bioRxiv preprint doi: https://doi.org/10.1101/461699; this version posted November 4, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts John Gatesya,b*, Daniel B. Sloanc, Jessica M. Warrenc, Richard H. Bakerb, Mark P. Simmonsc, and Mark S. Springerd aDivision of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA bSackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA cDepartment of Biology, Colorado State University, Fort Collins, CO 80523, USA dDepartment of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA *Corresponding author. E-mail addresses:
[email protected] (J. Gatesy). Key words: ASTRAL MP-EST coalescence gene tree incomplete lineage sorting species tree Abbreviations: ASTRAL, accurate species tree algorithm; ASTRID, accurate species trees from internode distances; ILS, incomplete lineage sorting; ML, maximum likelihood; MP-EST, maximum pseudo-likelihood for estimating species trees; MY, million years; NJ-ST, neighbor joining species tree; PCS, partitioned coalescence support; PP, posterior probability; STAR, species tree estimation using average ranks of coalescences; STEAC, species tree estimation using average coalescence times; UCE, ultraconserved element 1 bioRxiv preprint doi: https://doi.org/10.1101/461699; this version posted November 4, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.