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http://dx.doi.org/10.5635/ASED.2014.30.1.039

Tempo of Diversification of Global Amphibians: One-Constant Rate, One-Continuous Shift or Multiple-Discrete Shifts?  

Chen, Youhua (Department of Zoology, University of British Columbia)
Abstract
In this brief report, alternative time-varying diversification rate models were fitted onto the phylogeny of global amphibians by considering one-constant-rate (OCR), one-continuous-shift (OCS) and multiple-discrete- shifts (MDS) situations. The OCS diversification model was rejected by ${\gamma}$ statistic (${\gamma}=-5.556$, p<0.001), implying the existence of shifting diversification rates for global amphibian phylogeny. Through model selection, MDS diversification model outperformed OCS and OCR models using "laser" package under R environment. Moreover, MDS models, implemented using another R package "MEDUSA", indicated that there were sixteen shifts over the internal nodes for amphibian phylogeny. Conclusively, both OCS and MDS models are recommended to compare so as to better quantify rate-shifting trends of species diversification. MDS diversification models should be preferential for large phylogenies using "MEDUSA" package in which any arbitrary numbers of shifts are allowed to model.
Keywords
adaptive radiation; rate variation; maximum likelihood; model selection and comparison;
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1 Alfaro ME, Santini F, Brock C, Alamillo H, Dornburg A, Rabosky DL, Carnevale G, Harmon LJ, 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proceedings of the National Academy of Sciences of the United States of America, 106:13410-13414.   DOI   ScienceOn
2 Antonelli A, Sanmartin I, 2011. Mass extinction, gradual cooling, or rapid radiation? Reconstructing the spatiotemporal evolution of the ancient angiosperm genus Hedyosmum (Chloranthaceae) using empirical and simulated approaches. Systematic Biology, 60:596-615.   DOI   ScienceOn
3 Barraclough TG, Vogler AP, 2002. Recent diversification rates in North American Tiger beetles estimated from a dated mtDNA phylogenetic tree. Molecular Biology and Evolution, 19:1706-1716.   DOI   ScienceOn
4 Brown JW, FitzJohn RG, Alfaro ME, Harmon LJ, Eastman JM, 2013. MEDUSA: modeling evolutionary diversification using stepwise AIC. R Graphical Manual.
5 Buckley LB, Jetz W, 2007. Environmental and historical constraints on global patterns of amphibian richness. Proceedings of the Royal Society B: Biological Sciences, 274: 1167-1173.   DOI   ScienceOn
6 Chen YH, 2013. A phylogenetic subclade analysis of range sizes of endemic woody seed plant species of China: trait conservatism, diversification rates and evolutionary models. Journal of Systematics and Evolution, 51:590-600.   DOI
7 Fordyce JA, 2010a. Host shifts and evolutionary radiations of butterflies. Proceedings of the Royal Society B: Biological Sciences, 277:3735-3743.   DOI   ScienceOn
8 Fordyce JA, 2010b. Interpreting the gamma statistic in phylogenetic diversification rate studies: a rate decrease does not necessarily indicate an early burst. PLoS ONE, 5:e11781.   DOI   ScienceOn
9 Fritz SA, Rahbek C, 2012. Global patterns of amphibian phylogenetic diversity. Journal of Biogeography, 39:1373-1382.   DOI   ScienceOn
10 Gillespie RG, 2013. Adaptive radiation: convergence and nonequilibrium. Current Biology, 23:R71-R74.   DOI   ScienceOn
11 Grenyer R, Orme CDL, Jackson SF, Thomas GH, Davies RG, Davies TJ, Jones KE, Olson VA, Ridgely RS, Rasmussen PC, Ding TS, Bennett PM, Blackburn TM, Gaston KJ, Gittleman JL, Owens IPF, 2006. Global distribution and conservation of rare and threatened vertebrates. Nature, 444:93-96.   DOI   ScienceOn
12 Losos JB, 2010. Adaptive radiation, ecological opportunity, and evolutionary determinism. American Naturalist, 175:623-639.   DOI   ScienceOn
13 Harmon LJ, Losos JB, Jonathan Davies T, Gillespie RG, Gittleman JL, Bryan Jennings WB, Kozak KH, McPeek MA, Moreno-Roark F, Near TJ, Purvis A, Ricklefs RE, Schluter D, Schulte JA 2nd, Seehausen O, Sidlauskas BL, Torres- Carvajal O, Weir JT, Mooers AO, 2010. Early bursts of body size and shape evolution are rare in comparative data. Evolution, 64:2385-2396.
14 Harmon LJ, Weir JT, Brock CD, Glor RE, Challenger W, 2008. GEIGER: investigating evolutionary radiations. Bioinformatics, 24:129-131.   DOI   ScienceOn
15 Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO, 2012. The global diversity of birds in space and time. Nature, 491: 444-448.   DOI   ScienceOn
16 Myers EA, Burbrink FT, 2012. Ecological opportunity: trigger of adaptive radiation. Nature Education Knowledge, 3:23.
17 Paradis E, Claude J, Strimmer K, 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20: 289-290.   DOI   ScienceOn
18 Phillimore AB, Price TD, 2008. Density-dependent cladogenesis in birds. PLoS Biology, 6:e71.   DOI   ScienceOn
19 Pybus OG, Harvey PH, 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proceedings of the Royal Society B: Biological Sciences, 267:2267-2272.   DOI   ScienceOn
20 Pyron RA, Burbrink FT, 2012. Extinction, ecological opportunity, and the origins of global snake diversity. Evolution, 66: 163-178.   DOI   ScienceOn
21 Rabosky DL, 2006. Likelihood methods for detecting temporal shifts in diversification rates. Evolution, 60:1152-1164.   DOI
22 Pyron RA, Wiens JJ, 2011. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Molecular Phylogenetics and Evolution, 61:543-583.   DOI   ScienceOn
23 Qian H, 2009. Global comparisons of beta diversity among mammals, birds, reptiles and amphibians across spatial scales and taxonomic ranks. Journal of Systematics and Evolution, 47:509-514.   DOI
24 R Development Core Team, 2011. R: A Language and Environment for Statistical Computing [Internet]. R Foundation for Statistical Computing, Vienna, Accessed 1 Jan 2014, .
25 Rabosky DL, 2007. LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies. Evolutionary Bioinformatics Online, 2: 273-276.
26 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.   DOI   ScienceOn
27 Rabosky DL, Donnellan SC, Talaba AL, Lovette IJ, 2007. Exceptional among-lineage variation in diversification rates during the radiation of Australia's most diverse vertebrate clade. Proceedings of the Royal Society B: Biological Sciences, 274:2915-2923.   DOI   ScienceOn
28 Rabosky DL, Lovette IJ, 2008a. Density dependent diversification in North American wood warblers. Proceedings of the Royal Society B: Biological Sciences, 275:2363-2371.   DOI   ScienceOn
29 Rabosky DL, Slater GJ, Alfaro ME, 2012. Clade age and species richness are decoupled across the eukaryotic tree of life. PLoS Biology, 10:e1001381.   DOI
30 Rabosky DL, Lovette IJ, 2008b. Explosive evolutionary radiations: decreasing speciation or increasing extinction through time? Evolution, 62:1866-1875.   DOI   ScienceOn
31 Ricklefs RE, 2006. Global variation in the diversification rate of passerine birds. Ecology, 87:2468-2478.   DOI   ScienceOn
32 Roelants K, Gower DJ, Wilkinson M, Loader SP, Biju SD, Guillaume K, Moriau L, Bossuyt F, 2007. Global patterns of diversification in the history of modern amphibians. Proceedings of the National Academy of Sciences of the United States of America, 104:887-892.   DOI   ScienceOn
33 Santini F, Harmon LJ, Carnevale G, Alfaro ME, 2009. Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. BMC Evolutionary Biology, 9:194.   DOI   ScienceOn
34 Schluter D, 2000. The ecology of adaptive radiation. Oxford University Press, New York.
35 Wake DB, 1991. Declining amphibian populations. Science, 253,860.   DOI
36 Wake DB, 2007. Climate change implicated in amphibian and lizard declines. Proceedings of the National Academy of Sciences of the United States of America, 104:8201-8202.   DOI   ScienceOn
37 Wiens JJ, 2007. Global patterns of diversification and species richness in amphibians. American Naturalist, 170:S86-S106.   DOI   ScienceOn
38 Zimkus BM, Lawson L, Loader SP, Hanken J, 2012. Terrestrialization, miniaturization and rates of diversification in African Puddle frogs (Anura: Phrynobatrachidae). PLoS ONE, 7:e35118.   DOI
39 Wollenberg KC, Vieites DR, Glaw F, Vences M, 2011. Speciation in little: the role of range and body size in the diversification of Malagasy mantellid frogs. BMC Evolutionary Biology, 11:217.   DOI