Patterns of mammalian diversification in recent evolutionary times: Global tendencies and methodological issues

Journal of Evolutionary Biology

Volumn 24, Issue 12, 2011, Pages 2611-2623

  Soria Carrasco, V ^a   Castresana, J ^a  

^a INSTITUTE OF EVOLUTIONARY BIOLOGY CSIC UNIVERSITAT POMPEU FABRA   (Spain)

Author keywords

Diversification; Mammals; Niche saturation; Pleistocene glaciations; Sequence saturation

Indexed keywords

CYTOCHROME B;

EVOLUTIONARY BIOLOGY; GLACIATION; MAMMAL; METHODOLOGY; NICHE; PHYLOGENETICS; PHYLOGENY; PLEISTOCENE; RECONSTRUCTION; SPECIES DIVERSITY; TAXONOMY;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; EVOLUTION; GENETIC VARIABILITY; GENETICS; MAMMAL; METHODOLOGY; MITOCHONDRION; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; BIOLOGICAL EVOLUTION; CYTOCHROMES B; GENETIC VARIATION; MAMMALS; MITOCHONDRIA; MODELS, GENETIC; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

MAMMALIA;

EID: 81155151485     PISSN: 1010061X     EISSN: 14209101     Source Type: Journal    
DOI: 10.1111/j.1420-9101.2011.02384.x     Document Type: Article

References (72)

1. Akaike, H. 1974. A new look at the statistical model identification. IEEE Trans. Automat. Contr. 19: 716-723.
2. Alfaro, M.E., Santini, F., Brock, C., Alamillo, H., Dornburg, A., Rabosky, D.L. et al. 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc. Natl Acad. Sci. USA 106: 13410-13414.
3. Alroy, J. 1996. Constant extinction, constrained diversification, and uncoordinated stasis in North American mammals. Palaeogeogr. Palaeoclimatol. Palaeoecol. 127: 285-311.
4. Avise, J.C. & Walker, D. 1998. Pleistocene phylogeographic effects on avian populations and the speciation process. Proc. R. Soc. Lond. B Biol. Sci. 265: 457-463.
5. Avise, J.C., Walker, D. & Johns, G.C. 1998. Speciation durations and Pleistocene effects on vertebrate phylogeography. Proc. R. Soc. Lond. B Biol. Sci. 265: 1707-1712.
6. 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.
7. Bennett, K.D. 2004. Continuing the debate on the role of quaternary environmental change for macroevolution. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 359: 295-303.
8. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. & Sayers, E.W. 2009. GenBank. Nucleic Acids Res. 37: D26-D31.
9. 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.
10. Bininda-Emonds, O.R. 2007. Fast genes and slow clades: comparative rates of molecular evolution in mammals. Evol. Bioinform. Online 3: 59-85.
11. Bininda-Emonds, O.R., Gittleman, J.L. & Purvis, A. 1999. Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biol. Rev. 74: 143-175.
12. Bininda-Emonds, O.R., Cardillo, M., Jones, K.E., MacPhee, R.D., Beck, R.M., Grenyer, R. et al. 2007. The delayed rise of present-day mammals. Nature 446: 507-512.
13. Bokma, F. 2003. Testing for equal rates of cladogenesis in diverse taxa. Evolution 57: 2469-2474.
14. Brock, C.D., Harmon, L.J. & Alfaro, M.E. 2011. Testing for temporal variation in diversification rates when sampling is incomplete and nonrandom. Syst. Biol. 60: 410-419.
15. Brown, J.M., Hedtke, S.M., Lemmon, A.R. & Lemmon, E.M. 2010. When trees grow too long: investigating the causes of highly inaccurate Bayesian branch-length estimates. Syst. Biol. 59: 145-161.
16. Drummond, A.J. & Rambaut, A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7: 214.
17. Drummond, A.J., Ho, S.Y., Phillips, M.J. & Rambaut, A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4: e88.
18. Felsenstein, J. 1989. PHYLIP-phylogeny inference package (version 3.4). Cladistics 5: 164-166.
19. Guindon, S. & Gascuel, O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52: 696-704.
20. Harvey, P.H., May, R.M. & Nee, S. 1994. Phylogenies without fossils. Evolution 48: 523-529.
21. Heath, T.A., Zwickl, D.J., Kim, J. & Hillis, D.M. 2008. Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Syst. Biol. 57: 160-166.
22. Hewitt, G. 2000. The genetic legacy of the quaternary ice ages. Nature 405: 907-913.
23. Hey, J. 1992. Using phylogenetic trees to study speciation and extinction. Evolution 46: 627-640.
24. Johnson, N.K. & Cicero, C. 2004. New mitochondrial DNA data affirm the importance of Pleistocene speciation in North American birds. Evolution 58: 1122-1130.
25. Jones, K.E., Bininda-Emonds, O.R. & Gittleman, J.L. 2005. Bats, clocks, and rocks: diversification patterns in Chiroptera. Evolution 59: 2243-2255.
26. Kirkpatrick, M. & Slatkin, M. 1993. Searching for evolutionary patterns in the shape of a phylogenetic tree. Evolution 47: 1171-1181.
27. Klicka, J. & Zink, R.M. 1997. The importance of recent ice ages in speciation: a failed paradigm. Science 277: 1666-1669.
28. Kocher, T.D., Thomas, W.K., Meyer, A., Edwards, S.V., Pääbo, S., Villablanca, F.X. et al. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl Acad. Sci. USA 86: 6196-6200.
29. Kozak, K.H., Weisrock, D.W. & Larson, A. 2006. Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern North American woodland salamanders (Plethodontidae: Plethodon). Proc. R. Soc. Lond. B Biol. Sci. 273: 539-546.
30. Lister, A.M. 2004. The impact of quaternary ice ages on mammalian evolution. Philos. Trans. R. Soc. Lond. B Biol. Sci. 359: 221-241.
31. Marshall, D.C. 2010. Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees. Syst. Biol. 59: 108-117.
32. McPeek, M.A. 2008. The ecological dynamics of clade diversification and community assembly. Am. Nat. 172: E270-E284.
33. Moore, B.R., Chan, K.M.A. & Donoghue, M.J. 2004. Detecting diversification rate variation in supertrees. In: Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life (O.R. Bininda-Emonds, ed.), pp. 281-299. Kluwer Academic Publishers, Dordrecht, The Netherlands.
34. Nee, S. 2001. Inferring speciation rates from phylogenies. Evolution 55: 661-668.
35. Nee, S. 2006. Birth-death models in macroevolution. Ann. Rev. Ecol. Evol. Syst. 37: 1-17.
36. Nee, S., Mooers, A.O. & Harvey, P.H. 1992. Tempo and mode of evolution revealed from molecular phylogenies. Proc. Natl Acad. Sci. USA 89: 8322-8326.
37. Nee, S., May, R.M. & Harvey, P.H. 1994. The reconstructed evolutionary process. Philos. Trans. R. Soc. Lond. B Biol. Sci. 344: 305-311.
38. Paradis, E. 1997. Assessing temporal variations in diversification rates from phylogenies: estimation and hypothesis testing. Proc. R. Soc. Lond. B Biol. Sci. 264: 1141-1147.
39. Paradis, E., Claude, J. & Strimmer, K. 2004. APE: Analyses of Phylogenetics and Evolution in R Language. Bioinformatics 20: 289-290.
40. Pereira, S.L. & Baker, A.J. 2006. A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock. Mol. Biol. Evol. 23: 1731-1740.
41. Philippe, H. & Laurent, J. 1998. How good are deep phylogenetic trees? Curr. Opin. Genet. Dev. 8: 616-623.
42. Phillimore, A.B. & Price, T.D. 2008. Density-dependent cladogenesis in birds. PLoS Biol. 6: e71.
43. Posada, D. 2008. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25: 1253-1256.
44. Posada, D. & Crandall, K.A. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
45. Pybus, O.G. & Harvey, P.H. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Lond. B Biol. Sci. 267: 2267-2272.
46. Quental, T.B. & Marshall, C.R. 2010. Diversity dynamics: molecular phylogenies need the fossil record. Trends Ecol. Evol. 25: 434-441.
47. R Development Core Team 2010. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing Vienna, Austria.
48. Rabosky, D.L. 2006a. LASER: a maximum likelihood toolkit for detecting temporal shifts in diversifi cation rates from molecular phylogenies. Evol. Bioinform. Online 2: 257-260.
49. Rabosky, D.L. 2006b. Likelihood methods for detecting temporal shifts in diversification rates. Evolution 60: 1152-1164.
50. Rabosky, D.L. 2010. Extinction rates should not be estimated from molecular phylogenies. Evolution 64: 1816-1824.
51. Rabosky, D.L. & Lovette, I.J. 2008a. Density-dependent diversification in North American wood warblers. Proc. R. Soc. Lond. B Biol. Sci. 275: 2363-2371.
52. Rabosky, D.L. & Lovette, I.J. 2008b. Explosive evolutionary radiations: decreasing speciation or increasing extinction through time? Evolution 62: 1866-1875.
53. Rambaut, A. 2002. PhyloGen, Version 1.1. Department of Zoology, University of Oxford, Oxford.
54. Rambaut, A. & Grassly, N.C. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13: 235-238.
55. Revell, L.J., Harmon, L.J. & Glor, R.E. 2005. Underparameterized model of sequence evolution leads to bias in the estimation of diversification rates from molecular phylogenies. Syst. Biol. 54: 973-983.
56. Rüber, L. & Zardoya, R. 2005. Rapid cladogenesis in marine fishes revisited. Evolution 59: 1119-1127.
57. Sanderson, M.J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14: 1218-1231.
58. Sanderson, M.J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19: 101-109.
59. Sanderson, M.J. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19: 301-302.
60. Sanderson, M.J. & Donoghue, M.J. 1996. Reconstructing shifts in diversification rates on phylogenetic trees. Trends Ecol. Evol. 11: 15-20.
61. Schwartz, R.S. & Mueller, R.L. 2010. Branch length estimation and divergence dating: estimates of error in Bayesian and maximum likelihood frameworks. BMC Evol. Biol. 10: 5.
62. Sepkoski, J.J. 1998. Rates of speciation in the fossil record. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 353: 315-326.
63. Soria-Carrasco, V., Talavera, G., Igea, J. & Castresana, J. 2007. The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees. Bioinformatics 23: 2954-2956.
64. Stadler, T. 2011. Mammalian phylogeny reveals recent diversification rate shifts. Proc. Natl Acad. Sci. USA 108: 6187-6192.
65. Stajich, J.E., Block, D., Boulez, K., Brenner, S.E., Chervitz, S.A., Dagdigian, C. et al. 2002. The Bioperl toolkit: perl modules for the life sciences. Genome Res. 12: 1611-1618.
66. Weir, J.T. 2006. Divergent timing and patterns of species accumulation in lowland and highland neotropical birds. Evolution 60: 842-855.
67. Weir, J.T. & Schluter, D. 2004. Ice sheets promote speciation in boreal birds. Proc. R. Soc. Lond. B Biol. Sci. 271: 1881-1887.
68. Weir, J.T. & Schluter, D. 2008. Calibrating the avian molecular clock. Mol. Ecol. 17: 2321-2328.
69. Welch, J.J., Bininda-Emonds, O.R. & Bromham, L. 2008. Correlates of substitution rate variation in mammalian protein-coding sequences. BMC Evol. Biol. 8: 53.
70. Wertheim, J.O., Sanderson, M., Worobey, M. & Bjork, A. 2010. Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inference. Syst. Biol. 59: 1-8.
71. Wilson, D.E. & Reeder, D.M. 2005. Mammal Species of the World. A Taxonomic and Geographic Reference, 3rd edn. Johns Hopkins University Press, Baltimore.
72. Zink, R.M. & Slowinski, J.B. 1995. Evidence from molecular systematics for decreased avian diversification in the Pleistocene epoch. Proc. Natl Acad. Sci. USA 92: 5832-5835.