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45
Estimating Recombination Rates from Population Genetic Data
, 2000
"... We introduce a new method for estimating recombination rates from population genetic data. The method uses a computationallyintensive statistical procedure (importance sampling) to calculate the likelihood under a coalescentbased model. Detailed comparisons of the new algorithm with two existing m ..."
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Cited by 89 (11 self)
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We introduce a new method for estimating recombination rates from population genetic data. The method uses a computationallyintensive statistical procedure (importance sampling) to calculate the likelihood under a coalescentbased model. Detailed comparisons of the new algorithm with two existing methods (one based on importance sampling and one based on MCMC) show it to be substantially more efficient. (The improvement over the existing importance sampling scheme is typically by four orders of magnitude.) The existing approaches not infrequently led to misleading results on the problems we investigated. We also performed a simulation study to look at the properties of the maximum likelihood estimator (mle) of the recombination rate, and its robustness to misspecification of the demographic model.
Comparison of Bayesian and maximumlikelihood inference of population genetic parameters
 Bioinformatics
, 2006
"... doi:10.1093/bioinformatics/bti803 ..."
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Executive Summary
 Usability Inspection Methods
, 1994
"... The fact that membrane proteins are notoriously difficult to analyse using standard protocols for atomicresolution structure determination methods have motivated adaptation of these techniques to membrane protein studies as well as development of new technologies. With this motivation, liquidstate ..."
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Cited by 32 (0 self)
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The fact that membrane proteins are notoriously difficult to analyse using standard protocols for atomicresolution structure determination methods have motivated adaptation of these techniques to membrane protein studies as well as development of new technologies. With this motivation, liquidstate nuclear magnetic resonance (NMR) has recently been used with success for studies of peptides and membrane proteins in detergent micelles, and solidstate NMR has undergone a tremendous evolution towards characterization of membrane proteins in native membrane and oriented phospholipid bilayers. In this minireview, we describe some of the technological challenges behind these efforts and provide examples on their use in membrane biology.
Inferences from DNA data: population histories, evolutionary processes, and forensic match probabilities.
 Journal of Royal Statistics Society, Series A
, 2003
"... We develop a flexible class of... ..."
Inferring population history with DIY ABC: a userfriendly approach to Approximate Bayesian
, 2008
"... Computation ..."
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2003 Decline of North Atlantic eels: a fatal synergy
 Proc. R. Soc. B
"... Panmictic species pose particular problems for conservation because their welfare can be addressed effectively only on a global scale. We recently documented by means of microsatellite analysis that the European eel (Anguilla anguilla) is not panmictic but instead shows genetic isolation by distanc ..."
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Cited by 19 (4 self)
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Panmictic species pose particular problems for conservation because their welfare can be addressed effectively only on a global scale. We recently documented by means of microsatellite analysis that the European eel (Anguilla anguilla) is not panmictic but instead shows genetic isolation by distance. In this study, we extended the analysis to the American eel (A. rostrata) by applying identical analytical procedures and statistical power. Results obtained for the American eel were in sharp contrast with those obtained for the European eel: the null hypothesis of panmixia could not be rejected, and no isolation by distance was detected. This implies that the species must be managed as a single population. Using Bayesian statistics, we also found that the effective population sizes for both species were surprisingly low and that the populations had undergone severe contractions, most probably during the Wisconsinan glaciation. The apparent sensitivity of eels to climatic changes affecting the strength and position of the Gulf Stream 20 000 years ago is particularly worrying, given the effects of the ongoing global warming on the North Atlantic climate. Moreover, additional shortterm stresses such as surging glass eel prizes, overfishing and lethal parasitic infections negatively affect eel population size. The fascinating transatlantic migration and life cycle of Atlantic eels is also their Achilles ’ heel as these negative short and longterm effects will probably culminate in a fatal synergy if drastic conservation measures are not implemented to protect these international biological resources.
Models of microsatellite evolution
 Statistical Methods in Molecular Evolution, Series: Statistics for Biology and Health
, 2004
"... Microsatellites are simple sequence repeats in DNA, for example the motif AT repeated twentyfive times in a row. Microsatellites mutate by changing the number of their repeats, for example the (AT)25 mentioned in the previous sentence might become an (AT)24 or (AT)26 in that individual’s offspring. ..."
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Cited by 10 (2 self)
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Microsatellites are simple sequence repeats in DNA, for example the motif AT repeated twentyfive times in a row. Microsatellites mutate by changing the number of their repeats, for example the (AT)25 mentioned in the previous sentence might become an (AT)24 or (AT)26 in that individual’s offspring.
Accurate Computation of Likelihoods in the Coalescent with Recombination via Parsimony
"... Abstract. Understanding the variation of recombination rates across a given genome is crucial for disease gene mapping and for detecting signatures of selection, to name just a couple of applications. A widelyused method of estimating recombination rates is the maximum likelihood approach, and the ..."
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Cited by 5 (0 self)
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Abstract. Understanding the variation of recombination rates across a given genome is crucial for disease gene mapping and for detecting signatures of selection, to name just a couple of applications. A widelyused method of estimating recombination rates is the maximum likelihood approach, and the problem of accurately computing likelihoods in the coalescent with recombination has received much attention in the past. A variety of sampling and approximation methods have been proposed, but no single method seems to perform consistently better than the rest, and there still is great value in developing better statistical methods for accurately computing likelihoods. So far, with the exception of some twolocus models, it has remained unknown how the true likelihood exactly behaves as a function of model parameters, or how close estimated likelihoods are to the true likelihood. In this paper, we develop a deterministic, parsimonybased method of accurately computing the likelihood for multilocus input data of moderate size. We first find the set of all ancestral configurations (ACs) that occur in evolutionary histories with at most k crossover recombinations. Then, we compute the likelihood by summing over all evolutionary histories that can be constructed only using the ACs in that set. We allow for an arbitrary number of crossing over, coalescent and mutation events in a history, as long as the transitions stay within that restricted set of ACs. For given parameter values, by gradually increasing the bound k until the likelihood stabilizes, we can obtain an accurate estimate of the likelihood. At least for moderate crossover rates, the algorithmbased method described here opens up a new window of opportunities for testing and finetuning statistical methods for computing likelihoods. 1
Perfect Simulation from Population Genetic Models with Selection
, 2000
"... We consider using the ancestral selection graph to simulate samples from genetic models with selection. Currently the use of the ancestral selection graph to simulate such samples is limited. This is because the computational requirement for simulating such samples increases exponentially with the s ..."
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Cited by 5 (2 self)
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We consider using the ancestral selection graph to simulate samples from genetic models with selection. Currently the use of the ancestral selection graph to simulate such samples is limited. This is because the computational requirement for simulating such samples increases exponentially with the selection rate, and also due to the need to be able to simulate a sample of size 1 from the population at equilibrium. For the only case where the distribution of a sample of size one is known, that of parent independent mutations, more ecient simulation algorithms exist. We will show that by applying the idea of coupling from the past to the ancestral selection graph, samples can be simulated from a general Kallele model without knowledge of the distribution of a sample of size 1. Further, the computation involved in generating such samples appears to be less than that of simulating the ancestral selection graph until its ultimate ancestor. In particular, in the case of genic selection with...