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

• Published in: BMC genomics Vol. 17; no. S10; pp. 783 - 113
• Main Authors: Sayyari, Erfan, Mirarab, Siavash
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 11.11.2016; BioMed Central; BMC
• Subjects: Algorithms; Analysis; Animals; Birds - classification; Birds - genetics; Databases, Genetic; Genetic aspects; Genetic research; Incomplete lineage sorting; Mammals - classification; Mammals - genetics; Models, Genetic; Multi-species coalescent; Origin of species; Phylogeny; Quartet methods; Species tree; Quartet methods; Species tree; Multi-species coalescent; Incomplete lineage sorting
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-016-3098-z

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. 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. We show in simulated studies that DISTIQUE has comparable accuracy to leading coalescent-based summary methods and reduced running times.