Biomedical subjects

M A Beaumont

Publications and source records attributed to M A Beaumont.

10 recordsLinked to original sources

PubMed2006

A note on the accuracy of PAC-likelihood inference with microsatellite data.

Stephens and Donnelly have introduced a simple yet powerful importance sampling scheme for computing the likelihood in population genetic models. Fundamental to the method is an approximation to the conditional probability of the allelic type of an additional gene, given those currently in the sample. As noted by Li and Stephens, the product of these conditional probabilities for a sequence of draws that gives the frequency of allelic types in a sample is an approximation to the likelihood, and can be used directly in inference. The aim of this note is to demonstrate the high level of accuracy of "product of approximate conditionals" (PAC) likelihood when used with microsatellite data. Results obtained on simulated microsatellite data show that this strategy leads to a negligible bias over a wide range of the scaled mutation parameter theta. Furthermore, the sampling variance of likelihood estimates as well as the computation time are lower than that obtained with importance sampling on the whole range of theta. It follows that this approach represents an efficient substitute to IS algorithms in computer intensive (e.g. MCMC) inference methods in population genetics.

Gene Frequency↗

PubMed2005

Inference on microsatellite mutation processes in the invasive mite, Varroa destructor, using reversible jump Markov chain Monte Carlo.

Varroa destructor is a parasitic mite of the Eastern honeybee Apis cerana. Fifty years ago, two distinct evolutionary lineages (Korean and Japanese) invaded the Western honeybee Apis mellifera. This haplo-diploid parasite species reproduces mainly through brother-sister matings, a system which largely favors the fixation of new mutations. In a worldwide sample of 225 individuals from 21 locations collected on Western honeybees and analyzed at 19 microsatellite loci, a series of de novo mutations was observed. Using historical data concerning the invasion, this original biological system has been exploited to compare three mutation models with allele size constraints for microsatellite markers: stepwise (SMM) and generalized (GSM) mutation models, and a model with mutation rate increasing exponentially with microsatellite length (ESM). Posterior probabilities of the three models have been estimated for each locus individually using reversible jump Markov Chain Monte Carlo. The relative support of each model varies widely among loci, but the GSM is the only model that always receives at least 9% support, whatever the locus. The analysis also provides robust estimates of mutation parameters for each locus and of the divergence time of the two invasive lineages (67,000 generations with a 90% credibility interval of 35,000-174,000). With an average of 10 generations per year, this divergence time fits with the last post-glacial Korea-Japan land separation.

Animals↗

PubMed2004

Recent developments in genetic data analysis: what can they tell us about human demographic history?

Over the last decade, a number of new methods of population genetic analysis based on likelihood have been introduced. This review describes and explains the general statistical techniques that have recently been used, and discusses the underlying population genetic models. Experimental papers that use these methods to infer human demographic and phylogeographic history are reviewed. It appears that the use of likelihood has hitherto had little impact in the field of human population genetics, which is still primarily driven by more traditional approaches. However, with the current uncertainty about the effects of natural selection, population structure and ascertainment of single-nucleotide polymorphism markers, it is suggested that likelihood-based methods may have a greater impact in the future.

DNA, Satellite↗

PubMed2001

Immigration and the ephemerality of a natural population bottleneck: evidence from molecular markers.

Population bottlenecks are often invoked to explain low levels of genetic variation in natural populations, yet few studies have documented the direct genetic consequences of known bottlenecks in the wild. Empirical studies of natural population bottlenecks are therefore needed, because key assumptions of theoretical and laboratory studies of bottlenecks may not hold in the wild. Here we present microsatellite data from a severe bottleneck (95% mortality) in an insular population of song sparrows (Melospiza melodia). The major findings of our study are as follows: (i) The bottleneck reduced heterozygosity and allelic diversity nearly to neutral expectations, despite non-random survival of birds with respect to inbreeding and wing length. (ii) All measures of genetic diversity regained pre-bottleneck levels within two to three years of the crash. This rapid recovery was due to low levels of immigration. (iii) The rapid recovery occurred despite a coincident, strong increase in average inbreeding. These results show that immigration at levels that are hard to measure in most field studies can lead to qualitatively very different genetic outcomes from those expected from mutations only. We suggest that future theoretical and empirical work on bottlenecks and metapopulations should address the impact of immigration.

Animals↗

PubMed2001

Estimation of admixture proportions: a likelihood-based approach using Markov chain Monte Carlo.

When populations are separated for long periods and then brought into contact for a brief episode in part of their range, this can result in genetic admixture. To analyze this type of event we considered a simple model under which two parental populations (P1 and P2) mix and create a hybrid population (H). After that event, the three populations evolve under pure drift without exchange during T generations. We developed a new method, which allows the simultaneous estimation of the time since the admixture event (scaled by the population size t(i) = T/N(i), where N(i) is the effective population size of population i) and the contribution of one of two parental populations (which we call p1). This method takes into account drift since the admixture event, variation caused by sampling, and uncertainty in the estimation of the ancestral allele frequencies. The method is tested on simulated data sets and then applied to a human data set. We find that (i) for single-locus data, point estimates are poor indicators of the real admixture proportions even when there are many alleles; (ii) biallelic loci provide little information about the admixture proportion and the time since admixture, even for very small amounts of drift, but can be powerful when many loci are used; (iii) the precision of the parameters' estimates increases with sample size n = 50 vs. n = 200 but this effect is larger for the t(i)'s than for p1; and (iv) the increase in precision provided by multiple loci is quite large, even when there is substantial drift (we found, for instance, that it is preferable to use five loci than one locus, even when drift is 100 times larger for the five loci). Our analysis of a previously studied human data set illustrates that the joint estimation of drift and p1 can provide additional insights into the data.

Bayes Theorem↗

PubMed1999

Minisatellite mutational processes reduce F(st) estimates.

We have used a new method for binning minisatellite alleles (semi-automated allele aggregation) and report the extent of population diversity detectable by eleven minisatellite loci in 2,689 individuals from 19 human populations distributed widely throughout the world. Whereas population relationships are consistent with those found in other studies, our estimate of genetic differentiation (F(st)) between populations is less than 8%, which is lower than comparative estimates of between 10%-15% obtained by using other sources of polymorphism data. We infer that mutational processes are involved in reducing F(st) estimates from minisatellite data because, first, the lowest F(st) estimates are found at loci showing autocorrelated frequencies among alleles of similar size and, second, F(st) declines with heterozygosity but by more than predicted assuming simple models of mutation. These conclusions are consistent with the view that minisatellites are subject to selective or mutational constraints in addition to those expected under simple step-wise mutation models.

Alleles↗

PubMed1999

Detecting population expansion and decline using microsatellites.

This article considers a demographic model where a population varies in size either linearly or exponentially. The genealogical history of microsatellite data sampled from this population can be described using coalescent theory. A method is presented whereby the posterior probability distribution of the genealogical and demographic parameters can be estimated using Markov chain Monte Carlo simulations. The likelihood surface for the demographic parameters is complicated and its general features are described. The method is then applied to published microsatellite data from two populations. Data from the northern hairy-nosed wombat show strong evidence of decline. Data from European humans show weak evidence of expansion.

Demography↗

PubMed1993

Evolution of optimal behaviour in networks of Boolean automata.

This paper describes the response to selection for optimal behaviour in networks of Boolean automata. The networks considered are "open" in the sense that they receive an input and produce an output. The task that the nets are selected to solve is to maximize the mean "height" attained in a fixed number of iterations in "landscapes" that vary in their ruggedness. This is analogous to an organism with a fixed time budget that attempts to maximize its food intake in an environment where the food concentration varies in space. The results suggest that it is possible to select simple Boolean nets to respond adaptively to their inputs. Selection on simple environments produces a near "optimal" response. The response to complex environments is worse. The results suggest that nets selected on complex environments perform better on environments of different degrees of complexity than those selected on simple environments. Although nets with larger numbers of automata do not respond markedly better to selection, the variability in the response to selection is reduced. It appears to be difficult to predict the movements of nets from a study of the attractors of net with sensory units clamped at particular values. The cycle of bits in clamped nets can vary greatly with small changes in the inputs to the nets. The actual movement of nets does not, however, reflect this instability. It is concluded that networks of Boolean automata may be useful models with which to investigate different genetic algorithms. Furthermore, perturbations in such systems may give insights into the nature of pleiotropy and epistasis.

Algorithms↗

PubMed1988

The effect of lanthanum on nerve terminals in goldfish muscle after paralysis with tetanus toxin.

Lanthanum (1.9 mM) has previously been shown to produce a massive increase in the frequency of spontaneous miniature junction potentials at the neuromuscular junctions of goldfish fin muscles. In fins where transmission has been blocked by previous injection of tetanus toxin and where there are few (if any) spontaneous miniature potentials, lanthanum treatment is able to restore a modest frequency. The results of parallel experiments in which the ultrastructure of the nerve endings has been investigated by electron microscopy are reported. In normal goldfish muscles, the lanthanum-induced increase in frequency is accompanied by depletion of synaptic vesicles. In contrast, there is no depletion in tetanus toxin-paralysed nerve endings subjected to lanthanum treatment, which parallels the relative insensitivity of the endings to activation by lanthanum. Of particular interest is the finding that the lanthanum treatment of the toxin muscles apparently causes accumulation of vesicles in a row just inside the terminal membrane, both at synaptic and non-synaptic positions. The results are discussed with respect to the mechanisms of transmitter release and to the actions of tetanus toxin and lanthanum.

Animals↗

PubMed1988

Stabilizing selection and metabolism.

This paper attempts to provide a biochemical explanation for selection against extreme phenotypes. From current ideas on the analysis of metabolic control, it is argued that, on average, most mutations will reduce flux through metabolic pathways and change substrate pool concentrations in an arbitrary direction. Currently available experimental data suggests that there may be a positive relationship between flux and fitness. It is also argued that there may be a relationship between phenotypic traits and substrate pool concentrations. Given these premises, it is shown that intrinsic selective constraints occur against the production of extreme phenotypic variants.

Animals↗