ArticleGenetics2011
Joint inference of microsatellite mutation models, population history and genealogies using transdimensional Markov Chain Monte Carlo.
Article in Genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Bayesian Model Averaging of Parametric Coalescent Models for Phylodynamic Inference.Molecular biology and evolution · 2025Article
- Founder events and subsequent genetic bottlenecks underlie karyotype evolution in the Ibero-North African endemic Carex helodes.Annals of botany · 2024Article
- Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales.Systematic biology · 2021Article
- Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020.Nature communications · 2021Article
- Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework.Scientific reports · 2021Article
- BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.PLoS computational biology · 2019Article
- What factors shape genetic diversity in cetaceans?Ecology and evolution · 2018Article
- Genetic Variation of the Endangered Neotropical CatfishFrontiers in genetics · 2018Article
- Article
- The Genome as an Evolutionary Timepiece.Genome biology and evolution · 2016Review
- The triploid East African Highland Banana (EAHB) genepool is genetically uniform arising from a single ancestral clone that underwent population expansion by vegetative propagation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016Article
- Longitudinal analysis of Plasmodium falciparum genetic variation in Turbo, Colombia: implications for malaria control and elimination.Malaria journal · 2015Article
- Motif mismatches in microsatellites: insights from genome-wide investigation among 20 insect species.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Recent insertion/deletion (reINDEL) mutations: increasing awareness to boost molecular-based research in ecology and evolution.Ecology and evolution · 2015Article
- Challenges in analysis and interpretation of microsatellite data for population genetic studies.Ecology and evolution · 2014Review
- Microsatellite data show recent demographic expansions in sedentary but not in nomadic human populations in Africa and Eurasia.European journal of human genetics : EJHG · 2014Article
- Phylogenetic stochastic mapping without matrix exponentiation.Journal of computational biology : a journal of computational molecular cell biology · 2014Article
- Detecting past changes of effective population size.Evolutionary applications · 2014Article
- Article
- Factors influencing ascertainment bias of microsatellite allele sizes: impact on estimates of mutation rates.Genetics · 2013Article
Corrections and comments
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2 authors.
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Abstract
We provide a framework for Bayesian coalescent inference from microsatellite data that enables inference of population history parameters averaged over microsatellite mutation models. To achieve this we first implemented a rich family of microsatellite mutation models and related components in the software package BEAST. BEAST is a powerful tool that performs Bayesian MCMC analysis on molecular data to make coalescent and evolutionary inferences. Our implementation permits the application of existing nonparametric methods to microsatellite data. The implemented microsatellite models are based on the replication slippage mechanism and focus on three properties of microsatellite mutation: length dependency of mutation rate, mutational bias toward expansion or contraction, and number of repeat units changed in a single mutation event. We develop a new model that facilitates microsatellite model averaging and Bayesian model selection by transdimensional MCMC. With Bayesian model averaging, the posterior distributions of population history parameters are integrated across a set of microsatellite models and thus account for model uncertainty. Simulated data are used to evaluate our method in terms of accuracy and precision of estimation and also identification of the true mutation model. Finally we apply our method to a red colobus monkey data set as an example.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.