Abstract
Abstract We describe a method for co-estimating r = C/μ (where C is the per-site recombination rate and μ is the per-site neutral mutation rate) and Θ = 4Neμ (where Ne is the effective population size) from a population sample of molecular data. The technique is Metropolis-Hastings sampling: we explore a large number of possible reconstructions of the recombinant genealogy, weighting according to their posterior probability with regard to the data and working values of the parameters. Different relative rates of recombination at different locations can be accommodated if they are known from external evidence, but the algorithm cannot itself estimate rate differences. The estimates of Θ are accurate and apparently unbiased for a wide range of parameter values. However, when both Θ and r are relatively low, very long sequences are needed to estimate r accurately, and the estimates tend to be biased upward. We apply this method to data from the human lipoprotein lipase locus.
Keywords
Recombination rateRecombinationWeightingBiologyStatisticsPopulationMutation rateSampling (signal processing)Locus (genetics)Range (aeronautics)Sampling biasGeneticsMathematicsSample size determinationComputer scienceDemographyPhysicsGene
Affiliated Institutions
Related Publications
LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters
Abstract Summary: We present a Markov chain Monte Carlo coalescent genealogy sampler, LAMARC 2.0, which estimates population genetic parameters from genetic data. LAMARC can co-...
Direct estimates of human per nucleotide mutation rates at 20 loci causing mendelian diseases
I estimate per nucleotide rates of spontaneous mutations of different kinds in humans directly from the data on per locus mutation rates and on sequences of de novo nonsense nuc...
Estimate of the Mutation Rate per Nucleotide in Humans
Abstract Many previous estimates of the mutation rate in humans have relied on screens of visible mutants. We investigated the rate and pattern of mutations at the nucleotide le...
Patterns of DNA sequence polymorphism along chromosome 1 of maize ( <i>Zea mays</i> ssp. <i>mays</i> L.)
We measured sequence diversity in 21 loci distributed along chromosome 1 of maize ( Zea mays ssp. mays L.). For each locus, we sequenced a common sample of 25 individuals repres...
Statistical tests of neutrality of mutations.
Abstract Mutations in the genealogy of the sequences in a random sample from a population can be classified as external and internal. External mutations are mutations that occur...
Publication Info
- Year
- 2000
- Type
- article
- Volume
- 156
- Issue
- 3
- Pages
- 1393-1401
- Citations
- 212
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
212
OpenAlex
Cite This
Mary K. Kuhner,
Jon Yamato,
Joseph Felsenstein
(2000).
Maximum Likelihood Estimation of Recombination Rates From Population Data.
Genetics
, 156
(3)
, 1393-1401.
https://doi.org/10.1093/genetics/156.3.1393
Identifiers
- DOI
- 10.1093/genetics/156.3.1393