Construction of Gene and Species Trees from Sequence Data incl. Orthologs, Paralogs, and Xenologs

TL;DR

This paper introduces a new method for constructing gene and species trees from sequence data that includes orthologs, paralogs, and xenologs, thereby utilizing more comprehensive genomic information for phylogenetic analysis.

Contribution

The paper presents a novel approach to phylogenetic reconstruction that incorporates non-orthologous genes, expanding beyond traditional methods limited to 1:1 orthologs.

Findings

Method effectively uses larger gene sets including paralogs and xenologs.

Improves accuracy of species tree inference with diverse gene data.

Demonstrates robustness across different genomic datasets.

Abstract

Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged after a speciation) is crucial and lies at the heart of many genomic studies. However, existing methods that rely only on 1:1 orthologs to infer species trees are strongly restricted to a small set of allowed genes that provide information about the species tree. The use of larger gene sets that consist in addition of non-orthologous genes (e.g. so-called paralogous or xenologous genes) considerably increases the information about the evolutionary history of the respective species. In this work, we introduce a novel method to compute species phylogenies based on sequence data including orthologs, paralogs or even xenologs.