Accuracy of Molecular Dating with the Rho Statistic: Deviations from Coalescent Expectations Under a Range of Demographic Models

@inproceedings{Cox2008AccuracyOM,
  title={Accuracy of Molecular Dating with the Rho Statistic: Deviations from Coalescent Expectations Under a Range of Demographic Models},
  author={Murray P. Cox},
  booktitle={Human biology},
  year={2008}
}
  • M. Cox
  • Published in Human biology 29 May 2010
  • Biology
Abstract The ρ statistic is commonly used to infer chronological dates for molecular lineages, especially from mitochondrial DNA sequences obtained in anthropological contexts. Since this approach was described 12 years ago, it has been applied to estimate molecular dates in more than 200 studies, including some published in top-tier journals. However, this method has not been well evaluated, and the accuracy of dates obtained from the ρ statistic remains unknown, especially for genetic data… 
View on BioOne
ncbi.nlm.nih.gov
21 Citations
Highly Influential Citations
1
Background Citations
8
Methods Citations
3
Results Citations
2

21 Citations

Rectifying long-standing misconceptions about the ρ statistic for molecular dating
TLDR
It is concluded that ρ dating, alongside approaches such as maximum likelihood (ML) and Bayesian inference, remains a useful tool for genetic dating.
Counterbalancing the time-dependent effect on the human mitochondrial DNA molecular clock
TLDR
It is suggested that the demographic history of populations has a more decisive effect than purifying selection and/or mutational saturation on the time-dependent effect observed for the substitution rate, and a new method is proposed that corrects for this effect.
Chromosome as a chronicler: Genetic dating, historical events, and DNA-genealogic temptation
TLDR
Nonrecombinant portions of the genome, Y chromosome and mitochondrial DNA, are widely used for research on human population gene pools and reconstruction of their history, and rate estimations for Y-chromosomal STR haplotypes with threefold difference are obtained.
Reconstructing past changes in locus-specific recombination rates
TLDR
This work describes a new method, based on n-tuple dataset subsampling, to infer past changes in recombination rate from DNA sequences taken at a single time point, and shows for the first time that reconstructing historic recombination rates is possible in principle.
Climatic variability, plasticity, and dispersal: A case study from Lake Tana, Ethiopia.
Insights into matrilineal genetic structure, differentiation and ancestry of Armenians based on complete mitogenome data
TLDR
The authors' phylogeographic analysis reveals common ancestries for some mtDNA lineages shared by West Asians, Transcaucasians, Europeans, Central Asians and Armenians and reveals a remarkable degree of matrilineal genetic heterogeneity and weak population structuring of Armenians.
A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the last glacial maximum.
TLDR
It is demonstrated that maternal diversity on the plateau reflects mostly a northern East Asian ancestry, and phylogeographic analysis of plateau-specific sublineages revealed two primary components: pre-last glacial maximum (LGM) inhabitants and post-LGM immigrants.
Contradictions and Concordances in American Colonization Models
The traditional view of American colonization during the late Pleistocene has largely been conditioned on early conceptions of the timing and extent of continental glaciations and the age and…
Contradictions and Concordances in American Colonization Models
  • D. O’Rourke
  • Environmental Science
    Evolution: Education and Outreach
  • 2011
TLDR
Accumulating molecular genetic data raises new questions about the timing and population size of the initial colonization of the Americas, while a closer examination of glacial models suggests that a number of routes into the Americas may have been available until fairly late in the last glacial cycle.
Pliocene-Early Pleistocene Geological Events Structure Pacific Martens (Martes caurina).
The complex topography, climate, and geological history of Western North America have shaped contemporary patterns of biodiversity and species distributions in the region. Pacific martens (Martes…
...
...

References

SHOWING 1-10 OF 30 REFERENCES
Frequentist estimation of coalescence times from nucleotide sequence data using a tree-based partition.
TLDR
The method is applied to sequences of Y chromosomes and mtDNAs to estimate the coalescent times of human male and female populations and shows that in a wide range of situations, the point estimate has small bias and the confidence interval has at least the nominal coverage probability.
Inferring Human Population Sizes, Divergence Times and Rates of Gene Flow From Mitochondrial, X and Y Chromosome Resequencing Data
TLDR
It is surmised that ancestral African populations had already been geographically structured prior to the founding of ancestral Eurasian populations, and African populations are shown to experience low levels of mitochondrial DNA gene flow, but high levels of Y chromosome gene flow.
Dates from the molecular clock: how wrong can we be?
Inferring coalescence times from DNA sequence data.
TLDR
Extensions are presented that allow for the effects of uncertainty in knowledge of population size and mutation rates, for variability in population sizes, for regions of different mutation rate, and for inference concerning the coalescence time of the entire population.
Molecular clocks: when times are a-changin'.
Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies.
The length of the human generation interval is a key parameter when using genetics to date population divergence events. However, no consensus exists regarding the generation interval length, and a…
Testing for Archaic Hominin Admixture on the X Chromosome: Model Likelihoods for the Modern Human RRM2P4 Region From Summaries of Genealogical Topology Under the Structured Coalescent
TLDR
A new summary statistic called the minimum clade proportion (pmc) is defined, which quantifies the proportion of individuals from a specified geographic region in each of the two basal clades of a binary gene tree, and yields values that are significantly unlikely under the RAR model and fit expectations better under a range of archaic admixture scenarios.
BEAST: Bayesian evolutionary analysis by sampling trees
TLDR
BEAST is a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree that provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions.
When did the human population size start increasing?
TLDR
Analysis of frequency spectra of all available human nuclear sequence data sets by using a model of constant population size followed by exponential growth finds that under more complex demographic models, including a bottleneck or population subdivision, more of the data are compatible with long-term growth.
Indonesian Mitochondrial DNA and Its Opposition to a Pleistocene Era Origin of Proto-Polynesians in Island Southeast Asia
  • M. Cox
  • Biology
    Human biology
  • 2005
TLDR
The extant mtDNA evidence can no longer be viewed as favoring a Polynesian origin in eastern Indonesia, but instead remains consistent with an origin of proto-Polynesian peoples in southern China and Taiwan.
...
...