75 research outputs found
Efficient learning in ABC algorithms
Approximate Bayesian Computation has been successfully used in population
genetics to bypass the calculation of the likelihood. These methods provide
accurate estimates of the posterior distribution by comparing the observed
dataset to a sample of datasets simulated from the model. Although
parallelization is easily achieved, computation times for ensuring a suitable
approximation quality of the posterior distribution are still high. To
alleviate the computational burden, we propose an adaptive, sequential
algorithm that runs faster than other ABC algorithms but maintains accuracy of
the approximation. This proposal relies on the sequential Monte Carlo sampler
of Del Moral et al. (2012) but is calibrated to reduce the number of
simulations from the model. The paper concludes with numerical experiments on a
toy example and on a population genetic study of Apis mellifera, where our
algorithm was shown to be faster than traditional ABC schemes
Reliable ABC model choice via random forests
Approximate Bayesian computation (ABC) methods provide an elaborate approach
to Bayesian inference on complex models, including model choice. Both
theoretical arguments and simulation experiments indicate, however, that model
posterior probabilities may be poorly evaluated by standard ABC techniques. We
propose a novel approach based on a machine learning tool named random forests
to conduct selection among the highly complex models covered by ABC algorithms.
We thus modify the way Bayesian model selection is both understood and
operated, in that we rephrase the inferential goal as a classification problem,
first predicting the model that best fits the data with random forests and
postponing the approximation of the posterior probability of the predicted MAP
for a second stage also relying on random forests. Compared with earlier
implementations of ABC model choice, the ABC random forest approach offers
several potential improvements: (i) it often has a larger discriminative power
among the competing models, (ii) it is more robust against the number and
choice of statistics summarizing the data, (iii) the computing effort is
drastically reduced (with a gain in computation efficiency of at least fifty),
and (iv) it includes an approximation of the posterior probability of the
selected model. The call to random forests will undoubtedly extend the range of
size of datasets and complexity of models that ABC can handle. We illustrate
the power of this novel methodology by analyzing controlled experiments as well
as genuine population genetics datasets. The proposed methodologies are
implemented in the R package abcrf available on the CRAN.Comment: 39 pages, 15 figures, 6 table
A third-generation microsatellite-based linkage map of the honey bee, Apis mellifera, and its comparison with the sequence-based physical map
The meiotic map of the honey bee is presented, including the main features that emerged from comparisons with the sequence-based physical map. The map is based on 2,008 markers and is about 40 M long, corresponding to a recombination rate of 22 cM/Mb
Bridgehead Effect in the Worldwide Invasion of the Biocontrol Harlequin Ladybird
Recent studies of the routes of worldwide introductions of alien organisms suggest that many widespread invasions could have stemmed not from the native range, but from a particularly successful invasive population, which serves as the source of colonists for remote new territories. We call here this phenomenon the invasive bridgehead effect. Evaluating the likelihood of such a scenario is heuristically challenging. We solved this problem by using approximate Bayesian computation methods to quantitatively compare complex invasion scenarios based on the analysis of population genetics (microsatellite variation) and historical (first observation dates) data. We applied this approach to the Harlequin ladybird Harmonia axyridis (HA), a coccinellid native to Asia that was repeatedly introduced as a biocontrol agent without becoming established for decades. We show that the recent burst of worldwide invasions of HA followed a bridgehead scenario, in which an invasive population in eastern North America acted as the source of the colonists that invaded the European, South American and African continents, with some admixture with a biocontrol strain in Europe. This demonstration of a mechanism of invasion via a bridgehead has important implications both for invasion theory (i.e., a single evolutionary shift in the bridgehead population versus multiple changes in case of introduced populations becoming invasive independently) and for ongoing efforts to manage invasions by alien organisms (i.e., heightened vigilance against invasive bridgeheads)
Bases theoriques de l'amelioration genetique de l'Abeille
SIGLEINIST T 77632 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc
How did Man history affect Saccharomyces cerevisiae diversity?
International audienc
- …