The DOI matches its Crossref record; 16 of the 16 references it cites were found in a registry or an index.
Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling.
Open accessAbstract
We present a new way to make a maximum likelihood estimate of the parameter 4N mu (effective population size times mutation rate per site, or theta) based on a population sample of molecular sequences. We use a Metropolis-Hastings Markov chain Monte Carlo method to sample genealogies in proportion to the product of their likelihood with respect to the data and their prior probability with respect to a coalescent distribution. A specific value of theta must be chosen to generate the coalescent distribution, but the resulting trees can be used to evaluate the likelihood at other values of theta, generating a likelihood curve. This procedure concentrates sampling on those genealogies that contribute most of the likelihood, allowing estimation of meaningful likelihood curves based on relatively small samples. The method can potentially be extended to cases involving varying population size, recombination, and migration.
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Cites
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On the genealogy of large populations
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Cited by
Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
Huelsenbeck, J. P., Ronquist, F., Nielsen, R., & Bollback, J. P. (2001) · Science · doi:10.1126/science.1065889 · Cited by 2,737
Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
Rannala, B., & Yang, Z. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02338839 · Cited by 1,748
Markov Chasin Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees
Larget, B., & Simon, D. L. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026160 · Cited by 1,617
Distinguishing Migration From Isolation: A Markov Chain Monte Carlo Approach
Nielsen, R., & Wakeley, J. (2001) · Genetics · doi:10.1093/genetics/158.2.885 · Cited by 1,311
Approximate Bayesian Computation in Evolution and Ecology
Beaumont, M. A. (2010) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev-ecolsys-102209-144621 · Cited by 1,114
Metadata
- Authors
- Kuhner, M. K., Yamato, J., & Felsenstein, J.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 1995-08-01
- Volume
- 140
- Issue
- 4
- Pages
- 1421-1430
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W2124061807
- Cited by
- 451
- References
- 16
- FWCI
- 7.30
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Kuhner, M. K., Yamato, J., & Felsenstein, J. (1995). Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics. https://doi.org/10.1093/genetics/140.4.1421
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
