Weighted ASTRID: fast and accurate species trees from weighted internode distances

Background Species tree estimation is a basic step in many biological research projects, but is complicated by the fact that gene trees can differ from the species tree due to processes such as incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT), which can cause different regions within the genome to have different evolutionary histories (i.e., gene tree heterogeneity). One approach to estimating species trees in the presence of gene tree heterogeneity resulting from ILS operates by computing trees on each genomic region (i.e., computing gene trees) and then using these gene trees to define a matrix of average internode distances, where the internode distance in a tree T between two species x and y is the number of nodes in T between the leaves corresponding to x and y. Given such a matrix, a tree can then be computed using methods such as neighbor joining. Methods such as ASTRID and NJst (which use this basic approach) are provably statistically consistent, very fast (low degree polynomial time) and have had high accuracy under many conditions that makes them competitive with other popular species tree estimation methods. In this study, inspired by the very recent work of weighted ASTRAL, we present weighted ASTRID, a variant of ASTRID that takes the branch uncertainty on the gene trees into account in the internode distance. Results Our experimental study evaluating weighted ASTRID typically shows improvements in accuracy compared to the original (unweighted) ASTRID, and shows competitive accuracy against weighted ASTRAL, the state of the art. Our re-implementation of ASTRID also improves the runtime, with marked improvements on large datasets. Conclusions Weighted ASTRID is a new and very fast method for species tree estimation that typically improves upon ASTRID and has comparable accuracy to weighted ASTRAL, while remaining much faster. Weighted ASTRID is available at https://github.com/RuneBlaze/internode.

Automated summary

Species tree estimation is a fundamental step in many biological research projects, but is complicated by gene tree heterogeneity caused by processes such as incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer. In this study, we propose a new method called weighted ASTRID, which takes into account the branch uncertainty on gene trees to estimate the species tree. Experimental results show that weighted ASTRID improves accuracy compared to unweighted ASTRID and has comparable accuracy to weighted ASTRAL, while being faster.