Inferring different modes of natural selection using PoMos in RevBayes

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Description

The interplay between mutation, genetic drift, directional, and balancing selection in shaping populations’ diversity is highly convoluted and hard to disentangle. This requires sophisticated phylogenetic models that have high degrees of flexibility and can handle multi-individual data. For these purposes, our group has developed a polymorphism-aware phylogenetic set of models called PoMos. These models have recently been proven effective in inferring species trees as well as mutational effects, fixation biases and, in some cases, GC-bias rates of great apes and grasshoppers. For ease of use, the models are now implemented in the open-source Bayesian inference framework RevBayes. In this study, we further developed PoMos to study neutral, directional and, for the first time, balancing selection. The main benefit of our models for studying the balancing selection is that PoMos allow for ancestral polymorphisms that can be maintained, and parameters that can measure frequency-dependent selection. We have applied our new approach to a set of simulated data to test the inferential framework. We also investigate real sequences of African human populations to understand the evolutionary history of regions of the genome that are known to be under balancing selection driven by malarial parasites. [1] N. De Maio, D. Schrempf, and C. Kosiol, ‘PoMo: An Allele Frequency-Based Approach for Species Tree Estimation’, Systematic Biology, vol. 64, no. 6, pp. 1018-1031, Nov. 2015, doi: 10.1093/sysbio/syv048.[2] D. Schrempf, B. Q. Minh, N. De Maio, A. von Haeseler, and C. Kosiol, ‘Reversible polymorphism-aware phylogenetic models and their application to tree inference’, Journal of Theoretical Biology, vol. 407, pp. 362-370, Oct. 2016, doi: 10.1016/j.jtbi.2016.07.042.[3] R. Borges, G. J. Szöll_si, and C. Kosiol, ‘Quantifying GC-Biased Gene Conversion in Great Ape Genomes Using Polymorphism-Aware Models’, Genetics, vol. 212, no. 4, pp. 1321-1336, Aug. 2019, doi: 10.1534/genetics.119.302074.[4] R. Borges, B. Boussau, S. Höhna, R. J. Pereira, and C. Kosiol, ‘Polymorphism-aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes’, Methods in Ecology and Evolution, vol. 13, no. 11, pp. 2339-2346, 2022, doi: 10.1111/2041-210X.13980.[5] S. Höhna et al., ‘RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language’, Syst Biol, vol. 65, no. 4, pp. 726-736, Jul. 2016, doi: 10.1093/sysbio/syw021.
Period4 Jan 2023
Event titlePopulation Genetics Group Meeting
Event typeConference
LocationLondon, United KingdomShow on map
Degree of RecognitionNational