Time dependency of molecular rate estimates and systematic overestimation of recent divergence times.

No abstract is available for this paper.

• Publication year

  2005

• Venue

  Molecular biology and evolution

• Publication date

  2005-07-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1093/MOLBEV/MSI145PMID 15814826
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• The Primate Fossil Record

  2008influential reference
• On the constancy of the evolutionary rate of cistrons

  2005cited by this paper
• Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

  2005cited by this paper
• Precision of molecular time estimates.

  2004cited by this paper
• Quality assessment of the human genome sequence

  2004cited by this paper
• Is there a universal mtDNA clock for birds

  2004cited by this paper
• Tracing the decay of the historical signal in biological sequence data.

  2004cited by this paper
• Estimation of divergence times for major lineages of primate species.

  2003influential reference
• Timing the origin of New World monkeys.

  2003influential reference
• The pedigree rate of sequence divergence in the human mitochondrial genome: there is a difference between phylogenetic and pedigree rates.

  2003influential reference
• Molecular evidence for deep phylogenetic divergence in Mandrillus sphinx

  2003cited by this paper
• Patterns of Intra- and Interhost Nonsynonymous Variation Reveal Strong Purifying Selection in Dengue Virus

  2003cited by this paper
• Molecular phylogeography reveals island colonization history and diversification of western Indian Ocean sunbirds (Nectarinia: Nectariniidae).

  2003cited by this paper
• Phylogenetic network and physicochemical properties of nonsynonymous mutations in the protein-coding genes of human mitochondrial DNA.

  2003cited by this paper
• Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny.

  2002cited by this paper
• Rates of Evolution in Ancient DNA from Adélie Penguins

  2002cited by this paper
• Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus anthracis

  2002cited by this paper
• Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach.

  2002cited by this paper
• Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data.

  2002cited by this paper
• Positive and negative selection on the human genome.

  2001cited by this paper
• Initial sequencing and analysis of the human genome

  2001cited by this paper
• Codon-substitution models for heterogeneous selection pressure at amino acid sites.

  2000cited by this paper
• Molecular analysis of Neanderthal DNA from the northern Caucasus

  2000cited by this paper
• The mutation rate in the human mtDNA control region.

  2000influential reference
• The age of nonsynonymous and synonymous mutations in animal mtDNA and implications for the mildly deleterious theory.

  1999cited by this paper
• DNA sequence of the mitochondrial hypervariable region II from the neandertal type specimen.

  1999cited by this paper
• Estimating the rate of evolution of the rate of molecular evolution.

  1998cited by this paper
• Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K–Ar‐based ages of the Hawaiian Islands to estimate molecular evolutionary rates

  1998cited by this paper
• Mitochondrial mutation rate revisited: hot spots and polymorphism

  1998cited by this paper
• Preponderance of slightly deleterious polymorphism in mitochondrial DNA: nonsynonymous/synonymous rate ratio is much higher within species than between species.

  1998cited by this paper
• Body size effects and rates of cytochrome b evolution in tube-nosed seabirds.

  1998cited by this paper
• Neandertal DNA sequences and the origin of modern humans.

  1997cited by this paper
• PAML: a program package for phylogenetic analysis by maximum likelihood

  1997cited by this paper
• A high observed substitution rate in the human mitochondrial DNA control region

  1997cited by this paper
• How rapidly does the human mitochondrial genome evolve?

  1996cited by this paper
• A Mitochondrial CytochromeBPhylogeny of theAlectorisPartridges

  1996cited by this paper
• A mitochondrial cytochrome B phylogeny of the Alectoris partridges.

  1996cited by this paper
• Molecular divergence and phylogeny: rates and patterns of cytochrome b evolution in cranes.

  1996cited by this paper
• Reduced mtDNA diversity in the Ngöbé Amerinds of Panamá.

  1995cited by this paper
• Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs.

  1995cited by this paper
• Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods

  1994cited by this paper
• Sequencing errors and molecular evolutionary analysis.

  1992cited by this paper
• African populations and the evolution of human mitochondrial DNA.

  1991cited by this paper
• Extensive mitochondrial diversity within a single Amerindian tribe.

  1991cited by this paper
• The neutral theory of molecular evolution.

  1983influential reference
• Rapid evolution of animal mitochondrial DNA.

  1979cited by this paper
• Slightly Deleterious Mutant Substitutions in Evolution

  1973cited by this paper
• Department of Mathematics

  1894cited by this paper

• Historical Biogeography of the diverse Neotropical seasonal killifishes of the Austrolebias Genus Group: potential environmental drivers of diversification

  2026cites this paper
• Two Contrasting Demographic Processes Shape the Divergence and Evolution of the Widespread Arid Zone Specialist, Petrogale lateralis

  2026cites this paper
• Molecular Characterization of Complete Simian Foamy Virus Genomes from Three Colobine Monkeys Reveals Highly Divergent Evolutionary Trajectories and Identifies Transmission to Humans

  2026cites this paper
• Navigating "tip fog": Embracing uncertainty in tip measurements.

  2025cites this paper
• Evidence of long-term purging of mutation burden in killer whale Orcinus orca genomes

  2025cites this paper
• Integrated taxonomy using morphology and DNA sequences: recognition of a new species with comments on the geological history of the Liolaemus capillitas clade (Squamata: Iguania)

  2025cites this paper
• Tuberculosis susceptibility and inbreeding depression hinder ex-situ conservation in a critically endangered rainforest bird

  2025cites this paper
• Phylogenomics and structural modelling feature accelerated evolution of Oropouche virus: 1955 to 2024

  2025cites this paper
• A unified evolutionary framework to reconstruct the viral histories of human, simian, and prosimian immunodeficiency viruses across timescales

  2025cites this paper
• Phylogenetic Assessment of Gazella bennettii: A Genetic Framework for the Conservation of the Endangered Jebeer in Iran

  2025cites this paper
• Phylogenetics of Channel Island Deer Mice Based on the Cytochrome B Gene Sheds Light on Multiple Colonization Events and Supports Current Taxonomy

  2025cites this paper
• Genetic diversity and historical demography of the imperiled rattlesnake-master borer moth (Papaipema eryngii)

  2025cites this paper
• Coalescent-based branch length estimation improves dating of species trees

  2025cites this paper
• Phylogenetic meta-analysis of persistent SARS-CoV-2 infections in immunocompromised individuals highlights the challenges of robust evolutionary rate estimation caused by low genetic diversity

  2025cites this paper
• Reply to Zijlstra (2025) - Status of Indo-Burmese pangolin (Manis indoburmanica)

  2025influential citation
• The convergent genomic dynamism for aquatic adaptation in vascular plants.

  2025cites this paper
• Island Population Dynamics Since the Late Miocene: Comparative Phylogeography of Mammalian Species in Three Genera (Pentalagus, Diplothrix, and Tokudaia) Endemic to the Central Ryukyu Islands

  2025cites this paper
• Study of Cytochrome B Gene Variations in Avian Fauna of Sargodha

  2025cites this paper
• Revisiting evolutionary rate-time relationships

  2025influential citation
• Explainable machine learning reveals evolutionary signals in Influenza hemagglutinin

  2025cites this paper
• Demographic and genetic diversity of the genus Paralichthys in the Buenos Aires Coastal Ecosystem of the southwestern Atlantic

  2025cites this paper
• Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss

  2025cites this paper
• Rate-time scaling in phenotypic evolution: Limitations of current models in capturing temporal dynamics.

  2025cites this paper
• Untangling intergeneric mito-nuclear discordance: evidence for ancient introgression in two vole genera, Clethrionomys and Alticola (Rodentia, Cricetidae).

  2025cites this paper
• Evidence for Neolithic acquisition of the high pathogenic island by Escherichia coli followed by recent selection

  2025influential citation
• Species level hidden diversity within morphospecies: Anatolia-based evolution and cryptic species diversity in the Simulium (Wilhelmia) equinum species group (Diptera: Simuliidae)

  2024cites this paper
• Comparative Phylogeography of Vicariant Species of the Daphnia longispina s.lat. Complex (Crustacea: Cladocera) in Northern Eurasia

  2024cites this paper
• The distinct spatiotemporal evolutionary landscape of HBV and HDV largely determines the unique epidemic features of HDV globally.

  2024cites this paper
• Paleopteran molecular clock: Time drift and recent acceleration

  2024cites this paper
• South! Phylogeography of the Antarctic fairy shrimp Branchinecta gaini and its closest Patagonian congener Branchinecta granulosa reveals a long-term association of freshwater fauna with the southern continent

  2024cites this paper
• Mixture Models for Dating with Confidence

  2024cites this paper
• Analysis of Evolutionary Conservation, Expression Level, and Genetic Association at a Genome-wide Scale Reveals Heterogeneity Across Polygenic Phenotypes

  2024cites this paper
• Genetic Differentiation and Evolutionary Transition-Transversion Bias in Vertebrates by the Example of the CYTB Gene with Emphasis on Mammals and Primates

  2024cites this paper
• Phylogeography of Korean field mouse Apodemus peninsulae (Rodentia: Muridae): an update

  2024cites this paper
• Cassava brown streak virus evolves with a nucleotide-substitution rate that is typical for the family Potyviridae

  2024cites this paper
• What, if anything, is Galaxias vulgaris?

  2024cites this paper
• Rapid evolution of mitochondrion-related genes in haplodiploid arthropods

  2024cites this paper
• Genetic variation and taxonomic status of Dahl’s jird (Meriones dahli, rodentia, muridae)

  2024cites this paper
• The rate and nature of mitochondrial DNA mutations in human pedigrees.

  2024cites this paper
• Both high and low dispersal? Apparently contradictory genetic patterns in the Antarctic littorinid gastropod Laevilacunaria antarctica

  2024cites this paper
• Comparative phylogeography of vicariant species of the Daphnia longispina s.lat. complex (Crustacea: Cladocera) in North Eurasia

  2024cites this paper
• Navigating “tip fog”: Embracing uncertainty in tip measurements

  2024cites this paper
• HIV-1 Gag, Pol, and Env diversified with limited adaptation since the 1980s

  2024cites this paper
• Region-Specific Genetic Diversity of Black Rats (Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events

  2024cites this paper
• Noise leads to the perceived increase in evolutionary rates over short time scales

  2024cites this paper
• Comparing the transmission potential from sequence and surveillance data of 2009 North American influenza pandemic waves

  2023cites this paper
• Conceptual and empirical bridges between micro- and macroevolution

  2023cites this paper
• Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus

  2023cites this paper
• Beringia as a high‐latitude engine of avian speciation

  2023cites this paper
• Inferring phylogenetic structure, taxa hybridization, and divergence times within rock voles of subgenus Aschizomys (Cricetidae: Alticola) using quaddRAD sequencing and a cytb dataset

  2023cites this paper
• Phylogeography of Lasiopodomys gregalis (Rodentia: Cricetidae) in the southern part of its geographic range

  2023cites this paper
• Rapid host switching of Wolbachia and even more rapid turnover of their phages and incompatibility-causing loci

  2023influential citation
• Genetic Variability of the Long-Tailed Macaque (Macaca fascicularis) Populations in Urban Habitat in Padang City, West Sumatra, Indonesia

  2023influential citation
• DNA Identification of Parasitic Copepods Salmincola (Copepoda, Siphonostomatoida, Lernaeopodidae): Variability and Rate of Evolution of the Mitochondrial Cytochrome c Oxidase Subunit I Gene

  2023cites this paper
• Geologically calibrated mammalian tree and its correlation with global events, including the emergence of humans

  2023cites this paper
• Reversions mask the contribution of adaptive evolution in microbiomes

  2023cites this paper
• Contribution of small rodent communities (Muridae) to the history of West Central African savannas (case of Gabonese savannas): diversity, biogeographic affinities, phylogeography and paleoenvironmental analyses

  2023cites this paper
• Modeling the mosaic structure of bacterial genomes to infer their evolutionary history

  2023cites this paper
• Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses

  2023cites this paper
• Functional Duplication of the Short-Wavelength-Sensitive Opsin in Sea Snakes: Evidence for Reexpanded Color Sensitivity Following Ancestral Regression

  2023cites this paper
• Effects of Quaternary climatic oscillations over the Chacoan fauna: phylogeographic patterns in the southern three-banded armadillo Tolypeutes matacus (Cingulata: Chlamyphoridae)

  2023cites this paper
• Molecular evolution in introduced insect species—a mitochondrial perspective

  2023cites this paper
• Evaluating species boundaries using coalescent delimitation in pine-killing Monochamus (Coleoptera: Cerambycidae) sawyer beetles.

  2023cites this paper
• Wild pedigrees inform mutation rates and historic abundance in baleen whales

  2023cites this paper
• Reconstructing the evolutionary history of human, simian, and prosimian immunodeficiency viruses

  2023cites this paper
• Phylogeography and demographic history of the subterranean rodents belonging to the Ctenomys talarum phylogenetic group (Rodentia: Ctenomyidae)

  2023cites this paper
• Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

  2022cites this paper
• Mitochondrial DNA variation of the caracal (Caracal caracal) in Iran and range-wide phylogeographic comparisons

  2022cites this paper
• Phylogeography of the White-Toothed Shrews Crocidura suaveolens and Crocidura sibirica: Searching for the Geographical Homeland

  2022cites this paper
• Phylogeography reveals a panmictic population of the Chilean nylon shrimp along its exploitation range in the southeast Pacific Ocean

  2022cites this paper
• The Concept of the Modern Molecular Clock and Experience in Estimating Divergence Times of Eulipotyphla and Rodentia

  2022cites this paper
• Quaternary Environmental Changes Shaped Mitochondrial DNA Diversity in the Large Japanese Wood Mouse Apodemus speciosus in Hokkaido, Japan

  2022cites this paper
• Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale

  2022cites this paper
• A unified global genotyping framework of dengue virus serotype-1 for a stratified coordinated surveillance strategy of dengue epidemics

  2022cites this paper
• Mitogenomic phylogeny revealed the fine population structure of an endangered cyprinid fish Pseudorasbora pugnax in the Tokai region, central Japan

  2022cites this paper
• Variation in the Substitution Rates among the Human Mitochondrial Haplogroup U Sublineages

  2022cites this paper
• Temporal dynamics of mildly deleterious nonsynonymous substitutions in mitochondrial gene sequences in rodents and moles.

  2022cites this paper
• Phylogenomics and Historical Biogeography of West Indian Rock Iguanas (genus Cyclura).

  2022cites this paper
• Phylogeography of the White-Toothed Shrews Crocidura suaveolens and Crocidura sibirica: Searching for the Geographical Homeland

  2022cites this paper
• The scaling of diversification rates with age is likely explained by sampling bias

  2022cites this paper
• Disease-causing human viruses: novelty and legacy.

  2022cites this paper
• Genetic diversity and demography of Bufo japonicus and B. torrenticola (Amphibia: Anura: Bufonidae) influenced by the Quaternary climate

  2022cites this paper
• Relation between two evolutionary clocks reveal new insights in bacterial evolution

  2022cites this paper
• Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

  2022cites this paper
• Isolation and Divergence of Peromyscus melanotis Populations Across the Madrean Sky Islands in Arizona

  2022cites this paper
• Taxonomic re-appraisal for toothfish (Dissostichus: Notothenioidea) across the Antarctic Polar Front using genomic and morphological studies.

  2022cites this paper
• Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates

  2022cites this paper
• Phylogeography using mitogenomes: A rare Dipodidae, Sicista betulina, in North‐western Europe

  2022cites this paper
• Paleogenomics reveals independent and hybrid origins of two morphologically distinct wolf lineages endemic to Japan.

  2022cites this paper
• Gene duplication and rate variation in the evolution of plastid ACCase and Clp genes in angiosperms

  2022cites this paper
• Mitochondrial substitution rates estimation for divergence time analyses in modern birds based on full mitochondrial genomes

  2021cites this paper
• Pleistocene divergence in the absence of gene flow among populations of a viviparous reptile with intraspecific variation in sex determination

  2021influential citation
• Phylogeography and genetic diversity of the microbivalve Kidderia subquadrata, reveals new data from West Antarctic Peninsula

  2021cites this paper
• Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim.

  2021cites this paper
• Fast Bayesian inference of phylogenies from multiple continuous characters

  2021cites this paper
• Prisoner of War dynamics explains the time-dependent pattern of substitution rates in viruses

  2021cites this paper
• Diversification and geological history of the Liolaemus ornatus group (Squamata: Iguania) of Argentina including the recognition of a new species

  2021cites this paper
• BAYESIAN ADVENTURES AMONG HUMAN MITOCHONDRIAL LINEAGES

  2021cites this paper
• Karyotypic polymorphism of Crocidura tanakae (Eulipotyphla: Soricidae) and revision of the karyotype of C. attenuata in mainland China

  2021cites this paper
• Genetic diversity and population structure of Pacific herring Clupea pallasii in the Northeast Asia inferred from mtDNA marker

  2021cites this paper