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The Gene Structure and Expression Level Changes of the GH3 Gene Family in Brassica napus Relative to Its Diploid Ancestors

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Structural organization and functional divergence of high isoelectric point α-amylase genes in bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.)

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Molecular Phylogeny of the Sharks and Rays of Superorder Squalea Based on Mitochondrial Cytochrome b Gene

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Evaluation of candidate F-box genes for the pollen S of gametophytic self-incompatibility in the Pyrinae (Rosaceae) on the basis of their phylogenomic context

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GAI Homologues in the Hawaiian Silversword Alliance (Asteraceae-Madiinae): Molecular Evolution of Growth Regulators in a Rapidly Diversifying Plant Lineage

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Estimating Empirical Codon Hidden Markov Models

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Bifidochaetus, a new Arctic genus of freshwater Chaetonotida (Gastrotricha) from Spitsbergen revealed by an integrative taxonomic approach

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Inner Ear Genes Underwent Positive Selection and Adaptation in the Mammalian Lineage

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New candidate species most closely related to penguins

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The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring

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Mitochondrial genomes advance phylogenetic hypotheses for Tylenchina (Nematoda: Chromadorea)

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A system-level, molecular evolutionary analysis of mammalian phototransduction

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Evaluation of Methods to Detect Shifts in Directional Selection at the Genome Scale

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Comparative analysis of evolutionary modes in Mc1r coat color gene in wild mice and mustelids

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In silico identification of functional divergence between the multiple groEL gene paralogs in Chlamydiae

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Detecting natural selection in RNA virus populations using sequence summary statistics

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Are Residues in a Protein Folding Nucleus Evolutionarily Conserved?

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Adaptive Patterns of Mitogenome Evolution Are Associated with the Loss of Shell Scutes in Turtles

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A Rapidly Diverging EGF Protein Regulates Species-Specific Signal Transduction in Early Sea Urchin Development

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A murine specific expansion of the Rhox cluster involved in embryonic stem cell biology is under natural selection

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Nucleotide sequence of rbcL and phylogenetic relationships of Setchellanthus caeruleus (Setchellanthaceae)

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Empirical Analysis of the Most Relevant Parameters of Codon Substitution Models

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Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin

Meyer, A. G., Dawson, E. T., & Wilke, C. O. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2012.0334 · Cited by 29

Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence

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Egg Coat Proteins Across Metazoan Evolution

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Genome Wild Analysis and Molecular Understanding of the Aquaporin Diversity in Olive Trees (Olea Europaea L.)

Faize, M., Fumanal, B., Luque, F., Ramírez‐Tejero, J. A., Zou, Z., Qiao, X., Faize, L., Gousset‐Dupont, A., Roeckel‐Drevet, P., Label, P., et al. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21114183 · Cited by 29

Molecular evolution and diversification of the GRF transcription factor family

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A large accessory genome and high recombination rates may influence global distribution and broad host range of the fungal plant pathogen Claviceps purpurea

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Purifying selection in mitochondria, free-living and obligate intracellular proteobacteria.

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Repertoire and evolution of TNF superfamily in Crassostrea gigas: Implications for expansion and diversification of this superfamily in Mollusca

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Genetic variation in East-Adriatic populations of the Asian tiger mosquito, Aedes albopictus (Diptera: Culicidae), inferred from NADH5 and COI sequence variability

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Bayesian Comparisons of Codon Substitution Models

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Selection for Higher Gene Copy Number after Different Types of Plant Gene Duplications

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In Silico Comparative Transcriptome Analysis of Two Color Morphs of the Common Coral Trout (Plectropomus Leopardus)

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Applications of Ancestral Protein Reconstruction in Understanding Protein Function: GFP-Like Proteins

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Molecular and morphological phylogeny of Menispermaceae (Ranunculales)

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Molecular Evolution and Positive Selection of the Symbiotic Gene NORK in Medicago truncatula

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Improved techniques for the identification of pseudogenes

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A phylogenetic analysis of the pSymB replicon from the Sinorhizobium meliloti genome reveals a complex evolutionary history

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Correction: Molecular Evolution of Vertebrate Neurotrophins: Co-Option of the Highly Conserved Nerve Growth Factor Gene into the Advanced Snake Venom Arsenalf

Sunagar, K., Fry, B. G., Jackson, T., Casewell, N. R., Undheim, E. A. B., Vidal, N., Ali, S. A., King, G. F., Vasudevan, K., Vasconcelos, V. M., et al. (2013) · PLoS ONE · doi:10.1371/annotation/accecc73-91b2-45d4-bb33-774b1f394ca1 · Cited by 30

The role of metabolism in shaping enzyme structures over 400 million years

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Shifting habitats, morphology, and selective pressures: Developmental polyphenism in an adaptive radiation of Hawaiian spiders

Brewer, M. S., Carter, R. A., Croucher, P. J. P., & Gillespie, R. G. (2014) · Evolution · doi:10.1111/evo.12563 · Cited by 28

Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models

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The TIFY Gene Family in Wheat and its Progenitors: Genome-wide Identification, Evolution and Expression Analysis

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Adaptive Evolution Targets a piRNA Precursor Transcription Network

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Genome-Wide Analysis of Nubian Ibex Reveals Candidate Positively Selected Genes That Contribute to Its Adaptation to the Desert Environment

Chebii, V. J., Oyola, S. O., Kotzé, A., Entfellner, J.-B. D., Mutuku, J. M., & Agaba, M. K. (2020) · Animals · doi:10.3390/ani10112181 · Cited by 29

HYPERMUTABILITY OFHOXA13AAND FUNCTIONAL DIVERGENCE FROM ITS PARALOG ARE ASSOCIATED WITH THE ORIGIN OF A NOVEL DEVELOPMENTAL FEATURE IN ZEBRAFISH AND RELATED TAXA (CYPRINIFORMES)

Crow, K. D., Amemiya, C. T., Roth, J. J., & Wagner, G. P. (2009) · Evolution · doi:10.1111/j.1558-5646.2009.00657.x · Cited by 28

RIBOSOMAL RNA GENE DIVERSITY, EFFECTIVE POPULATION SIZE, AND EVOLUTIONARY LONGEVITY IN ASEXUAL GLOMEROMYCOTA

VanKuren, N. W., den Bakker, H. C., Morton, J. B., & Pawlowska, T. E. (2012) · Evolution · doi:10.1111/j.1558-5646.2012.01747.x · Cited by 28

Molecular adaptation in Rubisco: Discriminating between convergent evolution and positive selection using mechanistic and classical codon models

Parto, S., & Lartillot, N. (2018) · PLoS ONE · doi:10.1371/journal.pone.0192697 · Cited by 30

Exploring Molecular Evolution Reconstruction Using a Parallel Cloud Based Scientific Workflow

Ocaña, K., de Oliveira, D., Horta, F., Dias, J., Ogasawara, E., & Mattoso, M. (2012) · Lecture notes in computer science · doi:10.1007/978-3-642-31927-3_16 · Cited by 28

Positive Darwinian Selection Promotes Heterogeneity Among Members of the Antifreeze Protein Multigene Family

Swanson, W. J., & Aquadro, C. F. (2002) · Journal of Molecular Evolution · doi:10.1007/s00239-001-0030-0 · Cited by 28

Adaptive evolution after duplication of penaeidin antimicrobial peptides

Padhi, A., Verghese, B., Otta, S. K., Varghese, B., & Ramu, K. (2007) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2007.01.003 · Cited by 28

Pattern of synonymous and nonsynonymous substitutions: An indicator of mechanisms of molecular evolution

Ina, Y. (1996) · Journal of Genetics · doi:10.1007/bf02931754 · Cited by 28

Human–Mouse Gene Identification by Comparative Evidence Integration and Evolutionary AnalysisPreprint

Zhang, L., Pavlović, V., Cantor, C. R., & Kasif, S. (2003) · Genome Research · doi:10.1101/gr.703903 · Cited by 28

Similar Relative Mutation Rates in the Three Genetic Compartments of Mesostigma and Chlamydomonas

Hua, J., Smith, D. R., Borza, T., & Lee, R. W. (2011) · Protist · doi:10.1016/j.protis.2011.04.003 · Cited by 27

Selective constraints on protamine 2 in primates and rodents

Arévalo, L., Tourmente, M., Dopazo, H., Serra, F., & Roldán, E. R. S. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0588-1 · Cited by 27

Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response

Lynch, M. J., Walsh, T., Marszalowska, I., Webb, A. E., MacAogain, M., Rogers, T. R., Windle, H. J., Kelleher, D. P., O’Connell, M. J., & Loscher, C. E. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-0937-8 · Cited by 27

Identification and characterization of RING-finger ubiquitin ligase UBR7 in mammalian spermatozoa

Zimmerman, S. W., Yi, Y., Sutovsky, M., van Leeuwen, F. W., Conant, G. C., & Šutovský, P. (2014) · Cell and Tissue Research · doi:10.1007/s00441-014-1808-x · Cited by 29

Sequence Variation and Expression Analysis of Seed Dormancy- and Germination-Associated ABA- and GA-Related Genes in Rice Cultivars

Liu, F., Zhang, H., Wu, G., Sun, J., Hao, L., Ge, X., Yu, J. M., & Wang, W. (2011) · Frontiers in Plant Science · doi:10.3389/fpls.2011.00017 · Cited by 27

Isolation of Prasinoviruses of the Green Unicellular Algae Ostreococcus spp. on a Worldwide Geographical Scale

Bellec, L., Grimsley, N. H., & Desdevises, Y. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01799-09 · Cited by 27

Two mitochondrial genes under episodic positive selection in subterranean octodontoid rodents

Tomasco, I. H., & Lessa, E. P. (2013) · Gene · doi:10.1016/j.gene.2013.09.097 · Cited by 27

Isolation, annotation and applications of expressed sequence tags from the olive fly, Bactrocera oleae

Tsoumani, K. T., Augustinos, A. A., Kakani, E. G., Drosopoulou, E., Mavragani-Tsipidou, P., & Mathiopoulos, K. D. (2010) · Molecular Genetics and Genomics · doi:10.1007/s00438-010-0583-y · Cited by 27

Multilocus Patterns of Polymorphism and Selection Across the X Chromosome of Caenorhabditis remanei

Cutter, A. D. (2008) · Genetics · doi:10.1534/genetics.107.085803 · Cited by 27

Diversification of porcine MHC class II genes: evidence for selective advantage

Luetkemeier, E. S., Malhi, R. S., Beever, J. E., & Schook, L. B. (2009) · Immunogenetics · doi:10.1007/s00251-008-0348-5 · Cited by 27

Dating and functional characterization of duplicated genes in the apple (Malus domestica Borkh.) by analyzing EST data

Sanzol, J. (2010) · BMC Plant Biology · doi:10.1186/1471-2229-10-87 · Cited by 28

Molecular and Phenotypic Characterization of a Highly Evolved Type 2 Vaccine-Derived Poliovirus Isolated from Seawater in Brazil, 2014

Cassemiro, K. M. S. D. M., Burlandy, F. M., Barbosa, M. R. F., Chen, Q., Jorba, J. C., Hachich, E. M., Sato, M. I. Z., Burns, C. C., & da Silva, E. E. (2016) · PLoS ONE · doi:10.1371/journal.pone.0152251 · Cited by 27

Subgenome‐specific assembly of vitamin E biosynthesis genes and expression patterns during seed development provide insight into the evolution of oat genome

Gutierrez-Gonzalez, J. J., & Garvin, D. F. (2016) · Plant Biotechnology Journal · doi:10.1111/pbi.12571 · Cited by 27

Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) – Insights from transcriptome sequences

Yu, Y., Xiang, Q., Manos, P. S., Soltis, P. S., Soltis, P. S., Song, B., Cheng, S., Liu, X., & Wong, G. K. (2017) · PLoS ONE · doi:10.1371/journal.pone.0171361 · Cited by 29

Genomic Insights into Evolution of AdpA Family Master Regulators of Morphological Differentiation and Secondary Metabolism in Streptomyces

Rabyk, M., Yushchuk, O., Rokytskyy, I., Anisimova, M. O., & Ostash, B. O. (2018) · Journal of Molecular Evolution · doi:10.1007/s00239-018-9834-z · Cited by 27

Parallel Acceleration of Evolutionary Rates in Symbiont Genes Underlying Host Nutrition

Wernegreen, J. J., Richardson, A. O., & Moran, N. A. (2001) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.2001.0929 · Cited by 27

Comparative mapping, genomic structure, and expression analysis of eight pseudo-response regulator genes in Brassica rapa

Kim, J. A., Kim, J. S., Hong, J. K., Lee, Y.-H., Choi, B., Seol, Y., & Jeon, C. H. (2012) · Molecular Genetics and Genomics · doi:10.1007/s00438-012-0682-z · Cited by 27

Is the Synonymous Substitution Rate in Mammals Gene-Specific?

Williams, E. J. B., & Hurst, L. D. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004202 · Cited by 27

Estimation of genetic distances from human and mouse introns

Castresana, J. (2002) · Genome biology · doi:10.1186/gb-2002-3-6-research0028 · Cited by 27

Selection on Coding Regions Determined Hox7 Genes Evolution

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PAML (Phylogenetic Analysis by Maximum Likelihood)

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