Speciation dynamics during the global radiation of extant bats

Evolution

Volumn 69, Issue 6, 2015, Pages 1528-1545

  Shi, Jeff J ^a   Rabosky, Daniel L ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

BAMM; Chiroptera; Diversification rates; Macroevolution; Phylogenetic imbalance

Indexed keywords

BAT; BAYESIAN ANALYSIS; CLADISTICS; EVOLUTIONARY BIOLOGY; GENETIC DIFFERENTIATION; HETEROGENEITY; PHYLOGENETICS; PHYLOGENY; SPECIATION (BIOLOGY); SPECIES RICHNESS;

CHIROPTERA; STENODERMATINAE;

ANIMAL; BAT; BAYES THEOREM; BIODIVERSITY; BIOLOGICAL MODEL; CLASSIFICATION; FOSSIL; GENETICS; PHYLOGENY; SEQUENCE ALIGNMENT; SPECIES DIFFERENTIATION; TIME FACTOR;

ANIMALS; BAYES THEOREM; BIODIVERSITY; CHIROPTERA; FOSSILS; GENETIC SPECIATION; MODELS, GENETIC; PHYLOGENY; SEQUENCE ALIGNMENT; TIME FACTORS;

EID: 84931565695     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/evo.12681     Document Type: Article

References (101)

1. Aberer, A. J., D. Krompass, and A. Stamatakis. 2013. Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice. Syst. Biol. 62:162-166.
2. Agnarsson, I., C. M. Zambrana-Torrelio, N. P. Flores-Saldana, and L. J. May-Collado. 2011. A time-calibrated species-level phylogeny of bats (Chiroptera, Mammalia). PLoS Curr. 3. doi:10.1371/currents.RRN1212.
3. Alfaro, M. E., F. Santini, C. Brock, H. Alamillo, A. Dornburg, D. L. Rabosky, G. Carnevale, and L. J. Harmon. 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc. Natl. Acad. Sci. USA 106:13410-13414.
4. Almeida, F. C., N. P. Giannini, R. DeSalle, and N. B. Simmons. 2011. Evolutionary relationships of the old world fruit bats (Chiroptera, Pteropodidae): another star phylogeny? BMC Evol. Biol. 11:281.
5. Altekar, G., S. Dwarkadas, J. P. Huelsenbeck, and F. Ronquist. 2004. Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20:407-415.
6. Badgley, C., and J. A. Finarelli. 2013. Diversity dynamics of mammals in relation to tectonic and climatic history: comparison of three Neogene records from North America. Paleobiology 39:373-399.
7. Barker, F. K., K. J. Burns, J. Klicka, S. M. Lanyon, and I. J. Lovette. 2013. Going to extremes: contrasting rates of diversification in a recent radiation of new world passerine birds. Syst. Biol. 62:298-320.
8. Barnosky, A. D. 2001. Distinguishing the effects of the Red Queen and Court Jester on Miocene mammal evolution in the northern Rocky Mountains. J. Vertebr. Paleontol. 21:172-185.
9. Barraclough, T. G., and S. Nee. 2001. Phylogenetics and speciation. Trends Ecol. Evol. 16:391-399.
10. Benton, M. J. 1987. Progress and competition in macroevolution. Biol. Rev. 62:305-338.
11. Benton, M. J. 2009. The Red Queen and the Court Jester: species diversity and the role of biotic and abiotic factors through time. Science 323:728-732.
12. Bininda-Emonds, O. R. P., M. Cardillo, K. E. Jones, R. D. E. MacPhee, R. M. D. Beck, R. Grenyer, S. A. Price, R. A. Vos, J. L. Gittleman, and A. Purvis. 2007. The delayed rise of present-day mammals. Nature 446:507-512.
13. Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17:540-552.
14. Chan, K. M. A., and B. R. Moore. 2002. Whole-tree methods for detecting differential diversification rates. Syst. Biol. 51:855-865.
15. Cornell, H. V. 2013. Is regional species diversity bounded or unbounded? Biol. Rev. 88:140-165.
16. Dávalos, L. M., A. L. Cirranello, J. H. Geisler, and N. B. Simmons. 2012. Understanding phylogenetic incongruence: lessons from phyllostomid bats. Biol. Rev. 87:991-1024.
17. Dumont, E. R., L. M. Dávalos, A. Goldberg, S. E. Santana, K. Rex, and C. C. Voigt. 2012. Morphological innovation, diversification and invasion of a new adaptive zone. Proc. R. Soc. B Biol. Sci. 279:1797-1805.
18. Dumont, E. R., K. Samadevam, I. Grosse, O. M. Warsi, B. Baird, and L. M. Dávalos. 2014. Selection for mechanical advantage underlies multiple cranial optima in New World leaf-nosed bats. Evolution 68:1436-1449.
19. Eiting, T. P., and G. F. Gunnell. 2009. Global completeness of the bat fossil record. J. Mamm. Evol. 16:151-173.
20. Erwin, D. H., J. W. Valentine, and J. J. Sepkoski, Jr. 1987. A comparative study of diversification events: the early Paleozoic versus the Mesozoic. Evolution 41:1177-1186.
21. Etienne, R. S., and B. Haegeman. 2012. A conceptual and statistical framework for adaptive radiations with a key role for diversity dependence. Am. Nat. 180:E75-E89.
22. Farrell, B. D. 1998. "Inordinate fondness" explained: why are there so many beetles? Science 281:555-559.
23. Fenton, M. B. 2010. Convergences in the diversification of bats. Curr. Zool. 56:454-468.
24. FitzJohn, R. G., W. P. Maddison, and S. P. Otto. 2009. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Syst. Biol. 58:595-611.
25. Foote, M. 1993. Contributions of individual taxa to overall morphological disparity. Paleobiology 19:403-419.
26. Funk, D. J., and K. E. Omland. 2003. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst. 34:397-423.
27. Glor, R. E. 2010. Phylogenetic insights on adaptive radiation. Annu. Rev. Ecol. Evol. Syst. 41:251-270.
28. Gould, S. J., D. M. Raup, and J. J. Sepkoski, Jr. 1977. The shape of evolution: a comparison of real and random clades. Paleobiology 3:23-40.
29. Gould, S. J., N. L. Gilinsky, and R. Z. German. 1987. Asymmetry of lineages and the direction of evolutionary time. Science 236:1437-1441.
30. Harmon, L. J. 2012. An inordinate fondness for eukaryotic diversity. PLoS Biol. 10:e1001382.
31. Harmon, L. J., J. T. Weir, C. D. Brock, R. E. Glor, and W. Challenger. 2008. GEIGER: investigating evolutionary radiations. Bioinformatics 24:129-131.
32. Harrison, N., and C. A. Kidner. 2011. Next-generation sequencing and systematics: what can a billion base pairs of DNA sequence data do for you? Taxon 60:1552-1566.
33. Heath, T. A., D. J. Zwickl, J. Kim, and D. M. Hillis. 2008. Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Syst. Biol. 57:160-166.
34. Hinchliff, C. E., and E. H. Roalson. 2013. Using supermatrices for phylogenetic inquiry: an example using the sedges. Syst. Biol. 62:205-219.
35. Jones, K. E., A. Purvis, A. MacLarnon, O. R. P. Bininda-Emonds, and N. B. Simmons. 2002. A phylogenetic supertree of the bats (Mammalia: Chiroptera). Biol. Rev. 77:223-259.
36. Jones, K. E., O. R. P. Bininda-Emonds, and J. L. Gittleman. 2005. Bats, clocks, and rocks: diversification patterns in Chiroptera. Evolution 59:2243-2255.
37. Kass, R. E., and A. E. Raftery. 1995. Bayes factors. J. Am. Stat. Assoc. 90:773-795.
38. Kirkpatrick, M., and M. Slatkin. 1993. Searching for evolutionary patterns in the shape of a phylogenetic tree. Evolution 47:1171-1181.
39. Kisel, Y., L. McInnes, N. H. Toomey, and C. D. L. Orme. 2011. How diversification rates and diversity limits combine to create large-scale species-area relationships. Philos. Trans. R. Soc. B Biol. Sci. 366:2514-2525.
40. Knowles, L. L. 2009. Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes. Syst. Biol. 58:463-467.
41. Lack, J. B., and R. A. Van Den Bussche. 2010. Identifying the confounding factors in resolving phylogenetic relationships in Vespertilionidae. J. Mammal. 91:1435-1448.
42. Lamb, J. M., T. M. C. Ralph, T. Naidoo, P. J. Taylor, F. Ratrimomanarivo, W. T. Stanley, and S. M. Goodman. 2011. Toward a molecular phylogeny for the Molossidae (Chiroptera) of the Afro-Malagasy region. Acta Chiropterol. 13:1-16.
43. Magallón, S., and M. J. Sanderson. 2001. Absolute diversification rates in angiosperm clades. Evolution 55:1762-1780.
44. Martins, E. P., and T. F. Hansen. 1997. Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. Am. Nat. 149:646-667.
45. McPeek, M. A., and J. M. Brown. 2007. Clade age and not diversification rate explains species richness among animal taxa. Am. Nat. 169:E97-E106.
46. Meredith, R. W., J. E. Janečka, J. Gatesy, O. A. Ryder, C. A. Fisher, E. C. Teeling, A. Goodbla, E. Eizirik, T. L. L. Simão, T. Stadler, et al. 2011. Impacts of the Cretaceous terrestrial revolution and KPg extinction on mammal diversification. Science 334:521-524.
47. Miller-Butterworth, C. M., W. J. Murphy, S. J. O'Brien, D. S. Jacobs, M. S. Springer, and E. C. Teeling. 2007. A family matter: conclusive resolution of the taxonomic position of the long-fingered bats, Miniopterus. Mol. Biol. Evol. 24:1553-1561.
48. Moen, D., and H. Morlon. 2014. Why does diversification slow down? Trends Ecol. Evol. 29:190-197.
49. Monteiro, L. R., and M. R. Nogueira. 2011. Evolutionary patterns and processes in the radiation of phyllostomid bats. BMC Evol. Biol. 11:137.
50. Nee, S., A. O. Mooers, and P. H. Harvey. 1992. Tempo and mode of evolution revealed from molecular phylogenies. Proc. Natl. Acad. Sci. USA 89:8322-8326.
51. Nee, S., E. C. Holmes, R. M. May, and P. H. Harvey. 1994. Extinction rates can be estimated from molecular phylogenies. Philos. Trans. R. Soc. B Biol. Sci. 344:77-82.
52. Nowak, M. D. 1994. Walker's bats of the world. Johns Hopkins University Press, Baltimore.
53. Platt II, R. N., M. W. Vandewege, C. Kern, C. J. Schmidt, F. G. Hoffmann, and D. A. Ray. 2014. Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats. Mol. Biol. Evol. 31:1536-1545.
54. Purvis, A., and P. M. Agapow. 2002. Phylogeny imbalance: taxonomic level matters. Syst. Biol. 51:844-854.
55. Pybus, O. G., and P. H. Harvey. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. B Biol. Sci. 267:2267-2272.
56. Rabosky, D. L. 2009a. Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions. Ecol. Lett. 12:735-743.
57. Rabosky, D. L. 2009b. Ecological limits on clade diversification in higher taxa. Am. Nat. 173:662-674.
58. Rabosky, D. L. 2010. Extinction rates should not be estimated from molecular phylogenies. Evolution 64:1816-1824.
59. Rabosky, D. L. 2013. Diversity-dependence, ecological speciation, and the role of competition in macroevolution. Annu. Rev. Ecol. Evol. Syst. 44:481-502.
60. Rabosky, D. L. 2014. Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS One 9:e89543.
61. Rabosky, D. L., and I. J. Lovette. 2008. Explosive evolutionary radiations: decreasing speciation or increasing extinction through time? Evolution 62:1866-1875.
62. Rabosky, D. L., F. Santini, J. Eastman, S. A. Smith, B. Sidlauskas, J. Chang, and M. E. Alfaro. 2013. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nat. Commun. 4:1958.
63. Rabosky, D. L., S. C. Donellan, M. C. Grundler, and I. J. Lovette. 2014a. Analysis and visualization of complex macroevolutionary dynamics: an example from Australian scincid lizards. Syst. Biol. 63:610-627.
64. Rabosky, D. L., M. C. Grundler, C. J. R. Anderson, P. O. Title, J. J. Shi, J. W. Brown, H. Huang, and J. G. Larson. 2014b. BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees. Methods Ecol. Evol. 5:701-707.
65. Raia, P., F. Carotenuto, F. Passaro, P. Piras, D. Fulgione, L. Werdelin, J. Saarinen, and M. Fortelius. 2012. Rapid action in the Palaeogene, the relationship between phenotypic and taxonomic diversification in Coenozoic mammals. Proc. R. Soc. B Biol. Sci. 280:20122244.
66. Raup, D. M., S. J. Gould, T. J. M. Schopf, and D. S. Simberloff. 1973. Stochastic models of phylogeny and the evolution of diversity. J. Geol. 81:525-542.
67. Revell, L. J. 2012. Phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3:217-223.
68. Rojas, D., Á. Vale, V. Ferrero, and L. Navarro. 2012. The role of frugivory in the diversification of bats in the Neotropics. J. Biogeogr. 39:1948-1960.
69. Rosenzweig, M. L., and R. D. McCord. 1991. Incumbent replacement: evidence for long-term evolutionary progress. Paleobiology 17:202-213.
70. Sahney, S., M. J. Benton, and P. A. Ferry. 2010. Links between global taxonomic diversity, ecological diversity and the expansion of vertebrates on land. Biol. Lett. 6:544-547.
71. Salichos, L., and A. Rokas. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497:327-331.
72. Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19:101-109.
73. Sanderson, M. J., D. Boss, D. Chen, K. A. Cranston, and A. Wehe. 2008. The PhyLoTA browser: processing GenBank for molecular phylogenetics research. Syst. Biol. 57:335-346.
74. Santana, S. E., I. R. Grosse, and E. R. Dumont. 2012. Dietary hardness, loading behavior, and the evolution of skull form in bats. Evolution 66:2587-2598.
75. Schluter, D. 2000. The ecology of adaptive radiation. Oxford Univ. Press, Oxford, U.K.
76. Simmons, N. B. 2005a. An Eocene big bang for bats. Science 307:527-528.
77. Simmons, N. B. 2005b. Order Chiroptera. Pp. 312-529 in D. E. Wilson and D. M. Reeder, eds. Mammal species of the world: a taxonomic and geographic reference. Johns Hopkins Univ. Press, Baltimore, MD.
78. Simmons, N. B., and T. M. Conway. 2003. Evolution of ecological diversity in bats. Pp. 493-535 in T. H. Kunz and M. B. Fenton, eds. Bat ecology. Univ. of Chicago Press, Chicago, IL.
79. Simmons, N. B., K. L. Seymour, J. Habersetzer, and G. F. Gunnell. 2008. Primitive early Eocene bat from Wyoming and the evolution of flight and echolocation. Nature 451:818-821.
80. Simpson, G. G. 1953. The major features of evolution. Columbia City Press, New York.
81. Slater, G. J., L. J. Harmon, D. Wegmann, P. Joyce, L. J. Revell, and M. E. Alfaro. 2012. Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation. Evolution 66:752-762.
82. Smith, S. A., and C. W. Dunn. 2008. Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24:715-716.
83. Smith, S. A., and B. C. O'Meara. 2012. treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 28:2689-2690.
84. Smith, S. A., J. M. Beaulieu, and M. J. Donoghue. 2009. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evol. Biol. 9:37.
85. Springer, M. S., W. J. Murphy, E. Eizirik, and S. J. O'Brien. 2003. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc. Natl. Acad. Sci. USA 100:1056-1061.
86. Stadler, T., D. L. Rabosky, R. E. Ricklefs, and F. Bokma. 2014. On age and species richness of higher taxa. Am. Nat. 184:447-455.
87. Stamatakis, A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312-1313.
88. Stanley, S. M. 1979. Macroevolution: pattern and process. W.H. Freeman, San Francisco, CA.
89. Strathmann, R. R., and M. Slatkin. 1983. The improbability of animal phyla with few species. Paleobiology 9:97-106.
90. Talavera, G., and J. Castresana. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56:564-577.
91. Teeling, E. C., O. Madsen, R. A. Van Den Bussche, W. W. de Jong, M. J. Stanhope, and M. S. Springer. 2002. Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats. Proc. Natl. Acad. Sci. USA 99:1431-1436.
92. Teeling, E. C., O. Madsen, W. J. Murphy, M. S. Springer, and S. J. O'Brien. 2003. Nuclear gene sequences confirm an ancient link between New Zealand's short-tailed bat and South American noctilionoid bats. Mol. Phylogenet. Evol. 28:308-319.
93. Teeling, E. C., M. S. Springer, O. Madsen, P. J. J. Bates, S. J. O'Brien, and W. J. Murphy. 2005. A molecular phylogeny for bats illuminates biogeography and the fossil record. Science 307:580-584.
94. Teeling, E. C., S. Dool, and M. S. Springer. 2012. Phylogenies, fossils, and functional genes: the evolution of echolocation in bats. Pp. 1-22 in G. F. Gunnell and N. B. Simmons, eds. Evolutionary history of bats: fossils, molecules, and morphology. Cambridge Univ. Press, Cambridge, U.K.
95. Van Valen, L. 1979. The evolution of bats. Evol. Theory 4:103-121.
96. Vrba, E. S. 1992. Mammals as a key to evolutionary theory. J. Mammal. 73:1-28.
97. Weir, J. T., and T. D. Price. 2011. Limits to speciation inferred from times to secondary sympatry and ages of hybridizing species along a latitudinal gradient. Am. Nat. 177:462-469.
98. Wiens, J. J. 2011. The causes of species richness patterns across space, time, and clades and the role of "ecological limits." Q. Rev. Biol. 86:75-96.
99. Yoder, J. B., E. Clancey, S. Des Roches, J. M. Eastman, L. Gentry, W. Godsoe, T. J. Hagey, D. Jochimsen, B. P. Oswald, J. Robertson, et al. 2010. Ecological opportunity and the origin of adaptive radiations. J. Evol. Biol. 23:1581-1596.
100. Yu, W., Y. Wu, and G. Yang. 2014. Early diversification trend and Asian origin for extent bat lineages. J. Evol. Biol. 27:2204-2218.
101. Zanne, A. E., D. C. Tank, W. K. Cornwell, J. M. Eastman, S. A. Smith, R. G. FitzJohn, D. J. McGlinn, B. C. O'Meara, A. T. Moles, P. B. Reich, et al. 2014. Three keys to the radiation of angiosperms into freezing environments. Nature 506:89-92.