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

Meyer, Britta S., Matschiner, Michael and Salzburger, Walter (2015) A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach Molecular Phylogenetics and Evolution, 83 . pp. 56-71. DOI 10.1016/j.ympev.2014.10.009.

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Supplementary data:


• We provide a new phylogeny for Lake Tanganyika cichlids using 42 nuclear makers.
• Data concatenation and a Bayesian concordance analysis lead to congruent results.
• Gene tree discordance hints to past hybridization or incomplete lineage sorting.
• The Lamprologini are the sister-group to the ‘H-lineage’.
• The Eretmodini are nested within the ‘H-lineage’.

The species-flocks of cichlid fishes in the East African Great Lakes Victoria, Malawi and Tanganyika constitute the most diverse extant adaptive radiations in vertebrates. Lake Tanganyika, 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 morphological 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 level 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 sequencing with the 454 pyrosequencing 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 concatenated dataset and each marker individually, and performed a Bayesian concordance analysis and gene tree discordance tests. Overall, we find strong support for a position of the Oreochromini, Boulengerochromini, Bathybatini and Trematocarini outside of a clade combining the substrate spawning Lamprologini and the mouthbrooding tribes of the ‘H-lineage’, which are both strongly supported to be monophyletic. The Eretmodini are firmly placed within the ‘H-lineage’, as sister-group to the most species-rich tribe of cichlids, the Haplochromini. The phylogenetic 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. Discordance among gene trees and marker sets further suggests the occurrence of past hybridization and/or incomplete lineage sorting in the cichlid fishes of Lake Tanganyika.

Document Type: Article
Additional Information: All sequences are accessible in Genbank KP129679-KP131427 and KM263618-KM263752. Trees are deposited at Treebase (http://purl.org/phylo/treebase/phylows/study/TB2:S16660) WOS:000350008400007
Keywords: Adaptive radiation; Cichlidae; 454 amplicon sequencing; Hybridization; Incomplete lineage sorting
Research affiliation: OceanRep > GEOMAR > FB3 Marine Ecology > FB3-EV Evolutionary Ecology of Marine Fishes
Refereed: Yes
DOI etc.: 10.1016/j.ympev.2014.10.009
ISSN: 1055-7903
Related URLs:
Date Deposited: 02 Dec 2014 09:30
Last Modified: 13 Apr 2017 09:18
URI: http://eprints.uni-kiel.de/id/eprint/26096

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