Models of Microsatellite Evolution

Calabrese, Peter; Sainudiin, Raazesh

doi:10.1007/0-387-27733-1_10

Cited by 17 publications

(27 citation statements)

References 54 publications

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“…In the admixture models, the admixed (or hybrid) population is assumed to have an effective size N H . We note that in all models the loci are assumed to have the same per locus mutation rate m and to evolve according to the stepwise mutation model, as is usually assumed for microsatellites (see, for example, Calabrese and Sainudiin, 2005).…”

Section: Demographic Modelsmentioning

confidence: 99%

Population divergence with or without admixture: selecting models using an ABC approach

et al. 2011

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Genetic data have been widely used to reconstruct the demographic history of populations, including the estimation of migration rates, divergence times and relative admixture contribution from different populations. Recently, increasing interest has been given to the ability of genetic data to distinguish alternative models. One of the issues that has plagued this kind of inference is that ancestral shared polymorphism is often difficult to separate from admixture or gene flow. Here, we applied an approximate Bayesian computation (ABC) approach to select the model that best fits microsatellite data among alternative splitting and admixture models. We performed a simulation study and showed that with reasonably large data sets (20 loci) it is possible to identify with a high level of accuracy the model that generated the data. This suggests that it is possible to distinguish genetic patterns due to past admixture events from those due to shared polymorphism (population split without admixture). We then apply this approach to microsatellite data from an endangered and endemic Iberian freshwater fish species, in which a clustering analysis suggested that one of the populations could be admixed. In contrast, our results suggest that the observed genetic patterns are better explained by a population split model without admixture.

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Section: Demographic Modelsmentioning

confidence: 99%

Population divergence with or without admixture: selecting models using an ABC approach

et al. 2011

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“…As was mentioned before, many statistical models have been proposed for the microsatellite mutation process (Calabrese and Sainudiin 2005). However, only a few of these turned out to be applicable to our data.…”

Section: Discussionmentioning

confidence: 90%

“…Various statistical models have been proposed for the microsatellite mutation process (Calabrese and Sainudiin 2005), but no model has yet been identified as representing the single best, thereby testifying to the complexity of the mutation process. In any case, it is well established that the mutation rate of microsatellites (i) depends upon the respective repeat number (Xu et al 2000;Lai and Sun 2003;Kelkar et al 2008) and (ii) varies greatly across loci, which is partly due to the variable nature of the repeat motif itself (Kelkar et al 2008).…”

Section: "Mmentioning

confidence: 99%

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Empirical Evaluation Reveals Best Fit of a Logistic Mutation Model for Human Y-Chromosomal Microsatellites

et al. 2011

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The rate of microsatellite mutation is dependent upon both the allele length and the repeat motif, but the exact nature of this relationship is still unknown. We analyzed data on the inheritance of human Y-chromosomal microsatellites in father-son duos, taken from 24 published reports and comprising 15,285 directly observable meioses. At the six microsatellites analyzed (DYS19, DYS389I, DYS390, DYS391, DYS392, and DYS393), a total of 162 mutations were observed. For each locus, we employed a maximum-likelihood approach to evaluate one of several single-step mutation models on the basis of the data. For five of the six loci considered, a novel logistic mutation model was found to provide the best fit according to Akaike's information criterion. This implies that the mutation probability at the loci increases (nonlinearly) with allele length at a rate that differs between upward and downward mutations. For DYS392, the best fit was provided by a linear model in which upward and downward mutation probabilities increase equally with allele length. This is the first study to empirically compare different microsatellite mutation models in a locus-specific fashion.

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“…A review of microsatellite models can be found in Calabrese and Sainudiin (2004). A detailed analysis of these and other models was undertaken by in the context of the split time for humans and chimpanzees.…”

Section: Introductionmentioning

confidence: 99%

Microsatellite evolution: Markov transition functions for a suite of models

Watkins

2007

Theoretical Population Biology

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This paper takes from the collection of models considered by Whittaker et. al. (2003) derived from direct observation of microsatellite mutation in parent-child pairs and provides analytical expressions for the probability distributions for the change in number of repeats over any given number of generations. The mathematical framework for this analysis is the theory of Markov processes. We find these expressions using two approaches, approximating by circulant matrices and solving a partial differential equation satisfied by the generating function. The impact of the differing choice of models is examined using likelihood estimates for time to most recent common ancestor. The analysis presented here may play a role in elucidating the connections between these two approaches and shows promise in reconciling differences between estimates for mutation rates based on Whittaker's approach and methods based on phylogenetic analyses.

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Models of Microsatellite Evolution

Cited by 17 publications

References 54 publications

Population divergence with or without admixture: selecting models using an ABC approach

Population divergence with or without admixture: selecting models using an ABC approach

Empirical Evaluation Reveals Best Fit of a Logistic Mutation Model for Human Y-Chromosomal Microsatellites

Microsatellite evolution: Markov transition functions for a suite of models

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