Evolution, Molecular

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  Subject Areas on Research

  • "Good enough solutions" and the genetics of complex diseases. 
  • 17^th Century Variola Virus Reveals the Recent History of Smallpox. 
  • 50 million years of genomic stasis in endosymbiotic bacteria. 
  • A Heritable Missense Polymorphism in CDKN2A Confers Strong Risk of Childhood Acute Lymphoblastic Leukemia and Is Preferentially Selected during Clonal Evolution. 
  • A brief review of vertebrate sex evolution with a pledge for integrative research: towards 'sexomics'. 
  • A class of viral inducer of degradation of the necroptosis adaptor RIPK3 regulates virus-induced inflammation. 
  • A conservative test of genetic drift in the endosymbiotic bacterium Buchnera: slightly deleterious mutations in the chaperonin groEL. 
  • A dimensionless number for understanding the evolutionary dynamics of antigenically variable RNA viruses 
  • A high-resolution map of human evolutionary constraint using 29 mammals. 
  • A higher-level phylogenetic classification of the Fungi 
  • A metabolic enzyme for S-nitrosothiol conserved from bacteria to humans. 
  • A minimal TrpRS catalytic domain supports sense/antisense ancestry of class I and II aminoacyl-tRNA synthetases. 
  • A modular switch for spatial Ca2+ selectivity in the calmodulin regulation of CaV channels. 
  • A molecular phylogeny of the fern family Pteridaceae: assessing overall relationships and the affinities of previously unsampled genera 
  • A multi-locus assessment of connectivity and historical demography in the bluehead wrasse (Thalassoma bifasciatum). 
  • A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes. 
  • A new perspective on lower metazoan relationships from 18S rDNA sequences. 
  • A novel murine protein with no effect on iron homoeostasis is homologous with transferrin and is the putative inhibitor of carbonic anhydrase. 
  • A phylogeny of Adelanthaceae (Jungermanniales, Marchantiophyta) based on nuclear and chloroplast DNA markers, with comments on classification, cryptic speciation and biogeography. 
  • A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta). 
  • A pipeline to determine RT-PCR control genes for evolutionary studies: application to primate gene expression across multiple tissues 
  • A re-evaluation of 12S ribosomal RNA variability in Drosophila pseudoobscura. 
  • A refined model of the genomic basis for phenotypic variation in vertebrate hemostasis. 
  • A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability. 
  • A stochastic evolutionary model for protein structure alignment and phylogeny. 
  • A survey of plant and algal genomes and transcriptomes reveals new insights into the evolution and function of the cellulose synthase superfamily. 
  • A taxonomic monograph of Ipomoea integrated across phylogenetic scales. 
  • A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny. 
  • A voltage-gated calcium-selective channel encoded by a sodium channel-like gene. 
  • Abrupt deceleration of molecular evolution linked to the origin of arborescence in ferns. 
  • Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. 
  • Abundant raw material for cis-regulatory evolution in humans. 
  • Adaptive Evolution of the GDH2 Allosteric Domain Promotes Gliomagenesis by Resolving IDH1R132H-Induced Metabolic Liabilities. 
  • Adaptive Radiation Genomics of Two Ecologically Divergent Hawai'ian Honeycreepers: The 'akiapōlā'au and the Hawai'i 'amakihi. 
  • Adaptive Transcriptome Profiling of Subterranean Zokor, Myospalax baileyi, to High- Altitude Stresses in Tibet. 
  • Adaptive evolution and fixation of drug-resistant Plasmodium falciparum genotypes in pregnancy-associated malaria: 9-year results from the QuEERPAM study. 
  • Adaptive evolution drives the diversification of zinc-finger binding domains. 
  • Adaptive evolution: evaluating empirical support for theoretical predictions. 
  • African origin of the malaria parasite Plasmodium vivax. 
  • Allele-specific assay reveals functional variation in the chalcone synthase promoter of Arabidopsis thaliana that is compatible with neutral evolution. 
  • Alternative Splicing of the Delta-Opioid Receptor Gene Suggests Existence of New Functional Isoforms. 
  • Alu Insertion Polymorphisms as Evidence for Population Structure in Baboons. 
  • An Evolutionary Insertion in the Mxra8 Receptor-Binding Site Confers Resistance to Alphavirus Infection and Pathogenesis. 
  • An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes. 
  • An allele of HRAS1 3'variable number of tandem repeats is a frailty allele: implication for an evolutionarily-conserved pathway involved in longevity. 
  • An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes. 
  • An integrated map of genetic variation from 1,092 human genomes. 
  • Analyses on mutation patterns, detection of population bottlenecks, and suggestion of deleterious-compensatory evolution among members of the genus Potyvirus. 
  • Ancestral and consensus envelope immunogens for HIV-1 subtype C. 
  • Ancestral population genomics: the coalescent hidden Markov model approach. 
  • Ancient DNA from giant extinct lemurs confirms single origin of Malagasy primates. 
  • Ancient and recent positive selection transformed opioid cis-regulation in humans. 
  • Ancient bacterial endosymbionts of insects: Genomes as sources of insight and springboards for inquiry. 
  • Ancient co-speciation of simian foamy viruses and primates. 
  • Ancient single origin for Malagasy primates. 
  • Ankyrins and cellular targeting of diverse membrane proteins to physiological sites. 
  • Ant Olfaction: Smells Like an Insect, Develops Like a Mammal. 
  • Antisense-Derived HIV-1 Cryptic Epitopes Are Not Major Drivers of Viral Evolution during the Acute Phase of Infection. 
  • Aquaporins in Saccharomyces. Genetic and functional distinctions between laboratory and wild-type strains. 
  • Arabidopsis functional genomics. 
  • Ascaris haemoglobin is a nitric oxide-activated 'deoxygenase'. 
  • Axon guidance pathways served as common targets for human speech/language evolution and related disorders. 
  • Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation. 
  • Bacteriophage flux in endosymbionts (Wolbachia): infection frequency, lateral transfer, and recombination rates. 
  • Bacteriophages that infect Gram-negative bacteria as source of signal-arrest-release motif lysins. 
  • Balancing selection and trans-specific polymorphisms. 
  • Beta2-adrenergic receptor gene polymorphisms as systemic determinants of healthy aging in an evolutionary context. 
  • Biogeographic distribution of polyploidy and B chromosomes in the apomictic Boechera holboellii complex. 
  • Biotic interactions. Genomics and coevolution. 
  • Boechera, a model system for ecological genomics. 
  • Bone-associated gene evolution and the origin of flight in birds. 
  • Breaking evolution's chains: the prospect of deliberate genetic modification in humans. 
  • CD4 receptor diversity in chimpanzees protects against SIV infection. 
  • CD69 gene is differentially regulated in T and B cells by evolutionarily conserved promoter-distal elements. 
  • Caspases: an ancient cellular sword of Damocles. 
  • Chemokine (C-C motif) receptor 5-using envelopes predominate in dual/mixed-tropic HIV from the plasma of drug-naive individuals. 
  • Chemoreception scientists gather under the Florida sun: The 31st Annual Association for Chemoreception Sciences meeting. 
  • Chromosomal sex-determining regions in animals, plants and fungi. 
  • Chromosome rearrangements via template switching between diverged repeated sequences. 
  • Circular RNAs are abundant, conserved, and associated with ALU repeats. 
  • Cis-regulatory evolution of chalcone-synthase expression in the genus Arabidopsis. 
  • Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. 
  • Combining and comparing morphometric shape descriptors with a molecular phylogeny: the case of fruit type evolution in Bornean Lithocarpus (Fagaceae) 
  • Combining expression and comparative evolutionary analysis. The COBRA gene family. 
  • Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris. 
  • Comparative Genomic Analysis of the Pheromone Receptor Class 1 Family (V1R) Reveals Extreme Complexity in Mouse Lemurs (Genus, Microcebus) and a Chromosomal Hotspot across Mammals. 
  • Comparative RNA sequencing reveals substantial genetic variation in endangered primates. 
  • Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee. 
  • Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. 
  • Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). 
  • Comparative genetic mapping in Boechera stricta, a close relative of Arabidopsis. 
  • Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. 
  • Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. 
  • Comparative genomics and regulatory evolution: conservation and function of the Chs and Apetala3 promoters. 
  • Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens. 
  • Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi. 
  • Comparative genomics reveals insights into avian genome evolution and adaptation. 
  • Comparative genomics search for losses of long-established genes on the human lineage. 
  • Comparative linkage maps suggest that fission, not polyploidy, underlies near-doubling of chromosome number within monkeyflowers (Mimulus; Phrymaceae). 
  • 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. 
  • Comparison of ribosomal DNA ITS regions among geographic isolates of Cenococcum geophilum. 
  • Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: a case for the genetic coherence of rhizobial lineages. 
  • Complete genomic and epigenetic maps of human centromeres. 
  • Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. 
  • Complex evolutionary trajectories of sex chromosomes across bird taxa. 
  • Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics. 
  • Connecting recombination, nucleotide diversity and species divergence in Drosophila. 
  • Consensus and ancestral state HIV vaccines. 
  • Conservation and diversification of SCARECROW in maize. 
  • Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases. 
  • Conservation genomic analysis reveals ancient introgression and declining levels of genetic diversity in Madagascar's hibernating dwarf lemurs. 
  • Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation. 
  • Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee. 
  • Conservation, duplication, and loss of the Tor signaling pathway in the fungal kingdom. 
  • Conserved organization of centromeric chromatin in flies and humans. 
  • Context-dependent effects of whole-genome duplication during mammary tumor recurrence. 
  • Contrasting quaternary histories in an ecologically divergent sister pair of low-dispersing intertidal fish (Xiphister) revealed by multilocus DNA analysis. 
  • Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. 
  • Convergent adaptation of human lactase persistence in Africa and Europe. 
  • Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. 
  • Convergent evolution of chromosomal sex-determining regions in the animal and fungal kingdoms. 
  • Convergent evolution of escape from hepaciviral antagonism in primates. 
  • Convergent evolution of linked mating-type loci in basidiomycete fungi. 
  • Convergent transcriptional specializations in the brains of humans and song-learning birds. 
  • Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution 
  • Correlation between env V1/V2 region diversification and neutralizing antibodies during primary infection by simian immunodeficiency virus sm in rhesus macaques. 
  • Cryptococcus gattii virulence composite: candidate genes revealed by microarray analysis of high and less virulent Vancouver island outbreak strains. 
  • Crystal structure of molybdopterin synthase and its evolutionary relationship to ubiquitin activation. 
  • Cytoskeleton. Evolution in bacteria. 
  • DEPDC1/LET-99 participates in an evolutionarily conserved pathway for anti-tubulin drug-induced apoptosis. 
  • DNA copy number evolution in Drosophila cell lines. 
  • DNA sequence characterization and molecular evolution of MAT1 and MAT2 mating-type loci of the self-compatible ascomycete mold Neosartorya fischeri. 
  • Darwinian genomics and diversity in the tree of life. 
  • Dating branches on the tree of life using DNA. 
  • De novo transcriptomics reveal distinct phototransduction signaling components in the retina and skin of a color-changing vertebrate, the hogfish (Lachnolaimus maximus). 
  • Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing. 
  • Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification. 
  • Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants. 
  • Delimiting species without nuclear monophyly in Madagascar's mouse lemurs. 
  • Density dependence and population differentiation of genetic architecture in Impatiens capensis in natural environments. 
  • Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs. 
  • Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish. 
  • Different models, different trees: the geographic origin of PTLV-I. 
  • Differential patterns of male and female mtDNA exchange across the Atlantic Ocean in the blue mussel, Mytilus edulis. 
  • Differential regulation of genes by retrotransposons in rice promoters. 
  • Dinucleotide repeats in the Drosophila and human genomes have complex, length-dependent mutation processes. 
  • Distinct properties of cell-type-specific and shared transcription factor binding sites. 
  • Distinctive variation in the U3R region of the 5' Long Terminal Repeat from diverse HIV-1 strains. 
  • Divergence between the Drosophila pseudoobscura and D. persimilis genome sequences in relation to chromosomal inversions. 
  • Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. 
  • Divergence of protein kinase A catalytic subunits in Cryptococcus neoformans and Cryptococcus gattii illustrates evolutionary reconfiguration of a signaling cascade. 
  • Diversification before the most recent glaciation in Balanus glandula. 
  • Diversity considerations in HIV-1 vaccine selection. 
  • Do asexual polyploid lineages lead short evolutionary lives? A case study from the fern genus Astrolepis 
  • Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution. 
  • Drosophila p120catenin plays a supporting role in cell adhesion but is not an essential adherens junction component. 
  • Dynamic evolution of base composition: causes and consequences in avian phylogenomics. 
  • Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles. 
  • Dynamic functional evolution of an odorant receptor for sex-steroid-derived odors in primates. 
  • EAG2 potassium channel with evolutionarily conserved function as a brain tumor target. 
  • Early specialization of the superfast myosin in extraocular and laryngeal muscles. 
  • Ecological transition predictably associated with gene degeneration. 
  • Effect of alternating passage on adaptation of sindbis virus to vertebrate and invertebrate cells. 
  • Effects of inversions on within- and between-species recombination and divergence. 
  • Electron transfer mechanisms. 
  • Emergence of SARS-CoV-2 through recombination and strong purifying selection. 
  • Endangered species hold clues to human evolution. 
  • Endosymbiont evolution: predictions from theory and surprises from genomes. 
  • Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts. 
  • Endosymbiosis: lessons in conflict resolution. 
  • Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. 
  • Escape from adaptive conflict after duplication in an anthocyanin pathway gene. 
  • Estimation of primate speciation dates using local molecular clocks. 
  • Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach. 
  • Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. 
  • Evidence for a one-allele assortative mating locus. 
  • Evidence for a single loss of mineralized teeth in the common avian ancestor. 
  • Evidence for conservation of architecture and physical properties of Omp85-like proteins throughout evolution. 
  • Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein-coding genes. 
  • Evidence for reciprocal origins in Polypodium hesperium (Polypodiaceae): A fern model system for investigating how multiple origins shape allopolyploid genomes 
  • Evidence of adaptive divergence in plasticity: density- and site-dependent selection on shade-avoidance responses in Impatiens capensis. 
  • Evidence that the human pathogenic fungus Cryptococcus neoformans var. grubii may have evolved in Africa. 
  • Evolution and antiviral activity of a human protein of retroviral origin. 
  • Evolution and diversity in human herpes simplex virus genomes. 
  • Evolution and probable transmission of intersubtype recombinant human immunodeficiency virus type 1 in a Zambian couple. 
  • Evolution of ASPM coding variation in apes and associations with brain structure in chimpanzees. 
  • Evolution of DNA Methylation in Papio Baboons. 
  • Evolution of Pleopsidium (lichenized Ascomycota) S943 group I introns and the phylogeography of an intron-encoded putative homing endonuclease. 
  • Evolution of a malaria resistance gene in wild primates. 
  • Evolution of a tumorigenic property conferred by glycophosphatidyl-inositol membrane anchors of carcinoembryonic antigen gene family members during the primate radiation. 
  • Evolution of budding yeast prion-determinant sequences across diverse fungi. 
  • Evolution of calcium-carbonate skeletons in the Hydractiniidae. 
  • Evolution of drug-resistant viral populations during interruption of antiretroviral therapy. 
  • Evolution of flux control in the glucosinolate pathway in Arabidopsis thaliana 
  • Evolution of flux control in the glucosinolate pathway in Arabidopsis thaliana. 
  • Evolution of fungal sex chromosomes. 
  • Evolution of genes and genomes on the Drosophila phylogeny. 
  • Evolution of host range in Coleosporium ipomoeae, a plant pathogen with multiple hosts. 
  • Evolution of multiple paralogous adenosine kinase genes in the moss genus Hygroamblystegium: phylogenetic implications. 
  • Evolution of niche preference in Sphagnum peat mosses. 
  • Evolution of osmosensing OSCA1 Ca²⁺ channel family coincident with plant transition from water to land. 
  • Evolution of pathogenicity and sexual reproduction in eight Candida genomes. 
  • Evolution of regeneration and fission in annelids: insights from engrailed- and orthodenticle-class gene expression. 
  • Evolution of resistance to a multiple-herbivore community: genetic correlations, diffuse coevolution, and constraints on the plant's response to selection. 
  • Evolution of the 12 kDa FK506-binding protein gene. 
  • Evolution of the Wnt pathways. 
  • Evolution of the bipolar mating system of the mushroom Coprinellus disseminatus from its tetrapolar ancestors involves loss of mating-type-specific pheromone receptor function. 
  • Evolution of the cytoskeleton. 
  • Evolution of the mating type locus: insights gained from the dimorphic primary fungal pathogens Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii. 
  • Evolution of the sex-related locus and genomic features shared in microsporidia and fungi. 
  • Evolution of the trnF(GAA) gene in Arabidopsis relatives and the brassicaceae family: monophyletic origin and subsequent diversification of a plastidic pseudogene. 
  • Evolution, interactions, and biological networks. 
  • Evolution. CNCing is believing. 
  • Evolutionarily Conserved and Divergent Roles of Unfolded Protein Response (UPR) in the Pathogenic Cryptococcus Species Complex. 
  • Evolutionarily conserved role of calcineurin in phosphodegron-dependent degradation of phosphodiesterase 4D. 
  • Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees. 
  • Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites. 
  • Evolutionary and biomedical insights from a marmoset diploid genome assembly. 
  • Evolutionary and ecological functional genomics. 
  • Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, "subfossil" koala lemur Megaladapis edwardsi. 
  • Evolutionary biology: Genes to make new species. 
  • Evolutionary bottlenecks in the agents of tuberculosis, leprosy, and paratuberculosis. 
  • Evolutionary design on a budget: robustness and optimality of bacteriophage T7. 
  • Evolutionary dissociations between homologous genes and homologous structures. 
  • Evolutionary dynamics and information hierarchies in biological systems. 
  • Evolutionary dynamics of an Arabidopsis insect resistance quantitative trait locus. 
  • Evolutionary dynamics of dual-specificity self-incompatibility alleles. 
  • Evolutionary genetics in wild primates: combining genetic approaches with field studies of natural populations. 
  • Evolutionary genetics: gene replacement and the genetics of speciation. 
  • Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates. 
  • Evolutionary history of microsatellites in the obscura group of Drosophila. 
  • Evolutionary rate variation in anthocyanin pathway genes. 
  • Evolutionary relationships within the Neotropical, eusporangiate fern genus Danaea (Marattiaceae) 
  • Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication. 
  • Experimental analysis of sources of error in evolutionary studies based on Roche/454 pyrosequencing of viral genomes. 
  • Exploring syntenic conservation across genomes for phylogenetic studies of organisms subjected to horizontal gene transfers: A case study with Cyanobacteria and cyanolichens. 
  • Expression profiling and local adaptation of Boechera holboellii populations for water use efficiency across a naturally occurring water stress gradient. 
  • Extended ORF8 Gene Region Is Valuable in the Epidemiological Investigation of Severe Acute Respiratory Syndrome-Similar Coronavirus. 
  • Extensive changes in the expression of the opioid genes between humans and chimpanzees. 
  • Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. 
  • Extreme phenotypic divergence and the evolution of development. 
  • Fast Dissemination of New HIV-1 CRF02/A1 Recombinants in Pakistan. 
  • Feather development genes and associated regulatory innovation predate the origin of Dinosauria. 
  • Ferns diversified in the shadow of angiosperms. 
  • Fine-scale mapping of recombination rate in Drosophila refines its correlation to diversity and divergence. 
  • Fluorescence in situ hybridization analysis of keratinocyte growth factor gene amplification and dispersion in evolution of great apes and humans. 
  • Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing. 
  • For better or worse: genomic consequences of intracellular mutualism and parasitism. 
  • Functional Class I and II Amino Acid-activating Enzymes Can Be Coded by Opposite Strands of the Same Gene. 
  • Functional equivalence of an evolutionarily conserved RNA binding module. 
  • Functional evolution of an anthocyanin pathway enzyme during a flower color transition. 
  • Functional evolution of mammalian odorant receptors. 
  • Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination. 
  • GOBASE--a database of organelle and bacterial genome information. 
  • Gene conversion and linkage: effects on genome evolution and speciation. 
  • Gene conversion occurs within the mating-type locus of Cryptococcus neoformans during sexual reproduction. 
  • Gene expression and adaptive noncoding changes during human evolution. 
  • Gene expression divergence recapitulates the developmental hourglass model. 
  • Gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria. 
  • Gene flow between Drosophila pseudoobscura and D. persimilis. 
  • Gene flow happens. 
  • Gene loss and parallel evolution contribute to species difference in flower color. 
  • Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds. 
  • Gene transposition as a cause of hybrid sterility in Drosophila. 
  • Generators of phenotypic diversity in the evolution of pathogenic microorganisms. 
  • Genes translocated into the plastid inverted repeat show decelerated substitution rates and elevated GC content 
  • Genetic and Genomic Analyses Reveal Boundaries between Species Closely Related to Cryptococcus Pathogens. 
  • Genetic and evolutionary correlates of fine-scale recombination rate variation in Drosophila persimilis. 
  • Genetic and genomic evolution of sexual reproduction: echoes from LECA to the fungal kingdom. 
  • Genetic evidence for long-term population decline in a savannah-dwelling primate: inferences from a hierarchical bayesian model. 
  • Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. 
  • Genetic organization, length conservation, and evolution of RNA polymerase II carboxyl-terminal domain. 
  • Genetic relationships and evolution of genotypes of yellow fever virus and other members of the yellow fever virus group within the Flavivirus genus based on the 3' noncoding region. 
  • Genetic structure and genealogy in the Sphagnum subsecundum complex (Sphagnaceae: Bryophyta). 
  • Genetic variation in the 3' non-coding region of dengue viruses. 
  • Genetics. Enhancing gene regulation. 
  • Genome Architecture and Evolution of a Unichromosomal Asexual Nematode. 
  • Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii. 
  • Genome evolution in an insect cell: distinct features of an ant-bacterial partnership. 
  • Genome evolution in bacterial endosymbionts of insects. 
  • Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects. 
  • Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. 
  • Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways. 
  • Genome-wide mutagenesis of influenza virus reveals unique plasticity of the hemagglutinin and NS1 proteins. 
  • Genomic Characterization of the Evolutionary Potential of the Sea Urchin Strongylocentrotus droebachiensis Facing Ocean Acidification. 
  • Genomic erosion and extensive horizontal gene transfer in gut-associated Acetobacteraceae. 
  • Genomic resources for the endangered Hawaiian honeycreepers. 
  • Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction. 
  • Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species. 
  • Genomics and Transcriptomics Analyses of the Oil-Accumulating Basidiomycete Yeast Trichosporon oleaginosus: Insights into Substrate Utilization and Alternative Evolutionary Trajectories of Fungal Mating Systems. 
  • Genomics and expression profiles of the Hedgehog and Notch signaling pathways in sea urchin development. 
  • Genomics and genetics of human and primate y chromosomes. 
  • Geographic and evolutionary diversification of glucosinolates among near relatives of Arabidopsis thaliana (Brassicaceae). 
  • Geographic selection in the small heat shock gene complex differentiating populations of Drosophila pseudoobscura. 
  • Germline sequences of V(H)7183 gene family members in C57BL/6 mice demonstrate natural selection of particular sequences during recent evolution. 
  • Getting more from less: algorithms for rapid protein identification with multiple short peptide sequences. 
  • Giant ankyrin-G: a critical innovation in vertebrate evolution of fast and integrated neuronal signaling. 
  • Glioma progression is shaped by genetic evolution and microenvironment interactions. 
  • Glioma through the looking GLASS: molecular evolution of diffuse gliomas and the Glioma Longitudinal Analysis Consortium. 
  • Global Survey of Variation in a Human Olfactory Receptor Gene Reveals Signatures of Non-Neutral Evolution. 
  • Global analysis of the evolution and mechanism of echinocandin resistance in Candida glabrata. 
  • Global distribution, diversity hot spots and niche transitions of an astaxanthin-producing eukaryotic microbe. 
  • Global patterns in peatmoss biodiversity. 
  • Globally Relaxed Selection and Local Adaptation in Boechera stricta. 
  • Great ape genetic diversity and population history. 
  • HGT in the human and skin commensal Malassezia: A bacterially derived flavohemoglobin is required for NO resistance and host interaction. 
  • HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC. 
  • HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses. 
  • Has the chimpanzee Y chromosome been sequenced? 
  • Hedgehog signaling requires motile cilia in the sea urchin. 
  • Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition. 
  • High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men. 
  • High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq. 
  • High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems. 
  • Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified Southern hemisphere sister lineage 
  • History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae). 
  • Homeostasis and dynamic stability of the phenotype link robustness and plasticity. 
  • Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns 
  • Host-symbiont stability and fast evolutionary rates in an ant-bacterium association: cospeciation of camponotus species and their endosymbionts, candidatus blochmannia. 
  • How Big Is Your Y? A Genome-Sequence Based Estimate of the Size of the Male-Specific Region in Megaselia scalaris 
  • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. 
  • Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. 
  • Identification and evolution of an IS6110 low-copy-number Mycobacterium tuberculosis cluster. 
  • Identification of asteroid genera with species capable of larval cloning. 
  • Identification of cis-suppression of human disease mutations by comparative genomics. 
  • Identification of the mating-type (MAT) locus that controls sexual reproduction of Blastomyces dermatitidis. 
  • Identification, characterization, and evolution of a primate beta-defensin gene cluster. 
  • Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral. 
  • Identifying multiple origins of polyploid taxa: a multilocus study of the hybrid cloak fern (Astrolepis integerrima; Pteridaceae). 
  • Implications for proteasome nuclear localization revealed by the structure of the nuclear proteasome tether protein Cut8. 
  • Importance sampling for the infinite sites model. 
  • Imprinting evolution and the price of silence. 
  • In it for the long haul: evolutionary consequences of persistent endosymbiosis. 
  • InVEST: interactive and visual edge selection tool for constructing evolutionary trees. 
  • Incongruence between genetic and morphological diversity in Microcebus griseorufus of Beza Mahafaly. 
  • Incongruence between primary sequence data and the distribution of a mitochondrial atp1 group II intron among ferns and horsetails 
  • Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models. 
  • Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae. 
  • Inhibitor of apoptosis proteins in eukaryotic evolution and development: a model of thematic conservation. 
  • Initial sequencing and analysis of the human genome. 
  • Initial sequencing and comparative analysis of the mouse genome. 
  • Initiation of the Primate Genome Project. 
  • Insights from a chimpanzee adipose stromal cell population: opportunities for adult stem cells to expand primate functional genomics. 
  • Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). 
  • Intergenerational adaptations to stress are evolutionarily conserved, stress-specific, and have deleterious trade-offs. 
  • Intragenic duplication and divergence in the spectrin superfamily of proteins. 
  • Intraspecific phylogenetic congruence among multiple symbiont genomes. 
  • Intraspecific variation in symbiont genomes: bottlenecks and the aphid-buchnera association. 
  • Intronic cis-regulatory modules mediate tissue-specific and microbial control of angptl4/fiaf transcription. 
  • Investigating Conservation of the Cell-Cycle-Regulated Transcriptional Program in the Fungal Pathogen, Cryptococcus neoformans. 
  • Investigating evolutionary lag using the species-pairs evolutionary lag test (SPELT). 
  • Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. - Accepted at pacific symposium on biocomputing, 2016 
  • Is local adaptation in Mimulus guttatus caused by trade-offs at individual loci? 
  • Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species. 
  • Known mutator alleles do not markedly increase mutation rate in clinical Saccharomyces cerevisiae strains. 
  • LETM1, a gene deleted in Wolf-Hirschhorn syndrome, encodes an evolutionarily conserved mitochondrial protein. 
  • Lack of variation in voltage-gated sodium channels of common bottlenose dolphins (Tursiops truncatus) exposed to neurotoxic algal blooms. 
  • Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3. 
  • Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits. 
  • Levers and linkages: mechanical trade-offs in a power-amplified system. 
  • Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome. 
  • Looking for Darwin's footprints in the microbial world. 
  • Loss of centromere function drives karyotype evolution in closely related Malassezia species. 
  • Low frequency of paleoviral infiltration across the avian phylogeny. 
  • Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1. 
  • Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. 
  • Major histocompatibility complex variation and evolution at a single, expressed DQA locus in two genera of elephants. 
  • Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. 
  • Manipulation of insulin signaling phenocopies evolution of a host-associated polyphenism. 
  • Many globally isolated AD hybrid strains of Cryptococcus neoformans originated in Africa. 
  • Mapping the complexity of transcription control in higher eukaryotes. 
  • Mating-type locus of Cryptococcus neoformans: a step in the evolution of sex chromosomes. 
  • Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection. 
  • Melanoma Therapeutic Strategies that Select against Resistance by Exploiting MYC-Driven Evolutionary Convergence. 
  • Methicillin-resistant Staphylococcus aureus: an overview of basic and clinical research. 
  • MicroRNA regulation and interspecific variation of gene expression. 
  • Microevolution of Serial Clinical Isolates of Cryptococcus neoformans var. grubii and C. gattii. 
  • Microsatellite mutation models: insights from a comparison of humans and chimpanzees. 
  • Mistaken Identity: Another Bias in the Use of Relative Genetic Divergence Measures for Detecting Interspecies Introgression. 
  • Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3. 
  • Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs. 
  • Molecular Biology and Evolution of Cancer: From Discovery to Action. 
  • Molecular analysis of HLA-B35 alleles and their relationship to HLA-B15 alleles. 
  • Molecular and genetic evidence for a tetrapolar mating system in the basidiomycetous yeast Kwoniella mangrovensis and two novel sibling species. 
  • Molecular biology. Versatility of self-cleaving ribozymes. 
  • Molecular characterization of a highly divergent HIV type 1 isolate obtained early in the AIDS epidemic from the Democratic Republic of Congo. 
  • Molecular clock and recombination in primate Mhc genes. 
  • Molecular evidence of sequential evolution of DDT- and pyrethroid-resistant sodium channel in Aedes aegypti. 
  • Molecular evolution of X-linked accessory gland proteins in Drosophila pseudoobscura. 
  • Molecular evolution of a Drosophila homolog of human BRCA2. 
  • Molecular evolution of human immunodeficiency virus env in humans and monkeys: similar patterns occur during natural disease progression or rapid virus passage. 
  • Molecular evolution of the junctophilin gene family. 
  • Molecular evolutionary and structural analysis of the cytosolic DNA sensor cGAS and STING. 
  • Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates. 
  • Molecular evolutionary dynamics of cytochrome b in strepsirrhine primates: the phylogenetic significance of third-position transversions. 
  • Molecular footprint of Medawar's mutation accumulation process in mammalian aging. 
  • Molecular insights into the phylogeny and subgeneric classification of Frullania Raddi (Frullaniaceae, Porellales). 
  • Molecular phylogenetic analysis of the Papionina using concatenation and species tree methods. 
  • Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA. 
  • Molecular phylogeny of the Entomophthoromycota: 
  • Morning glory as a powerful model in ecological genomics: tracing adaptation through both natural and artificial selection. 
  • Motor proteins. 1: kinesins. 
  • Multiple Pathways to Homothallism in Closely Related Yeast Lineages in the Basidiomycota. 
  • Multiple colonisations of the western Indian Ocean by Pteropus fruit bats (Megachiroptera: Pteropodidae): the furthest islands were colonised first. 
  • Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans. 
  • Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification. 
  • Multiple hybrid formation in natural populations: concerted evolution of the internal transcribed spacer of nuclear ribosomal DNA (ITS) in North American Arabis divaricarpa (Brassicaceae). 
  • Multiple origins of high reciprocal symbiotic specificity at an intercontinental spatial scale among gelatinous lichens (Collemataceae, Lecanoromycetes). 
  • Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD. 
  • Muscle trade-offs in a power-amplified prey capture system. 
  • Mutagenesis from meiotic recombination is not a primary driver of sequence divergence between Saccharomyces species. 
  • Mutation and evolution of microsatellites in Drosophila melanogaster. 
  • Mutation exposed: a neutral explanation for extreme base composition of an endosymbiont genome. 
  • Mutation of Nogo-B receptor, a subunit of cis-prenyltransferase, causes a congenital disorder of glycosylation. 
  • Myosin VIIA, important for human auditory function, is necessary for Drosophila auditory organ development. 
  • N-myc regulates parkin expression. 
  • Natural infection of a household pet red-capped mangabey (Cercocebus torquatus torquatus) with a new simian immunodeficiency virus. 
  • Nature and distribution of large sequence polymorphisms in Saccharomyces cerevisiae. 
  • Neural correlates of mating system diversity: oxytocin and vasopressin receptor distributions in monogamous and non-monogamous Eulemur. 
  • Neuroscience and the fallacies of functionalism. 
  • Neutral Theory Is the Foundation of Conservation Genetics. 
  • Neutral evolution of the nonbinding region of the anthocyanin regulatory gene Ipmyb1 in Ipomoea. 
  • New Phytologist on plant evolution. 
  • New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. 
  • New insights into the phylogenetic distribution and evolutionary origins of the septins. 
  • Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria). 
  • Nonlinear developmental processes as sources of dominance. 
  • North American origin and recent European establishments of the amphi-Atlantic peat moss Sphagnum angermanicum. 
  • Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles. 
  • Nuclear ribosomal DNA sequence variation and evolution of spotted marsh-orchids (Dactylorhiza maculata group) 
  • Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny. 
  • Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida. 
  • On the evolutionary costs of self-incompatibility: incomplete reproductive compensation due to pollen limitation. 
  • On the origin of self-incompatibility haplotypes: transition through self-compatible intermediates. 
  • One species or at least eight? Delimitation and distribution of Frullania tamarisci (L.) Dumort. s. l. (Jungermanniopsida, Porellales) inferred from nuclear and chloroplast DNA markers. 
  • One thousand plant transcriptomes and the phylogenomics of green plants. 
  • Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss). 
  • Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution. 
  • Organization and evolution of a gene-rich region of the mouse genome: a 12.7-Mb region deleted in the Del(13)Svea36H mouse. 
  • Organization of the human aromatase p450 (CYP19) gene. 
  • Origin and Reversion of Omicron Core Mutations in the Evolution of SARS-CoV-2 Genomes. 
  • Origin and evolution of HIV-1 in breast milk determined by single-genome amplification and sequencing. 
  • Origin and evolution of large brains in toothed whales. 
  • Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. 
  • Origins and evolution of AIDS viruses. 
  • Origins and evolution of AIDS viruses: estimating the time-scale. 
  • Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae. 
  • Pan-cancer analysis of whole genomes. 
  • Parallel acceleration of evolutionary rates in symbiont genes underlying host nutrition. 
  • Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. 
  • Parallel molecular evolution of deletions and nonsense mutations in bacteriophage T7. 
  • Paralogous VDRs in teleosts:transition of nuclear receptor function 
  • Parasite-mediated evolution of the functional part of the MHC in primates. 
  • Partial shotgun sequencing of the Boechera stricta genome reveals extensive microsynteny and promoter conservation with Arabidopsis. 
  • Patterns of evolution of genes disrupted in expression in Drosophila species hybrids. 
  • Patterns of evolutionary rate variation among genes of the anthocyanin biosynthetic pathway. 
  • Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. 
  • Patterns of nucleotide variation and reproductive isolation between a Mimulus allotetraploid and its progenitor species. 
  • Peatmoss (Sphagnum) diversification associated with Miocene Northern Hemisphere climatic cooling? 
  • Peering ahead (cautiously). 
  • Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class. 
  • Pervasive gene conversion in chromosomal inversion heterozygotes. 
  • Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes. 
  • PhyloOncology: Understanding cancer through phylogenetic analysis. 
  • Phylogenetic analyses of morphological evolution in the gametophyte and sporophyte generations of the moss order Hookeriales (Bryopsida). 
  • Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA. 
  • Phylogenetic analysis of vertebrate lactate dehydrogenase (LDH) multigene families. 
  • Phylogenetic and biogeographic relationships of eastern Asian and eastern North American disjunct Suillus species (fungi) as inferred from nuclear ribosomal RNA ITS sequences. 
  • Phylogenetic evidence of a rapid radiation of pleurocarpous mosses (Bryophyta). 
  • Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. 
  • Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America. 
  • Phylogeny and evolution of Malagasy plated lizards. 
  • Phylogeny and evolution of aldehyde dehydrogenase-homologous folate enzymes. 
  • Phylogeny and evolution of medical species of Candida and related taxa: a multigenic analysis. 
  • Phylogeny and morphological evolution of the amblystegiaceae (Bryopsida). 
  • Phylogeny of Toll-like receptor signaling: adapting the innate response. 
  • Phylogeny of the leafy liverwort Ptilidium: cryptic speciation and shared haplotypes between the Northern and Southern Hemispheres. 
  • Phylogeographic structure and cryptic speciation in the trans-Antarctic moss Pyrrhobryum mnioides. 
  • Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci. 
  • Phylogeography's past, present, and future: 10 years after Avise, 2000. 
  • Phylotranscriptomic analysis of the origin and early diversification of land plants. 
  • Phytochrome diversity in green plants and the origin of canonical plant phytochromes 
  • Plant evolutionary genomics. 
  • Poliovirus and its cellular receptor: a molecular genetic dissection of a virus/receptor affinity interaction. 
  • Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune. 
  • Polymorphisms and evolutionary history of retrotransposon insertions in rice promoters. 
  • Population genetic analyses reveal the African origin and strain variation of Cryptococcus neoformans var. grubii. 
  • Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus. 
  • Population genetics of tandem trypsin inhibitor genes in Arabidopsis species with contrasting ecology and life history. 
  • Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans. 
  • Population perspectives on functional genomic variation in yeast. 
  • Positional cloning of zebrafish ferroportin1 identifies a conserved vertebrate iron exporter. 
  • Positive selection driving diversification in plant secondary metabolism. 
  • Positive selection on MMP3 regulation has shaped heart disease risk. 
  • Positive selection on a human-specific transcription factor binding site regulating IL4 expression. 
  • Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody. 
  • Predictability and irreversibility of genetic changes associated with flower color evolution in Penstemon barbatus. 
  • Preface to the special issue: ecological and evolutionary genomics of populations in nature. 
  • Preface. 
  • Primate phageomes are structured by superhost phylogeny and environment. 
  • Prolonged Adaptive Evolution of a Defensive Gene in the Solanaceae. 
  • Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution 
  • Properties of overlapping genes are conserved across microbial genomes. 
  • Protecting the hedgerow: p53 and hedgehog pathway interactions. 
  • Protein Serine/Threonine Phosphatases: Keys to Unlocking Regulators and Substrates. 
  • Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi. 
  • Purifying selection, sequence composition, and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont. 
  • R5 clade C SHIV strains with tier 1 or 2 neutralization sensitivity: tools to dissect env evolution and to develop AIDS vaccines in primate models. 
  • RNAi is a critical determinant of centromere evolution in closely related fungi. 
  • Radical alterations in the roles of homeobox genes during echinoderm evolution. 
  • Rapid evolution in plant chitinases: molecular targets of selection in plant-pathogen coevolution. 
  • Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thaliana and closely related species. 
  • Rapid evolution of cis-regulatory sequences via local point mutations. 
  • Rapid evolutionary innovation during an Archaean genetic expansion. 
  • RecDraw: a software package for the representation of HIV-1 recombinant structures. 
  • Recent divergence, intercontinental dispersal and shared polymorphism are shaping the genetic structure of amphi-Atlantic peatmoss populations. 
  • Recent evolution of the human pathogen Cryptococcus neoformans by intervarietal transfer of a 14-gene fragment. 
  • Recombination between retrotransposons as a source of chromosome rearrangements in the yeast Saccharomyces cerevisiae. 
  • Recombination hotspots flank the Cryptococcus mating-type locus: implications for the evolution of a fungal sex chromosome. 
  • Recombination modulates how selection affects linked sites in Drosophila. 
  • Recombination rate variation in closely related species. 
  • Recombining without Hotspots: A Comprehensive Evolutionary Portrait of Recombination in Two Closely Related Species of Drosophila. 
  • Reconciling extreme branch length differences: decoupling time and rate through the evolutionary history of filmy ferns 
  • Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. 
  • Reconstructing the early evolution of the Fungi using a six-gene phylogeny 
  • Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. 
  • Refugial isolation and range expansions drive the genetic structure of Oxyria sinensis (Polygonaceae) in the Himalaya-Hengduan Mountains. 
  • Relaxed constraint and evolutionary rate variation between basic helix-loop-helix floral anthocyanin regulators in Ipomoea. 
  • Relaxed natural selection alone does not permit transposable element expansion within 4,000 generations in Escherichia coli. 
  • Remote control of neuronal activity in transgenic mice expressing evolved G protein-coupled receptors. 
  • Repeat polymorphisms within gene regions: phenotypic and evolutionary implications. 
  • Repeated phenotypic changes highlight molecular targets of convergent evolution. 
  • Report of the fifth international workshop on human chromosome 1 mapping 1999. 
  • Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes. 
  • Retrotransposon insertion polymorphisms in six rice genes and their evolutionary history. 
  • Review of the systematic status of Sceloporus arenicolus Degenhardt and Jones, 1972 with an estimate of divergence time. 
  • Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets. 
  • SARS-CoV-2 Variants in Patients with Immunosuppression. 
  • SGP-1: prediction and validation of homologous genes based on sequence alignments. 
  • SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2. 
  • Selection is no more efficient in haploid than in diploid life stages of an angiosperm and a moss. 
  • Selective sweeps and intercontinental migration in the cosmopolitan moss Ceratodon purpureus (Hedw.) Brid. 
  • Selective trade-offs maintain alleles underpinning complex trait variation in plants. 
  • Sequence context of indel mutations and their effect on protein evolution in a bacterial endosymbiont. 
  • Sequence divergence of coiled coils--structural rods, myosin filament packing, and the extraordinary conservation of cohesins. 
  • Sex determination without sex chromosomes. 
  • Sex in fungi. 
  • Sex in the Mucoralean fungi. 
  • She Loves Me, She Loves Me Not: On the Dualistic Asexual/Sexual Nature of Dermatophyte Fungi. 
  • Should Y stay or should Y go: the evolution of non-recombining sex chromosomes. 
  • Signatures of demography and recombination at coding genes in naturally-distributed populations of Arabidopsis lyrata subsp. petraea. 
  • Simian immunodeficiency virus (SIV) envelope quasispecies transmission and evolution in infant rhesus macaques after oral challenge with uncloned SIVmac251: increased diversity is associated with neutralizing antibodies and improved survival in previously immunized animals. 
  • Single origin and subsequent diversification of central Andean endemic Umbilicaria species. 
  • Single origin of Malagasy Carnivora from an African ancestor. 
  • Six reference-quality genomes reveal evolution of bat adaptations. 
  • Slow algae, fast fungi: exceptionally high nucleotide substitution rate differences between lichenized fungi Omphalina and their symbiotic green algae Coccomyxa. 
  • Social environment is associated with gene regulatory variation in the rhesus macaque immune system. 
  • Spatial Genetic Structure of the Abundant and Widespread Peatmoss Sphagnum magellanicum Brid. 
  • Spatial pattern of nucleotide polymorphism indicates molecular adaptation in the bryophyte Sphagnum fimbriatum. 
  • Species delimitation in lemurs: multiple genetic loci reveal low levels of species diversity in the genus Cheirogaleus. 
  • Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. 
  • Statistical evaluation of the Rodin-Ohno hypothesis: sense/antisense coding of ancestral class I and II aminoacyl-tRNA synthetases. 
  • Strategies of genomic integration within insect-bacterial mutualisms. 
  • Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. 
  • Strong selection genome-wide enhances fitness tradeoffs across environments and episodes of selection 
  • Structural basis of selection and thermostability of laboratory evolved Bacillus subtilis lipase. 
  • Structural organization of the human MS4A gene cluster on Chromosome 11q12. 
  • Structures of naturally evolved CUP1 tandem arrays in yeast indicate that these arrays are generated by unequal nonhomologous recombination. 
  • Support for a monophyletic Lemuriformes: Overcoming incongruence between data partitions 
  • TRPV4 plays an evolutionary conserved role in the transduction of osmotic and mechanical stimuli in live animals. 
  • Temporal Stability of Molecular Diversity Measures in Natural Populations of Drosophila pseudoobscura and Drosophila persimilis. 
  • The AZFc region of the Y chromosome features massive palindromes and uniform recurrent deletions in infertile men. 
  • The DAZ gene cluster on the human Y chromosome arose from an autosomal gene that was transposed, repeatedly amplified and pruned. 
  • The DNA sequence of the human X chromosome. 
  • The ENCODE (ENCyclopedia Of DNA Elements) Project. 
  • The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes. 
  • The GRK4 subfamily of G protein-coupled receptor kinases. Alternative splicing, gene organization, and sequence conservation. 
  • The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense. 
  • The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. 
  • The Pan social brain: An evolutionary history of neurochemical receptor genes and their potential impact on sociocognitive differences. 
  • The Pheromone and Pheromone Receptor Mating-Type Locus Is Involved in Controlling Uniparental Mitochondrial Inheritance in Cryptococcus. 
  • The Pleistocene history of the sheepshead minnow (Cyprinodon variegatus): Non-equilibrium evolutionary dynamics within a diversifying species complex. 
  • The Rodin-Ohno hypothesis that two enzyme superfamilies descended from one ancestral gene: an unlikely scenario for the origins of translation that will not be dismissed. 
  • The Role of Brachyruy (T) During Gastrulations Movement in the Sea Urchin, Lytechinus variegatus 
  • The Time Scale of Recombination Rate Evolution in Great Apes. 
  • The accessible chromatin landscape of the human genome. 
  • The biology of the Cryptococcus neoformans species complex. 
  • The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods. 
  • The contribution of admixture to primate evolution. 
  • The control and execution of programmed cell death: an update. 
  • The cyclophilins. 
  • The deacetylase Sir2 from the yeast Clavispora lusitaniae lacks the evolutionarily conserved capacity to generate subtelomeric heterochromatin. 
  • The development of wing shape in Lepidoptera: mitotic density, not orientation, is the primary determinant of shape. 
  • The epigenetics of adaptation: focusing on epigenetic stability as an evolving trait. 
  • The essential sequence elements required for RNAP II carboxyl-terminal domain function in yeast and their evolutionary conservation. 
  • The evolution of chloroplast genes and genomes in ferns 
  • The evolution of control and distribution of adaptive mutations in a metabolic pathway 
  • The evolution of quantitative traits in complex environments 
  • The evolution of transcriptional regulation in eukaryotes. 
  • The evolutionary dynamics of alpha-satellite. 
  • The evolutionary dynamics of self-incompatibility systems. 
  • The evolutionary forest algorithm. 
  • The evolutionary significance of cis-regulatory mutations. 
  • The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. 
  • The genetic architecture of selection at the human dopamine receptor D4 (DRD4) gene locus. 
  • The genetic basis of a plant-insect coevolutionary key innovation. 
  • The genetics of speciation by reinforcement. 
  • The genome of a cave plant, Primulina huaijiensis, provides insights into adaptation to limestone karst habitats. 
  • The genome of a songbird. 
  • The genome of the green anole lizard and a comparative analysis with birds and mammals. 
  • The genome of the sea urchin Stongylocentrotus purpuratus 
  • The genomics of speciation in Drosophila: diversity, divergence, and introgression estimated using low-coverage genome sequencing. 
  • The geography of demography: long-term demographic studies and species distribution models reveal a species border limited by adaptation. 
  • The human gene for the type III isozyme of hexokinase: structure, basal promoter, and evolution. 
  • The integrity of a cholesterol-binding pocket in Niemann-Pick C2 protein is necessary to control lysosome cholesterol levels. 
  • The invertebrate deuterostomes: an introduction to their phylogeny, reproduction, development, and genomics. 
  • The lemur revolution starts now: the genomic coming of age for a non-model organism. 
  • The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. 
  • The narrow endemic Norwegian peat moss Sphagnum troendelagicum originated before the last glacial maximum. 
  • The naturalist in a world of genomics. 
  • The nature of robustness in development. 
  • The neutral theory and natural selection in the HLA region. 
  • The nonopisthokont septins: How many there are, how little we know about them, and how we might learn more. 
  • The roles of positive and negative selection in the molecular evolution of insect endosymbionts. 
  • The search for the fungal tree of life. 
  • The tardigrade Hypsibius dujardini, a new model for studying the evolution of development. 
  • The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. 
  • Theoretical and practical advances in genome halving. 
  • Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. 
  • Three periods of regulatory innovation during vertebrate evolution. 
  • Three-genome mosses: complex double allopolyploid origins for triploid gametophytes in Sphagnum. 
  • Time's arrow: heterochrony and the evolution of development. 
  • Timing the ancestor of the HIV-1 pandemic strains. 
  • Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level. 
  • Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection. 
  • Transcriptional regulation and the evolution of development. 
  • Transcriptome-mining for single-copy nuclear markers in ferns 
  • Transcriptomic analysis of sea star development through metamorphosis to the highly derived pentameral body plan with a focus on neural transcription factors. 
  • Transient expression of a winged-helix protein, MNF-beta, during myogenesis. 
  • Transitions in sexuality: recapitulation of an ancestral tri- and tetrapolar mating system in Cryptococcus neoformans. 
  • Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. 
  • Transmission ratio distortion in intraspecific hybrids of Mimulus guttatus: implications for genomic divergence. 
  • Treponema pallidum infection in the wild baboons of East Africa: distribution and genetic characterization of the strains responsible. 
  • Two classes of germline genes both derived from the V(H)1 family direct the formation of human antibodies that recognize distinct antigenic sites in the C2 domain of factor VIII. 
  • Two genetic changes in cis-regulatory elements caused evolution of petal spot position in Clarkia. 
  • Ultrabithorax function in butterfly wings and the evolution of insect wing patterns. 
  • Unifying genetic canalization, genetic constraint, and genotype-by-environment interaction: QTL by genomic background by environment interaction of flowering time in Boechera stricta. 
  • Unisexual reproduction drives evolution of eukaryotic microbial pathogens. 
  • Universal nomenclature for oxytocin-vasotocin ligand and receptor families. 
  • Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist. 
  • Unseen sex in ancient virgin fungi. 
  • Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case. 
  • Using a multigene phylogenetic analysis to assess generic delineation and character evolution in Verrucariaceae (Verrucariales, Ascomycota). 
  • Using comparative genomic data to test for fast-X evolution. 
  • Variation in Recombination Rate: Adaptive or Not? 
  • Variation in constraint versus positive selection as an explanation for evolutionary rate variation among anthocyanin genes. 
  • Variation in modes and rates of evolution in nuclear and mitochondrial ribosomal DNA in the mushroom genus Amanita (Agaricales, Basidiomycota): phylogenetic implications. 
  • Virologic failure in therapy-naive subjects on aplaviroc plus lopinavir-ritonavir: detection of aplaviroc resistance requires clonal analysis of envelope. 
  • Waiting for two mutations: with applications to regulatory sequence evolution and the limits of Darwinian evolution. 
  • What evidence is there for the existence of individual genes with antagonistic pleiotropic effects? 
  • When two is better than one. 
  • Which evolutionary processes influence natural genetic variation for phenotypic traits? 
  • Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds. 
  • Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences. 
  • Whole-genome positive selection and habitat-driven evolution in a shallow and a deep-sea urchin. 
  • Why ontogeny matters during adaptation: developmental niche construction and pleiotorpy across the life cycle in Arabidopsis thaliana. 
  • Widespread occurrence of spliceosomal introns in the rDNA genes of ascomycetes. 
  • Wingless Signaling: A Genetic Journey from Morphogenesis to Metastasis. 
  • Working at the interface of phylogenetics and population genetics: a biogeographical analysis of Triaenops spp. (Chiroptera: Hipposideridae). 
  • beta-arrestin-dependent, G protein-independent ERK1/2 activation by the beta2 adrenergic receptor. 
  • optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry 
• 

  Keywords of People

  • Alberts, Susan C., Robert F. Durden Distinguished Professor of Biology, Duke Science & Society
  • Bennett, Vann, George Barth Geller Distinguished Professor of Molecular Biology, Duke Cancer Institute
  • Carbrey, Jennifer Mehlman, Assistant Research Professor of Cell Biology, Cell Biology
  • Erickson, Harold Paul, James B. Duke Distinguished Professor Emeritus, Cell Biology
  • Ferrari, Guido, Professor in Surgery, Molecular Genetics and Microbiology
  • Hartemink, Alexander J., Professor in the Department of Computer Science, Biology
  • Kelsoe, Garnett H., James B. Duke Distinguished Professor of Immunology, Integrative Immunobiology
  • Magwene, Paul Mitaari, Professor of Biology, Biology
  • Mitchell-Olds, Thomas, Newman Ivey White Distinguished Professor of Biology, Biology
  • Noor, Mohamed A. F., Professor of Biology, Duke University
  • Shinohara, Mari L., Professor of Integrative Immunobiology, Cell Biology
  • Weinhold, Kent James, Joseph W. and Dorothy W. Beard Distinguished Professor of Experimental Surgery, Integrative Immunobiology
  • Wernegreen, Jennifer Jo, Lee Hill Snowdon Associate Professor, Environmental Sciences and Policy
  • Wray, Gregory Allan, Professor of Biology, Evolutionary Anthropology
  • Yoder, Anne Daphne, Braxton Craven Distinguished Professor of Evolutionary Biology, Duke Science & Society