Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes

PLoS Genetics

Volumn 11, Issue 11, 2015, Pages

  Lipson, Mark ^a   Loh, Po Ru ^b,c   Sankararaman, Sriram ^a,c   Patterson, Nick ^c   Berger, Bonnie ^c,d   Reich, David ^a,c,e  

^a HARVARD MEDICAL SCHOOL   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^e HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DIPLOIDY; GENETIC DISTANCE; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME; HETEROZYGOSITY; HUMAN; MUTATION RATE; NONHUMAN; PEDIGREE ANALYSIS; PHYLOGENY; ANIMAL; GENETICS; HOMINID; HUMAN GENOME; MOLECULAR EVOLUTION; MUTATION; PEDIGREE; POPULATION GENETICS;

ANIMALS; DIPLOIDY; EVOLUTION, MOLECULAR; GENETICS, POPULATION; GENOME, HUMAN; HOMINIDAE; HUMANS; MUTATION; MUTATION RATE; PEDIGREE; PHYLOGENY; RECOMBINATION, GENETIC;

EID: 84949256743     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1005550     Document Type: Article

References (43)

1. Scally A, Durbin R, (2012) Revising the human mutation rate: implications for understanding human evolution. Nat Rev Genet 13: 745–753. doi: 10.1038/nrg3295 22965354
2. Campbell CD, Eichler EE, (2013) Properties and rates of germline mutations in humans. Trends Genet 29: 575–584. doi: 10.1016/j.tig.2013.04.005 23684843
3. Ségurel L, Wyman MJ, Przeworski M, (2014) Determinants of mutation rate variation in the human germline. Annu Rev Genomics Hum Genet 15: 47–70. doi: 10.1146/annurev-genom-031714-125740 25000986
4. Li WH, Tanimura M, (1987) The molecular clock runs more slowly in man than in apes and monkeys. Nature 326: 93–96. doi: 10.1038/326093a0 3102974
5. Kimura M, (1968) Evolutionary rate at the molecular level. Nature 217: 624–626. doi: 10.1038/217624a0 5637732
6. Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, et al. (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328: 636–639. doi: 10.1126/science.1186802 20220176
7. Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, et al. (2011) Variation in genome-wide mutation rates within and between human families. Nat Genet 43: 712–714. doi: 10.1038/ng.862 21666693
8. Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, et al. (2012) Rate of de novo mutations and the importance of father’s age to disease risk. Nature 488: 471–475. doi: 10.1038/nature11396 22914163
9. Campbell CD, Chong JX, Malig M, Ko A, Dumont BL, et al. (2012) Estimating the human mutation rate using autozygosity in a founder population. Nat Genet 44: 1277–1281. doi: 10.1038/ng.2418 23001126
10. Besenbacher S, Liu S, Izarzugaza JM, Grove J, Belling K, et al. (2015) Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios. Nat Comm 6: 5969. doi: 10.1038/ncomms6969
11. Fu Q, Li H, Moorjani P, Jay F, Slepchenko SM, et al. (2014) Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514: 445–449. doi: 10.1038/nature13810 25341783
12. Fenner J, (2005) Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. Am J Phys Anthropol 128: 415–423. doi: 10.1002/ajpa.20188 15795887
13. Sun JX, Helgason A, Masson G, Ebenesersdóttir SS, Li H, et al. (2012) A direct characterization of human mutation based on microsatellites. Nat Genet 44: 1161–1165. doi: 10.1038/ng.2398 22922873
14. Myers S, Bottolo L, Freeman C, McVean G, Donnelly P, (2005) A fine-scale map of recombination rates and hotspots across the human genome. Science 310: 321–324. doi: 10.1126/science.1117196 16224025
15. The International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851–861. doi: 10.1038/nature06258 17943122
16. Kong A, Thorleifsson G, Gudbjartsson DF, Masson G, Sigurdsson A, et al. (2010) Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467: 1099–1103. doi: 10.1038/nature09525 20981099
17. Hinch AG, Tandon A, Patterson N, Song Y, Rohland N, et al. (2011) The landscape of recombination in African Americans. Nature 476: 170–175. doi: 10.1038/nature10336 21775986
18. Palamara PF, Francioli L, Genovese G, Wilton P, Gusev A, et al. (2015) Leveraging distant relatedness to quantify human mutation and gene conversion rates. Am J Hum Genet. 97. doi: 10.1016/j.ajhg.2015.10.006
19. Li H, Durbin R, (2011) Inference of human population history from individual whole-genome sequences. Nature 475: 493–496. doi: 10.1038/nature10231 21753753
20. Sankararaman S, Patterson N, Li H, Pääbo S, Reich D, (2012) The date of interbreeding between Neandertals and modern humans. PLoS Genet 8: e1002947. doi: 10.1371/journal.pgen.1002947 23055938
21. Williams A, Geneovese G, Dyer T, Truax K, Jun G, et al. (2015) Non-crossover gene conversions show strong GC bias and unexpected clustering in humans. eLife 4: e04637. doi: 10.7554/eLife.04637
22. Li H, (2014) Towards better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics 30: 2843–2851. doi: 10.1093/bioinformatics/btu356 24974202
23. Kong A, Thorleifsson G, Frigge ML, Masson G, Gudbjartsson DF, et al. (2014) Common and low-frequency variants associated with genome-wide recombination rate. Nat Genet 46: 11–16. doi: 10.1038/ng.2833 24270358
24. Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, et al. (2012) A high-coverage genome sequence from an archaic Denisovan individual. Science 338: 222–226. doi: 10.1126/science.1224344 22936568
25. Cochran G, Harpending H, (2013) Paternal age and genetic load. Hum Biol 85: 515–528. doi: 10.3378/027.085.0401 25019186
26. Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, et al. (2015) Genome-wide patterns and properties of de novo mutations in humans. Nat Genet 47: 822–826. doi: 10.1038/ng.3292 25985141
27. Neale BM, Kou Y, Liu L, Maayan A, Samocha KE, et al. (2012) Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature 485: 242–245. doi: 10.1038/nature11011 22495311
28. Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, et al. (2014) The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505: 43–49. doi: 10.1038/nature12886 24352235
29. Genome of the Netherlands Consortium (2014) Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat Genet 46: 818–825. doi: 10.1038/ng.3021 24974849
30. Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K, et al. (2012) A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS Genet 8: e1003125. doi: 10.1371/journal.pgen.1003125 23284294
31. Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, et al. (2013) Great ape genetic diversity and population history. Nature 499: 471–475. doi: 10.1038/nature12228 23823723
32. Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, et al. (2012) Insights into hominid evolution from the gorilla genome sequence. Nature 483: 169–175. doi: 10.1038/nature10842 22398555
33. Schiffels S, Durbin R, (2014) Inferring human population size and separation history from multiple genome sequences. Nat Genet 46: 919–925. doi: 10.1038/ng.3015 24952747
34. Iossifov I, Ronemus M, Levy D, Wang Z, Hakker I, et al. (2012) De novo gene disruptions in children on the autistic spectrum. Neuron 74: 285–299. doi: 10.1016/j.neuron.2012.04.009 22542183
35. Fromer M, Pocklington AJ, Kavanagh DH, Williams HJ, Dwyer S, et al. (2014) De novo mutations in schizophrenia implicate synaptic networks. Nature 506: 179–184. doi: 10.1038/nature12929 24463507
36. Iossifov I, ORoak BJ, Sanders SJ, Ronemus M, Krumm N, et al. (2014) The contribution of de novo coding mutations to autism spectrum disorder. Nature 515: 216–221. doi: 10.1038/nature13908 25363768
37. Harris K, (2015) Evidence for recent, population-specific evolution of the human mutation rate. Proc Natl Acad Sci U S A 112: 3439–3444. doi: 10.1073/pnas.1418652112 25733855
38. McVean GA, Cardin NJ, (2005) Approximating the coalescent with recombination. Philos Trans R Soc Lond B Biol Sci 360: 1387–1393. doi: 10.1098/rstb.2005.1673 16048782
39. Marjoram P, Wall JD, (2006) Fast “coalescent” simulation. BMC Genet 7: 16. doi: 10.1186/1471-2156-7-16 16539698
40. Coop G, Wen X, Ober C, Pritchard JK, Przeworski M, (2008) High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans. Science 319: 1395–1398. doi: 10.1126/science.1151851 18239090
41. Hellenthal G, Stephens M, (2007) mshot: modifying hudson’s ms simulator to incorporate crossover and gene conversion hotspots. Bioinformatics 23: 520–521. doi: 10.1093/bioinformatics/btl622 17150995
42. Hudson RR, (2002) Generating samples under a Wright–Fisher neutral model of genetic variation. Bioinformatics 18: 337–338. doi: 10.1093/bioinformatics/18.2.337 11847089
43. Jeffreys AJ, May CA, (2004) Intense and highly localized gene conversion activity in human meiotic crossover hot spots. Nat Genet 36: 151–156. doi: 10.1038/ng0404-427a 14704667