Likelihood methods are being developed for inference of migration rates and past demographic changes from population genetic data. We survey an approach for such inference using sequential importance sampling techniques derived from coalescent and diffusion theory. The consistent application and assessment of this approach has required the re-implementation of methods often considered in the context of computer experiments methods, in particular of Kriging which is used as a smoothing technique to infer a likelihood surface from likelihoods estimated in various parameter points, as well as reconsideration of methods for sampling the parameter space appropriately for such inference. We illustrate the performance and application of the whole tool chain on simulated and actual data, and highlight desirable developments in terms of data types and biological scenarios.
Diverses approches ont été développées pour l’inférence des taux de migration et des changements démographiques passés à partir de la variation génétique des populations. Nous décrivons une de ces approches utilisant des techniques d’échantillonnage pondéré séquentiel, fondées sur la modélisation par approches de coalescence et de diffusion de l’évolution de ces polymorphismes. L’application et l’évaluation systématique de cette approche ont requis la ré-implémentation de méthodes souvent considérées pour l’analyse de fonctions simulées, en particulier le krigeage, ici utilisé pour inférer une surface de vraisemblance à partir de vraisemblances estimées en différents points de l’espace des paramètres, ainsi que des techniques d’échantillonage de ces points. Nous illustrons la performance et l’application de cette série de méthodes sur données simulées et réelles, et indiquons les améliorations souhaitables en termes de types de données et de scénarios biologiques.
Mot clés : histoire démographique, processus de coalescence, échantillonnage pondéré, polymorphisme génétique
@article{JSFS_2018__159_3_142_0, author = {Rousset, Fran\c{c}ois and Beeravolu, Champak Reddy and Leblois, Rapha\"el}, title = {Likelihood computation and inference of demographic and mutational parameters from population genetic data under coalescent approximations}, journal = {Journal de la soci\'et\'e fran\c{c}aise de statistique}, pages = {142--166}, publisher = {Soci\'et\'e fran\c{c}aise de statistique}, volume = {159}, number = {3}, year = {2018}, zbl = {1406.92404}, language = {en}, url = {http://archive.numdam.org/item/JSFS_2018__159_3_142_0/} }
TY - JOUR AU - Rousset, François AU - Beeravolu, Champak Reddy AU - Leblois, Raphaël TI - Likelihood computation and inference of demographic and mutational parameters from population genetic data under coalescent approximations JO - Journal de la société française de statistique PY - 2018 SP - 142 EP - 166 VL - 159 IS - 3 PB - Société française de statistique UR - http://archive.numdam.org/item/JSFS_2018__159_3_142_0/ LA - en ID - JSFS_2018__159_3_142_0 ER -
%0 Journal Article %A Rousset, François %A Beeravolu, Champak Reddy %A Leblois, Raphaël %T Likelihood computation and inference of demographic and mutational parameters from population genetic data under coalescent approximations %J Journal de la société française de statistique %D 2018 %P 142-166 %V 159 %N 3 %I Société française de statistique %U http://archive.numdam.org/item/JSFS_2018__159_3_142_0/ %G en %F JSFS_2018__159_3_142_0
Rousset, François; Beeravolu, Champak Reddy; Leblois, Raphaël. Likelihood computation and inference of demographic and mutational parameters from population genetic data under coalescent approximations. Journal de la société française de statistique, Volume 159 (2018) no. 3, pp. 142-166. http://archive.numdam.org/item/JSFS_2018__159_3_142_0/
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