Origin and speciation of haplochromine fishes in East African crater lakes investigated by the analysis of their mtDNA, Mhc genes, and SINES

Max-Planck-Institut für Biologie, Abteilung Immungenetik, Tübingen, Germany.
Molecular Biology and Evolution (Impact Factor: 9.11). 10/2003; 20(9):1448-62. DOI: 10.1093/molbev/msg151
Source: PubMed


The Western Branch of the East African Great Rift Valley is pocketed with craters of extinct or dormant volcanoes. Many of the craters are filled with water, and the lakes are inhabited by fishes. The objective of the present study was to determine the amount and nature of genetic variation in haplochromine fishes inhabiting two of these crater lakes, Lake Lutoto and Lake Nshere, and to use this information to infer the origin and history of the two populations. To this end, sequences of mitochondrial (mt) DNA control region, exon 2 of major histocompatibility complex (Mhc) class II B genes, and short interspersed elements (SINEs) were analyzed. The results indicate that the Lake Nshere and Lake Lutoto fishes originated from different but related large founding populations derived from the Kazinga Channel, which connects Lake Edward and Lake George. Some of the genetic polymorphism that existed in the ancestral populations was lost in the populations of the two lakes. The polymorphism that has been retained has persisted for some 50000 generations (years). During this time, new mutations arose and became fixed in each of the two populations in the mtDNA, giving rise to sets of diagnostic substitutions. Each population evolved in isolation after the colonization of the lakes less than 50000 years ago. There appears to be no population structure within the crater lake fishes, and their present effective population sizes are in the order of 104 to 105 individuals. Comparisons with the endemic haplochromine species of Lake Victoria reveal interesting parallels, as well as differences, which may help to understand the nature of the speciation process.

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Available from: Naoko Takezaki, Mar 13, 2014
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    • "Current knowledge about the processes of diversification and speciation in cichlids is often derived from evolutionary patterns revealed in the phylogenetic trees of extant taxa (see e.g. Danley & Kocher, 2001; Sato et al., 2003; Barluenga et al., 2006; Wagner et al., 2012). With little concrete information on extinct species, however, a large knowledge gap remains. "
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    ABSTRACT: The sedimentary archive of Crater Lake Challa in East Africa contains abundant fossil teeth of cichlid fishes throughout at least the last 25,000 years. Here, we use morphometric analyses of oral teeth from the two extant Oreochromis species inhabiting Lake Challa to explore the feasibility of tracing adaptive modification of the cichlid trophic apparatus in the lake’s fossil record. We compared the performance of semi-landmark analysis (SLM) and elliptic Fourier analysis in capturing morphological variation in oral tooth crowns, and found that SLM, supplemented with tooth shaft measurements, ensured consistency with whole-body landmark analyses. Whole-body and tooth morphology data both allowed to discern between the indigenous Oreochromis hunteri and the recently introduced Oreochromis korogwe. Both species have an oral jaw arrangement of outer-row bicuspid and inner-rows tricuspid teeth, but O. hunteri has generally more slender teeth with a proportionally taller major cusp than O. korogwe, suggesting fine-scaled resource partitioning. Exploratory analysis of three fossil samples showed that the major tooth types of modern-day Oreochromis are also represented in the fossil record. Their total morphological variation is largely restricted to the morphospace occupied by contemporary teeth, suggesting a close functional relationship between ancient populations and their likely descendant, O. hunteri.
    Hydrobiologia 08/2015; 755(1). DOI:10.1007/s10750-015-2218-0 · 2.28 Impact Factor
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    • "Plausibility of the results was checked according to Schenekar and Weiss [40], using a range of substitution rates (0.01 to 0.1 substitutions per lineage per site per MY), taking into account the variability of reported values (e.g. [41-43]). "
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    ABSTRACT: The polytypic Nicaraguan Midas cichlids (Amphilophus cf. citrinellus) have been established as a model system for studying the mechanisms of speciation and patterns of diversification in allopatry and sympatry. The species assemblage in Crater Lake Apoyo has been accepted as a textbook example for sympatric speciation. Here, we present a first comprehensive data set of population genetic (mtDNA & AFLPs) proxies of species level differentiation for a representative set of individuals of all six endemic Amphilophus species occurring in Crater Lake Apoyo. AFLP genetic differentiation was partitioned into a neutral and non-neutral component based on outlier-loci detection approaches, and patterns of species divergence were explored with Bayesian clustering methods. Substantial levels of admixture between species were detected, indicating different levels of reproductive isolation between the six species. Analysis of neutral genetic variation revealed several A. zaliosus as being introgressed by an unknown contributor, hereby rendering the sympatrically evolving L. Apoyo flock polyphyletic. This is contrasted by the mtDNA analysis delivering a clear monophyly signal with Crater Lake Apoyo private haplotypes characterising all six described species, but also demonstrating different demographic histories as inferred from pairwise mismatch distributions.
    PLoS ONE 09/2013; 8(9):e74901. DOI:10.1371/journal.pone.0074901 · 3.23 Impact Factor
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    • "From Lake Malawi, evidence for deep introgression leaving a long-term signal in its haplochromine radiation [10, 14, 43], as well as evidence for more recent natural hybridisation [16, 50, 51] among Malawi cichlids, has been provided. In the Lake Victoria cichlid flock recent or ongoing hybridisation [52–54] presumably affects large parts of the species' genomes by homogenization [54, 55], hampering the reconstruction of its young evolutionary history [54, 56, 57], yet potentially seeding the process of speciation [58] but see [55]. In Cameroonian crater lakes the hybridisation of two ancient lineages resulted in the formation of a new and ecologically highly distinct species [59]. "
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    ABSTRACT: We present a comprehensive phylogenetic analysis of the Utaka, an informal taxonomic group of cichlid species from Lake Malawi. We analyse both nuclear and mtDNA data from five Utaka species representing two (Copadichromis and Mchenga) of the three genera within Utaka. Within three of the five analysed species we find two very divergent mtDNA lineages. These lineages are widespread and occur sympatrically in conspecific individuals in different areas throughout the lake. In a broader taxonomic context including representatives of the main groups within the Lake Malawi cichlid fauna, we find that one of these lineages clusters within the non-Mbuna mtDNA clade, while the other forms a separate clade stemming from the base of the Malawian cichlid radiation. This second mtDNA lineage was only found in Utaka individuals, mostly within Copadichromis sp. "virginalis kajose" specimens. The nuclear genes analysed, on the other hand, did not show traces of divergence within each species. We suggest that the discrepancy between the mtDNA and the nuclear DNA signatures is best explained by a past hybridisation event by which the mtDNA of another species introgressed into the ancestral Copadichromis sp. "virginalis kajose" gene pool.
    05/2012; 2012:865603. DOI:10.1155/2012/865603
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