DOI: 10.5061/dryad.8k0g5
title: Data from: Lake Tanganyika - a 'melting pot' of ancient and young cichlid lineages (Teleostei: Cichlidae)?

description: A long history of research focused on the East Africa cichlid radiations
 (EAR) revealed discrepancies between mtDNA and nuclear phylogenies,
 suggesting that interspecific hybridisation may have been significant
 during the radiation of these fishes. The approximately 250 cichlid
 species of Lake Tanganyika have their roots in a monophyletic African
 cichlid assemblage, but controversies remain about the precise
 phylogenetic origin and placement of different lineages and consequently
 about L. Tanganyika colonization scenarios. 3312 AFLP loci and the
 mitochondrial ND2 gene were genotyped for 91 species representing almost
 all major lacustrine and riverine haplotilapiine east African cichlid
 lineages with a focus on L. Tanganyika endemics. Explicitly testing for
 the possibility of ancient hybridisation events, a comprehensive
 phylogenetic network hypothesis is proposed for the origin and
 diversification of L. Tanganyika cichlids. Inference of discordant
 phylogenetic signal strongly suggests that the genomes of two endemic L.
 Tanganyika tribes, Eretmodini and Tropheini, are composed of an ancient
 mixture of riverine and lacustrine lineages. For the first time a strong
 monophyly signal of all non-haplochromine mouthbrooding species endemic to
 L. Tanganyika (“ancient mouthbrooders”) was detected. Further, in the
 genomes of early diverging L. Tanganyika endemics Trematocarini,
 Bathybatini, Hemibatini and Boulengerochromis genetic components of other
 lineages belonging to the East African Radiation appear to be present. In
 combination with recent palaeo-geological results showing that tectonic
 activity in the L. Tanganyika region resulted in highly dynamic and
 heterogeneous landscape evolution over the Neogene and Pleistocene, the
 novel phylogenetic data render a single lacustrine basin as the
 geographical cradle of the endemic L. Tanganyika cichlid lineages
 unlikely. Instead a scenario of a pre-rift origin of several independent
 L. Tanganyika precursor lineages which diversified in ancient rivers and
 precursor lakes and then amalgamated in the extant L. Tanganyika basin is
 put forward as an alternative: the 'melting pot Tanganyika'
 hypothesis.
description: AFLP_dataBinary matrix of nuclear AFLP loci which were generated using a modification of the method of Vos et al. 1995 as applied by Herder et al. 2006. The following 20 MseI/EcoRI primer pairs were used for selective amplification of fragments: AGG*-CTG; ACA*-CAA; ACA*-CTG; ACT*-CAA; AGG*-CTC; ACC*-CTA; ACT*-CAG; ACC*-CAT; AGG*-CTA; ACA*-CAT; ACT*-CTG; ACC*-CAG; ACT*-CTT; AGC*-CTC; AGG*-CAA; AGC*-CAC; AGG*-CTT; AGC*-CAG, ACT*-CAC, ACC*-CTC. Bands were visualized on an AB 3130 sequencer (Applied Biosystems) with size standard ROX 500XL. The Genemapper® v. 4.0. software (Applied Biosystems) was used for automatically scoring peaks between 50 and 499 bases for presence/absence. Three individuals were double genotyped to assess error rates. To correct for standard error of automated sequencers a bin correction was applied to the dataset following Schwarzer et al. 2011.