Comparing inference under the multispecies coalescent with and without recombination.
Mol Phylogenet Evol
; 181: 107724, 2023 04.
Article
en En
| MEDLINE
| ID: mdl-36720421
ABSTRACT
Accurate inference of population parameters plays a pivotal role in unravelling evolutionary histories. While recombination has been universally accepted as a fundamental process in the evolution of sexually reproducing organisms, it remains challenging to model it exactly. Thus, existing coalescent-based approaches make different assumptions or approximations to facilitate phylogenetic inference, which can potentially bring about biases in estimates of evolutionary parameters when recombination is present. In this article, we evaluate the performance of population parameter estimation using three methods-StarBEAST2, SNAPP, and diCal2-that represent three different types of inference. We performed whole-genome simulations in which recombination rates, mutation rates, and levels of incomplete lineage sorting were varied. We show that StarBEAST2 using short or medium-sized loci is robust to realistic rates of recombination, which is in agreement with previous studies. SNAPP, as expected, is generally unaffected by recombination events. Most surprisingly, diCal2, a method that is designed to explicitly account for recombination, performs considerably worse than other methods under comparison.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Genoma
/
Tasa de Mutación
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
Mol Phylogenet Evol
Asunto de la revista:
BIOLOGIA
/
BIOLOGIA MOLECULAR
Año:
2023
Tipo del documento:
Article