Crossref journal-article
Oxford University Press (OUP)
Molecular Biology and Evolution (286)
Bibliography

Fares, M. A., Byrne, K. P., & Wolfe, K. H. (2005). Rate Asymmetry After Genome Duplication Causes Substantial Long-Branch Attraction Artifacts in the Phylogeny of Saccharomyces Species. Molecular Biology and Evolution, 23(2), 245–253.

Authors 3
  1. Mario A. Fares (first)
  2. Kevin P. Byrne (additional)
  3. Kenneth H. Wolfe (additional)
References 33 Referenced 49
  1. Brinkmann, H., and H. Philippe. 1999. Archaea sister group of bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol. Biol. Evol.16:817–825. (10.1093/oxfordjournals.molbev.a026166)
  2. Byrne, K. P., and K. H. Wolfe. 2005. The yeast gene order browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15:1456–1461. (10.1101/gr.3672305)
  3. Cliften, P., P. Sudarsanam, A. Desikan, L. Fulton, B. Fulton, J. Majors, R. Waterston, B. A. Cohen, and M. Johnston. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science301:71–76. (10.1126/science.1084337)
  4. Conant, G. C., and A. Wagner. 2003. Asymmetric sequence divergence of duplicate genes. Genome Res.13:2052–2058. (10.1101/gr.1252603)
  5. Delsuc, F., H. Brinkmann, and H. Philippe. 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet.6:361–375. (10.1038/nrg1603)
  6. Dietrich, F. S., S. Voegeli, S. Brachat et al. (14 co-authors). 2004. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science304:304–307. (10.1126/science.1095781)
  7. Dujon, B., D. Sherman, G. Fischer et al. (67 co-authors). 2004. Genome evolution in yeasts. Nature430:35–44. (10.1038/nature02579)
  8. Felsenstein, J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool.27:401–410. (10.2307/2412923)
  9. Friedman, R., and A. L. Hughes. 2001. Gene duplication and the structure of eukaryotic genomes. Genome Res.11:373–381. (10.1101/gr.155801)
  10. Goldman, N., and Z. Yang. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol.11:725–736.
  11. Huelsenbeck, J. P., and K. A. Crandall. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst.28:437–466. (10.1146/annurev.ecolsys.28.1.437)
  12. Kellis, M., B. W. Birren, and E. S. Lander. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae.Nature428:617–624. (10.1038/nature02424)
  13. Kellis, M., N. Patterson, M. Endrizzi, B. Birren, and E. S. Lander. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature423:241–254. (10.1038/nature01644)
  14. Keogh, R. S., C. Seoighe, and K. H. Wolfe. 1998. Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi. Yeast14:443–457. (10.1002/(SICI)1097-0061(19980330)14:5<443::AID-YEA243>3.0.CO;2-L)
  15. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform.5:150–163. (10.1093/bib/5.2.150)
  16. Langkjaer, R. B., P. F. Cliften, M. Johnston, and J. Piskur. 2003. Yeast genome duplication was followed by asynchronous differentiation of duplicated genes. Nature421:848–852. (10.1038/nature01419)
  17. Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science290:1151–1155. (10.1126/science.290.5494.1151)
  18. Lynch, M., and V. Katju. 2004. The altered evolutionary trajectories of gene duplicates. Trends Genet.20:544–549. (10.1016/j.tig.2004.09.001)
  19. Nicholas, K. B., H. B. Nicholas Jr., and D. W. Deerfield II. 1997. GeneDoc: Analysis and visualization of genetic variation. EMBNET News 4:14.
  20. Notredame, C., D. G. Higgins, and J. Heringa. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol.302:205–217. (10.1006/jmbi.2000.4042)
  21. Reyes, A., G. Pesole, and C. Saccone. 2000. Long-branch attraction phenomenon and the impact of among-site rate variation on rodent phylogeny. Gene259:177–187. (10.1016/S0378-1119(00)00438-8)
  22. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol.4:406–425.
  23. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol.16:1114–1116. (10.1093/oxfordjournals.molbev.a026201)
  24. Souciet, J., M. Aigle, F. Artiguenave et al. (24 co-authors). 2000. Genomic exploration of the hemiascomycetous yeasts: 1. A set of yeast species for molecular evolution studies. FEBS Lett.487:3–12. (10.1016/S0014-5793(00)02272-9)
  25. Stefanovic, S., D. W. Rice, and J. D. Palmer. 2004. Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots? BMC Evol. Biol.4:35. (10.1186/1471-2148-4-35)
  26. Stiller, J. W., and B. D. Hall. 1999. Long-branch attraction and the rDNA model of early eukaryotic evolution. Mol. Biol. Evol.16:1270–1279. (10.1093/oxfordjournals.molbev.a026217)
  27. Thomarat, F., C. P. Vivarès, and M. Gouy. 2004. Phylogenetic analysis of the complete genome sequence of Encephalitozoon cuniculi supports the fungal origin of Microsporidia and reveals a high frequency of fast-evolving genes. J. Mol. Evol.59:780–791. (10.1007/s00239-004-2673-0)
  28. Van de Peer, Y., J. S. Taylor, I. Braasch, and A. Meyer. 2001. The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes. J. Mol. Evol.53:436–446. (10.1007/s002390010233)
  29. Whelan, S., and N. Goldman. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol.18:691–699. (10.1093/oxfordjournals.molbev.a003851)
  30. Wolfe, K. H., and D. C. Shields. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature387:708–713. (10.1038/42711)
  31. Wong, S., G. Butler, and K. H. Wolfe. 2002. Gene order evolution and paleopolyploidy in hemiascomycete yeasts. Proc. Natl. Acad. Sci. USA99:9272–9277. (10.1073/pnas.142101099)
  32. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci.13:555–556. (10.1093/bioinformatics/13.5.555)
  33. Yang, Z., R. Nielsen, N. Goldman, and A. M. Pedersen. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics155:431–449. (10.1093/genetics/155.1.431)
Dates
Type When
Created 19 years, 11 months ago (Oct. 5, 2005, 8:44 p.m.)
Deposited 4 years, 1 month ago (July 18, 2021, 5:24 a.m.)
Indexed 1 year, 6 months ago (March 1, 2024, 4:06 p.m.)
Issued 19 years, 11 months ago (Oct. 5, 2005)
Published 19 years, 11 months ago (Oct. 5, 2005)
Published Online 19 years, 11 months ago (Oct. 5, 2005)
Published Print 19 years, 7 months ago (Feb. 1, 2006)
Funders 0

None

@article{Fares_2005, title={Rate Asymmetry After Genome Duplication Causes Substantial Long-Branch Attraction Artifacts in the Phylogeny of Saccharomyces Species}, volume={23}, ISSN={0737-4038}, url={http://dx.doi.org/10.1093/molbev/msj027}, DOI={10.1093/molbev/msj027}, number={2}, journal={Molecular Biology and Evolution}, publisher={Oxford University Press (OUP)}, author={Fares, Mario A. and Byrne, Kevin P. and Wolfe, Kenneth H.}, year={2005}, month=oct, pages={245–253} }