Molecular Biology and Evolution

Article	Citations
TimeTree 5: An Expanded Resource for Species Divergence Times	388
New Methods to Calculate Concordance Factors for Phylogenomic Datasets	352
Corrigendum to: IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era	190
Recent Demographic History Inferred by High-Resolution Analysis of Linkage Disequilibrium	153
ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy	120
Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses	100
Asterid Phylogenomics/Phylotranscriptomics Uncover Morphological Evolutionary Histories and Support Phylogenetic Placement for Numerous Whole-Genome Duplications	86
GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene  Family Tree Inference under Gene Duplication, Transfer, and Loss	85
Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus	79
The Chicken Pan-Genome Reveals Gene Content Variation and a Promoter Region Deletion in IGF2BP1 Affecting Body Size	78
The Emergence of SARS-CoV-2 Variants of Concern Is Driven by Acceleration of the Substitution Rate	77
Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations	76
Herbicide Selection Promotes Antibiotic Resistance in Soil Microbiomes	71
Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function	66
Evolutionary Genomics of Structural Variation in Asian Rice (Oryza sativa) Domestication	61
Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens	59
Broccoli: Combining Phylogenetic and Network Analyses for Orthology Assignment	56
Gene Loss Predictably Drives Evolutionary Adaptation	56
Is Phylotranscriptomics as Reliable as Phylogenomics?	54
Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa	53
Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci	52
Venom Systems as Models for Studying the Origin and Regulation of Evolutionary Novelties	52
Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry	48
Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids	46
Ancient Hybridization with an Unknown Population Facilitated High-Altitude Adaptation of Canids	45

The Emergence of the Spike Furin Cleavage Site in SARS-CoV-2	42
Giant Starship Elements Mobilize Accessory Genes in Fungal Genomes	42
Comprehensive Species Sampling and Sophisticated Algorithmic Approaches Refute the Monophyly of Arachnida	41
Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes	40
Premetazoan Origin of Neuropeptide Signaling	40
Purifying Selection Determines the Short-Term Time Dependency of Evolutionary Rates in SARS-CoV-2 and pH1N1 Influenza	39
The Neandertal Progesterone Receptor	39
De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions	38
Spatiotemporal Evolution of the Global Species Diversity of Rhododendron	37
Ongoing Recombination in SARS-CoV-2 Revealed through Genealogical Reconstruction	36
Phylogeography Reveals Association between Swine Trade and the Spread of Porcine Epidemic Diarrhea Virus in China and across the World	36
Genome Resequencing Reveals Rapid, Repeated Evolution in the Colorado Potato Beetle	35
High and Highly Variable Spontaneous Mutation Rates in Daphnia	35
The Evolution of Human Cancer Gene Duplications across Mammals	34
Loss of Timeless Underlies an Evolutionary Transition within the Circadian Clock	34
Beginner's Guide on the Use of PAML to Detect Positive Selection	34
Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome	32
The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi	32
Phylotranscriptomics Resolves the Phylogeny of Pooideae and Uncovers Factors for Their Adaptive Evolution	32
Phenotype Bias Determines How Natural RNA Structures Occupy the Morphospace of All Possible Shapes	32
The Carbon Footprint of Bioinformatics	32
Evolution of the Insecticide Target Rdl in African Anopheles Is Driven by Interspecific and Interkaryotypic Introgression	32
A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy ofKlebsiella pneumoniaeStrains	32
Scalable Empirical Mixture Models That Account for Across-Site Compositional Heterogeneity	32
Giant Viruses Encode Actin-Related Proteins	31
ModelTeller: Model Selection for Optimal Phylogenetic Reconstruction Using Machine Learning	31
Nemertean, Brachiopod, and Phoronid Neuropeptidomics Reveals Ancestral Spiralian Signaling Systems	31
AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era	30
Synteny-Guided Resolution of Gene Trees Clarifies the Functional Impact of Whole-Genome Duplications	30
A Near-Deterministic Mutational Hotspot in Pseudomonas fluorescens Is Constructed by Multiple Interacting Genomic Features	30
Chaperone-Mediated Autophagy in the Light of Evolution: Insight from Fish	30
Functional Evolution of a Bark Beetle Odorant Receptor Clade Detecting Monoterpenoids of Different Ecological Origins	29
A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population	28
The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes	28
A Deep-Learning Approach for Inference of Selective Sweeps from the Ancestral Recombination Graph	28
Modeling Sequence-Space Exploration and Emergence of Epistatic Signals in Protein Evolution	28
Comparative Genomics Elucidates the Origin of a Supergene Controlling Floral Heteromorphism	28
Physical Constraints on Epistasis	28
Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees	28
Comprehensive and Functional Analysis of Horizontal Gene Transfer Events in Diatoms	27
Global Genetic Heterogeneity in Adaptive Traits	27
Noncoding Variation and Transcriptional Plasticity Promote Thermal Adaptation in Oysters by Altering Energy Metabolism	26
Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome	26
A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data	26
Allopatric and Sympatric Drivers of Speciation inAlviniconchaHydrothermal Vent Snails	26
Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies	26
SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss	26
Phylogenomic Analyses of Alismatales Shed Light into Adaptations to Aquatic Environments	25
De novo Mutations in Domestic Cat are Consistent with an Effect of Reproductive Longevity on Both the Rate and Spectrum of Mutations	25
Using GC Content to Compare Recombination Patterns on the Sex Chromosomes and Autosomes of the Guppy, Poecilia reticulata, and Its Close Outgroup Species	25

Detecting Selection in Multiple Populations by Modeling Ancestral Admixture Components	25
Positive Selection and Inactivation in the Vision and Hearing Genes of Cetaceans	25
Ancient Demographics Determine the Effectiveness of Genetic Purging in Endangered Lizards	25
Battle of the Sex Chromosomes: Competition between X and Y Chromosome-Encoded Proteins for Partner Interaction and Chromatin Occupancy Drives Multicopy Gene Expression and Evolution in Muroid Rodents	24
Genome-Wide Reconstruction of Rediploidization Following Autopolyploidization across One Hundred Million Years of Salmonid Evolution	24
Biases in demographic modelling affect our understanding of recent divergence	24
Placing Ancient DNA Sequences into Reference Phylogenies	24
Genome-Wide Association Analysis Identifies a Genetic Basis of Infectivity in a Model Bacterial Pathogen	24
Defective Satellite DNA Clustering into Chromocenters Underlies Hybrid Incompatibility in Drosophila	24
Prdm9Intersubspecific Interactions in Hybrid Male Sterility of House Mouse	24
Evolutionary Implications of the RNA N6-Methyladenosine Methylome in Plants	24
Endogenous Retroviruses Drive Lineage-Specific Regulatory Evolution across Primate and Rodent Placentae	23
Global Dynamics of Porcine Enteric Coronavirus PEDV Epidemiology, Evolution, and Transmission	23
Transcription Factors Evolve Faster Than Their Structural Gene Targets in the Flavonoid Pigment Pathway	23
Flexible Mixture Model Approaches That Accommodate Footprint Size Variability for Robust Detection of Balancing Selection	23
MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in 10 Years	22
Limited Introgression between Rock-Wallabies with Extensive Chromosomal Rearrangements	22
Adaptive Introgression Facilitates Adaptation to High Latitudes in European Aspen (Populus tremula L.)	22
Rethinking Opsins	22
Evolution of the SARS-CoV-2 Mutational Spectrum	22
Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells	22
Interspecific Gene Flow and the Evolution of Specialization in Black and White Rhinoceros	21
Neuronal Function and Dopamine Signaling Evolve at High Temperature in Drosophila	21
Recovery of Deleted Deep Sequencing Data Sheds More Light on the Early Wuhan SARS-CoV-2 Epidemic	21
Where Did SARS-CoV-2 Come From?	21
Dead-End Hybridization in Walnut Trees Revealed by Large-Scale Genomic Sequence Data	21
Chromosome Fissions and Fusions Act as Barriers to Gene Flow betweenBrenthisFritillary Butterflies	21
B2 SINE Copies Serve as a Transposable Boundary of DNA Methylation and Histone Modifications in the Mouse	21
Novel Doublesex Duplication Associated with Sexually Dimorphic Development of Dogface Butterfly Wings	20
Novel Classes and Evolutionary Turnover of Histone H2B Variants in the Mammalian Germline	20
Gradients Do Grow on Trees: A Linear-Time O(N)-Dimensional Gradient for Statistical Phylogenetics	20
Genomic Evidence for Speciation with Gene Flow in Broadcast Spawning Marine Invertebrates	20
Two Reference-Quality Sea Snake Genomes Reveal Their Divergent Evolution of Adaptive Traits and Venom Systems	20
A Simulation Study to Examine the Information Content in Phylogenomic Data Sets under the Multispecies Coalescent Model	20
Mitonuclear Coevolution, but not Nuclear Compensation, Drives Evolution of OXPHOS Complexes in Bivalves	20
Chromosomal Fusions Facilitate Adaptation to Divergent Environments in Threespine Stickleback	19
Distinguishing Felsenstein Zone from Farris Zone Using Neural Networks	19
Molecular Signatures of Placentation and Secretion Uncovered in Poeciliopsis Maternal Follicles	19
Mutation Load in Sunflower Inversions Is Negatively Correlated with Inversion Heterozygosity	19
Population Genetics and Signatures of Selection in Early Neolithic European Farmers	18
FishmiRNA: An Evolutionarily Supported MicroRNA Annotation and Expression Database for Ray-Finned Fishes	18
Quantitative Lipidomics and Spatial MS-Imaging Uncovered Neurological and Systemic Lipid Metabolic Pathways Underlying Troglomorphic Adaptations in Cave-Dwelling Fish	18
Recent Common Origin, Reduced Population Size, and Marked Admixture Have Shaped European Roma Genomes	18
Fold Evolution before LUCA: Common Ancestry of SH3 Domains and OB Domains	18
The Molecular Machinery of Gametogenesis inGeodiaDemosponges (Porifera): Evolutionary Origins of a Conserved Toolkit across Animals	18
Evolution of Sequence-Diverse Disordered Regions in a Protein Family: Order within the Chaos	18
Viral CpG Deficiency Provides No Evidence That Dogs Were Intermediate Hosts for SARS-CoV-2	18
Molecular Evolution across Mouse Spermatogenesis	18
Variable Spontaneous Mutation and Loss of Heterozygosity among Heterozygous Genomes in Yeast	17
MicroRNAs as Indicators into the Causes and Consequences of Whole-Genome Duplication Events	17
Rapid Decline of Ceftazidime Resistance in Antibiotic-Free and Sublethal Environments Is Contingent on Genetic Background	17
Evolution of Olfactory Receptors Tuned to Mustard Oils in Herbivorous Drosophilidae	17
Molluskan Dorsal–Ventral Patterning Relying on BMP2/4 and Chordin Provides Insights into Spiralian Development and Evolution	17
From Easy to Hopeless—Predicting the Difficulty of Phylogenetic Analyses	17
Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms	17
Citrullination Was Introduced into Animals by Horizontal Gene Transfer from Cyanobacteria	17
The Codon Statistics Database: A Database of Codon Usage Bias	16
Multiple Mechanisms of Photoreceptor Spectral Tuning inHeliconiusButterflies	16
Phylogenetic and Molecular Analyses Identify SNORD116 Targets Involved in the Prader–Willi Syndrome	16
Bidirectional Movement of Emerging H5N8 Avian Influenza Viruses Between Europe and Asia via Migratory Birds Since Early 2020	16
Evolutionary Processes in the Emergence and Recent Spread of the Syphilis Agent,Treponema pallidum	16
Replacement and Parallel Simplification of Nonhomologous Proteinases Maintain Venom Phenotypes in Rear-Fanged Snakes	16
Global Population Genomics of Two Subspecies ofCryptosporidium hominisduring 500 Years of Evolution	16
A CLAVATA3-like Gene Acts as a Gynoecium Suppression Function in White Campion	16
Deleterious Mutations Accumulate Faster in Allopolyploid Than Diploid Cotton (Gossypium) and Unequally between Subgenomes	16
Highly Replicated Evolution of Parapatric Ecotypes	16
Genome Analysis Traces Regional Dispersal of Rice in Taiwan and Southeast Asia	16
Frequent Retroviral Gene Co-option during the Evolution of Vertebrates	16
Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research	16
A Population-Genetic Lens into the Process of Gene Loss Following Whole-Genome Duplication	16
Degradation of the Repetitive Genomic Landscape in a Close Relative of Caenorhabditis elegans	16
Identification of RNA Virus–Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets	16
Comparative Analysis of Mammal Genomes Unveils Key Genomic Variability for Human Life Span	15
Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures	15
Positive Selection and Enhancer Evolution Shaped Lifespan and Body Mass in Great Apes	15
Tracing Bai-Yue Ancestry in Aboriginal Li People on Hainan Island	15
The Slowing Rate of CpG Depletion in SARS-CoV-2 Genomes Is Consistent with Adaptations to the Human Host	15
Host Adaptation inLegionellalesIs 1.9 Ga, Coincident with Eukaryogenesis	15
More Than One-to-Four via 2R: Evidence of an Independent Amphioxus Expansion and Two-Gene Ancestral Vertebrate State for MyoD-Related Myogenic Regulatory Factors (MRFs)	15
Antifungal Drug Concentration Impacts the Spectrum of Adaptive Mutations in Candida albicans	15

Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina	15
Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications	15
The Runaway Evolution of SARS-CoV-2 Leading to the Highly Evolved Delta Strain	15
In Vitro Evolution Reveals Noncationic Protein–RNA Interaction Mediated by Metal Ions	14
How a Scorpion Toxin Selectively Captures a Prey Sodium Channel: The Molecular and Evolutionary Basis Uncovered	14
Collagen Sequence Analysis Reveals Evolutionary History of Extinct West Indies Nesophontes (Island-Shrews)	14
The Mastigamoeba balamuthi Genome and the Nature of the Free-Living Ancestor of Entamoeba	14
Comparative Genomics Reveals Insights into the Divergent Evolution of Astigmatic Mites and Household Pest Adaptations	14
Domestication Shapes Recombination Patterns in Tomato	14
Duplication and Specialization of NUDX1 in Rosaceae Led to Geraniol Production in Rose Petals	14
Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum	14
Lateral Gene Transfer Acts As an Evolutionary Shortcut to Efficient C4 Biochemistry	14
Orthology Clusters from Gene Trees with Possvm	14
Attribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational Processes	14
Reconstructing the Evolutionary History of Chromosomal Races on Islands: A Genome-Wide Analysis of Natural House Mouse Populations	14
Butyrate Production Pathway Abundances Are Similar in Human and Nonhuman Primate Gut Microbiomes	13
The Transposition Rate Has Little Influence on the Plateauing Level of the P-element	13
Origin and Evolution of Nitrogen Fixation in Prokaryotes	13
Disentangling Signatures of Selection Before and After European Colonization in Latin Americans	13
Evolution of Gene Expression across Species and Specialized Zooids in Siphonophora	13
Selection Balancing at Innate Immune Genes: Adaptive Polymorphism Maintenance in Toll-Like Receptors	13
Is the Mutation Rate Lower in Genomic Regions of Stronger Selective Constraints?	13
Pervasive Phenotypic Impact of a Large Nonrecombining Introgressed Region in Yeast	13
Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study	13
Sexual Antagonism, Temporally Fluctuating Selection, and Variable Dominance Affect a Regulatory Polymorphism in Drosophila melanogaster	13
Warthog Genomes Resolve an Evolutionary Conundrum and Reveal Introgression of Disease Resistance Genes	13
Sympatric Recombination in Zoonotic Cryptosporidium Leads to Emergence of Populations with Modified Host Preference	13
Convergent Loss of Chemoreceptors across Independent Origins of Slave-Making in Ants	12
Inference of Gene Flow between Species under Misspecified Models	12
Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome	12
A New Paradigm of Multiheme Cytochrome Evolution by Grafting and Pruning Protein Modules	12
Population Genomics of Wall Lizards Reflects the Dynamic History of the Mediterranean Basin	12
Ancestral Sequence Reconstruction of a Cytochrome P450 Family Involved in Chemical Defense Reveals the Functional Evolution of a Promiscuous, Xenobiotic-Metabolizing Enzyme in Vertebrates	12
Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul	12
Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution	12
Novel Insights on Obligate Symbiont Lifestyle and Adaptation to Chemosynthetic Environment as Revealed by the Giant Tubeworm Genome	12
Endosperm Evolution by Duplicated and Neofunctionalized Type I MADS-Box Transcription Factors	12
A Transcriptomic Atlas Underlying Developmental Plasticity of Seasonal Forms of Bicyclus anynana Butterflies	12
Long-term Small Population Size, Deleterious Variation, and Altitude Adaptation in the Ethiopian Wolf, a Severely Endangered Canid	12
Model-Based Inference of Punctuated Molecular Evolution	12
Molecular Phylogeny Reveals the Past Transoceanic Voyages of Drywood Termites (Isoptera, Kalotermitidae)	11
Dissecting Genomic Determinants of Positive Selection with an Evolution-Guided Regression Model	11
Two Forms of Sexual Dimorphism in Gene Expression in Drosophila melanogaster: Their Coincidence and Evolutionary Genetics	11
Genomic Signatures of Recent Adaptation in a Wild Bumblebee	11
Episodes of Diversification and Isolation in Island Southeast Asian and Near Oceanian Male Lineages	11
Whole-Genome Duplication Facilitated the Evolution of C4 Photosynthesis in Gynandropsis gynandra	11
Speciation Underpinned by Unexpected Molecular Diversity in the Mycorrhizal Fungal GenusPisolithus	11
Changes in Ploidy Drive Reproduction Transition and Genomic Diversity in a Polyploid Fish Complex	11
Phylogenetic Articulation of Uric Acid Evolution in Mammals and How It Informs a Therapeutic Uricase	11
Higher Germline Mutagenesis of Genes with Stronger Testis Expressions Refutes the Transcriptional Scanning Hypothesis	11
PIQMEE: Bayesian Phylodynamic Method for Analysis of Large Data Sets with Duplicate Sequences	11
Dynamics and Impacts of Transposable Element Proliferation in the Drosophila nasuta Species Group Radiation	11
Reconstruction of Plastid Proteomes of Apicomplexans and Close Relatives Reveals the Major Evolutionary Outcomes of Cryptic Plastids	11
How Placenta Promotes the Successful Reproduction in High-Altitude Populations: A Transcriptome Comparison between Adaptation and Acclimatization	11
Polishing De Novo Nanopore Assemblies of Bacteria and Eukaryotes With FMLRC2	11
Genomic Impact of Whaling in North Atlantic Fin Whales	11
Coevolution in Hybrid Genomes: Nuclear-Encoded Rubisco Small Subunits and Their Plastid-Targeting Translocons Accompanying Sequential Allopolyploidy Events inTriticum	11
Consequences of Substitution Model Selection on Protein Ancestral Sequence Reconstruction	11
Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes	11
The Complex History of Genome Duplication and Hybridization in North American Gray Treefrogs	11
A Genomic Cluster Containing Novel and Conserved Genes is Associated with Cichlid Fish Dental Developmental Convergence	11
Looking through the Lens of the Ribosome Biogenesis Evolutionary History: Possible Implications for Archaeal Phylogeny and Eukaryogenesis	11
Parallel Genomic Changes Drive Repeated Evolution of Placentas in Live-Bearing Fish	11