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Approximate Bayesian Computation (ABC) in practice.
Pcadapt: An R Package to Perform Genome Scans for Selection Based on Principal Component Analysis
It is found that pcadapt and hapflk are the most powerful software in scenarios of population divergence and range expansion and it is a valuable tool for data analysis in molecular ecology.
Non-linear regression models for Approximate Bayesian Computation
A machine-learning approach to the estimation of the posterior density by introducing two innovations that fits a nonlinear conditional heteroscedastic regression of the parameter on the summary statistics, and then adaptively improves estimation using importance sampling.
abc: an R package for approximate Bayesian computation (ABC)
Approximate Bayesian computation (ABC) is devoted to complex models because it bypasses the evaluation of the likelihood function by comparing observed and simulated data.
Approximate Bayesian Computation: A Nonparametric Perspective
- M. Blum
- 3 April 2009
Approximate Bayesian Computation is a family of likelihood-free inference techniques that are well suited to models defined in terms of a stochastic generating mechanism. In a nutshell, Approximate…
Which random processes describe the tree of life? A large-scale study of phylogenetic tree imbalance.
The most popular model of phylogenetic trees is a branching process introduced by Yule, in which lineages split at random (Yule, 1924), and here the study of one major database of published phylogenies is reported.
Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History
Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification, and illustrated the importance of African genomic diversity in understanding human evolutionary history.
A comparative review of dimension reduction methods in approximate Bayesian computation
This article provides a comprehensive review and comparison of the performance of the principal methods of dimension reduction proposed in the ABC literature, split into three nonmutually exclusive classes consisting of best subset selection methods, projection techniques and regularization.
The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals
- S. Naderi, H. Rezaei, P. Taberlet
- BiologyProceedings of the National Academy of Sciences
- 18 November 2008
This study compared the genetic diversity of domestic goats to that of the modern representatives of their wild ancestor, the bezoar, by analyzing 473 samples collected over the whole distribution range of the latter species, and found no haplotype that could have been domesticated in the eastern half of the Iranian Plateau, nor further to the east.
Demographic History of European Populations of Arabidopsis thaliana
Evidence is found that a major migration wave occurred from east to west, affecting most of the sampled individuals, and the longitudinal gradient appears to result from the plant having spread in Europe from the east ∼10,000 years ago, with a rate of westward spread of ∼0.9 km/year.