Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes
Abstract The availability of population genomic data through new sequencing technologies gives unprecedented opportunities for estimating important evolutionary forces such as genetic drift, selection and mutation biases across organisms. Yet, analytical methods that can handle polymorphisms jointly...
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| Format: | Article |
| Language: | English |
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Wiley
2022-11-01
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| Series: | Methods in Ecology and Evolution |
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| Online Access: | https://doi.org/10.1111/2041-210X.13980 |
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| author | Rui Borges Bastien Boussau Sebastian Höhna Ricardo J. Pereira Carolin Kosiol |
| author_facet | Rui Borges Bastien Boussau Sebastian Höhna Ricardo J. Pereira Carolin Kosiol |
| author_sort | Rui Borges |
| collection | DOAJ |
| description | Abstract The availability of population genomic data through new sequencing technologies gives unprecedented opportunities for estimating important evolutionary forces such as genetic drift, selection and mutation biases across organisms. Yet, analytical methods that can handle polymorphisms jointly with sequence divergence across species are rare and not easily accessible to empiricists. We implemented polymorphism‐aware phylogenetic models (PoMos), an alternative approach for species tree estimation, in the Bayesian phylogenetic software RevBayes. PoMos naturally account for incomplete lineage sorting, which is known to cause difficulties for phylogenetic inference in species radiations, and scale well with genome‐wide data. Simultaneously, PoMos can estimate mutation and selection biases. We have applied our methods to resolve the complex phylogenetic relationships of a young radiation of Chorthippus grasshoppers, based on coding sequences. In addition to establishing a well‐supported species tree, we found a mutation bias favouring AT alleles and selection bias promoting the fixation of GC alleles, the latter consistent with GC‐biased gene conversion. The selection bias is two orders of magnitude lower than genetic drift, validating the critical role of nearly neutral evolutionary processes in species radiation. PoMos offer a wide range of models to reconstruct phylogenies and can be easily combined with existing models in RevBayes—for example, relaxed clock and divergence time estimation—offering new insights into the evolutionary processes underlying molecular evolution and, ultimately, species diversification. |
| format | Article |
| id | doaj-art-a4a8db0f114d464a88b36d8aacbf2e22 |
| institution | Kabale University |
| issn | 2041-210X |
| language | English |
| publishDate | 2022-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | Methods in Ecology and Evolution |
| spelling | doaj-art-a4a8db0f114d464a88b36d8aacbf2e222025-08-20T03:45:07ZengWileyMethods in Ecology and Evolution2041-210X2022-11-0113112339234610.1111/2041-210X.13980Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayesRui Borges0Bastien Boussau1Sebastian Höhna2Ricardo J. Pereira3Carolin Kosiol4Institut für Populationsgenetik, Vetmeduni Vienna Wien AustriaUniversité de Lyon, Université Claude Bernard Lyon 1 Villeurbanne FranceGeoBio‐Center, Ludwig‐Maximilians‐Universität München Munich GermanyDivision of Evolutionary Biology, Department of Biology II Ludwig‐Maximilians‐Universität München Martinsried GermanyInstitut für Populationsgenetik, Vetmeduni Vienna Wien AustriaAbstract The availability of population genomic data through new sequencing technologies gives unprecedented opportunities for estimating important evolutionary forces such as genetic drift, selection and mutation biases across organisms. Yet, analytical methods that can handle polymorphisms jointly with sequence divergence across species are rare and not easily accessible to empiricists. We implemented polymorphism‐aware phylogenetic models (PoMos), an alternative approach for species tree estimation, in the Bayesian phylogenetic software RevBayes. PoMos naturally account for incomplete lineage sorting, which is known to cause difficulties for phylogenetic inference in species radiations, and scale well with genome‐wide data. Simultaneously, PoMos can estimate mutation and selection biases. We have applied our methods to resolve the complex phylogenetic relationships of a young radiation of Chorthippus grasshoppers, based on coding sequences. In addition to establishing a well‐supported species tree, we found a mutation bias favouring AT alleles and selection bias promoting the fixation of GC alleles, the latter consistent with GC‐biased gene conversion. The selection bias is two orders of magnitude lower than genetic drift, validating the critical role of nearly neutral evolutionary processes in species radiation. PoMos offer a wide range of models to reconstruct phylogenies and can be easily combined with existing models in RevBayes—for example, relaxed clock and divergence time estimation—offering new insights into the evolutionary processes underlying molecular evolution and, ultimately, species diversification.https://doi.org/10.1111/2041-210X.13980Bayesian inferencegrasshoppersmutation biaspolymorphism‐aware phylogenetic modelsRevBayesselection |
| spellingShingle | Rui Borges Bastien Boussau Sebastian Höhna Ricardo J. Pereira Carolin Kosiol Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes Methods in Ecology and Evolution Bayesian inference grasshoppers mutation bias polymorphism‐aware phylogenetic models RevBayes selection |
| title | Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes |
| title_full | Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes |
| title_fullStr | Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes |
| title_full_unstemmed | Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes |
| title_short | Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes |
| title_sort | polymorphism aware estimation of species trees and evolutionary forces from genomic sequences with revbayes |
| topic | Bayesian inference grasshoppers mutation bias polymorphism‐aware phylogenetic models RevBayes selection |
| url | https://doi.org/10.1111/2041-210X.13980 |
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