A tribal level phylogeny of Lake Tanganyika cichlid fishes based
on a genomic multi-marker approach

Britta S. Meyer, Michael Matschiner, Walter Salzburger, 2015

Molecular Phylogenetics and Evolution 83 (2015) 56–71

Abstract
The species-flocks of cichlid fishes in the East African Great Lakes Victoria, Malawi and Tanganyika con-stitute the most diverse extant adaptive radiations in vertebrates. Lake Tangan yika, the oldest of the
lakes, harbors the morphologically and genetically most diverse assemblage of cichlids and contains
the highest number of endemic cichlid genera of all African lakes. Based on morpholog ical grounds,
the Tanganyikan cichlid species have been grouped into 12–16 distinct lineages, so-called tribes. While
the monophyly of most of the tribes is well established, the phylogenetic relationships among the tribes
remain largely elusive. Here, we present a new tribal leve l phylogenetic hypothesis for the cichlid fishes
of Lake Tanganyika that is based on the so far largest set of nuclear markers and a total alignment length
of close to 18 kb. Using next-generation amplicon sequenci ng with the 454 pyrosequ encing technology,
we compiled a dataset consisting of 42 nuclear loci in 45 East African cichlid species, which we subjected
to maximum likelihood and Bayesian inference phylogenetic analyses. We analyzed the entire concate-nated dataset and each marker individually, and performe d a Bayesian concordance analysis and gene
tree discordance tests. Overall, we find strong support for a position of the Oreo chromini, Boulengero-chromini, Bathybatini and Trematocarini outside of a clade combining the substrate spawning Lamprol-ogini and the mouthbr ooding tribes of the ‘H-lineage’, which are both strongly supported to be
monophyletic. The Eretmod ini are firmly placed within the ‘H-lineage’, as sister-group to the most spe-cies-r ich tribe of cichlids, the Haplochromini. The phylogene tic relationships at the base of the ‘H-lineage’
received less support, which is likely due to high speciation rates in the early phase of the radiation. Dis-corda nce among gene trees and marker sets further suggests the occurren ce of past hybridizat ion and/or
incompl ete lineage sorting in the cichlid fishes of Lake Tanganyika.

Marta