DupLoss-2: Improved phylogenomic species tree inference under gene duplication and loss

Accurate species tree reconstruction in the presence of widespread gene
duplication and loss is a challenging problem in eukaryote phylogenomics.
Many phylogenomics methods have been developed over the years to address
this challenge; these range from older methods based on gene tree
parsimony to newer quartet-based methods. In this work, we introduce
improved software for gene tree parsimony-based species tree
reconstruction under gene duplication and loss. The new software,
DupLoss-2, uses an improved procedure for computing gene losses and is far
more accurate and much easier to use than its previous version, released
over a decade ago. We thoroughly evaluate DupLoss-2 and eight other
existing methods, including ASTRAL-Pro, ASTRAL-Pro 2, DISCO-ASTRAL,
DISCO-ASTRID, FastMulRFS, and SpeciesRax, using existing benchmarking data
and find that DupLoss-2 outperforms all other methods on most of the
datasets. It delivers an average of almost 30% reduction in reconstruction
error compared to iGTP-Duploss, the previous version of this software, and
a 10% reduction compared to the best performing existing method. DupLoss-2
is written in C++ and is freely available open-source.