Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer

Abstract

With the increasing interest in recognizing the discordance between gene genealogies, various gene tree/species tree reconciliation methods have been developed. We present here the first attempt to assess and compare two such Bayesian methods, Bayesian estimation of species trees (BEST) and BUCKy (Bayesian untangling of concordance knots), in the presence of several known processes of gene tree discordance. DNA alignments were simulated under the influence of incomplete lineage sorting (ILS) and of horizontal gene transfer (HGT). BEST and BUCKy both account for uncertainty in gene tree estimation but differ substantially in their assumptions of what caused gene tree discordance. BEST estimates a species tree using the coalescent model, assuming that all gene tree discordance is due to ILS. BUCKy does not assume any specific biological process of gene tree discordance through the use of a nonparametric clustering of concordant genes. BUCKy estimates the concordance factor (CF) of a clade, which is defined as the proportion of genes that truly have the clade in their trees. The estimated concordance tree is then built from clades with the highest estimated CFs. Because of their different assumptions, it was expected that BEST would perform better in the presence of ILS and that BUCKy would perform better in the presence of HGT. As expected, the species tree was more accurately reconstructed by BUCKy in the presence of HGT, when the HGT events were unevenly placed across the species tree. BUCKy and BEST performed similarly in most other cases, including in the presence of strong ILS and of HGT events that were evenly placed across the tree. However, BUCKy was shown to underestimate the uncertainty in CF estimation, with short credibility intervals. Despite this, the discordance pattern estimated by BUCKy could be compared with the signature of ILS. The resulting test for the adequacy of the coalescent model proved to have low Type I error. It was powerful when HGT was the major source of discordance and when HGT events were unevenly placed across the species tree.

Evaluating evolutionary history in the face of high gene tree discordance in Australian Gehyra (Reptilia: Gekkonidae)

“…As gene trees inferred from different loci are often incongruent (Chung and Ané, 2011;Cranston, 2010;Degnan and Rosenberg, 2009), which can impact the statistical support of the overall estimated species tree and thus the robustness of hypotheses inferred from it, it is important to investigate the level of potential discordance between gene trees and evaluate the potential sources Gekkotans and other squamates 165-251 (flat prior) Sanders and Lee, 2007 All calibrations are based on fossils. A fuller justification for the use of these calibrations is available in Sanders and Lee (2007).…”

“…For this reason, our substitution rates are deliberately conservative, and thus the error bars surrounding nodes in the species tree are more likely to encompass the true divergence times of species than a more restrictive prior. Distinguishing between ILS and gene flow is a significant hurdle in the estimation of species trees, and the determination of evolutionary relationship between species and development of methods to distinguish between these two processes is ongoing (Chung and Ané, 2011). Thus, despite the fact that we recovered the same topology from multiple runs with different seeds, the low support values in our species tree estimation represent Species trees and gene tree discordance in Gehyra M Sistrom et al genuine uncertainty in estimating the species relationships among Australian Gehyra stemming from biological processes that make estimating accurate phylogenies inherently challenging.…”

“…Discordance between gene trees can be caused by both stochastic (for example, incorrect gene tree estimation) and technical (for example, paralogous sequences) errors (Chung and Ané, 2011). A number of biological processes, such as incomplete lineage sorting (ILS) and gene flow are known to create further discordance between gene trees (Maddison, 1997) and the underlying species tree.…”

“…Species tree methods represent a conceptual shift in phylogenetics in that the estimation gene and species trees is considered separately. These methods aim to account for discordance between gene trees in the estimation of species trees but make different inferences regarding the source of the discordance (Chung and Ané, 2011).…”

“…It is due to this ability to deal with certain levels of gene tree discordance that makes species tree methods also particularly useful for reconstructing the evolutionary history of recent and rapid radiations that have historically been problematic to reconstruct using more traditional phylogenetic methods (Edwards et al, 2007;McCormack et al, 2010;Rowe et al, 2010;Salichos and Rokas, 2013). However, species tree methods largely attribute discordance to ILS rather than technical errors or other biological phenomena (Chung and Ané, 2011). Despite some studies investigating the impact of discordance on the accuracy and interpretation of phylogenetic analyses (for example, Leaché, 2009;Reid et al, 2012), few empirical studies attempt to investigate the degree of discordance present or its potential sources.…”