Fig. 1: Whole-genome microsynteny-based species tree inference.

a Whole-genome data sets with all predicted genes are used for phylogeny reconstruction. b The synteny network approach first conducts all pairwise reciprocal genome comparisons, followed by synteny block detection. Syntenic anchor pairs from all syntenic blocks constitute the synteny network database (see Methods for details). c We analyzed all synteny clusters after clustering the entire network database. Synteny clusters vary in size and node compositions. Shared genomic rearrangements are reflected by cluster compositions. Specific anchor pairs shared by a lineage/species form specific clusters (e.g. Clusters 4–6). We account for the presence or absence of the same recurring anchors for multiple blocks derived from whole-genome or segmental duplications (e.g. for Species 2 and 3 in Clusters 2, 3, 5, and 8). d The phylogenomic profiling of all clusters constructs a binary matrix, where rows represent species and columns represent clusters. The synteny matrix comprehensively represents phylogenomic gene order dynamics. It transforms the concept of synteny comparisons from analyzing massive parallel coordinates plots into analyzing profiles of individual clusters/networks. Each cluster stands for a shared homologous ‘context’. For example, TE activity can cause genes to be transposed as insertions into new contexts or be lost from the original context (e.g. genes in Clusters 4–6). As long as such transpositions are shared by different genomes (e.g. genes in Clusters 4 and 6) or within the same genome because of whole-genome duplication (e.g. genes in Cluster 5), specific clusters will emerge and corresponding signals will be added to the matrix. This synteny matrix is used as the input for species tree inference by maximum likelihood (referred to as Syn-MRL).