Estimating divergence dates and substitution rates in the drosophila phylogeny

Molecular Biology and Evolution

Volumn 29, Issue 11, 2012, Pages 3459-3473

  Obbard, Darren J ^a   MacLennan, John ^b   Kim, Kang Wook ^c   Rambaut, Andrew ^a   O'Grady, Patrick M ^d   Jiggins, Francis M ^b  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c UNIVERSITY OF SHEFFIELD   (United Kingdom)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Drosophila; Hawai'i; mutation rate; phylogeny; relaxed clock; substitution rate

Indexed keywords

INSECT PROTEIN;

ARTICLE; DIVERGENCE RATE; DROSOPHILA; GENE MUTATION; GENE SEQUENCE; GENETIC MODEL; GENETIC PARAMETERS; GENETIC VARIABILITY; MOLECULAR CLOCK; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; MUTATION RATE; NONHUMAN; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS; SUBSTITUTION RATE; UNITED STATES;

ANIMALS; BASE SEQUENCE; CALIBRATION; DROSOPHILA; DROSOPHILA MELANOGASTER; GENETIC SPECIATION; GENETIC VARIATION; GENOME, INSECT; HAWAII; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MUTATION RATE; PHYLOGENY; TIME FACTORS; UNCERTAINTY; VOLCANIC ERUPTIONS;

EID: 84867767923     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss150     Document Type: Article

References (75)

1. Andolfatto P, Przeworski M. 2000. A genome-wide departure from the standard neutral model in natural populations of Drosophila. Genetics 156:257-172.
2. Ashburner M, Bodmer M, Lemeunier F. 1984. On the evolutionary relationaships of Drosophila melanogaster. Dev Genet. 4:295-312.
3. Atkinson IAE. 1970. Successional trends in the coastal and lowland forest of Mauna Loa and Kilauea volcanoes, Hawaii. Pacific Sci. 24: 387-400.
4. Begun DJ, Holloway AK, Stevens K, et al. 2007. Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol. 5:2534-2559.
5. Boake CRB, Price DK, Andreadis DK. 1998. Inheritance of behavioural differences between two interfertile, sympatric species, Drosophila silvestris and D. heteroneura. Heredity 80:642-650.
6. Bonacum J, O'Grady PM, Kambysellis M, DeSalle R. 2005. Phylogeny and age of diversification of the planitibia species group of the Hawaiian Drosophila. Mol Phylogenet Evol. 37:73-82.
7. Bromham L, Penny D. 2003. The modern molecular clock. Nat Rev Genet. 4:216-224.
8. Cao H, Wang X, Gao J, Prigent SR, Watabe H, Zhang Y, Chen H. 2011. Phylogeny of the African and Asian Phortica (Drosophilidae) deduced from nuclear and mitochondrial DNA sequences. Mol Phylogenet Evol. 61:677-685.
9. Carson HL. 1976. Inference of the time of origin of some Drosophila species. Nature 259:395-396.
10. Carson HL, Lockwood JP, Craddock EM. 1990. Extinction and recolonisation of local populations on a growing shield volcano. Proc Natl Acad Sci USA. 87:7055-7057.
11. Charlesworth D. 2010. Don't forget the ancestral polymorphisms. Heredity 105:509-510.
12. Clague DA, Dalrymple GB. 1987. Tectonics, geochronology and origin of the Hawaiian-Emperor volcanic chain. In: Decker RW, Wright TL, Stauffer PH, editors. US Geological Survey Professional Paper 1350. Washington (DC): US Government Printing Office. p. 1-55.
13. Clark AG, EisenMB, Smith DR, et al. (417 co-authors). 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
14. Cutter AD. 2008. Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate. Mol Biol Evol. 25:778-786.
15. Da Lage JL, Kergoat GJ, Maczkowiak F, Silvain JF, Cariou ML, Lachaise D. 2007. A phylogeny of Drosophilidae using the Amyrel gene: questioning the Drosophila melanogaster species group boundaries. J Zool Syst Evol Res. 45:47-63.
16. DePaolo DJ, Stolper EM. 1996. Models of Hawaiian volcano growth and plume structure: implications of results from the Hawaii Scientific Drilling Project. J Geophys Res Solid Earth. 101:11643-11654.
17. DeSalle R, Grimaldi DA. 1991. Morphological and molecular systematics of the Drosophilidae. Annu Rev Ecol Syst. 22:447-475.
18. Drummond AJ, Ho SY, Phillips MJ, Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4:699-710.
19. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214.
20. Easteal S, Oakeshott JG. 1985. Estimating divergence times of Drosophila species from DNA sequence comparisons. Mol Biol Evol. 2:87-91.
21. Fleischer RC, McIntosh CE, Tarr CL. 1998. Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K-Ar-based ages of the Hawaiian Islands to estimate molecular evolutionary rates. Mol Ecol. 7:533-545.
22. Fridriksson S. 2000. Vascular plants on Surtsey, Iceland, 1991-1998. Surtsey Res. 11:21-28.
23. Gao JJ, Hu YG, Toda MJ, Katoh T, Tamura K. 2011. Phylogenetic relationships between Sophophora and Lordiphosa, with proposition of a hypothesis on the vicariant divergences of tropical lineages between the Old and New Worlds in the family Drosophilidae. Mol Phylogenet Evol. 60:98-107.
24. Gao JJ, Watabe HA, Aotsuka T, Pang JF, Zhang YP. 2007. Molecular phylogeny of the Drosophila obscura species group, with emphasis on the Old World species. BMC Evol Biol. 7.
25. Grimaldi DA. 1987. Amber Fossil Drosophilidae (Diptera), with Particular Reference to the Hispaniolan taxa. Am Museum Novitates. 2880: 1-23.
26. Grimaldi DA. 1988. Relicts in the Drosophilidae (Diptera). In: Liebherr JK, editor. Zoogeography of Caribbean insects. Ithaca (NY): Cornell University Press. p. 183-213.
27. Grimaldi DA. 1990. A phylogenetic, revised classification of the genera in the Drosophilidae (Diptera). Bulletin of the American Museum of Natural History. New York: American Museum of Natural History. p. 139.
28. Guillou H, Sinton J, Laj C, Kissel C, Szeremeta N. 2000. New K-Ar ages of shield lavas from Waianae Volcano, Oahu, Hawaiian Archipelago. J Volcanol Geotherm Res. 96:229-242.
29. Haag-Liautard C, Dorris M, Maside X, Macaskill S, Halligan DL, Charlesworth B, Keightley PD. 2007. Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila. Nature 445:82-85.
30. Halligan DL, Keightley PD. 2006. Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison. Genome Res. 16:875-884.
31. Hardy DE. 1965. Diptera: Cyclorrhapha II, series Schizophora, section Acalypterae, family Drosophilidae. Honolulu (HI): University of Hawaii Press.
32. Hasegawa M, Kishino H, Yano TA. 1985. Dating of the the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22: 160-174.
33. Heads M. 2011. Old Taxa on young Islands:a critique of the use of island age to date island-endemic clades and calibrate phylogenies. Syst Biol. 60:204-218.
34. Heled J, Drummond AJ. 2010. Bayesian inference of species trees from multilocus data. Mol Biol Evol. 27:570-580.
35. Ho SY, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A. 2011. Time-dependent rates of molecular evolution. Mol Ecol. 20:3087-3101.
36. Ho SY, Larson G. 2006. Molecular clocks: when times are a-changin'. Trends Genet. 22:79-83.
37. Ho SY, Phillips MJ. 2009. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst Biol. 58: 367-380.
38. Ho SY, Shapiro B, Phillips MJ, Cooper A, Drummond AJ. 2007. Evidence for time dependency of molecular rate estimates. Syst Biol. 56: 515-522.
39. Keightley PD, Trivedi U, Thomson M, Oliver F, Kumar S, Blaxter ML. 2009. Analysis of the genome sequences of three Drosophila melanogaster spontaneousmutation accumulation lines. Genome Res. 19: 1195-1201.
40. Kellermann V, Loeschcke V, Hoffmann AA, Kristensen TN, Fløjgaard C, David JR, Svenning J-C, Overgaard J. Forthcoming 2012. Phylogenetic constraints in key functional traits behind species' climate niches: patterns of dessication and cold resistance across 95 Drosophila species. Evolution. Advance Access published May 28, 2012, doi:10.1111/j.1558-5646.2012.01685.x
41. Kopp A. 2006. Basal relationships in the Drosophila melanogaster species group. Mol Phylogenet Evol. 39:787-798.
42. Langley CH, Stevens K, Cardeno C, et al. (17 co-authors). 2012. Genomic variation in natural populations of Drosophila melanogaster. Genetics. Advance Access published June 5, 2012, doi:10.1534/genetics.112.142018
43. MacDonald GA, Katsura T. 1964. Chemical composition of Hawaiian lavas1. J Petrol. 5:82-133.
44. Moore JG, Clague DA. 1992. Volcano growth and evolution of the island of Hawaii. Geol Soc Am Bull. 104:1471-1484.
45. Moore JG, Clague DA, Normark WR. 1982. Diverse basalt types from Loihi seamount, Hawaii. Geology 10:88-92.
46. Nei M. 1971. Interspecific gene difference and evolutionary time estimated from electrophoretic data on protein identity. Am Nat. 105: 385.
47. O'Grady P, DeSalle R. 2008. Out of Hawaii: the origin and biogeography of the genus Scaptomyza (Diptera: Drosophilidae). Biol Lett. 4: 195-199.
48. O'Grady PM, Lapoint RT, Bonacum J, Lasola J, Owen E,Wu Y, DeSalle R. 2011. Phylogenetic and ecological relationships of the Hawaiian Drosophila inferred by mitochondrial DNA analysis. Mol Phylogenet Evol. 58:244-256.
49. Oliveira DC, Almeida FC, O'Grady PM, Armella MA, DeSalle R, Etges WJ. Forthcoming 2012. Monophyly, divergence times, and evolution of host plant use inferred from a revised phylogeny of the Drosophila repleta species group. Mol Phylogenet Evol. Advance Access published May 24, 2012, doi:10.1016/j.ympev. 2012.05.012
50. Pelandakis M, Solignac M. 1993. Molecular phylogeny of Drosophila based on ribosomal RNA sequences. J Mol Evol. 37:525-543.
51. Peterson DW, Moore RB. 1987. Geologic history and evolution of geologic concepts, Island of Hawaii. In: Decker RW, Wright TL, Stauffer PH, editors. Volcanism in Hawaii. U.S. Geological Survey Professional Paper 1350. Reston (VA): U.S. Geological Survey. p. 149-190.
52. Peterson GI, Masel J. 2009. Quantitative prediction of molecular clock and Ka/Ks at short timescales. Mol Biol Evol. 26:2595-2603.
53. Pollard DA, Iyer VN, Moses AM, Eisen MB. 2006. Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet. 2:1634-1647.
54. Price JP, Clague DA. 2002. How old is the Hawaiian biota? Geology and phylogeny suggest recent divergence. Proc R Soc London Ser B Biol Sci. 269:2429-2435.
55. Raghwani J, Thomas X, Koekkoek S, et al. (11 co-authors). 2012. The origin and evolution of the unique HCV circulating recombinant form 2k/1b. J Virol. 86:2212-2220.
56. Remsen J, DeSalle R. 1998. Character congruence of multiple data partitions and the origin of the Hawaiian Drosophilidae. Mol Phylogenet Evol. 9:225-235.
57. Remsen J, O'Grady P. 2002. Phylogeny of Drosophilinae (Diptera: Drosophilidae), with comments on combined analysis and character support. Mol Phylogenet Evol. 24:249-264.
58. Robe LJ, Loreto EL, Valente VL. 2010. Radiation of the "Drosophila" subgenus (Drosophilidae, Diptera) in the Neotropics. J Zool Syst Evol Res. 48:310-321.
59. Russo CA, Takezaki N, Nei M. 1995. Molecular phylogeny and divergence times of Drosophilid species. Mol Biol Evol. 12:391-404.
60. Schawaroch V. 2002. Phylogeny of a paradigm lineage: the Drosophila melanogaster species group (Diptera: Drosophilidae). Biol J Linnean Soc. 76:21-37.
61. Shapiro B, Rambaut A, Drummond AJ. 2006. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol. 23:7-9.
62. SharpWD, Renne PR. 2005. The Ar-40/Ar-39 dating of core recovered by the Hawaii Scientific Drilling Project (phase 2), Hilo, Hawaii. Geochem Geophys Geosyst. 6:18.
63. Sharp WD, Turrin BD, Renne PR, Lanphere MA. 1996. The 40Ar/39Ar and K/Ar dating of lavas from the Hilo 1-km core hole, Hawaii Scientific Drilling Project. J. Geophys Res. 101:11607-11616.
64. Sherrod DR, Sinton JM, Watkins SE, Brunt KM. 2007. Geologic map of the state of Hawai'i. U.S. Geological Survey Open-File Report 2007-1089. Reston (VA): U.S. Geological Survey.
65. Stearns HT. 1946. Geology of the Hawaiian islands. Hawaii (Terr.) Division of Hydrography. Bulletin. 8:106.
66. Tamura K, Nei M. 1993. Estimation of the the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 10:512-526.
67. Tamura K, Subramanian S, Kumar S. 2004. Temporal Patterns of Fruit Fly (Drosophila) Evolution Revealed by Mutation Clocks. Mol Biol Evol. 21:36-44.
68. Thomas JA, Welch JJ, Lanfear R, Bromham L. 2010. A Generation Time Effect on the Rate of Molecular Evolution in Invertebrates. Mol Biol Evol. 27:1173-1180.
69. Thomas RH, Hunt JA. 1993. Phylogenetic relationships in Drosophila-a conflict between molecualr and morphological data. Mol Biol Evol. 10:362-374.
70. Throckmorton LH. 1975. The phylogeny, ecology and geography of Drosophila. In: King RC, editor. Handbook of genetics. New York: Plenum. p. 421-469.
71. Van der Linde K, Houle D, Spicer GS, Steppan SJ. 2010. A supermatrixbased molecular phylogeny of the family Drosophilidae. Genet Res. 92:25-38.
72. Vicario S, Moriyama EN, Powell JR. 2007. Codon usage in twelve species of Drosophila. BMC Evol Biol. 7:226.
73. Wiegmann BM, Trautwein MD, Winkler IS, et al. 2011. Episodic radiations in the fly tree of life. Proc Natl Acad Sci USA. 108:5690-5695.
74. Yang Y, Hou Z-C, Qian Y-H, Kang H, Zeng Q-T. 2012. Increasing the data size to accurately reconstruct the phylogenetic relationships between nine subgroups of the Drosophila melanogaster species group (Drosophilidae, Diptera). Mol Phylogenet Evol. 62:214-223.
75. Zuckerkandl E, Pauling L. 1965. Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ, editors. Evolving genes and proteins. New York: Academic Press. p. 97-166.