Biology subjects

Mendes, F. K.

Publications and source records attributed to Mendes, F. K..

3 recordsLinked to original sources

bioRxiv2018

The perils of intralocus recombination for inferences of molecular convergence

Accurate inferences of convergence require that the appropriate tree topology be used. If there is a mismatch between the tree a trait has evolved along and the tree used for analysis, then false inferences of convergence (\"hemiplasy\") can occur. To avoid problems of hemiplasy when there are high levels of gene tree discordance with the species tree, researchers have begun to construct tree topologies from individual loci. However, due to intralocus recombination even locus-specific trees may contain multiple topologies within them. This implies that the use of individual tree topologies discordant with the species tree can still lead to incorrect inferences about molecular convergence. Here we examine the frequency with which single exons and single protein-coding genes contain multiple underlying tree topologies, in primates and Drosophila, and quantify the effects of hemiplasy when using trees inferred from individual loci. In both clades we find that there are most often multiple diagnosable topologies within single exons and whole genes, with 91% of Drosophila protein-coding genes containing multiple topologies. Because of this underlying topological heterogeneity, even using trees inferred from individual protein-coding genes results in 25% and 38% of substitutions falsely labeled as convergent in primates and Drosophila, respectively. While constructing local trees can reduce the problem of hemiplasy, our results suggest that it will be difficult to completely avoid false inferences of convergence. We conclude by suggesting several ways forward in the analysis of convergent evolution, for both molecular and morphological characters.

evolutionary biology↗

bioRxiv2018

Evolutionary inferences about quantitative traits are affected by underlying genealogical discordance

Modern phylogenetic methods used to study how traits evolve often require a single species tree as input, and do not take underlying gene tree discordance into account. Such approaches may lead to errors in phylogenetic inference because of hemiplasy -- the process by which single changes on discordant trees appear to be homoplastic when analyzed on a fixed species tree. Hemiplasy has been shown to affect inferences about discrete traits, but it is still unclear whether complications arise when quantitative traits are analyzed. In order to address this question and to characterize the effect of hemiplasy on traits controlled by a large number of loci, we present a multispecies coalescent model for quantitative traits evolving along a species tree. We demonstrate theoretically and through simulations that hemiplasy decreases the expected covariances in trait values between more closely related species relative to the covariances between more distantly related species. This effect leads to an overestimation of a traits evolutionary rate parameter, to a decrease of the traits phylogenetic signal, and to increased false positive rates in comparative methods such as the phylogenetic ANOVA. We also show that hemiplasy affects discrete, threshold traits that have an underlying continuous liability, leading to false inferences of convergent evolution. The number of loci controlling a quantitative trait appears to be irrelevant to the trends reported, for all analyses. Our results demonstrate that gene tree discordance and hemiplasy are a problem for all types of traits, across a wide range of methods. Our analyses also point to the conditions under which hemiplasy is most likely to be a factor, and suggest future approaches that may mitigate its effects.

evolutionary biology↗

bioRxiv2017

Why concatenation fails in the anomaly zone

AbstrctGenome-scale sequencing has been of great benefit in recovering species trees, but has not provided final answers. Despite the rapid accumulation of molecular sequences, resolving short and deep branches of the tree of life has remained a challenge, and has prompted the development of new strategies that can make the best use of available data. One such strategy - the concatenation of gene alignments - can be successful when coupled with many tree estimation methods, but has also been shown to fail when there are high levels of incomplete lineage sorting. Here, we focus on the failure of likelihood-based methods in retrieving a rooted, asymmetric four-taxon species tree from concatenated data when the species tree is in or near the anomaly zone - a region of parameter space where the most common gene tree does not match the species tree because of incomplete lineage sorting. First, we use coalescent theory to prove that most informative sites will support the species tree in the anomaly zone, and that as a consequence maximum-parsimony succeeds in recovering the species tree from concatenated data. We further show that maximum-likelihood tree estimation from concatenated data fails both inside and outside the anomaly zone, and that this failure is unconnected to the frequency of the most common gene tree. We provide support for a hypothesis that likelihood-based methods fail in and near the anomaly zone because discordant sites on the species tree have a lower likelihood than those that are discordant on alternative topologies. Our results confirm and extend previous reports of the failure and success of likelihood- and parsimony-based methods, and highlight avenues for future work improving the performance of methods aimed at recovering species tree.

evolutionary biology↗