DOI: 10.1038/ng1859. Population genomic analysis of outcrossing and recombination in yeast

Population genomic analysis of outcrossing and recombination in yeast

10.1038/ng1859

Crossref journal-article

Springer Science and Business Media LLC

Nature Genetics (297)

Bibliography

Ruderfer, D. M., Pratt, S. C., Seidel, H. S., & Kruglyak, L. (2006). Population genomic analysis of outcrossing and recombination in yeast. Nature Genetics, 38(9), 1077â1081.

Authors 4

Douglas M Ruderfer (first)
Stephen C Pratt (additional)
Hannah S Seidel (additional)
Leonid Kruglyak (additional)

References 27 Referenced 213

Mortimer, R.K. Evolution and variation of the yeast (Saccharomyces) genome. Genome Res. 10, 403–409 (2000). (10.1101/gr.10.4.403) / Genome Res. by RK Mortimer (2000)
Goffeau, A. et al. Life with 6,000 genes. Science 274, 546–563–7 (1996). (10.1126/science.274.5287.546) / Science by A Goffeau (1996)
Landry, C.R., Townsend, J.P., Hartl, D.L. & Cavalieri, D. Ecological and evolutionary genomics of Saccharomyces cerevisiae. Mol. Ecol. 15, 575–591 (2006). (10.1111/j.1365-294X.2006.02778.x) / Mol. Ecol. by CR Landry (2006)
Gu, Z. et al. Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 102, 1092–1097 (2005). (10.1073/pnas.0409159102) / Proc. Natl. Acad. Sci. USA by Z Gu (2005)
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). (10.1038/nature01644) / Nature by M Kellis (2003)
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). (10.1111/j.1567-1364.2006.00059.x) / FEMS Yeast Res. by E Aa (2006)
Fay, J.C. & Benavides, J.A. Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genet. 1, 66–71 (2005). (10.1371/journal.pgen.0010005) / PLoS Genet. by JC Fay (2005)
Johnson, L.J. et al. Population genetics of the wild yeast Saccharomyces paradoxus. Genetics 166, 43–52 (2004). (10.1534/genetics.166.1.43) / Genetics by LJ Johnson (2004)
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). (10.1093/molbev/msj102) / Mol. Biol. Evol. by A Carvajal-Rodriguez (2006)
Hey, J. & Wakeley, J. A coalescent estimator of the population recombination rate. Genetics 145, 833–846 (1997). (10.1093/genetics/145.3.833) / Genetics by J Hey (1997)
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). (10.1093/genetics/111.1.147) / Genetics by RR Hudson (1985)
Enjalbert, J. & David, J.L. Inferring recent outcrossing rates using multilocus individual heterozygosity: application to evolving wheat populations. Genetics 156, 1973–1982 (2000). (10.1093/genetics/156.4.1973) / Genetics by J Enjalbert (2000)
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). (10.1534/genetics.106.060863)
Baum, L.E. & Petrie, T. Statistical inference for probabilistic functions of finite state Markov chains. Ann. Math. Stat. 37, 1554–1563 (1966). (10.1214/aoms/1177699147) / Ann. Math. Stat. by LE Baum (1966)
Przeworski, M., Hudson, R.R. & Di Rienzo, A. Adjusting the focus on human variation. Trends Genet. 16, 296–302 (2000). (10.1016/S0168-9525(00)02030-8) / Trends Genet. by M Przeworski (2000)
Cherry, J.M. et al. Genetic and physical maps of Saccharomyces cerevisiae. Nature 387, 67–73 (1997). (10.1038/387067a0) / Nature by JM Cherry (1997)
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). (10.1002/yea.1200) / Yeast by G Liti (2005)
Reich, D.E. et al. Human genome sequence variation and the influence of gene history, mutation and recombination. Nat. Genet. 32, 135–142 (2002). (10.1038/ng947) / Nat. Genet. by DE Reich (2002)
McVean, G.A. A genealogical interpretation of linkage disequilibrium. Genetics 162, 987–991 (2002). (10.1093/genetics/162.2.987) / Genetics by GA McVean (2002)
Mortimer, R. & Polsinelli, M. On the origins of wine yeast. Res. Microbiol. 150, 199–204 (1999). (10.1016/S0923-2508(99)80036-9) / Res. Microbiol. by R Mortimer (1999)
Otto, S.P. & Lenormand, T. Resolving the paradox of sex and recombination. Nat. Rev. Genet. 3, 252–261 (2002). (10.1038/nrg761) / Nat. Rev. Genet. by SP Otto (2002)
Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004). (10.1186/gb-2004-5-2-r12) / Genome Biol. by S Kurtz (2004)
Bray, N. & Pachter, L. MAVID: constrained ancestral alignment of multiple sequences. Genome Res. 14, 693–699 (2004). (10.1101/gr.1960404) / Genome Res. by N Bray (2004)
Viterbi, A.J. Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Trans. Inf. Theory 13, 260–269 (1967). (10.1109/TIT.1967.1054010) / IEEE Trans. Inf. Theory by AJ Viterbi (1967)
Hudson, R.R. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18, 337–338 (2002). (10.1093/bioinformatics/18.2.337) / Bioinformatics by RR Hudson (2002)
Hein, J., Schierup, M.H. & Carsten, W. Gene Genealogies, Variation and Evolution (Oxford Univ. Press, New York, 2005). / Gene Genealogies, Variation and Evolution by J Hein (2005)
Hudson, R.R., Slatkin, M. & Maddison, W.P. Estimation of levels of gene flow from DNA sequence data. Genetics 132, 583–589 (1992). (10.1093/genetics/132.2.583) / Genetics by RR Hudson (1992)

Dates

Type	When
Created	19 years ago (Aug. 6, 2006, 1:36 p.m.)
Deposited	2 years, 3 months ago (May 18, 2023, 6:12 p.m.)
Indexed	1 month, 2 weeks ago (July 14, 2025, 11:30 p.m.)
Issued	19 years ago (Aug. 6, 2006)
Published	19 years ago (Aug. 6, 2006)
Published Online	19 years ago (Aug. 6, 2006)
Published Print	19 years ago (Sept. 1, 2006)

Funders 0

None

BibTeX

@article{Ruderfer_2006, title={Population genomic analysis of outcrossing and recombination in yeast}, volume={38}, ISSN={1546-1718}, url={http://dx.doi.org/10.1038/ng1859}, DOI={10.1038/ng1859}, number={9}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={Ruderfer, Douglas M and Pratt, Stephen C and Seidel, Hannah S and Kruglyak, Leonid}, year={2006}, month=aug, pages={1077–1081} }

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