Genome-wide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids-adapted clade of cichlids from the Congo River S. Elizabeth Alter (1,2,3)*, Jason Munshi-South (4), Melanie L. J. Stiassny (3,5) (1) Department of Biology, York College/The City University of New York, 94-20 Guy R. Brewer Blvd, Jamaica NY 11451 (2) The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016 (3) The Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY 10024 (4) Louis Calder Center—Biological Field Station, Fordham University, Armonk, NY 10504 (5) Department of Ichthyology, American Museum of Natural History, 79th Street and Central Article Park West, New York, NY 10024 Key words: diversification, phylogeography, fish, RAD-Seq, African biogeography *Corresponding author: S. Elizabeth Alter
[email protected] Phone: (650) 283-5629 Fax: (718) 262-2700 Running title: Phylogeography in rapids-adapted cichlids This article has been accepted for publication and undergone full peer review but has not Accepted been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/mec.13973 This article is protected by copyright. All rights reserved. Abstract: The lower Congo River (LCR) is a freshwater biodiversity hotspot in Africa characterized by some of the world's largest rapids. However, little is known about the evolutionary forces shaping this diversity, which include numerous endemic fishes. We investigated phylogeographic relationships in Teleogramma, a small clade of rheophilic cichlids, in the context of regional geography and hydrology.