Evolution, Molecular Concept

subject area of

• 17th Century Variola Virus Reveals the Recent History of Smallpox  Journal Articles
• d -Ala- d -Ala ligases from glycopeptide antibiotic-producing organisms are highly homologous to the enterococcal vancomycin-resistance ligases VanA and VanB  Journal Articles
• A Genomic Comparison of Faster-Sex, Faster-X, and Faster-Male Evolution Between Drosophila melanogaster and Drosophila pseudoobscura  Journal Articles
• A Large Pseudoautosomal Region on the Sex Chromosomes of the Frog Silurana tropicalis  Journal Articles
• A Population Genetics Model for Multiple Quantitative Traits Exhibiting Pleiotropy and Epistasis  Journal Articles
• A Single Amino Acid Change in the Response Regulator PhoP, Acquired during Yersinia pestis Evolution, Affects PhoP Target Gene Transcription and Polymyxin B Susceptibility  Journal Articles
• A Thermodynamic Basis for Prebiotic Amino Acid Synthesis and the Nature of the First Genetic Code  Journal Articles
• A Unified Model of Codon Reassignment in Alternative Genetic Codes  Journal Articles
• A brief review of vertebrate sex evolution with a pledge for integrative research: towards ‘sexomics’  Journal Articles
• A coalescent framework for comparing alternative models of population structure with genetic data: evolution of Celebes toads  Journal Articles
• A comprehensive genomic history of extinct and living elephants  Journal Articles
• A draft genome of Yersinia pestis from victims of the Black Death  Journal Articles
• A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code  Journal Articles
• A functionally divergent hydrogenosomal peptidase with protomitochondrial ancestry  Journal Articles
• A general mechanism for conditional expression of exaggerated sexually‐selected traits  Journal Articles
• A heteroplasmic mitochondrial complex I gene mutation in adult-onset dystonia  Journal Articles
• A high‐quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation  Journal Articles
• A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution  Journal Articles
• A phylogenetic analysis of the pSymB replicon from the Sinorhizobium meliloti genome reveals a complex evolutionary history  Journal Articles
• A phylogenomic framework and timescale for comparative studies of tunicates  Journal Articles
• A spliceosomal intron in Giardia lamblia  Journal Articles
• A unique Malpighian tubule architecture in Tribolium castaneum informs the evolutionary origins of systemic osmoregulation in beetles  Journal Articles
• Abundant sequence variation around the mitochondrial origin of replication in the human opportunistic yeast pathogen Candida albicans from a tropical island in China  Journal Articles
• Accelerated Evolutionary Rate of Housekeeping Genes in Tunicates  Journal Articles
• Aminoglycoside phosphotransferases: proteins, structure, and mechanism  Journal Articles
• An Evolutionary Genetic Perspective of Eating Disorders  Journal Articles
• An ancestral mitochondrial DNA resembling a eubacterial genome in miniature  Journal Articles
• An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models  Journal Articles
• Analysis of Canis mitochondrial DNA demonstrates high concordance between the control region and ATPase genes  Journal Articles
• Ancestry Influences the Fate of Duplicated Genes Millions of Years After Polyploidization of Clawed Frogs (Xenopus)  Journal Articles
• Ancient DNA and the tropics: a rodent's tale  Journal Articles
• Ancient selection for derived alleles at a GDF5 enhancer influencing human growth and osteoarthritis risk  Journal Articles
• Ancyromonadida: A New Phylogenetic Lineage Among the Protozoa Closely Related to the Common Ancestor of Metazoans, Fungi, and Choanoflagellates (Opisthokonta)  Journal Articles
• AnnoTree: visualization and exploration of a functionally annotated microbial tree of life  Journal Articles
• Armadillos exhibit less genetic polymorphism in North America than in South America: nuclear and mitochondrial data confirm a founder effect in Dasypus novemcinctus (Xenarthra)  Journal Articles
• Asymmetrical Evolution of Cytochrome bd Subunits  Journal Articles
• Bacterial evolution: Making a host-adapted bacterium  Journal Articles
• Bats and Coronaviruses  Journal Articles
• Bayesian Phylogenetics Using an RNA Substitution Model Applied to Early Mammalian Evolution  Journal Articles
• Botulinum neurotoxin homologs in non‐Clostridium species  Journal Articles
• Broad-sense sexual selection, sex gene pool evolution, and speciation  Journal Articles
• Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites  Journal Articles
• Caenorhabditis briggsae Recombinant Inbred Line Genotypes Reveal Inter-Strain Incompatibility and the Evolution of Recombination  Journal Articles
• Cancer phenomics: RET and PTEN as illustrative models  Journal Articles
• Characterization of a cetacean aromatase (CYP19) and the phylogeny and functional conservation of vertebrate aromatase  Journal Articles
• Characterization of the mouse lysosomal sialidase promoter  Journal Articles
• Childhood cerebellar tumours mirror conserved fetal transcriptional programs  Journal Articles
• Chimeric Structure of the NAD(P)+- and NADP+-dependent Malic Enzymes ofRhizobium (Sinorhizobium) meliloti  Journal Articles
• Chlamydiae-specific proteins and indels: novel tools for studies  Journal Articles
• Chromosomal Rearrangements between Serotype A and D Strains in Cryptococcus neoformans  Journal Articles
• Clades of huge phages from across Earth’s ecosystems  Journal Articles
• Co-operation between Polymerases and Nucleotide Synthetases in the RNA World  Journal Articles
• Codon Usage and Selection on Proteins  Journal Articles
• Codon Usage in Mitochondrial Genomes: Distinguishing Context-Dependent Mutation from Translational Selection  Journal Articles
• Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus  Journal Articles
• Coevolution of Codon Usage and tRNA Genes Leads to Alternative Stable States of Biased Codon Usage  Journal Articles
• Cold-Active Winter Rye Glucanases with Ice-Binding Capacity  Journal Articles
• Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum  Journal Articles
• Comments on “Evolutionary dynamics of RNA-like replicator systems”  Journal Articles
• Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution  Journal Articles
• Comparative chromosome painting of pronghorn (Antilocapra americana) and saola (Pseudoryx nghetinhensis) karyotypes with human and dromedary camel probes  Journal Articles
• Comparative molecular phylogeography of two Xenopus species, X. gilli and X. laevis, in the south‐western Cape Province, South Africa  Journal Articles
• Comparison of mitochondrial genomes provides insights into intron dynamics and evolution in the caterpillar fungus Cordyceps militaris  Journal Articles
• Compensatory neutral mutations and the evolution of RNA.  Journal Articles
• Conservation of Lotus and Arabidopsis Basic Helix-Loop-Helix Proteins Reveals New Players in Root Hair Development      Journal Articles
• Conserved Features and Evolutionary Shifts of the EDA Signaling Pathway Involved in Vertebrate Skin Appendage Development  Journal Articles
• Conserved domains of the class A scavenger receptors: evolution and function  Journal Articles
• Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth  Journal Articles
• Constraining the Time Interval for the Origin of Life on Earth  Journal Articles
• Contemporary Gene Flow is a Major Force Shaping the Aspergillus fumigatus Population in Auckland, New Zealand  Journal Articles
• Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.  Journal Articles
• Convergent evolution of signal-structure interfaces for maintaining symbioses  Journal Articles
• Correlations in the population structure of music, genes and language  Journal Articles
• DIVERSIFICATION OF SULAWESI MACAQUE MONKEYS: DECOUPLED EVOLUTION OF MITOCHONDRIAL AND AUTOSOMAL DNA  Journal Articles
• DNA Sequence Analyses Reveal Abundant Diversity, Endemism and Evidence for Asian Origin of the Porcini Mushrooms  Journal Articles
• DNA and the revolutions of molecular evolution, computational biology, and bioinformatics  Journal Articles
• DNAzymes: From Creation In Vitro to Application In Vivo  Journal Articles
• Darwin to DNA, molecules to morphology: the end of classical population genetics and the road ahead  Journal Articles
• Detecting recent speciation events: the case of the finless porpoise (genus Neophocaena)  Journal Articles
• Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum  Journal Articles
• Developmental Systems Drift and the Drivers of Sex Chromosome Evolution  Journal Articles
• Directionality in the evolution of influenza A haemagglutinin  Journal Articles
• Divergence, hybridization, and recombination in the mitochondrial genome of the human pathogenic yeast Cryptococcus gattii  Journal Articles
• Divergent subgenome evolution after allopolyploidization in African clawed frogs (Xenopus)  Journal Articles
• Divergent subgenome evolution in the allotetraploid frog Xenopus calcaratus  Journal Articles
• Diversity Considerations in HIV-1 Vaccine Selection  Journal Articles
• Does Gene Translocation Accelerate the Evolution of Laterally Transferred Genes?  Journal Articles
• Does your gene need a background check? How genetic background impacts the analysis of mutations, genes, and evolution  Journal Articles
• Drainage isolation and climate change-driven population expansion shape the genetic structures of Tuber indicum complex in the Hengduan Mountains region  Journal Articles
• Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization  Journal Articles
• EVOLUTION OF THE CLOSELY RELATED, SEX-RELATED GENES DM-W AND DMRT1 IN AFRICAN CLAWED FROGS (XENOPUS)  Journal Articles
• Ecological and physical barriers shape genetic structure of the Alpine porcini (Boletus reticuloceps)  Journal Articles
• Effects of contact structure on the transient evolution of HIV virulence  Journal Articles
• Elucidating Evolutionary Mechanisms and Variants of the Hammerhead Ribozyme Using In Vitro Selection  Journal Articles
• Emerging evolutionary paradigms in antibiotic discovery  Journal Articles
• Enzyme Evolution Explained (Sort Of)  Journal Articles
• Erratum to “Evidence for the monophyletic evolution of benzylisoquinoline alkaloid biosynthesis in angiosperms” [Phytochemistry 66 (2005) 1374–1393]  Journal Articles
• Estimating Selection Pressures from Limited Comparative Data  Journal Articles
• Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss  Journal Articles
• Estimation of Gene Insertion/Deletion Rates with Missing Data  Journal Articles
• Evidence for canalization of Distal‐less function in the leg of Drosophila melanogaster  Journal Articles
• Evidence for the monophyletic evolution of benzylisoquinoline alkaloid biosynthesis in angiosperms.  Journal Articles
• Evolution and persistence of influenza A and other diseases  Journal Articles
• Evolution of Eukaryotic Transcription: Insights From the Genome of Giardia lamblia  Journal Articles
• Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression  Journal Articles
• Evolution of Proteasome Regulators in Eukaryotes  Journal Articles
• Evolution of RAG-1 in Polyploid Clawed Frogs  Journal Articles
• Evolution of RNA Viruses: Reasons for the Existence of Separate Plus, Minus, and Double-Strand Replication Strategies  Journal Articles
• Evolution of Salmonella-Host Cell Interactions through a Dynamic Bacterial Genome  Journal Articles
• Evolution of Simple Sequence in Proteins  Journal Articles
• Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions  Journal Articles
• Evolution of Transcriptional Repressors Impacts Caenorhabditis Vulval Development  Journal Articles
• Evolution of an Enzyme from a Noncatalytic Nucleic Acid Sequence  Journal Articles
• Evolution of genes and genomes on the Drosophila phylogeny  Journal Articles
• Evolution of mitochondrial-encoded cytochrome oxidase subunits in endothermic fish: The importance of taxon-sampling in codon-based models  Journal Articles
• Evolution of protein interfaces in multimers and fibrils  Journal Articles
• Evolution of the Largest Mammalian Genome  Journal Articles
• Evolution of the RpoS Regulon: Origin of RpoS and the Conservation of RpoS-Dependent Regulation in Bacteria  Journal Articles
• Evolution of the nuclear-encoded cytochrome oxidase subunits in vertebrates  Journal Articles
• Evolutionary affinity of billfishes (Xiphiidae and Istiophoridae) and flatfishes (Plueronectiformes): Independent and trans-subordinal origins of endothermy in teleost fishes  Journal Articles
• Evolutionary analysis of selective constraints identifies ameloblastin (AMBN) as a potential candidate for amelogenesis imperfecta  Journal Articles
• Evolutionary and Functional Analyses of the Interaction between the Myeloid Restriction Factor SAMHD1 and the Lentiviral Vpx Protein  Journal Articles
• Evolutionary and cellular webs in benzylisoquinoline alkaloid biosynthesis  Journal Articles
• Evolutionary and functional diversity of the Pseudomonas type IVa pilin island  Journal Articles
• Evolutionary and mechanistic insights into substrate and product accommodation of CTP:phosphocholine cytidylyltransferase from Plasmodium falciparum  Journal Articles
• Evolutionary implications of the relationship between genome size and body size in flatworms and copepods  Journal Articles
• Evolutionary origins of two tightly linked mutations in arylsulfatase-A pseudodeficiency  Journal Articles
• Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis  Journal Articles
• Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction  Journal Articles
• Examining the molecular clock hypothesis for the contemporary evolution of the rabies virus.  Journal Articles
• Factors Affecting the Errors in the Estimation of Evolutionary Distances Between Sequences  Journal Articles
• Factors affecting germline mutations in a hypervariable microsatellite: A comparative analysis of six species of swallows (Aves: Hirundinidae)  Journal Articles
• Fluctuation domains in adaptive evolution  Journal Articles
• Fossil Rhabdoviral Sequences Integrated into Arthropod Genomes: Ontogeny, Evolution, and Potential Functionality  Journal Articles
• From p63 to p53 across p73  Journal Articles
• Functional Divergence in the Arabidopsis  -1,3-Glucanase Gene Family Inferred by Phylogenetic Reconstruction of Expression States  Journal Articles
• Fundamentals of Fungal Molecular Population Genetic Analyses  Journal Articles
• Fungal mitochondrial genomes and genetic polymorphisms  Journal Articles
• Gene Gain and Gene Loss in Streptococcus: Is It Driven by Habitat?  Journal Articles
• Gene duplication and divergence produce divergent MHC genotypes without disassortative mating  Journal Articles
• Genetic Changes Accompanying the Evolution of Host Specialization in Drosophila sechellia  Journal Articles
• Genome duplication events have led to a diversification in the CPT I gene family in fish  Journal Articles
• Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A  Journal Articles
• Genome sequence of the button mushroomAgaricus bisporusreveals mechanisms governing adaptation to a humic-rich ecological niche  Journal Articles
• Genomic Dynamics of Transposable Elements in the Western Clawed Frog (Silurana tropicalis)  Journal Articles
• Genomic insights into the evolution and ecology of botulinum neurotoxins  Journal Articles
• Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria  Journal Articles
• Haplotype-resolved genome of a papeda provides insights into the geographical origin and evolution of Citrus.  Journal Articles
• Heterotachy and long-branch attraction in phylogenetics  Journal Articles
• High divergence of reproductive tract proteins and their association with postzygotic reproductive isolation in Drosophila melanogaster and Drosophila virilis group species  Journal Articles
• High rates of lateral gene transfer are not due to false diagnosis of gene absence  Journal Articles
• Horizontal Gene Transfer Contributed to the Evolution of Extracellular Surface Structures: The Freshwater Polyp Hydra Is Covered by a Complex Fibrous Cuticle Containing Glycosaminoglycans and Proteins of the PPOD and SWT (Sweet Tooth) Families  Journal Articles
• Identification of a diphtheria toxin‐like gene family beyond the Corynebacterium genus  Journal Articles
• Identification of the Regulatory Logic Controlling Salmonella Pathoadaptation by the SsrA-SsrB Two-Component System  Journal Articles
• Increased Polymorphism Near Low-Complexity Sequences across the Genomes of Plasmodium falciparum Isolates  Journal Articles
• Increased Substitution Rates Surrounding Low-Complexity Regions within Primate Proteins  Journal Articles
• Inferring Bacterial Genome Flux While Considering Truncated Genes  Journal Articles
• Inferring sequence regions under functional divergence in duplicate genes  Journal Articles
• Influence of Humans on Evolution and Mobilization of Environmental Antibiotic Resistome  Journal Articles
• Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans.  Journal Articles
• Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster  Journal Articles
• Intron-specific patterns of divergence of lin-11 regulatory function in the C. elegans nervous system  Journal Articles
• JOINT RECONSTRUCTION OF DIVERGENCE TIMES AND LIFE-HISTORY EVOLUTION IN PLACENTAL MAMMALS USING A PHYLOGENETIC COVARIANCE MODEL  Journal Articles
• Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits  Journal Articles
• Lateral Gene Transfer Dynamics in the Ancient Bacterial GenusStreptomyces  Journal Articles
• Les datations moléculaires à l’heure de la génomique  Journal Articles
• Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals  Journal Articles
• Lessons from the Environmental Antibiotic Resistome  Journal Articles
• Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function  Journal Articles
• Local Molecular Clocks in Three Nuclear Genes: Divergence Times for Rodents and Other Mammals and Incompatibility Among Fossil Calibrations  Conferences
• Low Complexity Regions in Mammalian Proteins are Associated with Low Protein Abundance and High Transcript Abundance  Journal Articles
• Low-complexity sequences and single amino acid repeats: not just “junk” peptide sequences  Journal Articles
• Male sex drive and the masculinization of the genome  Journal Articles
• Mammalian Sperm Proteins Are Rapidly Evolving: Evidence of Positive Selection in Functionally Diverse Genes  Journal Articles
• Microbial systematics in the post-genomics era  Journal Articles
• Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements  Journal Articles
• Mitonuclear interactions and introgression genomics of macaque monkeys ( Macaca ) highlight the influence of behaviour on genome evolution  Journal Articles
• Modular Evolution and the Origins of Symmetry: Reconstruction of a Three-Fold Symmetric Globular Protein  Journal Articles
• Molecular Evolution of Cytochrome c Oxidase Underlies High-Altitude Adaptation in the Bar-Headed Goose  Journal Articles
• Molecular Evolution of Respiratory Syncytial Virus Fusion Gene, Canada, 2006–2010  Journal Articles
• Molecular Phylogeny of Living Xenarthrans and the Impact of Character and Taxon Sampling on the Placental Tree Rooting  Journal Articles
• Molecular Polymorphism and Divergence of Duplicated Genes in Tetraploid African Clawed Frogs <b><i>(Xenopus)</i></b>  Journal Articles
• Molecular evidence for increased regulatory conservation during metamorphosis, and against deleterious cascading effects of hybrid breakdown in Drosophila  Journal Articles
• Molecular evidence of sequential evolution of DDT- and pyrethroid-resistant sodium channel in Aedes aegypti  Journal Articles
• Molecular evolution of the vesicle coat component βCOP in Toxoplasma gondii  Journal Articles
• Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups  Journal Articles
• Molecular, developmental, and evolutionary genetic studies highlight rapid evolution of genes and genetic systems  Journal Articles
• Multicopy gene family evolution on primate Y chromosomes  Journal Articles
• Multilocus sequence analyses reveal extensive diversity and multiple origins of fluconazole resistance in Candida tropicalis from tropical China  Journal Articles
• Multiple Mechanisms Promote the Retained Expression of Gene Duplicates in the Tetraploid Frog Xenopus laevis  Journal Articles
• Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans  Journal Articles
• Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD  Journal Articles
• Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins  Journal Articles
• Naked but Not Hairless: The Pitfalls of Analyses of Molecular Adaptation Based on Few Genome Sequence Comparisons  Journal Articles
• Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes  Journal Articles
• Neurological Proteins Are Not Enriched For Repetitive Sequences  Journal Articles
• New Insights into 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Phylogeny, Evolution and Ecological Significance  Journal Articles
• New insights into Xenopus sex chromosome genomics from the Marsabit clawed frog X. borealis  Journal Articles
• Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae)  Journal Articles
• Non-neutral evolution and reciprocal monophyly of two expressed Mhc class II B genes in Leach’s storm-petrel  Journal Articles
• Novel Insights Into Immune Systems of Bats  Journal Articles
• Novel Molecular Signatures in the PIP4K/PIP5K Family of Proteins Specific for Different Isozymes and Subfamilies Provide Important Insights into the Evolutionary Divergence of this Protein Family  Journal Articles
• Novel molecular, structural and evolutionary characteristics of the phosphoketolases from bifidobacteria and Coriobacteriales  Journal Articles
• On selection in finite populations  Journal Articles
• On the Accessibility of Adaptive Phenotypes of a Bacterial Metabolic Network  Journal Articles
• Ontogeny and phylogeny: molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila  Journal Articles
• Origin and Spread of Photosynthesis Based upon Conserved Sequence Features in Key Bacteriochlorophyll Biosynthesis Proteins  Journal Articles
• Origin and evolution of gene families in Bacteria and Archaea  Journal Articles
• Origin of the RNA world: The fate of nucleobases in warm little ponds  Journal Articles
• OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals  Journal Articles
• Osteocalcin protein sequences of Neanderthals and modern primates  Journal Articles
• Partial 28S rDNA Sequences and the Antiquity of Hydrothermal Vent Endemic Gastropods  Journal Articles
• Pathways of Genetic Code Evolution in Ancient and Modern Organisms  Journal Articles
• Patterns of Bacterial Gene Movement  Journal Articles
• Pervasive Cryptic Epistasis in Molecular Evolution  Journal Articles
• Phage–antibiotic combinations: a promising approach to constrain resistance evolution in bacteria  Journal Articles
• Phenotypic Divergence along Geographic Gradients Reveals Potential for Rapid Adaptation of the White-Nose Syndrome Pathogen, Pseudogymnoascus destructans, in North America  Journal Articles
• Phylogenetic Analysis of the Cytochrome P450 3 (CYP3) Gene Family  Journal Articles
• Phylogenetic analysis of the 90 kD heat shock family of protein sequences and an examination of the relationship among animals, plants, and fungi species.  Journal Articles
• Phylogenetic and Functional Analysis of the Vertebrate Cytochrome P450 2 Family  Journal Articles
• Phylogenetic and functional analyses of the cytochrome P450 family 4  Journal Articles
• Phylogenetic reconciliation reveals the natural history of glycopeptide antibiotic biosynthesis and resistance  Journal Articles
• Phylogenomic Analysis and Predicted Physiological Role of the Proton-Translocating NADH:Quinone Oxidoreductase (Complex I) Across Bacteria  Journal Articles
• Phylogenomic and molecular marker based studies to clarify the evolutionary relationships amongst Anoxybacillus species and demarcation of the family Anoxybacillaceae and some of its constituent genera.  Journal Articles
• Phylogenomic and molecular markers based studies on clarifying the evolutionary relationships among Peptoniphilus species. Identification of several Genus-Level clades of Peptoniphilus species and transfer of some Peptoniphilus species to the genus Aedoeadaptatus  Journal Articles
• Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups  Journal Articles
• Phylogenomics and the reconstruction of the tree of life  Journal Articles
• Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B  Journal Articles
• Population Genetic Structure of Aldabra Giant Tortoises  Journal Articles
• Population Genetics Without Intraspecific Data  Journal Articles
• Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa  Journal Articles
• Possible Roles of Exceptionally Conserved Residues around the Selectivity Filters of Sodium and Calcium Channels  Journal Articles
• Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins  Journal Articles
• Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes  Journal Articles
• Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution  Journal Articles
• RNA Sequence Evolution With Secondary Structure Constraints: Comparison of Substitution Rate Models Using Maximum-Likelihood Methods  Journal Articles
• RNA secondary structure: physical and computational aspects  Journal Articles
• Rainbow trout exposed to benzo[a]pyrene yields conserved microRNA binding sites in DNA methyltransferases across 500 million years of evolution  Journal Articles
• Rapid Evolution Through Gene Duplication and Subfunctionalization of the Testes-Specific α4 Proteasome Subunits in DrosophilaSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY542377, AY542378, AY542379, AY542380, AY542381, AY542382, AY542383, AY542384, AY542385, AY542386, AY542387, AY542388, AY542389, AY542390, AY542391, AY542392, AY542393, AY542394, AY542395, AY542396, AY542397, AY542398, AY542399, AY542400, AY542401, AY542402, AY542403, AY542404, AY542405, AY542406, AY542407, AY542408, AY542409, AY542410, AY542411, AY542412, AY542413, AY542414, AY542415, AY542416, AY542417, AY542418, AY542419, AY542420, AY542421, AY542422, AY542423, AY542424, AY542425, AY542426, AY542427, AY542428, AY542429, AY542430, AY542431, AY542432.  Journal Articles
• Rapid Evolution of Outer Egg Membrane Proteins in the Drosophila melanogaster Subgroup: A Case of Ecologically Driven Evolution of Female Reproductive Traits  Journal Articles
• Rapid Evolution of cis-Regulatory Sequences via Local Point Mutations  Journal Articles
• Rapid Evolution of the Sex-Determining Gene, transformer: Structural Diversity and Rate Heterogeneity Among Sibling Species of Drosophila  Journal Articles
• Rapidly Evolving Genes of Drosophila: Differing Levels of Selective Pressure in Testis, Ovary, and Head Tissues Between Sibling Species  Journal Articles
• Reduced Representation Genome Sequencing Suggests Low Diversity on the Sex Chromosomes of Tonkean Macaque Monkeys  Journal Articles
• Regulatory Evolution of a Duplicated Heterodimer Across Species and Tissues of Allopolyploid Clawed Frogs (Xenopus)  Journal Articles
• Regulatory evolution at the host–pathogen interface  Journal Articles
• Relaxed Molecular Clock Provides Evidence for Long-Distance Dispersal of Nothofagus (Southern Beech)  Journal Articles
• Replication of an Egfr-Wing Shape Association in a Wild-Caught Cohort of Drosophila melanogaster  Journal Articles
• Resolving the root of the avian mitogenomic tree by breaking up long branches  Journal Articles
• Retroposed Elements and Their Flanking Regions Resolve the Evolutionary History of Xenarthran Mammals (Armadillos, Anteaters, and Sloths)  Journal Articles
• Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti  Journal Articles
• Searching for Substitution Rate Heterogeneity  Journal Articles
• Second-Pandemic Strain ofVibrio choleraefrom the Philadelphia Cholera Outbreak of 1849  Journal Articles
• Selection and Slippage Creating Serine Homopolymers  Journal Articles
• Sequence variation at the major histocompatibility complex DRB loci in beluga ( Delphinapterus leucas ) and narwhal ( Monodon monoceros )  Journal Articles
• Sex gene pool evolution and speciation: A new paradigm  Journal Articles
• Sex-Linked Mammalian Sperm Proteins Evolve Faster Than Autosomal Ones  Journal Articles
• Sex-Specific Functional Specialization and the Evolutionary Rates of Essential Fertility Genes  Journal Articles
• Sex-related genes, directional sexual selection, and speciation  Journal Articles
• 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  Journal Articles
• Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans  Journal Articles
• Signature Sequences in Diverse Proteins Provide Evidence of a Close Evolutionary Relationship Between the Deinococcus-Thermus Group and Cyanobacteria  Journal Articles
• Signature proteins that are distinctive of alpha proteobacteria  Journal Articles
• Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality  Journal Articles
• Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements  Journal Articles
• Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome  Journal Articles
• Tetracycline-resistant coliforms in the effluent of the main sewage treatment plant in Hamilton, Ontario — do they have a common ancestral strain?  Journal Articles
• The C. difficile toxin B membrane translocation machinery is an evolutionarily conserved protein delivery apparatus  Journal Articles
• The Composite Genome of the Legume Symbiont Sinorhizobium meliloti  Journal Articles
• The Divided Bacterial Genome: Structure, Function, and Evolution  Journal Articles
• The Evolution of tRNA-Leu Genes in Animal Mitochondrial Genomes  Journal Articles
• The Evolutionary Origins of Eukaryotic Protein Disulfide Isomerase Domains: New Evidence from the Amitochondriate Protist Giardia lamblia  Journal Articles
• The Genesis and Spread of Reassortment Human Influenza A/H3N2 Viruses Conferring Adamantane Resistance  Journal Articles
• The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution  Journal Articles
• The Location of Substitutions and Bacterial Genome Arrangements  Journal Articles
• The Pattern of Amino Acid Replacements in α/β-Barrels  Journal Articles
• The Phylogeny and Signature Sequences Characteristics ofFibrobacteres,Chlorobi, andBacteroidetes  Journal Articles
• The RNA World: molecular cooperation at the origins of life  Journal Articles
• The Recovery, Interpretation and Use of Ancient Pathogen Genomes  Journal Articles
• The Relationship Between the Rate of Molecular Evolution and the Rate of Genome Rearrangement in Animal Mitochondrial Genomes  Journal Articles
• The Rift Valley is a major barrier to dispersal of African clawed frogs (Xenopus) in Ethiopia  Journal Articles
• The Roles of Standing Genetic Variation and Evolutionary History in Determining the Evolvability of Anti-Predator Strategies  Journal Articles
• The advantage of recombination when selection is acting at many genetic Loci  Journal Articles
• The advantages and disadvantages of horizontal gene transfer and the emergence of the first species  Journal Articles
• The antibiotic resistome: the nexus of chemical and genetic diversity  Journal Articles
• The effects of environmental and genetic factors on the germination of basidiospores in the Cryptococcus gattii species complex  Journal Articles
• The evolution of antibiotic production rate in a spatial model of bacterial competition  Journal Articles
• The evolution of the class A scavenger receptors  Journal Articles
• The fate of laterally transferred genes: Life in the fast lane to adaptation or death  Journal Articles
• The inheritance of organelle genes and genomes: patterns and mechanisms  Journal Articles
• The natural history of antibiotics  Journal Articles
• The newly characterized colicin Y provides evidence of positive selection in pore-former colicin diversification During the time this manuscript was being prepared for publication, our colleague James V. Neel passed away. The other authors wish to dedicate this work to his memory. The GenBank accession number for the sequence reported in this paper is AF197335.  Journal Articles
• The odds of duplicate gene persistence after polyploidization  Journal Articles
• The origin recognition complex protein family  Journal Articles
• The paradox of HBV evolution as revealed from a 16th century mummy  Journal Articles
• The proto-oncogene C-KIT maps to canid B-chromosomes  Journal Articles
• The role of laterally transferred genes in adaptive evolution  Journal Articles
• The shortest telomeres drive karyotype evolution in transformed cells  Journal Articles
• The structural basis of molecular adaptation  Journal Articles
• Thrice better than once: quality control guidelines to validate new mitogenomes  Journal Articles
• Time Dependency of Molecular Rates in Ancient DNA Data Sets, A Sampling Artifact?  Journal Articles
• Tipping the scales: Evolution of the allometric slope independent of average trait size  Journal Articles
• Transcriptome data reveal conserved patterns of fruiting body development and response to heat stress in the mushroom-forming fungus Flammulina filiformis  Journal Articles
• Trends in DNA barcoding and metabarcoding  Journal Articles
• Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny  Journal Articles
• Tunicates and not cephalochordates are the closest living relatives of vertebrates  Journal Articles
• Uncorrected Nucleotide Bias in mtDNA Can Mimic the Effects of Positive Darwinian Selection  Journal Articles
• Uncovering rate variation of lateral gene transfer during bacterial genome evolution  Journal Articles
• Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods  Journal Articles
• Xenopus fraseri: Mr. Fraser, where did your frog come from?  Journal Articles
• Yersinia pestis: New Evidence for an Old Infection  Journal Articles
• [MOLECULAR EVOLUTION OF ION CHANNELS: AMINO ACID SEQUENCES AND 3D STRUCTURES].  Journal Articles
• p73 and p63: Why Do We Still Need Them?  Journal Articles
• zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters.  Journal Articles