Multilocus estimation of divergence times and ancestral effective population sizes of Oryza species and implications for the rapid diversification of the genus

New Phytologist

Volumn 198, Issue 4, 2013, Pages 1155-1164

  Zou, Xin Hui ^a   Yang, Ziheng ^b,c   Doyle, Jeff J ^d   Ge, Song ^a  

^a INSTITUTE OF BOTANY   (China)

^b INSTITUTE OF ZOOLOGY   (China)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

^d Department of Obstetrics Gynecology   (United States)

Author keywords

Divergence time; Oryza; Population size; Rapid diversification; Relaxed clock

Indexed keywords

DIVERGENCE; EVOLUTION; EVOLUTIONARY BIOLOGY; GRASS; MIOCENE; PHYLOGENY; PLIOCENE; POPULATION SIZE;

ARTICLE; BAYES THEOREM; CALIBRATION; GENE LOCUS; GENETIC VARIABILITY; GENETICS; MONTE CARLO METHOD; PHYLOGENY; POPULATION DENSITY; PROBABILITY; RICE; STATISTICAL MODEL; TIME;

BAYES THEOREM; CALIBRATION; GENETIC LOCI; GENETIC VARIATION; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; MONTE CARLO METHOD; ORYZA SATIVA; PHYLOGENY; POPULATION DENSITY; TIME FACTORS;

ORYZA;

EID: 84877589138     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/nph.12230     Document Type: Article

References (76)

1. Aggarwal RK, Brar DS, Khush GS. 1997. Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization. Molecular and General Genetics 254: 1-12.
2. Ai B, Wang ZS, Ge S. 2012. Genome size is not correlated with effective population size in the Oryza. Evolution 66: 3302-3310.
3. Ammiraju JSS, Lu F, Sanyal A, Yu Y, Song X, Jiang N, Pontaroli AC, Rambo T, Currie J, Collura K et al. 2008. Dynamic evolution of Oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell 20: 3191-3209.
4. Arbogast BS, Edwards SV, Wakeley J, Beerli P, Slowinski JB. 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annual Review of Ecology and Systematics 33: 707-740.
5. Broughton RE, Harrison RG. 2003. Nuclear gene genealogies reveal historical, demographic and selective factors associated with speciation in field crickets. Genetics 163: 1389-1401.
6. Burgess R, Yang Z. 2008. Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Molecular Biology and Evolution 25: 1979-1994.
7. Cerling TE, Harris JM, MacFadden BJ, Leakey MG, Quade J, Eisenmann V, Ehleringer JR. 1997. Global vegetation change through the Miocene/Pliocene boundary. Nature 389: 153-158.
8. Charlesworth B. 2009. Effective population size and patterns of molecular evolution and variation. Nature Reviews Genetics 10: 195-205.
9. Chen FC, Li WH. 2001. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. American Journal of Human Genetics 68: 444-456.
10. Davies TJ, Barraclough TG, Chase MW, Soltis PS, Soltis DE, Savolainen V. 2004. Darwin's abominable mystery: insights from a supertree of the angiosperms. Proceedings of the National Academy of Sciences, USA 101: 1904-1909.
11. 4 grasslands: integrating evolutionary and ecosystem science. Science 328: 587-591.
12. Fuchs J, Ohlson JI, Ericson PGP, Pasquet E. 2007. Synchronous intercontinental splits between assemblages of woodpeckers suggested by molecular data. Zoologica Scripta 36: 11-25.
13. Gaut BS. 1998. Molecular clocks and nucleotide substitution rates in higher plants. In: Hecht MK, MacIntyre RJ, Clegg MT, eds. Evolutionary biology. New York, NY, USA: Plenum Press, 93-120.
14. Gaut BS, Morton BR, McCaig BC, Clegg MT. 1996. Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proceedings of the National Academy of Sciences, USA 93: 10 274-10 279.
15. Ge S, Sang T, Lu BR, Hong DY. 1999. Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proceedings of the National Academy of Sciences, USA 96: 14 400-14 405.
16. Guo YL, Ge S. 2005. Molecular phylogeny of Oryzeae (Poaceae) based on DNA sequences from chloroplast, mitochondrial, and nuclear genomes. American Journal of Botany 92: 1548-1558.
17. Heaney LR. 1991. A synopsis of climatic and vegetational change in Southeast-Asia. Climatic Change 19: 53-61.
18. Heer O. 1855. Flora tertiaria helvetiae. Paris, France: Winterthur.
19. Inoue J, Donoghue PCJ, Yang ZH. 2010. The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Systematic Biology 59: 74-89.
20. Jacobs BF, Kingston JD, Jacobs LL. 1999. The origin of grass-dominated ecosystems. Annals of the Missouri Botanical Garden. Missouri Botanical Garden 86: 590-643.
21. Janis CM. 1993. Tertiary mammal evolution in the context of changing climates, vegetation, and tectonic events. Annual Review of Ecology and Systematics 24: 467-500.
22. Jennings WB, Edwards SV. 2005. Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution 59: 2033-2047.
23. Khush GS. 2001. Green revolution: the way forward. Nature Reviews Genetics 2: 815-822.
24. Kimura M. 1983. The neutral theory of molecular evolution. Cambridge, UK: Cambridge University Press.
25. Krause J, Unger T, Nocon A, Malaspinas AS, Kolokotronis SO, Stiller M, Soibelzon L, Spriggs H, Dear PH, Briggs AW et al. 2008. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evolutionary Biology 8: 220.
26. Kumar S, Hedges SB. 1998. A molecular timescale for vertebrate evolution. Nature 392: 917-920.
27. Lajeunesse TC. 2005. "Species" radiations of symbiotic dinoflagellates in the Atlantic and Indo-Pacific since the Miocene-Pliocene transition. Molecular Biology and Evolution 22: 570-581.
28. Lindstrom SC, Olsen JL, Stam WT. 1996. Recent radiation of the Palmariaceae (rhodophyta). Journal of Phycology 32: 457-468.
29. Lu F, Ammiraju JSS, Sanyal A, Zhang SL, Song RT, Chen JF, Li GS, Sui Y, Song X, Cheng ZK et al. 2009. Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proceedings of the National Academy of Sciences, USA 106: 2071-2076.
30. Machado CA, Kliman RM, Markert JA, Hey J. 2002. Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Molecular Biology and Evolution 19: 472-488.
31. 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.
32. McKenna DD, Farrell BD. 2006. Tropical forests are both evolutionary cradles and museums of leaf beetle diversity. Proceedings of the National Academy of Sciences, USA 103: 10 947-10 951.
33. Notredame C, Higgins DG, Heringa J. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 302: 205-217.
34. Pond SL, Frost SD, Muse SV. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679.
35. Posada D. 2001. Unveiling the molecular clock in the presence of recombination. Molecular Biology and Evolution 18: 1976-1978.
36. Prasad V, Stromberg CA, Leache AD, Samant B, Patnaik R, Tang L, Mohabey DM, Ge S, Sahni A. 2011. Late Cretaceous origin of the rice tribe provides evidence for early diversification in Poaceae. Nature Communications 2: 480.
37. Quade J, Solounias N, Cerling TE. 1994. Stable isotopic evidence from paleosol carbonates and fossil teeth in Greece for forest or woodlands over the past 11 Ma. Palaeogeography, Palaeoclimatology, Palaeoecology 108: 41-53.
38. R Development Core Team. 2008. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. URL http://www.R-project.org.
39. Rambaut A, Drummond AJ. 2007. Tracer v1.4. [WWW document] URL http://beast.bio.ed.ac.uk/Tracer.
40. Rannala B, Yang ZH. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645-1656.
41. Rannala B, Yang Z. 2007. Inferring speciation times under an episodic molecular clock. Systematic Biology 56: 453-466.
42. Rice WR. 1989. Analyzing tables of statistical tests. Evolution 43: 223-225.
43. Richardson JE, Pennington RT, Pennington TD, Hollingsworth PM. 2001. Rapid diversification of a species-rich genus of neotropical rain forest trees. Science 293: 2242-2245.
44. Rokas A, Carroll SB. 2006. Bushes in the tree of life. PLoS Biology 4: e352.
45. Roy MS, Sponer R, Fjeldsa J. 2001. Molecular systematics and evolutionary history of akalats (Genus Sheppardia): a pre-Pleistocene radiation in a group of African forest birds. Molecular Phylogenetics and Evolution 18: 74-83.
46. Sang T, Ge S. 2007. Genetics and phylogenetics of rice domestication. Current Opinion in Genetics & Development 17: 533-538.
47. Sanyal A, Ammiraju JS, Lu F, Yu Y, Rambo T, Currie J, Kollura K, Kim HR, Chen J, Ma J et al. 2010. Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in sorghum. Molecular Biology and Evolution 27: 2487-2506.
48. Satta Y, Hickerson M, Watanabe H, O'hUigin C, Klein J. 2004. Ancestral population sizes and species divergence times in the primate lineage on the basis of intron and BAC end sequences. Journal of Molecular Evolution 59: 478-487.
49. Second G. 1985. Evolutionary relationships in the sativa group of Oryza based on isozyme data. Genetics, Selection, Evolution 17: 89-114.
50. Soltis DE, Kuzoff RK. 1995. Discordance between nuclear and chloroplast phylogenies in the Heuchera group (Saxifragaceae). Evolution 49: 727-742.
51. Stromberg CAE. 2005. Decoupled taxonomic radiation and ecological expansion of open-habitat grasses in the Cenozoic of North America. Proceedings of the National Academy of Sciences, USA 102: 11 980-11 984.
52. Takahata N. 1986. An attempt to estimate the effective size of the ancestral species common to two extant species from which homologous genes are sequenced. Genetical Research 48: 187-190.
53. Takahata N, Satta Y. 1997. Evolution of the primate lineage leading to modern humans: phylogenetic and demographic inferences from DNA sequences. Proceedings of the National Academy of Sciences, USA 94: 4811-4815.
54. Takahata N, Satta Y, Klein J. 1995. Divergence time and population-size in the lineage leading to modern humans. Theoretical Population Biology 48: 198-221.
55. Tang L, Zou XH, Achoundong G, Potgieter C, Second G, Zhang DY, Ge S. 2010. Phylogeny and biogeography of the rice tribe (Oryzeae): evidence from combined analysis of 20 chloroplast fragments. Molecular Phylogenetics and Evolution 54: 266-277.
56. Thorne JL, Kishino H. 2002. Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology 51: 689-702.
57. Thorne JL, Kishino H, Painter IS. 1998. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution 15: 1647-1657.
58. Tiffney BH, Manchester SR. 2001. The use of geological and paleontological evidence in evaluating plant phylogeographic hypotheses in the Northern Hemisphere tertiary. International Journal of Plant Sciences 162: S3-S17.
59. Vaughan DA, Kadowaki K, Kaga A, Tomooka N. 2005. On the phylogeny and biogeography of the genus Oryza. Breeding Science 55: 113-122.
60. Vaughan DA, Morishima H, Kadowaki K. 2003. Diversity in the Oryza genus. Current Opinion in Plant Biology 6: 139-146.
61. Voelker G, Rohwer S, Outlaw DC, Bowie RCK. 2009. Repeated trans-Atlantic dispersal catalysed a global songbird radiation. Global Ecology and Biogeography 18: 41-49.
62. Wall JD. 2003. Estimating ancestral population sizes and divergence times. Genetics 163: 395-404.
63. White SE, Doebley JF. 1999. The molecular evolution of terminal ear1, a regulatory gene in the genus Zea. Genetics 153: 1455-1462.
64. Wing RA, Ammiraju JS, Luo M, Kim H, Yu Y, Kudrna D, Goicoechea JL, Wang W, Nelson W, Rao K et al. 2005. The Oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species. Plant Molecular Biology 59: 53-62.
65. Won YJ, Sivasundar A, Wang Y, Hey J. 2005. On the origin of Lake Malawi cichlid species: a population genetic analysis of divergence. Proceedings of the National Academy of Sciences, USA 102(Suppl 1): 6581-6586.
66. Yang Z. 1997. On the estimation of ancestral population sizes of modern humans. Genetical Research 69: 111-116.
67. Yang Z. 2002. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162: 1811-1823.
68. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24: 1586-1591.
69. Yang Z. 2010. A likelihood ratio test of speciation with gene flow using genomic sequence data. Genome Biology and Evolution 2: 200-211.
70. Yang Z, Rannala B. 2006. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Molecular Biology and Evolution 23: 212-226.
71. Zachos J, Pagani M, Sloan L, Thomas E, Billups K. 2001. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292: 686-693.
72. Zhang LB, Ge S. 2007. Multilocus analysis of nucleotide variation and speciation in Oryza officinalis and its close relatives. Molecular Biology and Evolution 24: 769-783.
73. Zhou HF, Zheng XM, Wei RX, Second G, Vaughan DA, Ge S. 2008. Contrasting population genetic structure and gene flow between Oryza rufipogon and Oryza nivara. TAG. Theoretical and Applied Genetics. 117: 1181-1189.
74. Zhou RC, Zeng K, Wu W, Chen XS, Yang ZH, Shi SH, Wu CI. 2007. Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves. Molecular Biology and Evolution 24: 2746-2754.
75. Zhu QH, Ge S. 2005. Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytologist 167: 249-265.
76. Zou XH, Zhang FM, Zhang JG, Zang LL, Tang L, Wang J, Sang T, Ge S. 2008. Analysis of 142 genes resolves the rapid diversification of the rice genus. Genome Biology 9: R49.