Molecular Biology and Evolution 19:908-917 (2002)
© 2002 Society for Molecular Biology and Evolution
Codon-Substitution Models for Detecting Molecular Adaptation at Individual Sites Along Specific Lineages
*Galton Laboratory, Department of Biology, University College London;
Department of Biometrics, Cornell University
The nonsynonymous (amino acid–altering) to synonymous (silent) substitution rate ratio (
= dN/dS) provides a measure of natural selection at the protein level, with = 1, >1, and <1, indicating neutral evolution, purifying selection, and positive selection, respectively. Previous studies that used this measure to detect positive selection have often taken an approach of pairwise comparison, estimating substitution rates by averaging over all sites in the protein. As most amino acids in a functional protein are under structural and functional constraints and adaptive evolution probably affects only a few sites at a few time points, this approach of averaging rates over sites and over time has little power. Previously, we developed codon-based substitution models that allow the ratio to vary either among lineages or among sites. In this paper we extend previous models to allow the ratio to vary both among sites and among lineages and implement the new models in the likelihood framework. These models may be useful for identifying positive selection along prespecified lineages that affects only a few sites in the protein. We apply those branch-site models as well as previous branch- and site-specific models to three data sets: the lysozyme genes from primates, the tumor suppressor BRCA1 genes from primates, and the phytochrome (PHY) gene family in angiosperms. Positive selection is detected in the lysozyme and BRCA genes by both the new and the old models. However, only the new models detected positive selection acting on lineages after gene duplication in the PHY gene family. Additional tests on several data sets suggest that the new models may be useful in detecting positive selection after gene duplication in gene family evolution.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  H. Shan, L. Zahn, S. Guindon, P. K. Wall, H. Kong, H. Ma, C. W. dePamphilis, and J. Leebens-Mack Evolution of Plant MADS Box Transcription Factors: Evidence for Shifts in Selection Associated with Early Angiosperm Diversification and Concerted Gene Duplications Mol. Biol. Evol., October 1, 2009; 26(10): 2229 - 2244. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. B. Geyer and H.A. Lessios Lack of Character Displacement in the Male Recognition Molecule, Bindin, in Altantic Sea Urchins of the Genus Echinometra Mol. Biol. Evol., September 1, 2009; 26(9): 2135 - 2146. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Albu, X. J. Min, G. B. Golding, and D. Hickey Nucleotide Substitution Bias within the Genus Drosophila Affects the Pattern of Proteome Evolution Gen Biol Evol, August 21, 2009; 2009(0): 288 - 293. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P.-A. Christin, E. Samaritani, B. Petitpierre, N. Salamin, and G. Besnard Evolutionary Insights on C4 Photosynthetic Subtypes in Grasses from Genomics and Phylogenetics Gen Biol Evol, August 13, 2009; 2009(0): 221 - 230. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Guirao-Rico and M. Aguade Positive Selection Has Driven the Evolution of the Drosophila Insulin-Like Receptor (InR) at Different Timescales Mol. Biol. Evol., August 1, 2009; 26(8): 1723 - 1732. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Fletcher and Z. Yang INDELible: A Flexible Simulator of Biological Sequence Evolution Mol. Biol. Evol., August 1, 2009; 26(8): 1879 - 1888. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Besnard, A. M. Muasya, F. Russier, E. H. Roalson, N. Salamin, and P.-A. Christin Phylogenomics of C4 Photosynthesis in Sedges (Cyperaceae): Multiple Appearances and Genetic Convergence Mol. Biol. Evol., August 1, 2009; 26(8): 1909 - 1919. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Chattopadhyay, S. J. Weissman, V. N. Minin, T. A. Russo, D. E. Dykhuizen, and E. V. Sokurenko High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection PNAS, July 28, 2009; 106(30): 12412 - 12417. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T.-K. Seo and H. Kishino Statistical Comparison of Nucleotide, Amino Acid, and Codon Substitution Models for Evolutionary Analysis of Protein-Coding Sequences Syst Biol, June 29, 2009; (2009) syp015v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Ikeda, N. Fujii, and H. Setoguchi Molecular Evolution of Phytochromes in Cardamine nipponica (Brassicaceae) Suggests the Involvement of PHYE in Local Adaptation Genetics, June 1, 2009; 182(2): 603 - 614. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Mallick, S. Gnerre, P. Muller, and D. Reich The difficulty of avoiding false positives in genome scans for natural selection Genome Res., May 1, 2009; 19(5): 922 - 933. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. J. Weadick and B. S.W. Chang Molecular Evolution of the {beta}{gamma} Lens Crystallin Superfamily: Evidence for a Retained Ancestral Function in {gamma}N Crystallins? Mol. Biol. Evol., May 1, 2009; 26(5): 1127 - 1142. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Nozawa, Y. Suzuki, and M. Nei Reliabilities of identifying positive selection by the branch-site and the site-prediction methods PNAS, April 21, 2009; 106(16): 6700 - 6705. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Gao, P. Sherman, L. Luo, J. Bowie, and S. Zhu Structural and functional characterization of two genetically related meucin peptides highlights evolutionary divergence and convergence in antimicrobial peptides FASEB J, April 1, 2009; 23(4): 1230 - 1245. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Miyake, N. Takebayashi, and D. E. Wolf Possible Diversifying Selection in the Imprinted Gene, MEDEA, in Arabidopsis Mol. Biol. Evol., April 1, 2009; 26(4): 843 - 857. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-L. Liu, Y. Zhuang, P. Zhang, and K. L. Adams Comparative Analysis of Structural Diversity and Sequence Evolution in Plant Mitochondrial Genes Transferred to the Nucleus Mol. Biol. Evol., April 1, 2009; 26(4): 875 - 891. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. J. Binford, M. R. Bodner, M. H.J. Cordes, K. L. Baldwin, M. R. Rynerson, S. N. Burns, and P. A. Zobel-Thropp Molecular Evolution, Functional Variation, and Proposed Nomenclature of the Gene Family That Includes Sphingomyelinase D in Sicariid Spider Venoms Mol. Biol. Evol., March 1, 2009; 26(3): 547 - 566. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Wallis Prolactin in the Afrotheria: characterization of genes encoding prolactin in elephant (Loxodonta africana), hyrax (Procavia capensis) and tenrec (Echinops telfairi) J. Endocrinol., February 1, 2009; 200(2): 233 - 240. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. S. Baucom, J. C. Estill, J. Leebens-Mack, and J. L. Bennetzen Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome Genome Res., February 1, 2009; 19(2): 243 - 254. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Girirajan, L. Chen, T. Graves, T. Marques-Bonet, M. Ventura, C. Fronick, L. Fulton, M. Rocchi, R. S. Fulton, R. K. Wilson, et al. Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites Genome Res., February 1, 2009; 19(2): 178 - 190. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Anisimova and C. Kosiol Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models Mol. Biol. Evol., February 1, 2009; 26(2): 255 - 271. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Ding and I. J. Kullo Evolutionary Genetics of Coronary Heart Disease Circulation, January 27, 2009; 119(3): 459 - 467. [Full Text] [PDF]
|
|
|
|
 |
|
 W. Delport, K. Scheffler, and C. Seoighe Models of coding sequence evolution Brief Bioinform, January 1, 2009; 10(1): 97 - 109. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Proux, R. A. Studer, S. Moretti, and M. Robinson-Rechavi Selectome: a database of positive selection Nucleic Acids Res., January 1, 2009; 37(suppl_1): D404 - D407. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. M. Kuhn, D. Karolchik, A. S. Zweig, T. Wang, K. E. Smith, K. R. Rosenbloom, B. Rhead, B. J. Raney, A. Pohl, M. Pheasant, et al. The UCSC Genome Browser Database: update 2009 Nucleic Acids Res., January 1, 2009; 37(suppl_1): D755 - D761. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X-j Luo, H-b Diao, J-k Wang, H Zhang, Z-m Zhao, and B Su Association of haplotypes spanning PDZ-GEF2, LOC728637 and ACSL6 with schizophrenia in Han Chinese J. Med. Genet., December 1, 2008; 45(12): 818 - 826. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Albu, X. J. Min, D. Hickey, and B. Golding Uncorrected Nucleotide Bias in mtDNA Can Mimic the Effects of Positive Darwinian Selection Mol. Biol. Evol., December 1, 2008; 25(12): 2521 - 2524. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Kryazhimskiy, G. A Bazykin, J. Plotkin, and J. Dushoff Directionality in the evolution of influenza A haemagglutinin Proc R Soc B, November 7, 2008; 275(1650): 2455 - 2464. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P.-A. Christin, N. Salamin, A. M. Muasya, E. H. Roalson, F. Russier, and G. Besnard Evolutionary Switch and Genetic Convergence on rbcL following the Evolution of C4 Photosynthesis Mol. Biol. Evol., November 1, 2008; 25(11): 2361 - 2368. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Ali and R. Meier Positive Selection in ASPM Is Correlated with Cerebral Cortex Evolution across Primates but Not with Whole-Brain Size Mol. Biol. Evol., November 1, 2008; 25(11): 2247 - 2250. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Maheshwari, J. Wang, and D. A. Barbash Recurrent Positive Selection of the Drosophila Hybrid Incompatibility Gene Hmr Mol. Biol. Evol., November 1, 2008; 25(11): 2421 - 2430. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. A. Studer, S. Penel, L. Duret, and M. Robinson-Rechavi Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes Genome Res., September 1, 2008; 18(9): 1393 - 1402. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Wang, A. Diehl, F. Wu, J. Vrebalov, J. Giovannoni, A. Siepel, and S. D. Tanksley Sequencing and Comparative Analysis of a Conserved Syntenic Segment in the Solanaceae Genetics, September 1, 2008; 180(1): 391 - 408. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. L. Kosakovsky Pond, A. F.Y. Poon, A. J. Leigh Brown, and S. D.W. Frost A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and Its Application to Influenza A Virus Mol. Biol. Evol., September 1, 2008; 25(9): 1809 - 1824. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. C. Almeida and R. DeSalle Evidence of Adaptive Evolution of Accessory Gland Proteins in Closely Related Species of the Drosophila repleta Group Mol. Biol. Evol., September 1, 2008; 25(9): 2043 - 2053. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. D. Rodgers and D. K. Garikipati Clinical, Agricultural, and Evolutionary Biology of Myostatin: A Comparative Review Endocr. Rev., August 1, 2008; 29(5): 513 - 534. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. C. Nickel, D. L. Tefft, K. Goglin, and M. D. Adams An Empirical Test for Branch-Specific Positive Selection Genetics, August 1, 2008; 179(4): 2183 - 2193. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zhao and R. J. Epstein Programmed Genetic Instability: A Tumor-Permissive Mechanism for Maintaining the Evolvability of Higher Species through Methylation-Dependent Mutation of DNA Repair Genes in the Male Germ Line Mol. Biol. Evol., August 1, 2008; 25(8): 1737 - 1749. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T.-K. Seo and H. Kishino Synonymous Substitutions Substantially Improve Evolutionary Inference from Highly Diverged Proteins Syst Biol, June 1, 2008; 57(3): 367 - 377. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Hernandez-Sanchez, A. Mansilla, F. de Pablo, and R. Zardoya Evolution of the Insulin Receptor Family and Receptor Isoform Expression in Vertebrates Mol. Biol. Evol., June 1, 2008; 25(6): 1043 - 1053. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Q. Xu, C.-H. C. Cheng, P. Hu, H. Ye, Z. Chen, L. Cao, L. Chen, Y. Shen, and L. Chen Adaptive Evolution of Hepcidin Genes in Antarctic Notothenioid Fishes Mol. Biol. Evol., June 1, 2008; 25(6): 1099 - 1112. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. G. Artieri, W. Haerty, B. P. Gupta, and R. S. Singh Sexual Selection and Maintenance of Sex: Evidence from Comparisons of Rates of Genomic Accumulation of Mutations and Divergence of Sex-Related Genes in Sexual and Hermaphroditic Species of Caenorhabditis Mol. Biol. Evol., May 1, 2008; 25(5): 972 - 979. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Houzelstein, I. R. Goncalves, A. Orth, F. Bonhomme, and P. Netter Lgals6, a 2-Million-Year-Old Gene in Mice: A Case of Positive Darwinian Selection and Presence/Absence Polymorphism Genetics, March 1, 2008; 178(3): 1533 - 1545. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M.-S. Shiao, B.-Y. Liao, M. Long, and H.-T. Yu Adaptive Evolution of the Insulin Two-Gene System in Mouse Genetics, March 1, 2008; 178(3): 1683 - 1691. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. F. Storz, F. G. Hoffmann, J. C. Opazo, and H. Moriyama Adaptive Functional Divergence Among Triplicated {alpha}-Globin Genes in Rodents Genetics, March 1, 2008; 178(3): 1623 - 1638. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. C. Nickel, D. Tefft, and M. D. Adams Human PAML browser: a database of positive selection on human genes using phylogenetic methods Nucleic Acids Res., January 11, 2008; 36(suppl_1): D800 - D808. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. A. Ramm, P. L. Oliver, C. P. Ponting, P. Stockley, and R. D. Emes Sexual Selection and the Adaptive Evolution of Mammalian Ejaculate Proteins Mol. Biol. Evol., January 1, 2008; 25(1): 207 - 219. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Chen, S. F. Perry, S. Aris-Brosou, C. Selva, and T. W. Moon Characterization and functional divergence of the {alpha}1-adrenoceptor gene family: insights from rainbow trout (Oncorhynchus mykiss) Physiol Genomics, December 19, 2007; 32(1): 142 - 153. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Heger and C. P. Ponting Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes Genome Res., December 1, 2007; 17(12): 1837 - 1849. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Haerty, S. Jagadeeshan, R. J. Kulathinal, A. Wong, K. Ravi Ram, L. K. Sirot, L. Levesque, C. G. Artieri, M. F. Wolfner, A. Civetta, et al. Evolution in the Fast Lane: Rapidly Evolving Sex-Related Genes in Drosophila Genetics, November 1, 2007; 177(3): 1321 - 1335. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Y. Low, H. L. Ng, C. J. Morton, M. W. Parker, P. Batterham, and C. Robin Molecular Evolution of Glutathione S-Transferases in the Genus Drosophila Genetics, November 1, 2007; 177(3): 1363 - 1375. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. T. Gerrard and A. Meyer Positive Selection and Gene Conversion in SPP120, a Fertilization-Related Gene, during the East African Cichlid Fish Radiation Mol. Biol. Evol., October 1, 2007; 24(10): 2286 - 2297. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Starrett and E. R Waters Positive natural selection has driven the evolution of the Hsp70s in Diguetia spiders Biol Lett, August 22, 2007; 3(4): 439 - 444. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. M Sweeney, D. L Des Marais, Y.-E. Andrew Ban, and S. Johnsen Evolution of graded refractive index in squid lenses J R Soc Interface, August 22, 2007; 4(15): 685 - 698. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. H. Orsi, D. R. Ripoll, M. Yeung, K. K. Nightingale, and M. Wiedmann Recombination and positive selection contribute to evolution of Listeria monocytogenes inlA Microbiology, August 1, 2007; 153(8): 2666 - 2678. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Wagner Rapid Detection of Positive Selection in Genes and Genomes Through Variation Clusters Genetics, August 1, 2007; 176(4): 2451 - 2463. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Yang PAML 4: Phylogenetic Analysis by Maximum Likelihood Mol. Biol. Evol., August 1, 2007; 24(8): 1586 - 1591. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. C. Choi, A. Hobolth, D. M. Robinson, H. Kishino, and J. L. Thorne Quantifying the Impact of Protein Tertiary Structure on Molecular Evolution Mol. Biol. Evol., August 1, 2007; 24(8): 1769 - 1782. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Tarraga, I. Medina, L. Arbiza, J. Huerta-Cepas, T. Gabaldon, J. Dopazo, and H. Dopazo Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics Nucleic Acids Res., July 13, 2007; 35(suppl_2): W38 - W42. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Kosiol, I. Holmes, and N. Goldman An Empirical Codon Model for Protein Sequence Evolution Mol. Biol. Evol., July 1, 2007; 24(7): 1464 - 1479. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. J. Barkman, T. R. Martins, E. Sutton, and J. T. Stout Positive Selection for Single Amino Acid Change Promotes Substrate Discrimination of a Plant Volatile-Producing Enzyme Mol. Biol. Evol., June 1, 2007; 24(6): 1320 - 1329. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Ruano-Rubio and M. A. Fares Testing the Neutral Fixation of Hetero-Oligomerism in the Archaeal Chaperonin CCT Mol. Biol. Evol., June 1, 2007; 24(6): 1384 - 1396. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. D. Frentiu, G. D. Bernard, C. I. Cuevas, M. P. Sison-Mangus, K. L. Prudic, and A. D. Briscoe Colloquium Papers: Adaptive evolution of color vision as seen through the eyes of butterflies PNAS, May 15, 2007; 104(suppl_1): 8634 - 8640. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Anisimova and Z. Yang Multiple Hypothesis Testing to Detect Lineages under Positive Selection that Affects Only a Few Sites Mol. Biol. Evol., May 1, 2007; 24(5): 1219 - 1228. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Rhesus Macaque Genome Sequencing and Analysis Cons, R. A. Gibbs, J. Rogers, M. G. Katze, R. Bumgarner, G. M. Weinstock, E. R. Mardis, K. A. Remington, R. L. Strausberg, J. C. Venter, et al. Evolutionary and Biomedical Insights from the Rhesus Macaque Genome Science, April 13, 2007; 316(5822): 222 - 234. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Seoighe, F. Ketwaroo, V. Pillay, K. Scheffler, N. Wood, R. Duffet, M. Zvelebil, N. Martinson, J. McIntyre, L. Morris, et al. A Model of Directional Selection Applied to the Evolution of Drug Resistance in HIV-1 Mol. Biol. Evol., April 1, 2007; 24(4): 1025 - 1031. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M.-L. Wu, T.-P. Lin, M.-Y. Lin, Y.-P. Cheng, and S.-Y. Hwang Divergent Evolution of the Chloroplast Small Heat Shock Protein Gene in the Genera Rhododendron (Ericaceae) and Machilus (Lauraceae) Ann. Bot., March 1, 2007; 99(3): 461 - 475. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Doron-Faigenboim and T. Pupko A Combined Empirical and Mechanistic Codon Model Mol. Biol. Evol., February 1, 2007; 24(2): 388 - 397. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Hernandez-Hernandez, L. P. Martinez-Castilla, and E. R. Alvarez-Buylla Functional Diversification of B MADS-Box Homeotic Regulators of Flower Development: Adaptive Evolution in Protein-Protein Interaction Domains after Major Gene Duplication Events Mol. Biol. Evol., February 1, 2007; 24(2): 465 - 481. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. L. Bauer DuMont, H. A. Flores, M. H. Wright, and C. F. Aquadro Recurrent Positive Selection at Bgcn, a Key Determinant of Germ Line Differentiation, Does Not Appear to be Driven by Simple Coevolution with Its Partner Protein Bam Mol. Biol. Evol., January 1, 2007; 24(1): 182 - 191. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. A. Bazykin, J. Dushoff, S. A. Levin, and A. S. Kondrashov Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites PNAS, December 19, 2006; 103(51): 19396 - 19401. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Subramanian and S. Kumar Higher Intensity of Purifying Selection on >90% of the Human Genes Revealed by the Intrinsic Replacement Mutation Rates Mol. Biol. Evol., December 1, 2006; 23(12): 2283 - 2287. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Riginos, D. Wang, and A. J. Abrams Geographic Variation and Positive Selection on M7 Lysin, an Acrosomal Sperm Protein in Mussels (Mytilus spp.) Mol. Biol. Evol., October 1, 2006; 23(10): 1952 - 1965. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Izagirre, I. Garcia, C. Junquera, C. de la Rua, and S. Alonso A Scan for Signatures of Positive Selection in Candidate Loci for Skin Pigmentation in Humans Mol. Biol. Evol., September 1, 2006; 23(9): 1697 - 1706. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. M. Turner and H. E. Hoekstra Adaptive Evolution of Fertilization Proteins within a Genus: Variation in ZP2 and ZP3 in Deer Mice (Peromyscus) Mol. Biol. Evol., September 1, 2006; 23(9): 1656 - 1669. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. H. Thomas Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants Genome Res., August 1, 2006; 16(8): 1017 - 1030. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Andres, L. S. Maroja, S. M. Bogdanowicz, W. J. Swanson, and R. G. Harrison Molecular Evolution of Seminal Proteins in Field Crickets Mol. Biol. Evol., August 1, 2006; 23(8): 1574 - 1584. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. M. Akey, W. J. Swanson, J. Madeoy, M. Eberle, and M. D. Shriver TRPV6 exhibits unusual patterns of polymorphism and divergence in worldwide populations Hum. Mol. Genet., July 1, 2006; 15(13): 2106 - 2113. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Conde, J. M. Vaquerizas, H. Dopazo, L. Arbiza, J. Reumers, F. Rousseau, J. Schymkowitz, and J. Dopazo PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W621 - W625. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Benderoth, S. Textor, A. J. Windsor, T. Mitchell-Olds, J. Gershenzon, and J. Kroymann Positive selection driving diversification in plant secondary metabolism PNAS, June 13, 2006; 103(24): 9118 - 9123. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Guindon, M. Black, and A. Rodrigo Control of the False Discovery Rate Applied to the Detection of Positively Selected Amino Acid Sites Mol. Biol. Evol., May 1, 2006; 23(5): 919 - 926. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. V. Pereira, F. M. Salzano, A. Mostowska, W. H. Trzeciak, A. Ruiz-Linares, J. A. B. Chies, C. Saavedra, C. Nagamachi, A. M. Hurtado, K. Hill, et al. Natural selection and molecular evolution in primate PAX9 gene, a major determinant of tooth development PNAS, April 11, 2006; 103(15): 5676 - 5681. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. L. Chen, C.-S. Hung, J. Xu, C. S. Reigstad, V. Magrini, A. Sabo, D. Blasiar, T. Bieri, R. R. Meyer, P. Ozersky, et al. Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach PNAS, April 11, 2006; 103(15): 5977 - 5982. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Bodilis and S. Barray Molecular evolution of the major outer-membrane protein gene (oprF) of Pseudomonas. Microbiology, April 1, 2006; 152(Pt 4): 1075 - 1088. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. P. Rooney, J. L. Swezey, R. Friedman, D. W. Hecht, and C. W. Maddox Analysis of Core Housekeeping and Virulence Genes Reveals Cryptic Lineages of Clostridium perfringens That Are Associated With Distinct Disease Presentations Genetics, April 1, 2006; 172(4): 2081 - 2092. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. H. Zakon, Y. Lu, D. J. Zwickl, and D. M. Hillis Sodium channel genes and the evolution of diversity in communication signals of electric fishes: Convergent molecular evolution PNAS, March 7, 2006; 103(10): 3675 - 3680. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Civetta, S. A. Rajakumar, B. Brouwers, and J. P. Bacik Rapid Evolution and Gene-Specific Patterns of Selection for Three Genes of Spermatogenesis in Drosophila Mol. Biol. Evol., March 1, 2006; 23(3): 655 - 662. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Shi and J. Zhang Contrasting Modes of Evolution Between Vertebrate Sweet/Umami Receptor Genes and Bitter Receptor Genes Mol. Biol. Evol., February 1, 2006; 23(2): 292 - 300. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Tang and C.-I Wu A New Method for Estimating Nonsynonymous Substitutions and Its Applications to Detecting Positive Selection Mol. Biol. Evol., February 1, 2006; 23(2): 372 - 379. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Dvornyk Subfamilies of cpmA, a gene involved in circadian output, have different evolutionary histories in cyanobacteria Microbiology, January 1, 2006; 152(1): 75 - 84. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. L Clark, J. E Aagaard, and W. J Swanson Evolution of reproductive proteins from animals and plants Reproduction, January 1, 2006; 131(1): 11 - 22. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Kivisild, P. Shen, D. P. Wall, B. Do, R. Sung, K. Davis, G. Passarino, P. A. Underhill, C. Scharfe, A. Torroni, et al. The Role of Selection in the Evolution of Human Mitochondrial Genomes Genetics, January 1, 2006; 172(1): 373 - 387. [Abstract] [Full Text] [PDF]
|
|