Three tree priors and five datasets: A study of the effect of tree priors in Indo-European phylogenetics

TL;DR

This study investigates how different tree priors influence Bayesian phylogenetic inferences of the Indo-European language family, revealing that prior choice affects root age estimates and support for the Steppe origin hypothesis.

Contribution

It systematically compares three tree priors across multiple datasets, highlighting their impact on phylogenetic results in Indo-European studies.

Findings

Support for the Steppe origin hypothesis varies with tree prior.

Uniform and FBD priors are more suitable than Coalescent for Indo-European data.

Root age estimates differ depending on the chosen prior.

Abstract

The age of the root of the Indo-European language family has received much attention since the application of Bayesian phylogenetic methods by Gray and Atkinson(2003). The root age of the Indo-European family has tended to decrease from an age that supported the Anatolian origin hypothesis to an age that supports the Steppe origin hypothesis with the application of new models (Chang et al., 2015). However, none of the published work in the Indo-European phylogenetics studied the effect of tree priors on phylogenetic analyses of the Indo-European family. In this paper, I intend to fill this gap by exploring the effect of tree priors on different aspects of the Indo-European family's phylogenetic inference. I apply three tree priors---Uniform, Fossilized Birth-Death (FBD), and Coalescent---to five publicly available datasets of the Indo-European language family. I evaluate the posterior distribution of the trees from the Bayesian analysis using Bayes Factor, and find that there is support for the Steppe origin hypothesis in the case of two tree priors. I report the median and 95% highest posterior density (HPD) interval of the root ages for all the three tree priors. A model comparison suggested that either Uniform prior or FBD prior is more suitable than the Coalescent prior to the datasets belonging to the Indo-European language family.