Estimating allele age and selection coefficient from time-serial data

Genetics

Volumn 192, Issue 2, 2012, Pages 599-607

  Malaspinas, Anna Sapfo ^a   Malaspinas, Orestis ^b,c   Evans, Steven N ^d   Slatkin, Montgomery ^d  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b INSTITUT JEAN LE ROND D ALEMBERT   (France)

^c UNIVERSITY OF GENEVA   (Switzerland)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALLELE; ARTICLE; CHROMOSOME; DOMESTICATION; GENE FREQUENCY; GENE LOCUS; GENOMICS; MUTATIONAL ANALYSIS; NATURAL SELECTION; POPULATION GENETIC PARAMETERS; PRIORITY JOURNAL; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; TIME SERIES ANALYSIS;

AGE FACTORS; ALLELES; ANIMALS; ANIMALS, DOMESTIC; COLOR; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENETICS, POPULATION; HORSES; MODELS, GENETIC; MODELS, THEORETICAL; MUTATION; PIGMENTS, BIOLOGICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC;

EQUIDAE;

EID: 84867176367     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.140939     Document Type: Article

References (34)

1. Anderson, E. C., E. G. Williamson, and E. A. Thompson, 2000 Monte Carlo evaluation of the likelihood for Ne from temporally spaced samples. Genetics 156: 2109-2118.
2. Barrett, R., and D. Schluter, 2008 Adaptation from standing genetic variation. Trends Ecol. Evol. 23(1): 38-44.
3. Bollback, J. P., and J. P. Huelsenbeck, 2007 Clonal interference is alleviated by high mutation rates in large populations. Mol. Biol. Evol. 24(6): 1397-1406.
4. Bollback, J. P., T. L. York, and R. Nielsen, 2008 Estimation of 2Nes from temporal allele frequency data. Genetics 179: 497-502.
5. Cieslak, M., M. Pruvost, N. Benecke, M. Hofreiter, A. Morales et al., 2010 Origin and history of mitochondrial DNA lineages in domestic horses. PLoS ONE 5(12): e15311.
6. Drummond, A. J., and A. Rambaut, 2007 BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7: 214.
7. Durrett, R., 2008 Probability Models for DNA Sequence Evolution, Ed. 2. Springer, New York.
8. Ewens, W. J., 2004 Mathematical Population Genetics, Ed. 2. Springer, New York.
9. Fisher, R., 1922 On the dominance ratio. Proc. R. Soc. 42: 321-341.
10. Gresham, D., M. M. Desai, C. M. Tucker, H. T. Jenq, D. A. Pai et al., 2008 The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet. 4(12): e1000303.
11. Gutenkunst, R. N., R. D. Hernandez, S. H. Williamson, and C. D. Bustamante, 2009 Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5(10): e1000695.
12. Hamilton, D., 1994 Time Series Analysis. Princeton University Press, Princeton, NH.
13. Hunter, J. D., 2007 Matplotlib: A 2d graphics environment. Comput. Sci. Eng. 9(3): 90-95.
14. Jazin, E., H. Soodyall, P. Jalonen, E. Lindholm, M. Stoneking et al., 1998 Mitochondrial mutation rate revisited: hot spots and polymorphism. Nat. Genet. 18(2): 109-110.
15. Jones, E., T. Oliphant, P. Peterson et al. 2001 {SciPy}: open source scientific tools for {Python}. http://www.scipy.org/.
16. Lalueza-Fox, C., H. Rompler, D. Caramelli, C. Staubert, G. Catalano et al., 2007 Amelanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science 318(5855): 1453-1455.
17. Ludwig, A., M. Pruvost, M. Reissmann, N. Benecke, G. A. Brockmann et al., 2009 Coat color variation at the beginning of horse domestication. Science 324(5926): 485.
18. Nakata, M., 2010 The MPACK (MBLAS/MLAPACK): a multiple precision arithmetic version of BLAS and LAPACK. http://mplapack.sourceforge.net/.
19. Nelder, J. A., and R. Mead, 1965 A simplex method for function minimization. Computer Journal 7: 303-313.
20. Nelson, M. I., and E. C. Holmes, 2007 The evolution of epidemic influenza. Nat. Rev. Genet. 8(3): 196-205.
21. Oliphant, T., 2006 Guide to NumPy. Trelgol Publishing.
22. Outram, A. K., N. A. Stear, R. Bendrey, S. Olsen, A. Kasparov et al., 2009 The earliest horse harnessing and milking. Science 323 (5919): 1332-1335.
23. Rasmussen, M., Y. Li, S. Lindgreen, J. S. Pedersen, A. Albrechtsen et al., 2010 Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463(7282): 757-762.
24. Reich, D., R. E. Green, M. Kircher, J. Krause, N. Patterson et al., 2010 Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468(7327): 1053-1060.
25. Rieder, S., S. Taourit, D. Mariat, B. Langlois, and G. Guerin, 2001 Mutations in the agouti (ASIP), the extension (MC1R), and the brown (TYRP1) loci and their association to coat color phenotypes in horses (Equus caballus). Mamm. Genome 12(6): 450-455.
26. Rusk, N., 2009 Targeting ancient DNA. Nat. Methods 6: 629.
27. Slatkin, M., and B. Rannala, 2000 Estimating allele age. Annu. Rev. Genomics Hum. Genet. 1: 225-249.
28. Song, Y., and M. Steinrucken, 2012 A simple method for finding explicit analytic transition densities of diffusion processes with general diploid selection. Genetics 190: 1117-1129.
29. Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei et al., 2011 MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28(10): 2731-2739.
30. Van Kampen, N., 1992 Stochastic Processes in Physics and Chemistry. Elsevier, New York.
31. Waples, R. S., 1989 A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics 121: 379-391.
32. Wichman, H. A., J. Millstein, and J. J. Bull, 2005 Adaptive molecular evolution for 13,000 phage generations: a possible arms race. Genetics 170: 19-31.
33. Williamson, E. G., and M. Slatkin, 1999 Using maximum likelihood to estimate population size from temporal changes in allele frequencies. Genetics 152: 755-761.
34. Wright, S., 1931 Evolution in Mendelian populations. Genetics 16: 97-159.