Rapid radiation, ancient incomplete lineage sorting and ancient hybridization in the endemic Lake Tanganyika cichlid tribe Tropheini Stephan Koblmüller a, * , Bernd Egger a,b , Christian Sturmbauer a , Kristina M. Sefc a a Department of Zoology, Karl-Franzens-University Graz, Universitätsplatz 2, A-8010 Graz, Austria b Zoological Institute, University of Basel, 4051 Basel, Switzerland article info Article history: Received 5 August 2009 Revised 28 September 2009 Accepted 29 September 2009 Available online 21 October 2009 Keywords: AFLP Homoplasy excess test Introgression mtDNA Phylogeny abstract The evolutionary history of the endemic Lake Tanganyika cichlid tribe Tropheini, the sister group of the species flocks of Lake Malawi and the Lake Victoria region, was reconstructed from 2009 bp DNA sequence of two mitochondrial genes (ND2 and control region) and from 1293 AFLP markers. A period of rapid cladogenesis at the onset of the diversification of the Tropheini produced a multitude of special- ized, predominantly rock-dwelling aufwuchs-feeders that now dominate in Lake Tanganyika’s shallow habitat. Nested within the stenotopic rock-dwellers is a monophyletic group of species, which also utilize more sediment-rich habitat. Most of the extant species date back to at least 0.7 million years ago. Several instances of disagreement between AFLP and mtDNA tree topology are attributed to ancient incomplete lineage sorting, introgression and hybridization. A large degree of correspondence between AFLP cluster- ing and trophic types indicated fewer cases of parallel evolution of trophic ecomorphology than previ- ously inferred from mitochondrial data. Ó 2009 Elsevier Inc. All rights reserved. 1. Introduction Together with the Darwin’s finches on the Galápagos Islands, the Hawaiian honeycreepers or the Caribbean anoline lizards, the cichlid species flocks of the East African Great Lakes Tanganyika (LT), Malawi (LM) and Victoria (LV) with their hundreds of endemic species belong to the most spectacular vertebrate examples for rapid speciation in confined environments (Fryer and Iles, 1972; Seehausen, 2006). Such species flocks provide ample opportunity for evolutionary biologists to gain insights into the processes creat- ing organismic diversity (e.g. Grant, 1981; Losos, 1994; Kornfield and Smith, 2000; Schluter, 2000; Kocher, 2004), but also pose ma- jor challenges to the phylogenetic analyses underlying the study of diversification. Oftentimes, attempts to resolve the chronology of rapid cladogenesis remain unsuccessful until exceedingly large datasets or more suitable marker types yield sufficient phyloge- netic resolution (e.g. Yoder and Irwin, 1999; Zwickl and Hillis, 2002; Rokas and Carroll, 2005; Jian et al., 2008). Moreover, under particular circumstances, multiple cladogenetic events may indeed occur simultaneously and result in hard polytomies in the phyloge- netic reconstruction (Sturmbauer et al., 2003). With an age of 9–12 million years, LT is the oldest of the three East African Great Lakes and harbors the morphologically, ecolog- ically and behaviorally most diverse cichlid species assemblage, currently consisting of 200 valid species (Koblmüller et al., 2008a), with several more awaiting scientific description. The age and distinctness of the LT cichlids facilitated their systematic treat- ment to some degree. Based on morphology, the species were orga- nized into 12 (Poll, 1986) or 16 (Takahashi, 2003) mostly endemic tribes, which are well supported by molecular data (Koblmüller et al., 2008a). Intra-tribal diversification, however, proved more difficult to resolve due to the condensed sequence of cladogenetic events, incomplete lineage sorting and introgression between spe- cies and genera. Interestingly, molecular phylogenies revealed a remarkable concurrence of periods of rapid cladogenesis, perhaps associated with environmental changes, in several different tribes: Lamprologini (Koblmüller et al., 2007a), Limnochromini (Duftner et al., 2005), Bathybatini (Koblmüller et al., 2005), and Ectodini (Koblmüller et al., 2004). With 24 described species (Koblmüller et al., 2008a), the Tro- pheini are one of the more species-rich cichlid tribes in LT. Although endemic to LT, the Tropheini were shown to constitute a lineage of the Haplochromini, the most species-rich and wide- spread cichlid tribe, and actually represent the sister group to the two species flocks of Lake Malawi and the Lake Victoria region and of some riverine species (Salzburger et al., 2005; Koblmüller et al., 2008b). All Tropheini species inhabit shallow, at least par- tially rocky habitat and feed on aufwuchs or invertebrates. In the strictly rock-dwelling genera Tropheus and Petrochromis, most spe- cies are highly specialized aufwuchs-feeders with restricted dis- persal over unsuitable habitat (Sturmbauer and Dallinger, 1995), 1055-7903/$ - see front matter Ó 2009 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2009.09.032 * Corresponding author. Fax: +43 316 380 9875. E-mail address: stephan.koblmueller@uni-graz.at (S. Koblmüller). Molecular Phylogenetics and Evolution 55 (2010) 318–334 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev