Cargando…
Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site Plus Gamma Model
The invariable site plus [Formula: see text] model (I [Formula: see text] is widely used to model rate heterogeneity among alignment sites in maximum likelihood and Bayesian phylogenetic analyses. The proof that the I [Formula: see text] continuous [Formula: see text] model is identifiable (model pa...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6204645/ https://www.ncbi.nlm.nih.gov/pubmed/29186593 http://dx.doi.org/10.1093/sysbio/syx092 |
_version_ | 1783366075119828992 |
---|---|
author | Nguyen, Lam-Tung von Haeseler, Arndt Minh, Bui Quang |
author_facet | Nguyen, Lam-Tung von Haeseler, Arndt Minh, Bui Quang |
author_sort | Nguyen, Lam-Tung |
collection | PubMed |
description | The invariable site plus [Formula: see text] model (I [Formula: see text] is widely used to model rate heterogeneity among alignment sites in maximum likelihood and Bayesian phylogenetic analyses. The proof that the I [Formula: see text] continuous [Formula: see text] model is identifiable (model parameters can be inferred correctly given enough data) has increased the creditability of its application to phylogeny reconstruction. However, most phylogenetic software implement the I [Formula: see text] discrete [Formula: see text] model, whose identifiability is likely but unproven. How well the parameters of the I [Formula: see text] discrete [Formula: see text] model are estimated is still disputed. Especially the correlation between the fraction of invariable sites and the fractions of sites with a slow evolutionary rate is discussed as being problematic. We show that optimization heuristics as implemented in frequently used phylogenetic software (PhyML, RAxML, IQ-TREE, and MrBayes) cannot always reliably estimate the shape parameter, the proportion of invariable sites, and the tree length. Here, we propose an improved optimization heuristic that accurately estimates the three parameters. While research efforts mainly focus on tree search methods, our results signify the equal importance of verifying and developing effective estimation methods for complex models of sequence evolution. |
format | Online Article Text |
id | pubmed-6204645 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-62046452018-10-31 Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site Plus Gamma Model Nguyen, Lam-Tung von Haeseler, Arndt Minh, Bui Quang Syst Biol Points of View The invariable site plus [Formula: see text] model (I [Formula: see text] is widely used to model rate heterogeneity among alignment sites in maximum likelihood and Bayesian phylogenetic analyses. The proof that the I [Formula: see text] continuous [Formula: see text] model is identifiable (model parameters can be inferred correctly given enough data) has increased the creditability of its application to phylogeny reconstruction. However, most phylogenetic software implement the I [Formula: see text] discrete [Formula: see text] model, whose identifiability is likely but unproven. How well the parameters of the I [Formula: see text] discrete [Formula: see text] model are estimated is still disputed. Especially the correlation between the fraction of invariable sites and the fractions of sites with a slow evolutionary rate is discussed as being problematic. We show that optimization heuristics as implemented in frequently used phylogenetic software (PhyML, RAxML, IQ-TREE, and MrBayes) cannot always reliably estimate the shape parameter, the proportion of invariable sites, and the tree length. Here, we propose an improved optimization heuristic that accurately estimates the three parameters. While research efforts mainly focus on tree search methods, our results signify the equal importance of verifying and developing effective estimation methods for complex models of sequence evolution. Oxford University Press 2018-05 2017-11-27 /pmc/articles/PMC6204645/ /pubmed/29186593 http://dx.doi.org/10.1093/sysbio/syx092 Text en © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For Permissions, please email: journals.permissions@oup.com |
spellingShingle | Points of View Nguyen, Lam-Tung von Haeseler, Arndt Minh, Bui Quang Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site Plus Gamma Model |
title | Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site Plus Gamma Model |
title_full | Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site Plus Gamma Model |
title_fullStr | Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site Plus Gamma Model |
title_full_unstemmed | Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site Plus Gamma Model |
title_short | Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site Plus Gamma Model |
title_sort | complex models of sequence evolution require accurate estimators as exemplified with the invariable site plus gamma model |
topic | Points of View |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6204645/ https://www.ncbi.nlm.nih.gov/pubmed/29186593 http://dx.doi.org/10.1093/sysbio/syx092 |
work_keys_str_mv | AT nguyenlamtung complexmodelsofsequenceevolutionrequireaccurateestimatorsasexemplifiedwiththeinvariablesiteplusgammamodel AT vonhaeselerarndt complexmodelsofsequenceevolutionrequireaccurateestimatorsasexemplifiedwiththeinvariablesiteplusgammamodel AT minhbuiquang complexmodelsofsequenceevolutionrequireaccurateestimatorsasexemplifiedwiththeinvariablesiteplusgammamodel |