Phylogeny of the Lake Tanganyika Cichlid Species Flock and Its Relationship to the Central and East African Haplochromine Cichlid Fish Faunas

Abstract

Lake Tanganyika, the oldest of the East African Great Lakes, harbors the ecologically, morphologically, and behaviorally most complex of all assemblages of cichlid fishes, consisting of about 200 described species. The evolutionary old age of the cichlid assemblage, its extreme degree of morphological differentiation, the lack of species with intermediate morphologies, and the rapidity of lineage formation have made evolutionary reconstruction difficult. The number and origin of seeding lineages, particularly the possible contribution of riverine haplochromine cichlids to endemic lacustrine lineages, remains unclear. Our phylogenetic analyses, based on mitochondrial DNA sequences of three gene segments of 49 species (25% of all described species, up to 2,400 bp each), yield robust phylogenies that provide new insights into the Lake Tanganyika adaptive radiation as well as into the origin of the Central- and East-African haplochromine faunas. Our data suggest that eight ancient African lineages may have seeded the Tanganyikan cichlid radiation. One of these seeding lineages, probably comprising substrate spawning Lamprologus-like species, diversified into six lineages that evolved mouthbrooding during the initial stage of the radiation. All analyzed haplochromines from surrounding rivers and lakes seem to have evolved within the radiating Tanganyikan lineages. Thus, our findings contradict the current hypothesis that ancestral riverine haplochromines colonized Lake Tanganyika to give rise to at least part of its spectacular endemic cichlid species assemblage. Instead, the early phases of the Tanganyikan radiation affected Central and East African rivers and lakes. The haplochromines may have evolved in the Tanganyikan basin before the lake became a hydrologically and ecologically closed system and then secondarily colonized surrounding rivers. Apparently, therefore, the current diversity of Central and East African haplochromines represents a relatively young and polyphyletic fauna that evolved from or in parallel to lineages now endemic to Lake Tanganyika.

The puzzling phylogeography of the haplochromine cichlid fish Astatotilapia burtoni

“…Amplification of a 374‐bp fragment of the mitochondrial control region (d‐loop) was conducted using published primers (L‐Pro‐F and TDK‐D; Kocher et al., 1989; Salzburger, Meyer, Baric, Verheyen, & Sturmbauer, 2002) and following a published protocol (Theis et al., 2014). PCR products were purified with Exo‐SAP‐IT (USB) and Sanger‐sequenced on an ABI 3130 xl genetic analyzer using the BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems).…”

Molecular Characterization of Two Endothelin Pathways in East African Cichlid Fishes

“…In this study, we analyzed two components of the endothelin system in 26 species of cichlid fishes from Lake Tanganyika, East Africa, belonging to 14 different tribes, thus representing a great portion of the diversity of East African cichlids (Salzburger et al 2002. The samples were collected during two consecutive expeditions to Lake Tanganyika in 2007 and 2008 (see Supplementary Table 1 for specimen information).…”

“…For the cod data sets, sliding window analyses of the K a /K s ratio were also performed with the same program with a window size of 25 and an overlap of 10 bp. This comparison was performed between different groups defined on the basis of existing phylogenies (e.g., outgroup species, and the three large Tanganyikan cichlid clades haplochromines, lamprologines, and ectodines; see, e.g., Salzburger et al 2002Salzburger et al , 2005Salzburger et al , 2007 and the remaining samples.…”

“…Likelihood ratio tests (LRTs) were carried out with jModeltest 0.1.1 (Guindon and Gascuel 2003;Posada 2008) and Bayesian information criterion and corrected Akaike information criteria were used to determine the best-fitting models of nucleotide substitutions. These models were used in the maximum likelihood (ML) search in PAUP* 4.0 (Swofford 2002) with T. polylepis and O. tanganicae as outgroup species (see Salzburger et al 2002). To test the robustness of the resulting topologies, we conducted bootstrap analyses with 100 replicates.…”

“…Both the obtained ML phylogeny (see above) and an independent tree based on sequences of the mitochondrial ND2 gene (Salzburger et al 2002 were used for reconstructions of the d n /d s ratios on the branches of the J Mol Evol (2011) 73:355-368 359 phylogeny. The Suzuki-Gojobori derived adaptation selection tool was then used (P = 0.05) to visualize the d n /d s ratios on a branch-scaled tree.…”