Are sympatrically speciating Midas cichlid fish special? Patterns of morphological and genetic variation in the closely related species Archocentrus centrarchus

Established empirical cases of sympatric speciation are scarce, although there is an increasing consensus that sympatric speciation might be more common than previously thought. Midas cichlid fish are one of the few substantiated cases of sympatric speciation, and they formed repeated radiations in crater lakes. In contrast, in the same environment, such radiation patterns have not been observed in other species of cichlids and other families of fish. We analyze morphological and genetic variation in a cichlid species (Archocentrus centrarchus) that co‐inhabits several crater lakes with the Midas species complex. In particular, we analyze variation in body and pharyngeal jaw shape (two ecologically important traits in sympatrically divergent Midas cichlids) and relate that to genetic variation in mitochondrial control region and microsatellites. Using these four datasets, we analyze variation between and within two Nicaraguan lakes: a crater lake where multiple Midas cichlids have been described and a lake where the source population lives. We do not observe any within‐lake clustering consistent across morphological traits and genetic markers, suggesting the absence of sympatric divergence in A. centrarchus. Genetic differentiation between lakes was low and morphological divergence absent. Such morphological similarity between lakes is found not only in average morphology, but also when analyzing covariation between traits and degree of morphospace occupation. A combined analysis of the mitochondrial control region in A. centrarchus and Midas cichlids suggests that a difference between lineages in the timing of crater lake colonization cannot be invoked as an explanation for the difference in their levels of diversification. In light of our results, A. centrarchus represents the ideal candidate to study the genomic differences between these two lineages that might explain why some lineages are more likely to speciate and diverge in sympatry than others.     

Genomic signatures of divergent selection and speciation patterns in a ‘natural experiment’, the young parallel radiations of Nicaraguan crater lake cichlid fishes

Divergent selection is the main driving force in sympatric ecological speciation and may also play a strong role in divergence between allopatric populations. Characterizing the genome‐wide impact of divergent selection often constitutes a first step in unravelling the genetic bases underlying adaptation and ecological speciation. The Midas cichlid fish (Amphilophus citrinellus) species complex in Nicaragua is a powerful system for studying evolutionary processes. Independent colonizations of isolated young crater lakes by Midas cichlid populations from the older and great lakes of Nicaragua resulted in the repeated evolution of adaptive radiations by intralacustrine sympatric speciation. In this study we performed genome scans on two repeated radiations of crater lake species and their great lake source populations (1030 polymorphic AFLPs, n ～ 30 individuals per species). We detected regions under divergent selection (0.3% in the crater lake Xiloá flock and 1.7% in the older crater lake Apoyo radiation) that might be responsible for the sympatric diversifications. We find no evidence that the same genomic regions have been involved in the repeated evolution of parallel adaptations across crater lake flocks. However, there is some genetic parallelism apparent (seven out of 51 crater lake to great lake outlier loci are shared; 13.7%) that is associated with the allopatric divergence of both crater lake flocks. Interestingly, our results suggest that the number of outlier loci involved in sympatric and allopatric divergence increases over time. A phylogeny based on the AFLP data clearly supports the monophyly of both crater lake species flocks and indicates a parallel branching order with a primary split along the limnetic‐benthic axis in both radiations.     

The Midas cichlid species complex: incipient sympatric speciation in Nicaraguan cichlid fishes?

Abstract Sympatric speciation is a contentious concept, although theoretical models as well as empirical evidence support its relevance in evolutionary biology. The Midas cichlid species complex (Amphilophus citrinellus, labiatus, zaliosus) from several crater lakes in Nicaragua fits several of the key characteristics of a sympatric speciation model. In particular, in A. citrinellus (i) strong assortative mating on the basis of colour polymorphism and (ii) ecological differentiation based on morphological polymorphisms involving the feeding apparatus and body shape might both be mechanisms of incipient speciation. Seven microsatellite markers and mtDNA control region sequences [836 base pairs (bp)] were used to study the population genetic structure of 519 specimens of Midas cichlid populations from the two Great Lakes Managua and Nicaragua, and three crater lakes in Nicaragua, Central America. The three named species of the species complex occupy different ecological niches, are morphologically distinct and can be distinguished genetically. We uncovered allopatric genetic differentiation of populations of A. citrinellus from different lakes and distant locations within Lake Managua and, more interestingly, incipient genetic differentiation of several sympatric populations based on colouration (in A. citrinellus and A. labiatus) but not on the morphology of the pharyngeal jaws (in A. citrinellus). Sexual selection and assortative mating might be the driven forces of diversification within named species. The Midas cichlid species complex in Nicaragua is an excellent model system for the study of the incipient stages of adaptation, speciation and the formation of species flocks.     

CRATER LAKE HABITAT PREDICTS MORPHOLOGICAL DIVERSITY IN ADAPTIVE RADIATIONS OF CICHLID FISHES

Adaptive radiations provide an excellent opportunity for studying the correlates and causes for the origin of biodiversity. In these radiations, species diversity may be influenced by either the ecological and physical environment, intrinsic lineage effects, or both. Disentangling the relative contributions of these factors in generating biodiversity remains a major challenge in understanding why a lineage does or does not radiate. Here, we examined morphological variation in body shape for replicate flocks of Nicaraguan Midas cichlid fishes and tested its association with biological and physical characteristics of their crater lakes. We found that variability of body elongation, an adaptive trait in freshwater fishes, is mainly predicted by average lake depth (N = 6, P < 0.001, R² = 0.96). Other factors considered, including lake age, surface area, littoral zone area, number of co‐occurring fish species, and genetic diversity of the Midas flock, did not significantly predict morphological variability. We also showed that lakes with a larger littoral zone have on average higher bodied Midas cichlids, indicating that Midas cichlid flocks are locally adapted to their crater lake habitats. In conclusion, we found that a lake's habitat predicts the magnitude and the diversity of body elongation in repeated cichlid adaptive radiations.     

Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times

Background  

After a volcano erupts, a lake may form in the cooled crater and become an isolated aquatic ecosystem. This makes fishes in crater lakes informative for understanding sympatric evolution and ecological diversification in barren environments. From a geological and limnological perspective, such research offers insight about the process of crater lake ecosystem establishment and speciation. In the present study we use genetic and coalescence approaches to infer the colonization history of Midas cichlid fishes (Amphilophus cf. citrinellus) that inhabit a very young crater lake in Nicaragua-the ca. 1800 year-old Lake Apoyeque. This lake holds two sympatric, endemic morphs of Midas cichlid: one with large, hypertrophied lips (~20% of the total population) and another with thin lips. Here we test the associated ecological, morphological and genetic diversification of these two morphs and their potential to represent incipient speciation.     

Sampling genetic diversity in the sympatrically and allopatrically speciating Midas cichlid species complex over a 16 year time series

Background  

Speciation often occurs in complex or uncertain temporal and spatial contexts. Processes such as reinforcement, allopatric divergence, and assortative mating can proceed at different rates and with different strengths as populations diverge. The Central American Midas cichlid fish species complex is an important case study for understanding the processes of speciation. Previous analyses have demonstrated that allopatric processes led to species formation among the lakes of Nicaragua as well as sympatric speciation that is occurring within at least one crater lake. However, since speciation is an ongoing process and sampling genetic diversity of such lineages can be biased by collection scheme or random factors, it is important to evaluate the robustness of conclusions drawn on individual time samples.     

Incipient speciation in sympatric Nicaraguan crater lake cichlid fishes: sexual selection versus ecological diversification.

The growing body of empirical evidence for sympatric speciation has been complemented by recent theoretical treatments that have identified evolutionary conditions conducive to speciation in sympatry. The Neotropical Midas cichlid (Amphilophus citrinellum) fits both of the key characteristics of these models, with strong assortative mating on the basis of a colour polymorphism coupled with trophic and ecological differentiation derived from a polymorphism in their pharyngeal jaws. We used microsatellite markers and a 480 bp fragment of the mitochondrial DNA control region to study four polymorphic populations of the Midas cichlid from three crater lakes and one large lake in Nicaragua in an investigation of incipient sympatric speciation. All populations were strongly genetically differentiated on the basis of geography. We identified strong genetic separation based on colour polymorphism for populations from Lake Nicaragua and one crater lake (Lake Apoyo), but failed to find significant genetic structuring based on trophic differences and ecological niche separation in any of the four populations studied. These data support the idea that sexual selection through assortative mating contributes more strongly or earlier during speciation in sympatry than ecological separation in these cichlids. The long-term persistence of divergent cichlid ecotypes (as measured by the percentage sequence divergence between populations) in Central American crater lakes, despite a lack of fixed genetic differentiation, differs strikingly from the patterns of extremely rapid speciation in the cichlids in Africa, including its crater lakes. It is unclear whether extrinsic environmental factors or intrinsic biological differences, e.g. in the degree of phenotypic plasticity, promote different mechanisms and thereby rates of speciation of cichlid fishes from the Old and New Worlds.     

Genetic, Comparative Genomic, and Expression Analyses of the Mc1r Locus in the Polychromatic Midas Cichlid Fish (Teleostei, Cichlidae Amphilophus sp.) Species Group

Natural populations of the Midas cichlid species in several different crater lakes in Nicaragua exhibit a conspicuous color polymorphism. Most individuals are dark and the remaining have a gold coloration. The color morphs mate assortatively and sympatric population differentiation has been shown based on neutral molecular data. We investigated the color polymorphism using segregation analysis and a candidate gene approach. The segregation patterns observed in a mapping cross between a gold and a dark individual were consistent with a single dominant gene as a cause of the gold phenotype. This suggests that a simple genetic architecture underlies some of the speciation events in the Midas cichlids. We compared the expression levels of several candidate color genes Mc1r, Ednrb1, Slc45a2, and Tfap1a between the color morphs. Mc1r was found to be up regulated in the gold morph. Given its widespread association in color evolution and role on melanin synthesis, the Mc1r locus was further investigated using sequences derived from a genomic library. Comparative analysis revealed conserved synteny in relation to the majority of teleosts and highlighted several previously unidentified conserved non-coding elements (CNEs) in the upstream and downstream regions in the vicinity of Mc1r. The identification of the CNEs regions allowed the comparison of sequences from gold and dark specimens of natural populations. No polymorphisms were found between in the population sample and Mc1r showed no linkage to the gold phenotype in the mapping cross, demonstrating that it is not causally related to the color polymorphism in the Midas cichlid.     

Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes

Determining the genetic bases of adaptations and their roles in speciation is a prominent issue in evolutionary biology. Cichlid fish species flocks are a prime example of recent rapid radiations, often associated with adaptive phenotypic divergence from a common ancestor within a short period of time. In several radiations of freshwater fishes, divergence in ecomorphological traits — including body shape, colour, lips and jaws — is thought to underlie their ecological differentiation, specialization and, ultimately, speciation. The Midas cichlid species complex (Amphilophus spp.) of Nicaragua provides one of the few known examples of sympatric speciation where species have rapidly evolved different but parallel morphologies in young crater lakes. This study identified significant QTL for body shape using SNPs generated via ddRAD sequencing and geometric morphometric analyses of a cross between two ecologically and morphologically divergent, sympatric cichlid species endemic to crater Lake Apoyo: an elongated limnetic species (Amphilophus zaliosus) and a high‐bodied benthic species (Amphilophus astorquii). A total of 453 genome‐wide informative SNPs were identified in 240 F₂ hybrids. These markers were used to construct a genetic map in which 25 linkage groups were resolved. Seventy‐two segregating SNPs were linked to 11 QTL. By annotating the two most highly supported QTL‐linked genomic regions, genes that might contribute to divergence in body shape along the benthic–limnetic axis in Midas cichlid sympatric adaptive radiations were identified. These results suggest that few genomic regions of large effect contribute to early stage divergence in Midas cichlids.     

Phylogeography and Evolution of the Tanganyikan Cichlid Genus Tropheus Based upon Mitochondrial DNA Sequences

Abstract Lake Tanganyika harbors the oldest and most diverse species flock of cichlid fish. Many species are subdivided into numerous genetically and phenotypically distinct populations. Their present distribution and genetic structure were shaped by a series of lake level fluctuations which caused cycles of isolation and admixis and promoted dispersal events. One of the best examples of this phenomenon is the genus Tropheus. We present a comprehensive mtDNA phylogeny based upon 365 individuals of 55 populations from all over Lake Tanganyika, which suggests an almost-contemporaneous origin of eight major mitochondrial lineages about 700 Ka ago. While the distribution of seven lineages is restricted to particular sections of the lake shore, one lineage was found to have a much more widespread distribution. This particular lineage is subdivided into four sublineages which seem to have originated from a single dispersal event about 400 Ka. By using a molecular clock estimate in combination with geological data we derived a hypothetical scenario for the colonization history of Tropheus. Thereby we show a high degree of concordance between major changes of the lake level in the recent history of Lake Tanganyika and three distinct diversification events in this genus.     

Phylogeography,colonization and population history of the Midas cichlid species complex (<Emphasis Type="Italic">Amphilophus</Emphasis> spp.) in the Nicaraguan crater lakes

Background  

Elucidation of the mechanisms driving speciation requires detailed knowledge about the phylogenetic relationships and phylogeography of the incipient species within their entire ranges as well as their colonization history. The Midas cichlid species complex Amphilophus spp. has been proven to be a powerful model system for the study of ecological specialization, sexual selection and the mechanisms of sympatric speciation. Here we present a comprehensive and integrative phylogeographic analysis of the complete Midas Cichlid species complex in Nicaragua (> 2000 individuals) covering the entire distributional range, using two types of molecular markers (the mitochondrial DNA control region and 15 microsatellites). We investigated the majority of known lake populations of this species complex and reconstructed their colonization history in order to distinguish between alternative speciation scenarios.     

Rapid adaptation to a novel light environment: The importance of ontogeny and phenotypic plasticity in shaping the visual system of Nicaraguan Midas cichlid fish (Amphilophus citrinellus spp.)

Colonization of novel habitats is typically challenging to organisms. In the initial stage after colonization, approximation to fitness optima in the new environment can occur by selection acting on standing genetic variation, modification of developmental patterns or phenotypic plasticity. Midas cichlids have recently colonized crater Lake Apoyo from great Lake Nicaragua. The photic environment of crater Lake Apoyo is shifted towards shorter wavelengths compared to great Lake Nicaragua and Midas cichlids from both lakes differ in visual sensitivity. We investigated the contribution of ontogeny and phenotypic plasticity in shaping the visual system of Midas cichlids after colonizing this novel photic environment. To this end, we measured cone opsin expression both during development and after experimental exposure to different light treatments. Midas cichlids from both lakes undergo ontogenetic changes in cone opsin expression, but visual sensitivity is consistently shifted towards shorter wavelengths in crater lake fish, which leads to a paedomorphic retention of their visual phenotype. This shift might be mediated by lower levels of thyroid hormone in crater lake Midas cichlids (measured indirectly as dio2 and dio3 gene expression). Exposing fish to different light treatments revealed that cone opsin expression is phenotypically plastic in both species during early development, with short and long wavelength light slowing or accelerating ontogenetic changes, respectively. Notably, this plastic response was maintained into adulthood only in the derived crater lake Midas cichlids. We conclude that the rapid evolution of Midas cichlids’ visual system after colonizing crater Lake Apoyo was mediated by a shift in visual sensitivity during ontogeny and was further aided by phenotypic plasticity during development.     

Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation

One of the most celebrated examples of sympatric speciation in nature are monophyletic radiations of cichlid fishes endemic to Cameroon crater lakes. However, phylogenetic inference of monophyly may not detect complex colonization histories involving some allopatric isolation, such as double invasions obscured by genome‐wide gene flow. Population genomic approaches are better suited to test hypotheses of sympatric speciation in these cases. Here, we use comprehensive sampling from all four sympatric crater lake cichlid radiations in Cameroon and outgroups across Africa combined with next‐generation sequencing to genotype tens of thousands of SNPs. We find considerable evidence of gene flow between all four radiations and neighboring riverine populations after initial colonization. In a few cases, some sympatric species are more closely related to outgroups than others, consistent with secondary gene flow facilitating their speciation. Our results do not rule out sympatric speciation in Cameroon cichlids, but rather reveal a complex history of speciation with gene flow, including allopatric and sympatric phases, resulting in both reproductively isolated species and incipient species complexes. The best remaining non‐cichlid examples of sympatric speciation all involve assortative mating within microhabitats. We speculate that this feature may be necessary to complete the process of sympatric speciation in nature.     

Depth-dependent abundance of Midas Cichlid fish (Amphilophus spp.) in two Nicaraguan crater lakes

The Midas Cichlid species complex (Amphilophus spp.) in Central America serves as a prominent model system to study sympatric speciation and parallel adaptive radiation, since small arrays of equivalent ecotype morphs have evolved independently in different crater lakes. While the taxonomy and evolutionary history of the different species are well resolved, little is known about basic ecological parameters of Midas Cichlid assemblages. Here, we use a line transect survey to investigate the depth-dependent abundance of Amphilophus spp. along the shores of two Nicaraguan crater lakes, Apoyo and Xiloá. We find a considerable higher density of Midas cichlids in Lake Xiloá as compared to Lake Apoyo, especially at the shallowest depth level. This might be due to the higher eutrophication level of Lake Xiloá and associated differences in food availability, and/or the presence of a greater diversity of niches in that lake. In any case, convergent forms evolved despite noticeable differences in size, age, eutrophication level, and carrying capacity. Further, our data provide abundance and density estimates for Midas Cichlid fish, which serve as baseline for future surveys of these ecosystems and are also relevant to past and future modeling of ecological speciation.     

Phylogeography and Evolution of the Tanganyikan Cichlid Genus <Emphasis Type="Italic">Tropheus</Emphasis> Based upon Mitochondrial DNA Sequences

Lake Tanganyika harbors the oldest and most diverse species flock of cichlid fish. Many species are subdivided into numerous genetically and phenotypically distinct populations. Their present distribution and genetic structure were shaped by a series of lake level fluctuations which caused cycles of isolation and admixis and promoted dispersal events. One of the best examples of this phenomenon is the genus Tropheus. We present a comprehensive mtDNA phylogeny based upon 365 individuals of 55 populations from all over Lake Tanganyika, which suggests an almost-contemporaneous origin of eight major mitochondrial lineages about 700 Ka ago. While the distribution of seven lineages is restricted to particular sections of the lake shore, one lineage was found to have a much more widespread distribution. This particular lineage is subdivided into four sublineages which seem to have originated from a single dispersal event about 400 Ka. By using a molecular clock estimate in combination with geological data we derived a hypothetical scenario for the colonization history of Tropheus. Thereby we show a high degree of concordance between major changes of the lake level in the recent history of Lake Tanganyika and three distinct diversification events in this genus.     

A dark shell hiding great variability: a molecular insight into the evolution and conservation of melanic Daphnia populations in the Alps

Zooplanktonic microcrustaceans of the Daphnia pulex group appear highly differentiated at high altitudes as a result of alternative colonizations and quick local adaptation to harsh environments. In particular, the occurrence of deeply differentiated mountain lineages of European Daphnia pulicaria (EuPC) is highly related to glacial advances and retreats during the Pleistocene. Nowadays, one single ancient EuPC lineage survives in the Pyrenees, with another inhabiting the High Tatra Mountains. Much less is known about populations inhabiting the Alps, where EuPC populations are extremely rare. Recently, four new melanic populations have been discovered in lakes in the Western Italian Alps, offering the opportunity to study their origin and adaptations. We inferred phylogenetic relationships of melanic high‐mountain populations in order to disentangle their history and clarify the colonization patterns of alpine populations. Molecular data suggest that dark populations originated from at least two ancestors, one genetically close to boreal haplotypes, the other apparently related to refugial populations that survived in southern Europe. Therefore, dark pigmentation and obligate parthenogenesis evolved independently within both lineages inhabiting the studied lakes as extreme local adaptations to the alpine environment. Finally, since impacts of human‐related activities and climate changes on mountain species are known to be dramatic, we pose strong issues for the conservation of these extremely localized endemisms. © 2014 The Linnean Society of London     

Phylogeography and speciation in the <Emphasis Type="Italic">Pseudocrenilabrus philander</Emphasis> species complex in Zambian Rivers

Haplochromine cichlids form the most species-rich lineage of cichlid fishes that both colonized almost all river systems in Africa and radiated to species flocks in several East African lakes. The enormous diversity of lakes is contrasted by a relatively poor albeit biogeographically clearly structured species diversity in rivers. The present study analyzed the genetic structure and phylogeographic history of species and populations of the genus Pseudocrenilabrus in Zambian rivers that span two major African drainage systems, the Congo- and the Zambezi-system. The mtDNA phylogeny identifies four major lineages, three of which occur in the Congo-system and one in the Zambezi system. Two of the Congo-clades (Lake Mweru and Lunzua River) comprise distinct albeit yet undescribed species, while the fish of the third Congo-drainage clade (Chambeshi River and Bangweulu swamps), together with the fish of the Zambezi clade (Zambezi and Kafue River) are assigned to Pseudocrenilabrus philander. Concerning the intraspecific genetic diversity observed in the sampled rivers, most populations are highly uniform in comparison to lacustrine haplochromines, suggesting severe founder effects and/or bottlenecking during their history. Two bursts of diversification are reflected in the structure of the linearized tree. The first locates at about 3.9% mean sequence divergence and points to an almost simultaneous colonization of the sampled river systems. Subsequent regional diversification (with about 1% mean sequence divergence) occurred contemporaneously within the Kafue River and the Zambezi River. The clear-cut genetic biogeographic structure points to the dominance of geographic speciation in this lineage of riverine cichlid fishes, contrasting the importance of in situ diversification observed in lake cichlids.     

COLOR ASSORTATIVE MATING CONTRIBUTES TO SYMPATRIC DIVERGENCE OF NEOTROPICAL CICHLID FISH

It is still debated vigorously whether sexual selection can result in speciation without physical barriers to gene flow. In this study, we used field data and molecular methods to investigate the gold–normal color polymorphism in two endemic cichlid fish species of crater lake Xiloá, Nicaragua. We found significant assortative mating by color in both Amphilophus xiloaensis and A. sagittae . Focusing on A. xiloaensis , microsatellite allele frequencies, an assignment test, and model-based cluster analysis demonstrates significant and clear genetic differentiation ( F _ST= 0.03) between gold and normal individuals in sympatry. In addition, we find genetic differentiation between all three sympatric and ecologically distinct Midas cichlid species of Lake Xiloá, A. amarillo , A. sagittae , and A. xiloaensis ( F _ST= 0.03 – 0.19), and clear genetic isolation of these species from their closest relative ( A. citrinellus ) in the neighboring great lake Managua. The A. xiloaensis gold morph is genetically more distinct from the lake's other two Midas cichlid species than is A. xiloaensis -normal. Thus, we have identified sexual isolation based on color that is evident in population genetics and mate choice. Our results suggest that sexual selection through color assortative mating may play an important role in incipient sympatric speciation in Midas cichlids of Nicaragua.     

Parallel evolution in Ugandan crater lakes: repeated evolution of limnetic body shapes in haplochromine cichlid fish

Background

The enormous diversity found in East African cichlid fishes in terms of morphology, coloration, and behavior have made them a model for the study of speciation and adaptive evolution. In particular, haplochromine cichlids, by far the most species-rich lineage of cichlids, are a well-known textbook example for parallel evolution. Southwestern Uganda is an area of high tectonic activity, and is home to numerous crater lakes. Many Ugandan crater lakes were colonized, apparently independently, by a single lineage of haplochromine cichlids. Thereby, this system could be considered a natural experiment in which one can study the interaction between geographical isolation and natural selection promoting phenotypic diversification.

Results

We sampled 13 crater lakes and six potentially-ancestral older lakes and, using both mitochondrial and microsatellite markers, discovered strong genetic and morphological differentiation whereby (a) geographically close lakes tend to be genetically more similar and (b) three different geographic areas seem to have been colonized by three independent waves of colonization from the same source population. Using a geometric morphometric approach, we found that body shape elongation (i.e. a limnetic morphology) evolved repeatedly from the ancestral deeper-bodied benthic morphology in the clear and deep crater lake habitats.

Conclusions

A pattern of strong genetic and morphological differentiation was observed in the Ugandan crater lakes. Our data suggest that body shape changes have repeatedly evolved into a more limnetic-like form in several Ugandan crater lakes after independent waves of colonization from the same source population. The observed morphological changes in crater lake cichlids are likely to result from a common selective regime.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0287-3) contains supplementary material, which is available to authorized users.     

Phylogeographic history of the genus Tropheus,a lineage of rock-dwelling cichlid fishes endemic to Lake Tanganyika

Lake Tanganyika contains the oldest and most complex flock of cichlid fishes counting about 200 endemic species. It is comprised of 16 ecologically, morphologically and genetically highly distinct tribes. Many species are further subdivided into arrays of geographic morphs, each colonizing particular sections of the shore line. The genus Tropheus represents the most spectacular and best studied example for this phenomenon, counting more than 100 distinctly colored populations and sister species, some living in sympatry. Their present distribution and genetic structure was shaped by a series of lake level fluctuations which caused cycles of isolation and secondary admixis. The present study extends previous work on the phylogeography of Tropheus and aims at the fine-scale reconstruction of the origin and spread of lineages in the central and southern basin of the lake. The previously defined mtDNA lineages were evaluated on the basis of statistical parsimony networks. Haplotype networks were created for each lineage and related to their centers of diversity in terms of present distribution. A linearized tree analysis and a mismatch distribution analysis corroborate two of the three radiation waves suggested in earlier works, but the new data suggest a different primary colonization scenario for the southern basin.