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Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Precision of molecular time estimates

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Precision of molecular time estimates

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Phylogenetic dating with confidence intervals using mean path lengths

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Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

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r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock

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RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

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Bayesian Morphological Clock Methods Resurrect Placoderm Monophyly and Reveal Rapid Early Evolution in Jawed Vertebrates

inferredcites →https://doi.org/10.1098/rsbl.2011.0710openalex-snapshot

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Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors

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A mixed relaxed clock model

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Molecular‐clock methods for estimating evolutionary rates and timescales

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Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences

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Isolation of Infective Zika Virus from Urine and Saliva of Patients in Brazil

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inferred← citeshttps://doi.org/10.1080/14772000.2023.2246476openalex-snapshot

Return of the prodigal son: morphology and molecular phylogenetic relationships of a new Antarctic fish leech (Hirudinea: Piscicolidae) imply a bipolar biogeographic pattern

inferred← citeshttps://doi.org/10.1086/733931openalex-snapshot

Colonization Dynamics Explain the Decoupling of Species Richness and Morphological Disparity in Syngnatharian Fishes across Oceans

inferred← citeshttps://doi.org/10.1093/aob/mcad008openalex-snapshot

Evolution of hygrophytic plant species in the Anatolia–Caucasus region: insights from phylogenomic analyses ofCardamineperennials

inferred← citeshttps://doi.org/10.1093/aob/mcaf110openalex-snapshot

Climatic oscillations, dispersibility and adaptability behind worldwide mountain radiations of the Helichrysum–Anaphalis–Pseudognaphalium (HAP) clade (Compositae)

inferred← citeshttps://doi.org/10.1093/bioinformatics/btab307openalex-snapshot

Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies

inferred← citeshttps://doi.org/10.1093/botlinnean/boad011openalex-snapshot

Morphological and anatomical evolution of species of Valeriana (Caprifoliaceae) during the uplift of the Andean range

inferred← citeshttps://doi.org/10.1093/cz/zoad027openalex-snapshot

Evolution, divergence, and convergence in the mandibles of opossums (Didelphidae, Didelphimorphia)

inferred← citeshttps://doi.org/10.1093/evolut/qpae142openalex-snapshot

Evolution and functional implications of stinger shape in ants

inferred← citeshttps://doi.org/10.1093/g3journal/jkab071openalex-snapshot

Comparative genome analyses suggest a hemibiotrophic lifestyle and virulence differences for the beech bark disease fungal pathogens Neonectria faginata and Neonectria coccinea

inferred← citeshttps://doi.org/10.1093/g3journal/jkad294openalex-snapshot

Unveiling the evolutionary history of lingonberry ( Vaccinium vitis-idaea L.) through genome sequencing and assembly of European and North American subspecies

inferred← citeshttps://doi.org/10.1093/gbe/evab251openalex-snapshot

Assessing Rapid Relaxed-Clock Methods for Phylogenomic Dating

inferred← citeshttps://doi.org/10.1093/gbe/evae027openalex-snapshot

The Genome of Plasmodium gonderi: Insights into the Evolution of Human Malaria Parasites

inferred← citeshttps://doi.org/10.1093/gbe/evae199openalex-snapshot

Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock

inferred← citeshttps://doi.org/10.1093/gbe/evy118openalex-snapshot

RelTime Relaxes the Strict Molecular Clock throughout the Phylogeny

inferred← citeshttps://doi.org/10.1093/genetics/iyaf084openalex-snapshot

Enabling data-driven discoveries in evolutionary genetics and genomics

inferred← citeshttps://doi.org/10.1093/gigascience/giae036openalex-snapshot

Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi

inferred← citeshttps://doi.org/10.1093/gigascience/giz116openalex-snapshot

A draft genome assembly of halophyte Suaeda aralocaspica, a plant that performs C4 photosynthesis within individual cells

inferred← citeshttps://doi.org/10.1093/ismejo/wraf039openalex-snapshot

Genome diversification of symbiotic fungi in beetle-fungus mutualistic symbioses

inferred← citeshttps://doi.org/10.1093/jcbiol/ruaf007openalex-snapshot

Discovery of new montane crab (Brachyura: Sesarmidae: Sesarma Say, 1817) in Hispaniola highlights the impact of incumbent island biotas on colonization and diversification

inferred← citeshttps://doi.org/10.1093/jhered/esac060openalex-snapshot

Genomic analyses of gray fox lineages suggest ancient divergence and secondary contact in the southern Great Plains

inferred← citeshttps://doi.org/10.1093/jmammal/gyaf006openalex-snapshot

Systematics and historical biogeography of Crunomys and Maxomys (Muridae: Murinae), with the description of a new species from Sulawesi and new genus-level classification

inferred← citeshttps://doi.org/10.1093/molbev/msaa049openalex-snapshot

Relative Efficiencies of Simple and Complex Substitution Models in Estimating Divergence Times in Phylogenomics

inferred← citeshttps://doi.org/10.1093/molbev/msaa222openalex-snapshot

Log Transformation Improves Dating of Phylogenies

inferred← citeshttps://doi.org/10.1093/molbev/msab129openalex-snapshot

The Evolution Pathway of Ammonia-Oxidizing Archaea Shaped by Major Geological Events

inferred← citeshttps://doi.org/10.1093/molbev/msad264openalex-snapshot

Forty Years of Inferential Methods in the Journals of the Society for Molecular Biology and Evolution

inferred← citeshttps://doi.org/10.1093/molbev/msae023openalex-snapshot

Mapping Geological Events and Nitrogen Fixation Evolution Onto the Timetree of the Evolution of Nitrogen-Fixation Genes

inferred← citeshttps://doi.org/10.1093/molbev/msaf101openalex-snapshot

MEGA-GPT: Artificial Intelligence Guidance and Building Analytical Protocols Using MEGA Software

inferred← citeshttps://doi.org/10.1093/molbev/msz014openalex-snapshot

A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies

inferred← citeshttps://doi.org/10.1093/molbev/msz236openalex-snapshot

Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times

inferred← citeshttps://doi.org/10.1093/pnasnexus/pgae057openalex-snapshot

Gene inversion led to the emergence of brackish archaeal heterotrophs in the aftermath of the Cryogenian Snowball Earth

inferred← citeshttps://doi.org/10.1093/sysbio/syaa009openalex-snapshot

Identification of Hidden Population Structure in Time-Scaled Phylogenies

inferred← citeshttps://doi.org/10.1093/sysbio/syaa095openalex-snapshot

Confronting Sources of Systematic Error to Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes)

inferred← citeshttps://doi.org/10.1093/sysbio/syae020openalex-snapshot

Sequential Bayesian Phylogenetic Inference

inferred← citeshttps://doi.org/10.1093/sysbio/syae034openalex-snapshot

Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model

inferred← citeshttps://doi.org/10.1093/sysbio/syag041openalex-snapshot

Phylogenomic Challenges in Polyploid-Rich Lineages: Insights from Paralog Processing and Reticulation Methods Using the Complex Genus Packera (Asteraceae: Senecioneae)

inferred← citeshttps://doi.org/10.1093/sysbio/syag060openalex-snapshot

Exploring Incongruence in a Plant Genus with Relatively Recent Polyploidy and Cytoplasmic Discordance

inferred← citeshttps://doi.org/10.1093/sysbio/syy082openalex-snapshot

Golden Orbweavers Ignore Biological Rules: Phylogenomic and Comparative Analyses Unravel a Complex Evolution of Sexual Size Dimorphism

inferred← citeshttps://doi.org/10.1093/zoolinnean/zlad150openalex-snapshot

A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

inferred← citeshttps://doi.org/10.1093/zoolinnean/zlae078openalex-snapshot

Diversification over deep and shallow temporal scales in the Holarctic genus Perpolita (Gastropoda: Gastrodontidae)

inferred← citeshttps://doi.org/10.1098/rsos.240064openalex-snapshot

Novel phylogenomic inference and ‘Out of Asia’ biogeography of cobras, coral snakes and their allies

inferred← citeshttps://doi.org/10.1101/2020.02.14.949339openalex-snapshot

Relative efficiencies of simple and complex substitution models in estimating divergence times in phylogenomics

inferred← citeshttps://doi.org/10.1101/2020.11.11.376459openalex-snapshot

Stepwise Bayesian Phylogenetic Inference

inferred← citeshttps://doi.org/10.1101/2022.09.22.508453openalex-snapshot

Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi

inferred← citeshttps://doi.org/10.1101/2022.11.08.515629openalex-snapshot

The genome of the brackish-water malaria vector Anopheles aquasalis

inferred← citeshttps://doi.org/10.1101/2023.09.02.556036openalex-snapshot

Comparative phylogenomic analyses of SNP versus full locus datasets: insights and recommendations for researchers

inferred← citeshttps://doi.org/10.1101/2023.09.04.556188openalex-snapshot

Schizosaccharomyces versatilis represents a distinct evolutionary lineage

inferred← citeshttps://doi.org/10.1101/2023.10.18.563010openalex-snapshot

Phylogenomics, biogeography, and trait evolution of the Boletaceae (Boletales, Agaricomycetes, Basidiomycota)

inferred← citeshttps://doi.org/10.1101/2023.10.26.564281openalex-snapshot

Phylogenomics reveals the deep ocean as an accelerator for evolutionary diversification in anglerfishes

inferred← citeshttps://doi.org/10.1101/2024.03.05.583480openalex-snapshot

Flame-forged divergence? Ancient human fires and the evolution of diurnal and nocturnal lineages in Mediterranean geckos

inferred← citeshttps://doi.org/10.1101/2024.08.08.607167openalex-snapshot

Footprints of human migration in the population structure of wild wine yeast

inferred← citeshttps://doi.org/10.1101/2024.08.23.609317openalex-snapshot

Phylogenomics, Classification, and Lifestyle Evolution in Raft- and Nursery web- Spiders (Araneae: Dolomedidae and Pisauridae)

inferred← citeshttps://doi.org/10.1101/2024.09.12.612680openalex-snapshot

Homoploid Hybridization Resolves the Origin of Octoploid Strawberries

inferred← citeshttps://doi.org/10.1101/2024.09.27.615508openalex-snapshot

The topography of gene tree topology space in a plant genus with a legacy of recent polyploidy and introgression

inferred← citeshttps://doi.org/10.1101/2024.10.09.617500openalex-snapshot

Genome diversification of symbiotic fungi in beetle-fungus mutualistic symbiosis

inferred← citeshttps://doi.org/10.1101/2025.03.07.25323493openalex-snapshot

On-Campus Dormitories as Viral Transmission Sinks: Phylodynamic Insights into Student Housing Networks During the COVID-19 Pandemic

inferred← citeshttps://doi.org/10.1101/2025.08.25.672084openalex-snapshot

Parasitism-mediated horizontal transfer of a functional cytochrome P450 gene entails transposon colonization in newly gained introns

inferred← citeshttps://doi.org/10.1101/2025.10.11.681805openalex-snapshot

Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus

inferred← citeshttps://doi.org/10.1101/2025.11.03.686292openalex-snapshot

Shedding light on Amazonian phylogeographic patterns and evolutionary history of night monkeys (Genus: Aotus ) using reconstructed fecal metagenomic shotgun sequencing

inferred← citeshttps://doi.org/10.1101/346635openalex-snapshot

A new method for detecting autocorrelation of evolutionary rates in large phylogenies

inferred← citeshttps://doi.org/10.1101/536656openalex-snapshot

Molecular dating for phylogenies containing a mix of populations and species

inferred← citeshttps://doi.org/10.1101/809541openalex-snapshot

Large DNA virus promoted the endosymbiotic evolution to make a photosynthetic eukaryote

inferred← citeshttps://doi.org/10.1111/1749-4877.12538openalex-snapshot

Impact of the Miocene orogenesis on Kaloula spp. radiation and implication of local refugia on genetic diversification

inferred← citeshttps://doi.org/10.1111/1755-0998.13233openalex-snapshot

Chromosome‐level genome assembly of the coastal horseshoe crab (Tachypleus gigas)

inferred← citeshttps://doi.org/10.1111/1755-0998.13249openalex-snapshot

Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches

inferred← citeshttps://doi.org/10.1111/1755-0998.13447openalex-snapshot

The endangered White Sands pupfish (Cyprinodon tularosa) genome reveals low diversity and heterogenous patterns of differentiation

inferred← citeshttps://doi.org/10.1111/1755-0998.14075openalex-snapshot

Comparative Genomics Points to Ecological Drivers of Genomic Divergence Among Intertidal Limpets

inferred← citeshttps://doi.org/10.1111/ddi.70166openalex-snapshot

Conservation Priority Areas Based on Phylogenetic Diversity Are Sensitive to Methods of Phylogenetic Inference and Divergence Time Estimation

inferred← citeshttps://doi.org/10.1111/ele.70169openalex-snapshot

Phylogenomic Evidence of Fire Regime Changes: The Case of a Resprouting Juniper

inferred← citeshttps://doi.org/10.1111/jbi.15097openalex-snapshot

Tiny Hunters Along the Alpine Fault: Integrative Phylobiogeography Demonstrates High Geographic Structure in a Forest‐Dwelling Aotearoa Harvester Genus (Arachnida, Triaenonychidae: Algidia)

inferred← citeshttps://doi.org/10.1111/jbi.70229openalex-snapshot

Autapomorphic Giantism Associated With Vicariance: A Test of the Island Rule

inferred← citeshttps://doi.org/10.1111/jbi.70305openalex-snapshot

The Making of a Continental Radiation: The History of Carduus (Compositae) From the Messinian Salinity Crisis to Pliocene–Pleistocene Ecological Opportunities

inferred← citeshttps://doi.org/10.1111/jfb.15927openalex-snapshot

A new discovery of cryptic species in barred sand burrower Limnichthys fasciatus (Pisces: Creediidae) from the western Pacific, with evolutionary perspectives of anti‐equatorial species

inferred← citeshttps://doi.org/10.1111/jipb.13466openalex-snapshot

Climate‐influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone

inferred← citeshttps://doi.org/10.1111/jse.13137openalex-snapshot

Target enrichment data reveal rapid divergence with reticulate evolution of Maianthemum (Asparagaceae: Convallarioideae) in the Himalayan‐Hengduan Mountains and eastern Asia

inferred← citeshttps://doi.org/10.1111/mec.17669openalex-snapshot

Footprints of Human Migration in the Population Structure of Wild Baker's Yeast

inferred← citeshttps://doi.org/10.1111/mec.70130openalex-snapshot

Ancient Introgression Explains Mitochondrial Genome Capture and Mitonuclear Discordance Among South American Collared Tropidurus Lizards

inferred← citeshttps://doi.org/10.1111/njb.04103openalex-snapshot

Molecular evidence to support the transfer of Enteromorpha ovata to genus Ulva and evaluate its divergence using multi‐locus time‐calibrated phylogeny

inferred← citeshttps://doi.org/10.1111/nph.20076openalex-snapshot

Ad fontes : divergence‐time estimation and the age of angiosperms

inferred← citeshttps://doi.org/10.1111/syen.12684openalex-snapshot

Inconsistent performance of multi‐type genomic data in phylogenomics of neuropteridan insects, with solutions toward conflicting results

inferred← citeshttps://doi.org/10.1111/syen.12694openalex-snapshot

Phylogenomics unveils Afrotropical origin, trans‐oceanic global diversification and climatic niche conservatism in the sedentary Zodariidae ant spiders

inferred← citeshttps://doi.org/10.1111/syen.70057openalex-snapshot

Mixture models unveil the origin of the enigmatic Satyrinae butterfly genera Calisto and Llorenteana (Lepidoptera, Nymphalidae, Satyrinae)

inferred← citeshttps://doi.org/10.1111/tpj.14765openalex-snapshot

Polyploidization events shaped the transcription factor repertoires in legumes (Fabaceae)

inferred← citeshttps://doi.org/10.1128/msphere.00913-24openalex-snapshot

Metagenomic and phylogenetic analyses reveal gene-level selection constrained by bacterial phylogeny, surrounding oxalate metabolism in the gut microbiota

inferred← citeshttps://doi.org/10.1128/msphere.00931-21openalex-snapshot

Comparative Genomic Analysis Reveals Preserved Features in Organohalide-Respiring Sulfurospirillum Strains

inferred← citeshttps://doi.org/10.1128/msystems.00602-21openalex-snapshot

Comparative Genomics Provides Insights into the Genetic Diversity and Evolution of the DPANN Superphylum

inferred← citeshttps://doi.org/10.1128/msystems.00867-20openalex-snapshot

Insights into the Metabolism and Evolution of the Genus Acidiphilium , a Typical Acidophile in Acid Mine Drainage

inferred← citeshttps://doi.org/10.1128/spectrum.01692-21openalex-snapshot

Construction and Analysis of the Complete Genome Sequence of Leprosy Agent Mycobacterium lepromatosis

inferred← citeshttps://doi.org/10.1128/spectrum.02271-25openalex-snapshot

Characterization of Proteus mirabilis isolated from ticks collected in Isiolo and Kilifi Counties, Kenya

inferred← citeshttps://doi.org/10.1128/spectrum.03441-25openalex-snapshot

Evolutionary dynamics of endogenous densoviruses NS1 proteins reveal ancient codivergence with their Platyhelminth hosts

inferred← citeshttps://doi.org/10.1128/spectrum.04570-22openalex-snapshot

Deciphering the Origin of DNA Viruses (Replication-Associated Parvo-NS1) That Infect Vertebrates from Invertebrate-Infecting Viruses

inferred← citeshttps://doi.org/10.1134/s0032945225601964openalex-snapshot

Genetic Divergence in Catfish of Odisha (India) Based on DNA-Barcoding Data

inferred← citeshttps://doi.org/10.1134/s2079086422050024openalex-snapshot

The Concept of the Modern Molecular Clock and Experience in Estimating Divergence Times of Eulipotyphla and Rodentia

inferred← citeshttps://doi.org/10.1177/1176934319855988openalex-snapshot

The Estimated Pacemaker for Great Apes Supports the Hominoid Slowdown Hypothesis

inferred← citeshttps://doi.org/10.1186/s12862-019-1455-7openalex-snapshot

On estimating evolutionary probabilities of population variants

inferred← citeshttps://doi.org/10.1186/s12862-025-02456-xopenalex-snapshot

Inbreeding does not reduce major histocompatibility complex diversity in the banded mongoose

inferred← citeshttps://doi.org/10.1186/s12864-022-09030-5openalex-snapshot

Assessing the relative performance of fast molecular dating methods for phylogenomic data

inferred← citeshttps://doi.org/10.1186/s12864-025-12171-yopenalex-snapshot

Next-generation sequencing, assembly, annotation, and phylogenomic analysis of the complete mitochondrial genome of the painted lady butterfly Vanessa cardui (Linnaeus, 1758) (Insecta: Lepidoptera: Nymphalidae)

inferred← citeshttps://doi.org/10.1186/s12915-025-02351-3openalex-snapshot

Dokdo sea lion Zalophus japonicus genome reveals its evolutionary trajectory before extinction

inferred← citeshttps://doi.org/10.1186/s12917-025-04612-3openalex-snapshot

First detection and molecular characterization of Chaphamaparvovirus galliform in broiler and turkey flocks in Türkiye

inferred← citeshttps://doi.org/10.1186/s12917-025-04675-2openalex-snapshot

De-novo assembled mitochondrial genome of Bhadawari buffalo (Bubalus bubalis) reveals close divergence to Egyptian buffalo

inferred← citeshttps://doi.org/10.1186/s12920-024-01890-yopenalex-snapshot

Exploring the extrachromosomal plasmid rDNA of Naegleria fowleri AY27 genotype II: A human brain-eating amoeba via high-throughput sequencing

inferred← citeshttps://doi.org/10.1186/s13071-020-04475-7openalex-snapshot

Investigation of the piroplasm diversity circulating in wildlife and cattle of the greater Kafue ecosystem, Zambia

inferred← citeshttps://doi.org/10.1186/s13071-023-05914-xopenalex-snapshot

Genomic analyses indicate the North American Ap-ha variant of the tick-vectored bacterium Anaplasma phagocytophilum was introduced from Europe

inferred← citeshttps://doi.org/10.1186/s40168-023-01728-2openalex-snapshot

Metagenomic characterization of a novel non-ammonia-oxidizing Thaumarchaeota from hadal sediment

inferred← citeshttps://doi.org/10.1186/s40529-022-00332-1openalex-snapshot

Morphology, mating system and taxonomy of Volvox africanus (Volvocaceae, Chlorophyceae) from Thailand

inferred← citeshttps://doi.org/10.1242/bio.059181openalex-snapshot

exTREEmaTIME: a method for incorporating uncertainty into divergence time estimates

inferred← citeshttps://doi.org/10.1266/ggs.20-00046openalex-snapshot

Three nuclear protein-coding genes corroborate a recent phylogenomic model of the Branchiopoda (Crustacea) and provide estimates of the divergence times of the major branchiopodan taxa

inferred← citeshttps://doi.org/10.12688/f1000research.28421.1openalex-snapshot

Sequence diversity and evolution of infectious bursal disease virus in Iraq

inferred← citeshttps://doi.org/10.1371/journal.pbio.2006035openalex-snapshot

Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution

inferred← citeshttps://doi.org/10.1371/journal.pbio.3002682openalex-snapshot

Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1007046openalex-snapshot

A new method for inferring timetrees from temporally sampled molecular sequences

inferred← citeshttps://doi.org/10.1371/journal.pgen.1008365openalex-snapshot

Convergent evolution of linked mating-type loci in basidiomycete fungi

inferred← citeshttps://doi.org/10.1371/journal.pgen.1008935openalex-snapshot

Horizontal transmission and recombination maintain forever young bacterial symbiont genomes

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