SPAGETI: Stabilizing Phylogenetic Assessment with Gene Evolutionary Tree Indices

TL;DR

This paper introduces SPAGETI, a method that improves species tree estimation by weighting genes according to their evolutionary signal and rate differences, addressing conflicts in gene-based phylogenetic analyses.

Contribution

It develops an enhanced weighting approach for gene trees that accounts for varying evolutionary rates, improving the accuracy of species tree inference.

Findings

Better confidence estimation for species trees.

Improved handling of gene rate heterogeneity.

More accurate phylogenetic reconstructions.

Abstract

The standard approach to estimate species trees is to align a selected set of genes, concatenate the alignments and then estimate a consensus tree. However, individual genes contain differing levels of evolutionary information, either supporting or conflicting with the consensus. Based on individual gene evolutionary tree, a recent study has demonstrated that this approach may result in incorrect solutions and developed the internode certainty (IC) heuristic for estimating the confidence of splits made on the consensus tree. Although an improvement, this heuristic neglects the differing rates of molecular evolution in individual genes. Here I develop an improved version of this method such that each gene is proportionally weighted based on its overall signal and specifically with the imbalanced signal for each node represented with gene tree.