The distribution of deleterious genetic variation in human populations

Current Opinion in Genetics and Development

Volumn 29, Issue , 2014, Pages 139-146

  Lohmueller, Kirk E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EFFECTIVE POPULATION SIZE; EXOME; GENE FREQUENCY; GENE SEGREGATION; GENETIC DIFFERENCE; GENETIC LOAD; GENETIC MODEL; GENETIC VARIABILITY; GENOME ANALYSIS; HOMO NEANDERTHALENSIS; HOMOZYGOSITY; HUMAN; INBREEDING; MUTATIONAL ANALYSIS; NATURAL SELECTION; POLYMERASE CHAIN REACTION; REVIEW; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGICAL MODEL; GENETIC SELECTION; GENETICS; GENOTYPE; HUMAN GENOME; POPULATION GENETICS;

GENE FREQUENCY; GENETIC LOAD; GENETIC VARIATION; GENETICS, POPULATION; GENOME, HUMAN; GENOTYPE; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC;

EID: 84906497659     PISSN: 0959437X     EISSN: 18790380     Source Type: Journal    
DOI: 10.1016/j.gde.2014.09.005     Document Type: Review

References (45)

1. Eyre-Walker A., Keightley P.D. The distribution of fitness effects of new mutations. Nat Rev Genet 2007, 8:610-618.
2. Boyko A.R., Williamson S.H., Indap A.R., Degenhardt J.D., Hernandez R.D., Lohmueller K.E., Adams M.D., Schmidt S., Sninsky J.J., Sunyaev S.R., et al. Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet 2008, 4:e1000083.
3. Eyre-Walker A. Evolution in health and medicine Sackler colloquium: genetic architecture of a complex trait and its implications for fitness and genome-wide association studies. Proc Natl Acad Sci U S A 2010, 107(Suppl. 1):1752-1756.
4. Ohta T. Slightly deleterious mutant substitutions in evolution. Nature 1973, 246:96-98.
5. Ohta T. Mutational pressure as the main cause of molecular evolution and polymorphism. Nature 1974, 252:351-354.
6. Ohta T. The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 1992, 23:263-286.
7. Nei M., Suzuki Y., Nozawa M. The neutral theory of molecular evolution in the genomic era. Annu Rev Genomics Hum Genet 2010, 11:265-289.
8. Akashi H., Osada N., Ohta T. Weak selection and protein evolution. Genetics 2012, 192:15-31.
9. Voight B.F., Adams A.M., Frisse L.A., Qian Y., Hudson R.R., Di Rienzo A. Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc Natl Acad Sci U S A 2005, 102:18508-18513.
10. Keinan A., Mullikin J.C., Patterson N., Reich D. Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans. Nat Genet 2007, 39:1251-1255.
11. Wall J.D., Lohmueller K.E., Plagnol V. Detecting ancient admixture and estimating demographic parameters in multiple human populations. Mol Biol Evol 2009, 26:1823-1827.
12. Lohmueller K.E., Bustamante C.D., Clark A.G. Methods for human demographic inference using haplotype patterns from genomewide single-nucleotide polymorphism data. Genetics 2009, 182:217-231.
13. Coventry A., Bull-Otterson L.M., Liu X., Clark A.G., Maxwell T.J., Crosby J., Hixson J.E., Rea T.J., Muzny D.M., Lewis L.R., et al. Deep resequencing reveals excess rare recent variants consistent with explosive population growth. Nat Commun 2010, 1:131.
14. Tennessen J.A., Bigham A.W., O'Connor T.D., Fu W., Kenny E.E., Gravel S., McGee S., Do R., Liu X., Jun G., et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 2012, 337:64-69.
15. Nelson M.R., Wegmann D., Ehm M.G., Kessner D., St Jean P., Verzilli C., Shen J., Tang Z., Bacanu S.A., Fraser D., et al. An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 2012, 337:100-104.
16. Gazave E., Ma L., Chang D., Coventry A., Gao F., Muzny D., Boerwinkle E., Gibbs R.A., Sing C.F., Clark A.G., et al. Neutral genomic regions refine models of recent rapid human population growth. Proc Natl Acad Sci U S A 2014, 111:757-762.
17. Lohmueller K.E., Indap A.R., Schmidt S., Boyko A.R., Hernandez R.D., Hubisz M.J., Sninsky J.J., White T.J., Sunyaev S.R., Nielsen R., et al. Proportionally more deleterious genetic variation in European than in African populations. Nature 2008, 451:994-997.
18. Campbell M.C., Tishkoff S.A. African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping. Annu Rev Genomics Hum Genet 2008, 9:403-433.
19. Kidd J.M., Gravel S., Byrnes J., Moreno-Estrada A., Musharoff S., Bryc K., Degenhardt J.D., Brisbin A., Sheth V., Chen R., et al. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet 2012, 91:660-671.
20. Lohmueller K.E. The impact of population demography and selection on the genetic architecture of complex traits. PLoS Genet 2014, 10:e1004379.
21. Fu W., O'Connor T.D., Jun G., Kang H.M., Abecasis G., Leal S.M., Gabriel S., Rieder M.J., Altshuler D., Shendure J., et al. Analysis of 6515 exomes reveals the recent origin of most human protein-coding variants. Nature 2013, 493:216-220.
22. Szpiech Z.A., Xu J., Pemberton T.J., Peng W., Zollner S., Rosenberg N.A., Li J.Z. Long runs of homozygosity are enriched for deleterious variation. Am J Hum Genet 2013, 93:90-102.
23. Casals F., Hodgkinson A., Hussin J., Idaghdour Y., Bruat V., de Maillard T., Grenier J.C., Gbeha E., Hamdan F.F., Girard S., et al. Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans. PLoS Genet 2013, 9:e1003815.
24. Lim E.T., Würtz P., Havulinna A.S., Palta P., Tukiainen T., Rehnström K., Esko T., Mägi R., Inouye M., Lappalainen T., et al. Distribution and medical impact of loss-of-function variants in the Finnish founder population. PLoS Genet 2014, 10:e1004494.
25. Prufer K., Racimo F., Patterson N., Jay F., Sankararaman S., Sawyer S., Heinze A., Renaud G., Sudmant P.H., de Filippo C., et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 2014, 505:43-49.
26. Castellano S., Parra G., Sanchez-Quinto F.A., Racimo F., Kuhlwilm M., Kircher M., Sawyer S., Fu Q., Heinze A., Nickel B., et al. Patterns of coding variation in the complete exomes of three Neandertals. Proc Natl Acad Sci U S A 2014, 111:6666-6671.
27. Simons Y.B., Turchin M.C., Pritchard J.K., Sella G. The deleterious mutation load is insensitive to recent population history. Nat Genet 2014, 46:220-224.
28. Haldane J.B.S. The effect of variation on fitness. Am Nat 1937, 71:337-349.
29. Agrawal A.F., Whitlock M.C. Mutation load: the fitness of individuals in populations where deleterious alleles are abundant. Annu Rev Ecol Syst 2012, 43:115-135.
30. Charlesworth B., Charlesworth D. Elements of Evolutionary Genetics 2010, Roberts and Company, Greenwood Village, CO.
31. Gazave E., Chang D., Clark A.G., Keinan A. Population growth inflates the per-individual number of deleterious mutations and reduces their mean effect. Genetics 2013, 195:969-978.
32. Goode D.L., Cooper G.M., Schmutz J., Dickson M., Gonzales E., Tsai M., Karra K., Davydov E., Batzoglou S., Myers R.M., et al. Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes. Genome Res 2010, 20:301-310.
33. Kimura M., Maruyama T. The mutational load with epistatic gene interactions in fitness. Genetics 1966, 54:1337-1351.
34. Jasnos L., Korona R. Epistatic buffering of fitness loss in yeast double deletion strains. Nat Genet 2007, 39:550-554.
35. Lesecque Y., Keightley P.D., Eyre-Walker A. A resolution of the mutation load paradox in humans. Genetics 2012, 191:1321-1330.
36. Peischl S., Dupanloup I., Kirkpatrick M., Excoffier L. On the accumulation of deleterious mutations during range expansions. Mol Ecol 2013, 22:5972-5982.
37. Do R., Balick D., Li H., Adzhubei I., Sunyaev S., Reich D. No evidence that natural selection has been less effective at removing deleterious mutations in Europeans than in West Africans 2014, arxiv:14024896.
38. Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics 1983, 105:437-460.
39. Keinan A., Clark A.G. Recent explosive human population growth has resulted in an excess of rare genetic variants. Science 2012, 336:740-743.
40. Tennessen J.A., O'Connor T.D., Bamshad M.J., Akey J.M. The promise and limitations of population exomics for human evolution studies. Genome Biol 2011, 12:127.
41. Slotte T., Hazzouri K.M., Agren J.A., Koenig D., Maumus F., Guo Y.L., Steige K., Platts A.E., Escobar J.S., Newman L.K., et al. The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet 2013, 45:831-835.
42. Brandvain Y., Slotte T., Hazzouri K.M., Wright S.I., Coop G. Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella. PLoS Genet 2013, 9:e1003754.
43. Torkamani A., Pham P., Libiger O., Bansal V., Zhang G., Scott-Van Zeeland A.A., Tewhey R., Topol E.J., Schork N.J. Clinical implications of human population differences in genome-wide rates of functional genotypes. Front Genet 2012, 3:211.
44. Hodgkinson A., Casals F., Idaghdour Y., Grenier J.C., Hernandez R.D., Awadalla P. Selective constraint, background selection, and mutation accumulation variability within and between human populations. BMC Genomics 2013, 14:495.
45. Subramanian S. The abundance of deleterious polymorphisms in humans. Genetics 2012, 190:1579-1583.