Elevated substitution rates estimated from ancient DNA sequences

No abstract is available for this paper.

• Publication year

  2007

• Venue

  Biology Letters

• Publication date

  2007-12-22

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1098/rsbl.2007.0377PMID 17785261PMCID PMC2391221
• 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.

• Evidence for time dependency of molecular rate estimates.

  2007cited by this paper
• Alarm bells for the molecular clock? No support for Ho et al.'s model of time-dependent molecular rate estimates.

  2007influential reference
• 217 000-year-old DNA sequences of green sulfur bacteria in Mediterranean sapropels and their implications for the reconstruction of the paleoenvironment.

  2007cited by this paper
• Relaxed Phylogenetics and Dating with Confidence

  2006cited by this paper
• Can deleterious mutations explain the time dependency of molecular rate estimates?

  2006cited by this paper
• Genomic Sequencing of Pleistocene Cave Bears

  2005cited by this paper
• Time dependency of molecular rate estimates and systematic overestimation of recent divergence times.

  2005cited by this paper
• Bayesian coalescent inference of past population dynamics from molecular sequences.

  2005cited by this paper
• Rise and Fall of the Beringian Steppe Bison

  2004cited by this paper
• Reconciling historical processes and population structure in the sooty tern Sterna fuscata

  2004cited by this paper
• The pedigree rate of sequence divergence in the human mitochondrial genome: there is a difference between phylogenetic and pedigree rates.

  2003cited by this paper
• DnaSP, DNA polymorphism analyses by the coalescent and other methods

  2003influential reference
• Statistical properties of new neutrality tests against population growth.

  2002cited by this paper
• A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times

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

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

  2002cited by this paper
• High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans.

  2000cited by this paper
• Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies

  2000cited by this paper
• PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees

  1997influential reference
• Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

  1997cited by this paper
• Evolutionary relationship of DNA sequences in finite populations.

  1983cited by this paper
• Rapid evolution of animal mitochondrial DNA.

  1979cited by this paper
• The Theory of Probability

  1922cited by this paper
• Department of Mathematics

  1894cited by 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
• A comparison of genomic diversity and demographic history of the North Atlantic and Southwest Atlantic southern right whales

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

  2023cites this paper
• Variation in the Substitution Rates among the Human Mitochondrial Haplogroup U Sublineages

  2022cites this paper
• Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species

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

  2021cites this paper
• BAYESIAN ADVENTURES AMONG HUMAN MITOCHONDRIAL LINEAGES

  2021cites this paper
• Mitogenomics and the genetic differentiation of contemporary Balaena mysticetus (Cetacea) from Svalbard

  2020cites this paper
• Using pre‐ and postexploitation samples to assess the impact of commercial whaling on the genetic characteristics of eastern North Pacific gray and humpback whales and to compare methods used to infer historic demography

  2020cites this paper
• Genetic Diversity of Ligidium Isopods in Hokkaido and Niigata, Northern Japan, Based on Mitochondrial DNA Analysis

  2020cites this paper
• Rapid loss of flight in the Aldabra white-throated rail

  2019cites this paper
• Demographic analysis of cyanobacteria based on the mutation rates estimated from an ancient ice core

  2018influential citation
• Deposited in DRO : 31 January 2018 Version of attached

  2018cites this paper
• Out of Africa: demographic and colonization history of the Algerian mouse (Mus spretus Lataste)

  2018cites this paper
• Eco-Evolutionary Processes Generating Diversity Among Bottlenose Dolphin, Tursiops truncatus, Populations off Baja California, Mexico

  2018cites this paper
• Guidelines for genetic data analysis

  2018cites this paper
• Low genetic diversity after a bottleneck in a population of a critically endangered migratory marine turtle species

  2017cites this paper
• Strong population structure in a species manipulated by humans since the Neolithic: the European fallow deer (Dama dama dama)

  2017cites this paper
• A comparison of methods for estimating substitution rates from ancient DNA sequence data

  2017cites this paper
• Phylogeography and population structure in highly mobile marine taxa in the western Indian Ocean : bottlenose dolphins (Tursiops spp.) and common dolphins (Delphinus sp.)

  2016cites this paper
• Post-glacial habitat release and incipient speciation in the genus Delphinus

  2016cites this paper
• Population differentiation in the context of Holocene climate change for a migratory marine species, the southern elephant seal

  2016cites this paper
• Resolving the ancestry of Austronesian-speaking populations

  2016cites this paper
• The importance of phylogenetic model assessment for macroevolutionary inference

  2016cites this paper
• Animal movement on short and long time scales and the effect on genetic diversity in cold-adapted species

  2016cites this paper
• The Roles of Taxonomy and Systematics in Bat Conservation

  2016cites this paper
• Post-glacial colonization of Europe by the wood mouse, Apodemus sylvaticus: evidence of a northern refugium and dispersal with humans

  2016cites this paper
• Inferences from tip‐calibrated phylogenies: a review and a practical guide

  2016cites this paper
• articlePhylogeographic history of grey wolves in Europe

  2015cites this paper
• Bucking the trend: genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean

  2015cites this paper
• Problems and Cautions With Sequence Mismatch Analysis and Bayesian Skyline Plots to Infer Historical Demography.

  2015cites this paper
• Micro‐evolutionary diversification among Indian Ocean parrots: temporal and spatial changes in phylogenetic diversity as a consequence of extinction and invasion

  2015cites this paper
• Geographically contrasting biodiversity reductions in a widespread New Zealand seabird

  2015influential citation
• The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data.

  2015cites this paper
• Model misspecification confounds the estimation of rates and exaggerates their time dependency

  2015influential citation
• Time‐dependent estimates of molecular evolutionary rates: evidence and causes

  2015influential citation
• Time Clustered Sampling Can Inflate the Inferred Substitution Rate in Foot-And-Mouth Disease Virus Analyses

  2015cites this paper
• Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA

  2015cites this paper
• Contrasting population genetic structure among freshwater-resident and anadromous lampreys: the role of demographic history, differential dispersal and anthropogenic barriers to movement

  2015cites this paper
• Lack of support for the time‐dependent molecular evolution hypothesis

  2015influential citation
• Ancient DNA: Results and prospects (The 30th anniversary)

  2015cites this paper
• Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences

  2015cites this paper
• Using Ancient DNA to Understand Evolutionary and Ecological Processes

  2014cites this paper
• Ancient DNA and the tropics: a rodent's tale

  2014cites this paper
• Influence of Holocene environmental change and anthropogenic impact on the diversity and distribution of roe deer

  2014cites this paper
• Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology

  2014cites this paper
• Land-Bridge Calibration of Molecular Clocks and the Post-Glacial Colonization of Scandinavia by the Eurasian Field Vole Microtus agrestis

  2014influential citation
• Improved Calibration of the Human Mitochondrial Clock Using Ancient Genomes

  2014cites this paper
• Rapid increase in southern elephant seal genetic diversity after a founder event

  2014cites this paper
• Phylogeography and population dynamics of the white-sided dolphin (Lagenorhynchus acutus) in the North Atlantic

  2014influential citation
• The evolutionary and behavioural ecology of a European lamprey species pair (Lampetra fluviatilis and L. planeri) : conservation concerns and anthropogenic impacts

  2014cites this paper
• Land Bridge Calibration of Rates of Molecular Evolution in a Widespread Rodent

  2014cites this paper
• Pleistocene sea level fluctuations and the phylogeography of the dugong in Australian waters

  2014cites this paper
• Phylogenomics of the killer whale indicates ecotype divergence in sympatry

  2014cites this paper
• Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts

  2013cites this paper
• A new genus of rodent from wallacea (Rodentia: Muridae: Murinae: Rattini), and its implication for biogeography and Indo-Pacific Rattini systematics

  2013cites this paper
• Mitogenomic analyses from ancient DNA.

  2013cites this paper
• The insect molecular clock

  2013cites this paper
• Evaluating Purifying Selection in the Mitochondrial DNA of Various Mammalian Species

  2013cites this paper
• Investigating patterns of animal domestication using ancient DNA

  2013cites this paper
• Molecular phylogeny of the Indian Ocean Terpsiphone paradise flycatchers: undetected evolutionary diversity revealed amongst island populations.

  2013cites this paper
• Expansion dating: calibrating molecular clocks in marine species from expansions onto the Sunda Shelf Following the Last Glacial Maximum.

  2012cites this paper
• Molecular evolutionary and epidemiological dynamics of a highly pathogenic fish rhabdovirus, the spring viremia of carp virus (SVCV).

  2012cites this paper
• Ancient DNA from marine mammals: studying long-lived species over ecological and evolutionary timescales.

  2012cites this paper
• Global phylogeography and evolution of chelonid fibropapilloma-associated herpesvirus.

  2012cites this paper
• Ancient human DNA.

  2012cites this paper
• A glimpse on the pattern of rodent diversification: a phylogenetic approach

  2012cites this paper
• Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages.

  2012cites this paper
• A molecular approach to Neanderthal extinction

  2012cites this paper
• Selective Constraints Determine the Time Dependency of Molecular Rates for Human Nuclear Genomes

  2012cites this paper
• Faunal histories from Holocene ancient DNA.

  2011cites this paper
• Bayesian estimation of substitution rates from ancient DNA sequences with low information content.

  2011cites this paper
• Ancient hybridization and an Irish origin for the modern polar bear matriline.

  2011cites this paper
• Possible cryptic stock structure for minke whales in the North Atlantic: Implications for conservation and management

  2011cites this paper
• Time‐dependent rates of molecular evolution

  2011influential citation
• Population genetic history of the British roe deer (Capreolus capreolus) and its implications for diversity and fitness

  2011cites this paper
• The influence of glacial epochs and habitat dependence on the diversity and phylogeography of a coastal dolphin species: Lagenorhynchus albirostris

  2010influential citation
• THE STATE OF THE FIELD: Combining contemporary and ancient DNA in population genetic and phylogeographical studies

  2010cites this paper
• European water fragmentation in a top cetacean predator : the harbour Genetic and historic evidence for climate-driven population

  2010cites this paper
• The evolution of the mitochondrial DNA in tuatara (Sphenodon punctatus) : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Evolutionary Genetics, Massey University, Auckland, New Zealand

  2010cites this paper
• Rates of Molecular Evolution and Phylogenomic Inference

  2010cites this paper
• Using genetic evidence to evaluate four palaeoanthropological hypotheses for the timing of Neanderthal and modern human origins.

  2010cites this paper
• Palaeoecology and population demographics of the extinct New Zealand moa (Aves: Dinornithiformes).

  2010cites this paper
• Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses

  2010influential citation
• articlePhylogeographic history of grey wolves in Europe

  2010cites this paper
• Genetic and historic evidence for climate-driven population fragmentation in a top cetacean predator: the harbour porpoises in European water

  2010cites this paper
• Evolution and maintenance of divergent lineages in an endangered freshwater fish, Macquaria australasica

  2010cites this paper
• Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times.

  2009influential citation
• First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns

  2009influential citation
• Mitochondrial phylogeography of the European ground squirrel, Spermophilus citellus, yields evidence on refugia for steppic taxa in the southern Balkans

  2009cites this paper
• Rapid Response of a Marine Mammal Species to Holocene Climate and Habitat Change

  2009cites this paper
• Time dependency of molecular rates in ancient DNA data sets, a sampling artifact?

  2009cites this paper
• Using Classical Population Genetics Tools with Heterochroneous Data: Time Matters!

  2009cites this paper
• HISTORICAL POPULATION GENETICS OF CALLORHINUS URSINUS (NORTHERN FUR SEALS) FROM THE ALEUTIAN ISLANDS

  2009influential citation
• Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods

  2009influential citation
• Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: a general demographic model for mammals?

  2009cites this paper
• Genetic structure of the asiatic black bear in Japan using mitochondrial DNA analysis.

  2009influential citation
• Do complex population histories drive higher estimates of substitution rate in phylogenetic reconstructions?

  2009cites this paper
• Comparing Evolutionary Patterns and Variability in the Mitochondrial Control Region and Cytochrome b in Three Species of Baleen Whales

  2008cites this paper
• Evolutionary history of the critically endangered Cozumel dwarf carnivores inferred from mitochondrial DNA analyses

  2008influential citation