 An almost infinite sites modelAlejandra Avalos-Pacheco, Cronjäger, Mathias C., Paul A. Jenkins and Jotun Hein Theoretical Population Biology, 2024, vol. 160, issue C, 49-61 Abstract: A main challenge in molecular evolution is to find computationally efficient mutation models with flexible assumptions that properly reflect genetic variation. The infinite sites model assumes that each mutation event occurs at a site never previously mutant, i.e. it does not allow recurrent mutations. This is reasonable for low mutation rates and makes statistical inference much more tractable. However, recurrent mutations are common enough to be observable from genetic variation data, even in species with low per-site mutation rates such as humans. The finite sites model on the other hand allows for recurrent mutations but is computationally unfeasible to work with in most cases. In this work, we bridge these two approaches by developing a novel molecular evolution model, the almost infinite sites model, that both admits recurrent mutations and is tractable. We provide a recursive characterization of the likelihood of our proposed model under complete linkage and outline a parsimonious approximation scheme for computing it. Keywords: Coalescent; Molecular evolution; Infinite sites; Finite sites; Parsimony; Sampling distribution (search for similar items in EconPapers) Downloads: (external link) Related works: Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text Persistent link: https://EconPapers.repec.org/RePEc:eee:thpobi:v:160:y:2024:i:c:p:49-61 DOI: 10.1016/j.tpb.2024.10.001 Access Statistics for this article Theoretical Population Biology is currently edited by Jeremy Van Cleve More articles in Theoretical Population Biology from Elsevier |
Is your work missing from RePEc? Here is how to contribute.
Questions or problems? Check the EconPapers FAQ or send mail to .
EconPapers is hosted by the
School of Business at Örebro University.