The effect of inappropriate calibration: three case studies in molecular ecology (Q28755767)

5

0 references

James Haile

4

0 references

Urmas Saarma

2

object named as

Urmas Saarma

0 references

Ross Barnett

object named as

Ross Barnett

3

0 references

Simon Y. W. Ho

Creative Commons Attribution 4.0 International

1

object named as

Simon Y W Ho

0 references

language of work or name

English

0 references

publication date

20 February 2008

0 references

published in

PLOS One

0 references

volume

3

0 references

issue

2

0 references

page(s)

e1615

0 references

copyright license

start time

20 February 2008

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

maintained by WikiProject

1 reference

DNA evidence for historic population size and past ecosystem impacts of gray whales

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Elevated substitution rates estimated from ancient DNA sequences

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

The latitudinal gradient in recent speciation and extinction rates of birds and mammals

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Molecular evidence for species-level distinctions in clouded leopards

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Paleontological evidence to date the tree of life

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Relaxed phylogenetics and dating with confidence

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Bayesian coalescent inference of past population dynamics from molecular sequences

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Ice sheets promote speciation in boreal birds

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Lack of phylogeography in European mammals before the last glaciation

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

The tempo of avian diversification during the Quaternary

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

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

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Genomic ancestry of the American puma (Puma concolor)

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Speciation durations and Pleistocene effects on vertebrate phylogeography

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Pleistocene phylogeographic effects on avian populations and the speciation process

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Abundant mitochondrial DNA variation and world-wide population structure in humpback whales

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

The genetic legacy of the Quaternary ice ages

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Comparative phylogeography and postglacial colonization routes in Europe

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Evidence for time dependency of molecular rate estimates

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Molecular clocks: when times are a-changin'

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Rise and fall of the Beringian steppe bison

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Staying out in the cold: glacial refugia and mitochondrial DNA phylogeography in ancient European brown bears

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Genetic variation in Holocene bowhead whales from Svalbard

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Bayesian estimation of sequence damage in ancient DNA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

The tempo of avian diversification: a comment on Johnson and Cicero

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Mutation hot spots in mammalian mitochondrial DNA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Mitochondrial phylogenetics and evolution of mysticete whales.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

New mitochondrial DNA data affirm the importance of Pleistocene speciation in North American birds

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Molecular phylogeography reveals island colonization history and diversification of western Indian Ocean sunbirds (Nectarinia: Nectariniidae).

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Rates of evolution in ancient DNA from Adélie penguins.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Dynamics of Pleistocene population extinctions in Beringian brown bears

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Historical population size change of bowhead whales inferred from DNA sequence polymorphism data.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

The age of nonsynonymous and synonymous mutations in animal mtDNA and implications for the mildly deleterious theory

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K-Ar-based ages of the Hawaiian Islands to estimate molecular evolutionary rates

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

A mitochondrial cytochrome B phylogeny of the Alectoris partridges.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Phylogeography of brown bears (Ursus arctos) of Alaska and paraphyly within the Ursidae

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Calibration of mitochondrial DNA evolution in geese

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

New approaches to dating suggest a recent age for the human mtDNA ancestor

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2229648

Glacial cycles and the tempo of avian speciation

3 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

Evidence for reproductive isolation between cave bear populations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

Mitogenetic structure of brown bears (Ursus arctos L.) in northeastern Europe and a new time frame for the formation of European brown bear lineages.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

Ancient DNA enables timing of the pleistocene origin and holocene expansion of two adélie penguin lineages in antarctica

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

Can deleterious mutations explain the time dependency of molecular rate estimates?

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

Estimation of the mtDNA mutation rate in aging mice by proteome analysis and mathematical modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

The genealogy of a sequence subject to purifying selection at multiple sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

Age and growth estimates of bowhead whales ( Balaena mysticetus ) via aspartic acid racemization

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

Mitochondrial DNA polymorphism, phylogeography, and conservation genetics of the brown bear Ursus arctos in Europe.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

Mitochondrial DNA Phylogeography of the North American Brown Bear and Implications for Conservation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

Microevolution of the mitochondrial DNA control region in the Japanese brown bear (Ursus arctos) population.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

Ancient DNA analyses reveal high mitochondrial DNA sequence diversity and parallel morphological evolution of late pleistocene cave bears

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

Diet and Co-ecology of Pleistocene Short-Faced Bears and Brown Bears in Eastern Beringia

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

Alarm bells for the molecular clock? No support for Ho et al.'s model of time-dependent molecular rate estimates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

Pleistocene brown bears in the mid-continent of North America

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

Global Changes During the Last 3 Million Years: Climatic Controls and Biotic Responses

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

Relativity for molecular clocks

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001615

The detection of shared and ancestral polymorphisms

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18286172

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0001615

1 reference

3772431

ADS bibcode

2008PLoSO...3.1615H

0 references

3772431

1 reference

1 reference

1 reference