Estimation of demo-genetic model probabilities with Approximate Bayesian Computation using linear discriminant analysis on summary statistics

Molecular Ecology Resources
Arnaud EstoupJean-Marie Cornuet

Abstract

Comparison of demo-genetic models using Approximate Bayesian Computation (ABC) is an active research field. Although large numbers of populations and models (i.e. scenarios) can be analysed with ABC using molecular data obtained from various marker types, methodological and computational issues arise when these numbers become too large. Moreover, Robert et al. (Proceedings of the National Academy of Sciences of the United States of America, 2011, 108, 15112) have shown that the conclusions drawn on ABC model comparison cannot be trusted per se and required additional simulation analyses. Monte Carlo inferential techniques to empirically evaluate confidence in scenario choice are very time-consuming, however, when the numbers of summary statistics (Ss) and scenarios are large. We here describe a methodological innovation to process efficient ABC scenario probability computation using linear discriminant analysis (LDA) on Ss before computing logistic regression. We used simulated pseudo-observed data sets (pods) to assess the main features of the method (precision and computation time) in comparison with traditional probability estimation using raw (i.e. not LDA transformed) Ss. We also illustrate the method on real microsatellit...Continue Reading

References

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Citations

Sep 24, 2013·Trends in Ecology & Evolution·Sam C BanksRod Peakall
Jun 25, 2014·PloS One·Michael StocksStéphane De Mita
Mar 22, 2016·Royal Society Open Science·Cornelya F C KlütschPaul J Wilson
Oct 11, 2015·Molecular Ecology·Dilli P RijalInger G Alsos
Nov 22, 2015·Bioinformatics·Pierre PudloChristian P Robert
Dec 17, 2014·Molecular Ecology·Dietrich GotzekDeWayne Shoemaker
Oct 15, 2013·Molecular Ecology Resources·Diego F Alvarado-Serrano, L Lacey Knowles
Jan 15, 2015·Molecular Ecology·Camille Roux, John R Pannell
Jul 18, 2015·BMC Evolutionary Biology·Maria Teresa CabriaRafael Zardoya
Oct 10, 2014·Proceedings. Biological Sciences·Marie LouisBenoit Simon-Bouhet
Sep 12, 2019·Proceedings of the National Academy of Sciences of the United States of America·Sean F RyanDeWayne Shoemaker
Mar 27, 2021·Current Biology : CB·Michael C FontaineFrançois Delmotte

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