Altenhoff, A. | Search bioRxiv

bioRxiv2024

EdgeHOG: fine-grained ancestral gene order inference at tree-of-life scale

Ancestral genomes are essential for studying the diversification of life from the last universal common ancestor to modern organisms. Methods have been proposed to infer ancestral gene order, but they lack scalability, limiting the depth to which gene neighborhood evolution can be traced back. We introduce edgeHOG, a tool designed for accurate ancestral gene order inference with linear time complexity. Validated on various benchmarks, edgeHOG was applied to the entire OMA orthology database, encompassing 2,845 extant genomes across all domains of life. This represents the first tree-of-life scale inference, resulting in 1,133 ancestral genomes. In particular, we reconstructed ancestral contigs for the last common ancestor of eukaryotes, dating back around 1.8 billion years, and observed significant functional association among neighboring genes. The method also dates gene adjacencies, revealing conserved histone clusters and rapid sex chromosome rearrangements, enabling computational inference of these features.

evolutionary biology↗

bioRxiv2017

Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree

Medium to large phylogenetic gene trees constructed from datasets of different species density and taxonomic range are rarely topologically consistent because of missing phylogenetic signal, non-phylogenetic signal and error. In this study, we first use simulations to show that taxon sampling unequally affects nodes in a gene tree, which likely contributes to controversial conclusions from taxon sampling experiments and contradicting species phylogenies such as for the boreoeutherians. Hence, because it is unlikely that a large gene tree can be reconstructed correctly based on a single optimized dataset, we take a two-step approach for the construction of model gene trees. First, stable and unstable clades are identified by comparing phylogenetic trees inferred from multiple datasets and data types (nucleotide, amino acid, codon) from the same gene family. Subsequently, data subsets are optimized for the analysis of individual uncertain clades. Results are summarized in form of a model tree that illustrates the evolutionary relationship of gene loci. A case study shows how a seemingly complex gene phylogeny becomes increasingly consistent with the reference species tree by attentive taxon sampling and subtree analysis. The procedure is progressively introduced to SwissTree (http://swisstree.vital-it.ch), a resource of high confidence model gene (locus) trees. Finally we demonstrate the usefulness of SwissTree for orthology benchmarking.

bioinformatics↗