Selective constraints determine the time dependency of molecular rates for human nuclear genomes

Genome Biology and Evolution

Volumn 4, Issue 11, 2012, Pages 1127-1132

  Subramanian, Sankar ^a   Lambert, David M ^a  

^a GRIFFITH UNIVERSITY   (Australia)

Author keywords

Deleterious polymorphisms; Natural selection; Population genetic theory; Rates of evolution; Time dependency

Indexed keywords

CELL NUCLEUS; DNA SEQUENCE; GENETIC SELECTION; GENETICS; HUMAN; HUMAN GENOME; LETTER; MUTATION RATE; PHYLOGENY; PHYSIOLOGY; POPULATION GENETICS; RACE; REPRODUCTIVE FITNESS; SINGLE NUCLEOTIDE POLYMORPHISM; TIME;

CELL NUCLEUS; CONTINENTAL POPULATION GROUPS; GENETIC FITNESS; GENETICS, POPULATION; GENOME, HUMAN; HUMANS; MUTATION RATE; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA; TIME FACTORS;

EID: 84876019991     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evs092     Document Type: Article

References (48)

1. Bandelt HJ. 2008. Clock debate: when times are a-changin': time dependency of molecular rate estimates: tempest in a teacup. Heredity 100: 1-2.
2. Bentley DR, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-59.
3. Burridge CP, Craw D, Fletcher D, Waters JM. 2008. Geological dates and molecular rates: fish DNA sheds light on time dependency. Mol Biol Evol. 25:624-633.
4. Conrad DF, et al. 2010. Variation in genome-wide mutation rates within and between human families. Nat Genet. 43:712-714.
5. Cooper GM, et al. 2005. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 15:901-913.
6. Debruyne R, Poinar HN. 2009. Time dependency of molecular rates in ancient DNA data sets, a sampling artifact? Syst Biol. 58:348-360.
7. Denver DR,Morris K, Lynch M, Thomas WK. 2004. High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature 430:679-682.
8. Emerson BC. 2007. Alarmbells for the molecular clock? No support for Ho et al.'s model of time-dependent molecular rate estimates. Syst Biol. 56:337-345.
9. Endicott P, Ho SY. 2008. A Bayesian evaluation of human mitochondrial substitution rates. Am J Hum Genet. 82:895-902.
10. Garcia-Moreno J. 2004. Is there a universal mtDNA clock for birds? J Avian Biol. 35:465-468.
11. Gronau I, et al. 2011. Bayesian inference of ancient human demography from individual genome sequences. Nat Genet. 43:1031-1034.
12. Haag-Liautard C, et al. 2007. Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila. Nature 445:82-85.
13. Hay JM, et al. 2008. Rapid molecular evolution in a living fossil. Trends Genet. 24:106-109.
14. Henn BM, Gignoux CR, Feldman MW, Mountain JL. 2009. Characterizing the time dependency of human mitochondrial DNA mutation rate estimates. Mol Biol Evol. 26:217-230.
15. Ho SY, Kolokotronis SO, Allaby RG. 2007. Elevated substitution rates estimated from ancient DNA sequences. Biol Lett. 3:702-705.
16. Ho SY, et al. 2011. Time-dependent rates ofmolecular evolution. Mol Ecol. 20:3087-3101.
17. Ho SYW, Phillips MJ, Cooper A, Drummond AJ. 2005. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol. 22:1561-1568.
18. Holmes EC. 2003. Patterns of intra- and interhost nonsynonymous variation reveal strong purifying selection in dengue virus. J Virol. 77: 11296-11298.
19. Howell N, et al. 2003. The pedigree rate of sequence divergence in the human mitochondrial genome: there is a difference between phylogenetic and pedigree rates. Am J Hum Genet. 72:659-670.
20. Kim JI, et al. 2009. A highly annotated whole-genome sequence of a Korean individual. Nature 460:1011-1015.
21. Kimura M. 1983. The neutral theory of molecular evolution. Cambridge (UK): Cambridge University Press.
22. Kivisild T, et al. 2006. The role of selection in the evolution of human mitochondrial genomes. Genetics 172:373-387.
23. Kong A, et al. 2012. Rate of de novo mutations and the importance of father's age to disease risk. Nature 488:471-475.
24. Lambert DM, et al. 2002. Rates of evolution in ancient DNA from Adelie penguins. Science 295:2270-2273.
25. Levy S, et al. 2007. The diploid genome sequence of an individual human. PLoS Biol. 5:e254.
26. Li H, Durbin R. 2011. Inference of human population history from individual whole-genome sequences. Nature 475:493-496.
27. Li Y, et al. 2010. Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet. 42: 969-972.
28. Marth GT, Czabarka E, Murvai J, Sherry ST. 2004. The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics 166:351-372.
29. Millar CD, et al. 2008. Mutation and evolutionary rates in Adelie penguins from the Antarctic. PLoS Genet. 4:e1000209.
30. Nachman MW, Crowell SL. 2000. Estimate of the mutation rate per nucleotide in humans. Genetics 156:297-304.
31. Nelson MR, et al. 2012. An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 337: 100-104.
32. Parsons TJ, et al. 1997. A high observed substitution rate in the human mitochondrial DNA control region. Nat Genet. 15:363-368.
33. Pereira L, et al. 2011. Comparing phylogeny and the predicted pathogenicity of protein variations reveals equal purifying selection across the global human mtDNA diversity. Am J Hum Genet. 88: 433-439.
34. Roach JC, et al. 2010. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328:636-639.
35. Rocha EPC, et al. 2006. Comparisons of dN/dS are time dependent for closely related bacterial genomes. J Theor Biol. 239:226-235.
36. Schuster SC, et al. 2010. Complete Khoisan and Bantu genomes from southern Africa. Nature 463:943-947.
37. Subramanian S. 2009. Temporal trails of natural selection in human mitogenomes. Mol Biol Evol. 26:715-717.
38. Subramanian S. 2012. The abundance of deleterious polymorphisms in humans. Genetics 190:1579-1583.
39. Subramanian S, et al. 2009. High mitogenomic evolutionary rates and time dependency. Trends Genet. 25:482-486.
40. Subramanian S, Lambert DM. 2011. Time dependency of molecular evolutionary rates? Yes and no. Genome Biol Evol. 3:1324-1328.
41. Sun JX, et al. 2012. A direct characterization of human mutation based on microsatellites. Nat Genet. 44:1161-1165.
42. Tennessen JA, et al. 2012. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337: 64-69.
43. Tishkoff SA, et al. 2009. The genetic structure and history of Africans and African Americans. Science 324:1035-1044.
44. Wang J, et al. 2008. The diploid genome sequence of an Asian individual. Nature 456:60-65.
45. Xue Y, et al. 2009. Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree. Curr Biol. 19:1453-1457.
46. Yang ZH. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
47. Zhivotovsky LA, et al. 2004. The effective mutation rate at Y chromosome short tandem repeats, with application to human populationdivergence time. Am J Hum Genet. 74:50-61.
48. Zhivotovsky LA, Underhill PA, Feldman MW. 2006. Difference between evolutionarily effective and germ line mutation rate due to stochastically varying haplogroup size. Mol Biol Evol. 23:2268-2270.