Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction

BACKGROUND: Inferring species trees from gene trees using the coalescent-based summary methods has been the subject of much attention, yet new scalable and accurate methods are needed. RESULTS: We introduce DISTIQUE, a new statistically consistent summary method for inferring species trees from gene trees under the coalescent model. We generalize our results to arbitrary phylogenetic inference problems; we show that two arbitrarily chosen leaves, called anchors, can be used to estimate relative distances between all other pairs of leaves by inferring relevant quartet trees. This results in a family of distance-based tree inference methods, with running times ranging between quadratic to quartic in the number of leaves. CONCLUSIONS: We show in simulated studies that DISTIQUE has comparable accuracy to leading coalescent-based summary methods and reduced running times. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3098-z) contains supplementary material, which is available to authorized users.