Dissecting incongruence between concatenation- and quartet-based approaches in phylogenomic data

Xing-Xing Shen, Jacob Steenwyk & Antonis Rokas
Topological conflict or incongruence is widespread in phylogenomic data. Concatenation- and coalescent-based approaches often result in incongruent topologies, but the causes of this conflict can be difficult to characterize. We examined incongruence stemming from conflict between likelihood-based signal (quantified by the difference in gene-wise log likelihood score or ΔGLS) and quartet-based topological signal (quantified by the difference in gene-wise quartet score or ΔGQS) for every gene in three phylogenomic studies in animals, fungi, and plants,...
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These counts follow the COUNTER Code of Practice, meaning that Internet robots and repeats within a certain time frame are excluded.
What does this mean?