute to divergence. Curr. Biol. 17:940-946.
53. Knowles, L. L. 2000. Tests of Pleistocene speciation in montane grasshoppers (genus Melanoplus) from the sky islands of western North America. Evolution 54:1337-1348.
54. Knowles, L. L. 2001. Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers. Mol. Ecol. 10:691-701.
55. Knowles, L. L. 2010. Sampling strategies for species-tree estimation. Pp. 163-173 in L. L. Knowles and L. S. Kubatko, eds. Estimating species trees: practical and theoretical aspects. Wiley-Blackwell, Oxford, U.K .
56. Knowles, L. L., and B. C. Carstens 2007. Estimating a geographically explicit model of population divergence. Evolution 61:477-493.
57. Kronforst, M. R., L. G. Young, L. M. Blume, and L. E. Gilbert 2006. Multilocus analyses of admixture and introgression among hybridizing Heliconius butterflies. Evolution 60:1254-1268.
58. Krosby, M., and S. Rohwer 2009. A 2000 km genetic wake yields evidence for northern glacial refugia and hybrid zone movement in a pair of songbirds. Proc. R. Soc. Lond. B. 276:615-621.
59. Kubatko, L. S., and J. H. Degnan 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56:17-24.
60. Lessa, E. P., J. A. Cook, and J. L. Patton 2003. Genetic footprints of demographic expansion in North America, but not Amazonia, during the Late Quaternary. Proc. Natl. Acad. Sci. USA 100:10331-10334.
61. Lovette, I. J., and E. Bermingham 1999. Explosive speciation in the New World Dendroica warblers. Proc. R. Soc. Lond. B. 266:1629-1636.
62. Maddison, W. P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
63. Maddison, W. P., and L. L. Knowles 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.
64. McCormack, J., and J. Brown 2008. Mexican Jay (Aphelocoma ultramarina). in A. Poole, ed. The birds of North America Online. Cornell Laboratory of Ornithology, Ithaca, NY Available at .
65. McCormack, J., and T. Smith 2008. Niche expansion leads to small-scale adaptive divergence along an elevation gradient in a medium-sized passerine bird. Proc. R. Soc. Lond. B. 275:2155-2164.
66. McCormack, J. E., B. S. Bowen, and T. B. Smith 2008a. Integrating paleoecology and genetics of bird populations in two sky island archipelagos. BMC Biol. 6:28.
67. McCormack, J. E., L. L. Knowles, and H. Huang 2009. Maximum-likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. Syst. Biol. 58:501-508.
68. McCormack, J. E., A. T. Peterson, E. Bonaccorso, and T. B. Smith 2008b. Speciation in the highlands of Mexico: genetic and phenotypic divergence in the Mexican jay (Aphelocoma ultramarina). Mol. Ecol. 17:2505-2521.
69. McCormack, J. E., A. J. Zellmer, and L. L. Knowles 2010. Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation? Insights from tests with niche models. Evolution 64:1231-1244.
70. McKay, B., and R. Zink 2010. The causes of mitochondrial gene tree paraphyly in birds. Mol. Phylo. Evol. 54:647-650.
71. Milne, I., F. Wright, G. Rowe, D. Marshall, D. Husmeier, and G. McGuire 2004. TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments. Bioinformatics 20:1806-1807.
72. Morgan, G. 2005. The Great American Biotic Interchange in Florida. Bull. Fla. Mus. Nat. Hist. 45:271-311.
73. Muster, C., W. Maddison, S. Uhlmann, T. Berendonk, and A. Vogler 2009. Artic-alpine distributions-metapopulations on a continental scale? Am. Nat. 173:313-326.
74. Nylander, J. A. A. 2004. MrModeltest v2. Program distributed by the author, Evolutionary Biology Centre, Uppsala University, Sweden .
75. Nylander, J. A. A., J. C. Wilgenbusch, D. L. Warren, and D. L. Swofford 2008. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. Bioinformatics 24:581-583.
76. Peterson, A., and R. D. Holt 2003. Niche differentiation in Mexican birds: using point occurrences to detect ecological innovation. Ecol. Lett. 6:774-782.
77. Peterson, A. T. 1991a. Geographic variation in the ontogeny of beak coloration of gray-breasted jays Aphelocoma ultramarina. Condor 93:448-452.
78. Peterson, A. T. 1991b. New distributional information on the Aphelocoma jays. Bull. Br. Ornithol. Club 111:28-33.
79. Peterson, A. T. 1992. Phylogeny and rates of molecular evolution in the Aphelocoma jays (Corvidae). Auk 109:133-147.
80. Peterson, A. T., and D. B. Burt 1992. Phylogenetic history of social evolution and habitat use in the Aphelocoma jays. Anim. Behav. 44:859-866.
81. Peterson, A. T., E. Martinez-Meyer, and C. Gonzalez-Salazar 2004. Reconstructing the Pleistocene geography of the Aphelocoma jays (Corvidae). Divers Distrib. 10:237-246.
82. Peterson, A. T., and N. Vargas-Barajas 1993. Ecological diversity in scrub jays, Aphelocoma coerulescens. Pp. 309-317 in T. P. Ramamoorthy, A. Lot, R. Bye and J. Fa, eds. The biological diversity of Mexico: origins and distribution. Oxford Univ. Press, Oxford, U.K .
83. Petit, R., and L. Excoffier 2009. Gene flow and species delimitation. Trends Ecol. Evol. 27:386-393.
84. Pitelka, F. A. 1951. Speciation and ecological distribution in American jays of the genus Aphelocoma. Univ. of California Press, Berkeley and Los Angeles, California .
85. Price, T., and M. Bouvier 2002. The evolution of F1 postzygotic incompatibilities in birds. Evolution 56:2083-2089.
86. Rice, N. H., E. Martinez-Meyer, and A. T. Peterson 2003. Ecological niche differentiation in the Aphelocoma jays: a phylogenetic perspective. Biol. J. Linn. Soc. 80:369-383.
87. Riddle, B. R. 1995. Molecular biogeography in the pocket mice (Perognathus and Chaetodipus) and grasshopper mice (Onychomys): the late Cenozoic development of a North American aridlands rodent guild. J. Mammal. 76:283-301.
88. Riddle, B. R. 1996. The molecular phylogenetic bridge between deep and shallow history in continental biotas. Trends Ecol. Evol. 11:207-211.
89. Ronquist, F., and J. P. Huelsenbeck 2003. MrBayes 3: Bayesian phlogenetic inference under mixed models. Bioinformatics 19:1572-1574.
90. Saetre, G. P., T. Moum, S. Bures, M. Kral, M. Adamjan, and J. Moreno 1997. A sexually selected character displacement in flycatchers reinforces premating isolation. Nature 387:589-592.
91. Sanderson, M. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301-302.
92. Smith, C. I., and B. D. Farrell 2005. Range expansions in the flightless longhorn cactus beetles, Moneilema gigas and Moneilema armatum, in response to Pleistocene climate changes. Mol. Ecol. 14:1025-1044.
93. Stephens, M., N. Smith, and P. Donnelly 2001. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68:978-989.
94. Subramanian, S., D. R. Denver, C. D. Millar, T. Heupink, A. Aschrafi, S. D. Emslie, C. Baroni, and D. M. Lambert 2009. High mitogenomic evolutionary rates and time dependency. Trends Genetics 25:482-486.
95. Swofford, D. L. 2000. PAUP*. phylogenetic analysis using parsimony (*and other methods). Ver 4.0b. Sinauer Associates, Sunderland, Massachusetts .
96. Tegelström, H., and H. P. Gelter 1990. Haldane's rule and sex biased gene flow between two hybridizing flycatcher species (Ficedula albicollis and F. hypoleuca, Aves: Muscicapidae). Evolution 44:2012-2021.
97. Thorne, J. L., and H. Kishino 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51:689-702.
98. Van Devender, T. 2002. The Sonoran desert tortoise. Univ. of Arizona Press and the Arizona-Sonora Desert Museum, Tucson, Arizona .
99. Watson, D. M. 2005. Diagnosable versus distinct: evaluating species limits in birds. BioScience 55:60-68.
100. Webb, I. T., and P. Bartlein 1992. Global changes during the last 3 million years: climatic controls and biotic responses. Annu. Rev. Ecol. Syst. 23:141-173.
101. Weir, J., D. Schluter, and E. Bermingham 2010. The Great American Biotic Interchange in birds. Proc. Natl. Acad. Sci. USA 106:21737-21742.
102. Weir, J. T., and D. Schluter 2004. Ice sheets promote speciation in boreal birds. Proc. R. Soc. Lond. B. 271:1881-1887.
103. Weir, J. T., and D. Schluter 2007. The latitudinal gradient in recent speciation and extinction rates of birds and mammals. Science 315:1574-1576.
104. Weir, J. T., and D. Schluter 2008. Calibrating the avian molecular clock. Mol. Ecol. 17:2321-2328.
105. Wells, J. 2007. Birder's conservation handbook: 100 North American birds at risk. Princeton Univ. Press, Princeton, New Jersey .
106. Woolfenden, G., and J. Fitzpatrick 1985. The Florida Scrub-Jay: demography of a cooperatively-breeding bird. Princeton Univ. Press, Princeton, New Jersey .
107. Woolfenden, G. E., and J. W. Fitzpatrick 1996. Florida Scrub-Jay (Aphelocoma coerulescens). in A. Poole, ed. The birds of North America online. Cornell Laboratory of Ornithology, Ithaca, New York Available at .
108. Yang, Z. H., and B. Rannala 2006. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23:212-226.
109. Zachos, J., M. Pagani, L. Sloan, E. Thomas, and K. Billups 2001. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292:686-693.
110. Zwickl, D. J. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. diss., University of Texas at Austin .