Population genomic analysis of outcrossing and recombination in yeast

Nature Genetics

Volumn 38, Issue 9, 2006, Pages 1077-1081

  Ruderfer, Douglas M ^a   Pratt, Stephen C ^a   Seidel, Hannah S ^a   Kruglyak, Leonid ^a  

^a PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL DIVISION; CORRELATION ANALYSIS; DATA ANALYSIS; FUNGAL STRAIN; GENE LINKAGE DISEQUILIBRIUM; GENE SEQUENCE; GENEALOGY; GENETIC ANALYSIS; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOMICS; GENOTYPE; MOLECULAR EVOLUTION; NONHUMAN; OUTCROSSING; PHENOTYPE; POPULATION GENETICS; PRIORITY JOURNAL; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES PARADOXUS; YEAST;

CROSSES, GENETIC; DATABASES, GENETIC; GENETICS, POPULATION; GENOME, FUNGAL; LINKAGE DISEQUILIBRIUM; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC; SACCHAROMYCES CEREVISIAE;

EUKARYOTA; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES PARADOXUS; SACCHAROMYCETALES;

EID: 33748288159     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1859     Document Type: Article

References (27)

1. Mortimer, R.K. Evolution and variation of the yeast (Saccharomyces) genome. Genome Res. 10, 403-409 (2000).
2. Goffeau, A. et al. Life with 6,000 genes. Science 274, 546-563-7 (1996).
3. Landry, C.R., Townsend, J.P., Hartl, D.L. & Cavalieri, D. Ecological and evolutionary genomics of Saccharomyces cerevisiae. Mol. Ecol. 15, 575-591 (2006).
4. Gu, Z. et al. Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 102, 1092-1097 (2005).
5. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E.S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241-254 (2003).
6. Aa, E., Townsend, J.P., Adams, R.I., Nielsen, K.M. & Taylor, J.W. Population structure and gene evolution in Saccharomyces cerevisiae. FEMS Yeast Res. 6, 702-715 (2006).
7. Fay, J.C. & Benavides, J.A. Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genet. 1, 66-71 (2005).
8. Johnson, L.J. et al. Population genetics of the wild yeast Saccharomyces paradoxus. Genetics 166, 43-52 (2004).
9. Carvajal-Rodriguez, A., Crandall, K.A. & Posada, D. Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method. Mol. Biol. Evol. 23, 817-827 (2006).
10. Hey, J. & Wakeley, J. A coalescent estimator of the population recombination rate. Genetics 145, 833-846 (1997).
11. Hudson, R.R. & Kaplan, N.L. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111, 147-164 (1985).
12. Enjalbert, J. & David, J.L. Inferring recent outcrossing rates using multilocus individual heterozygosity: application to evolving wheat populations. Genetics 156, 1973-1982 (2000).
13. Ronald, J., Tang, H. & Brem, R.B. Genome-wide evolutionary rates in laboratory and wild yeast. Genetics, published online 2 July 2006 (doi:10.1534/genetics.106.060863).
14. Baum, L.E. & Petrie, T. Statistical inference for probabilistic functions of finite state Markov chains. Ann. Math. Stat. 37, 1554-1563 (1966).
15. Przeworski, M., Hudson, R.R. & Di Rienzo, A. Adjusting the focus on human variation. Trends Genet. 16, 296-302 (2000).
16. Cherry, J.M. et al. Genetic and physical maps of Saccharomyces cerevisiae. Nature 387, 67-73 (1997).
17. Liti, G., Peruffo, A., James, S.A., Roberts, I.N. & Louis, E.J. Inferences of evolutionary relationships from a population survey of LTR-retrotransposons and telomeric-associated sequences in the Saccharomyces sensu stricto complex. Yeast 22, 177-192 (2005).
18. Reich, D.E. et al. Human genome sequence variation and the influence of gene history, mutation and recombination. Nat. Genet. 32, 135-142 (2002).
19. McVean, G.A. A genealogical interpretation of linkage disequilibrium. Genetics 162, 987-991 (2002).
20. Mortimer, R. & Polsinelli, M. On the origins of wine yeast. Res. Microbiol. 150, 199-204 (1999).
21. Otto, S.P. & Lenormand, T. Resolving the paradox of sex and recombination. Nat. Rev. Genet. 3, 252-261 (2002).
22. Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).
23. Bray, N. & Pachter, L. MAVID: constrained ancestral alignment of multiple sequences. Genome Res. 14, 693-699 (2004).
24. Viterbi, A.J. Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Trans. Inf. Theory 13, 260-269 (1967).
25. Hudson, R.R. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18, 337-338 (2002).
26. Hein, J., Schierup, M.H. & Carsten, W. Gene Genealogies, Variation and Evolution (Oxford Univ. Press, New York, 2005).
27. Hudson, R.R., Slatkin, M. & Maddison, W.P. Estimation of levels of gene flow from DNA sequence data. Genetics 132, 583-589 (1992).