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Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny

Ku, H., Vision, T., Liu, J., & Tanksley, S. D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.160271297 · Cited by 402 · see citing works

A random effects branch-site model for detecting episodic diversifying selection

Kosakovsky Pond, S. L., Murrell, B., Fourment, M., Frost, S. D. W., Delport, W., & Scheffler, K. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr125 · Cited by 400 · see citing works

Evidence for Variable Selective Pressures at MC1R

Harding, R. M., Healy, E., Ray, A. J., Ellis, N. S., Flanagan, N., Todd, C., Dixon, C., Sajantila, A., Jackson, I. J., Birch-Machin, M. A., et al. (2000) · The American Journal of Human Genetics · doi:10.1086/302863 · Cited by 389 · see citing works

Codon-Substitution Models to Detect Adaptive Evolution that Account for Heterogeneous Selective Pressures Among Site Classes

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Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood

Siepel, A. C. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msh039 · Cited by 375 · see citing works

Probability Models for DNA Sequence Evolution

Durrett, R. (2002) · Probability and its applications · doi:10.1007/978-1-4757-6285-3 · Cited by 366 · see citing works

Leishmania and the Leishmaniases: A Parasite Genetic Update and Advances in Taxonomy, Epidemiology and Pathogenicity in Humans

Bañuls, A., Hidé, M., & Prugnolle, F. (2007) · Advances in Parasitology/Advances in parasitology · doi:10.1016/s0065-308x(06)64001-3 · Cited by 362 · see citing works

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

Koenig, D., Jiménez‐Gómez, J. M., Kimura, S., Fulop, D., Chitwood, D. H., Headland, L. R., Kumar, R. S., Covington, M. F., Devisetty, U. K., Tat, A. V., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1309606110 · Cited by 362 · see citing works

Comparison of Likelihood and Bayesian Methods for Estimating Divergence Times Using Multiple Gene Loci and Calibration Points, with Application to a Radiation of Cute-Looking Mouse Lemur Species

Yang, Z., & Yoder, A. D. (2003) · Systematic Biology · doi:10.1080/10635150390235557 · Cited by 357 · see citing works

Evolution of reproductive proteins from animals and plants

Clark, N. L., Aagaard, J. E., & Swanson, W. J. (2005) · Reproduction · doi:10.1530/rep.1.00357 · Cited by 357 · see citing works

The importance of proper model assumption in bayesian phylogenetics.

Lemmon, A. R., & Moriarty, E. C. (2004) · Systematic Biology · doi:10.1080/10635150490423520 · Cited by 356 · see citing works

Empirical and Hierarchical Bayesian Estimation of Ancestral States

Huelsenbeck, J. P., & Bollback, J. P. (2001) · Systematic Biology · doi:10.1080/10635150119871 · Cited by 356 · see citing works

Sperm wars and the evolution of male fertility

Simmons, L. W., & Fitzpatrick, J. L. (2012) · Reproduction · doi:10.1530/rep-12-0285 · Cited by 344 · see citing works

Multiple Paleopolyploidizations during the Evolution of the Compositae Reveal Parallel Patterns of Duplicate Gene Retention after Millions of Years

Barker, M. S., Kane, N. C., Matvienko, M., Kozik, A., Michelmore, R. W., Knapp, S. J., & Rieseberg, L. H. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn187 · Cited by 342 · see citing works

Mining EST databases to resolve evolutionary events in major crop species

Schlueter, J. A., Dixon, P. M., Granger, C. L., Grant, D., Clark, L. G., Doyle, J. J., & Shoemaker, R. C. (2004) · Genome · doi:10.1139/g04-047 · Cited by 338 · see citing works

Evolution of Arabidopsis microRNA families through duplication eventsPreprint

Maher, C. A., Stein, L. D., & Ware, D. (2006) · Genome Research · doi:10.1101/gr.4680506 · Cited by 334 · see citing works

Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach

Stern, A., Doron‐Faigenboim, A., Erez, E., Martz, E., Bacharach, E., & Pupko, T. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm382 · Cited by 331 · see citing works

Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage

Yang, Z., & Nielsen, R. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msm284 · Cited by 331 · see citing works

Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes

Cannon, S. B., Sterck, L., Rombauts, S., Sato, S., Cheung, F., Gouzy, J., Wang, X., Mudge, J., Vasdewani, J., Schiex, T., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603228103 · Cited by 330 · see citing works

Evolution of the chicken Toll-like receptor gene family: A story of gene gain and gene loss

Temperley, N. D., Berlin, S., Paton, I. R., Griffin, D. K., & Burt, D. W. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-62 · Cited by 327 · see citing works

Analysis of Two in Planta Expressed LysM Effector Homologs from the FungusMycosphaerella graminicolaReveals Novel Functional Properties and Varying Contributions to Virulence on Wheat

Marshall, R., Kombrink, A., Motteram, J., Loza‐Reyes, E., Lucas, J. A., Hammond-Kosack, K. E., Thomma, B. P. H. J., & Rudd, J. J. (2011) · PLANT PHYSIOLOGY · doi:10.1104/pp.111.176347 · Cited by 326 · see citing works

Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies

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The KA/KS Ratio Test for Assessing the Protein-Coding Potential of Genomic Regions: An Empirical and Simulation StudyPreprint

Nekrutenko, A., Makova, K. D., & Li, W. (2001) · Genome Research · doi:10.1101/gr.200901 · Cited by 324 · see citing works

Causes of evolutionary rate variation among protein sites

Echave, J., Spielman, S. J., & Wilke, C. O. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2015.18 · Cited by 323 · see citing works

Phylogenetic systematics turns over a new leaf

Lewis, P. O. (2001) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(00)02025-5 · Cited by 320 · see citing works

Codon substitution models based on residue similarity and their applications

Liu, X., Liu, H., Guo, W., & Yu, K. (2012) · Gene · doi:10.1016/j.gene.2012.07.075 · Cited by 1 · see citing works

An Empirical Codon Model for Protein Sequence Evolution

Kosiol, C., Holmes, I. H., & Goldman, N. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm064 · Cited by 186 · see citing works

Advantages of a Mechanistic Codon Substitution Model for Evolutionary Analysis of Protein-Coding Sequences

Miyazawa, S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028892 · Cited by 18 · see citing works

An Empirical Examination of the Utility of Codon-Substitution Models in Phylogeny Reconstruction

Ren, F., Tanaka, H., & Yang, Z. (2005) · Systematic Biology · doi:10.1080/10635150500354688 · Cited by 168 · see citing works

A codon model of nucleotide substitution with selection on synonymous codon usage

Kubatko, L. S., Shah, P., Herbei, R., & Gilchrist, M. A. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2015.08.026 · Cited by 16 · see citing works