A statistical framework of model comparison and model validation is essential to resolving the debates over concatenation and coalescent models in phylogenomic data analysis. A set of statistical tests are here applied and developed to evaluate and compare the adequacy of substitution, concatenation, and multispecies coalescent (MSC) models across 47 phylogenomic data sets collected across tree of life. Tests for substitution models and the concatenation assumption of topologically concordant gene trees suggest that a poor fit of substitution models (44% of loci rejecting the substitution model) and concatenation models (38% of loci rejecting the hypothesis of topologically congruent gene trees) is widespread. Logistic regression shows that the proportions of GC content and informative sites are both negatively correlated with the fit of substitution models across loci. Moreover, a substantial violation of the concatenation assumption of congruent gene trees is consistently observed across 6 major groups (birds, mammals, fish, insects, reptiles, and others, including other invertebrates). In contrast, among those loci adequately described by a given substitution model, the proportion of loci rejecting the MSC model is 11%, significantly lower than those rejecting the substitution and concatenation models, and Bayesian model comparison strongly favors the MSC over concatenation across all data sets. Species tree inference suggests that loci rejecting the MSC have little effect on species tree estimation. Due to computational constraints, the Bayesian model validation and comparison analyses were conducted on the reduced data sets. A complete analysis of phylogenomic data requires the development of efficient algorithms for phylogenetic inference. Nevertheless, the concatenation assumption of congruent gene trees rarely holds for phylogenomic data with more than 10 loci. Thus, for large phylogenomic data sets, model comparison analyses are expected to consistently and more strongly favor the coalescent model over the concatenation model. Our analysis reveals the value of model validation and comparison in phylogenomic data analysis, as well as the need for further improvements of multilocus models and computational tools for phylogenetic inference.
- Downloaded 296 times
- Download rankings, all-time:
- Site-wide: 98,569
- In evolutionary biology: 5,052
- Year to date:
- Site-wide: 144,037
- Since beginning of last month:
- Site-wide: None
Downloads over time
Distribution of downloads per paper, site-wide
- 27 Nov 2020: The website and API now include results pulled from medRxiv as well as bioRxiv.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!