Genetic variation and demographic history of the Haplochromis laparogramma group of Lake Victoria-An analysis based on SINEs and mitochondrial DNA

More than 500 endemic haplochromine cichlid species inhabit Lake Victoria. This striking species diversity is a classical example of recent explosive adaptive radiation thought to have happened within the last similar to 15,000 years. In this study, we examined the population structure and historical demography of 3 pelagic haplochromine cichlid species that resemble in morphology and have similar niche, Haplochromis (Yssichromis) laparogramma, Haplochromis (Y.) pyrrhocephalus, and Haplochromis (Y.) sp. "glaucocephalus". We investigated the sequences of the mitochondrial DNA control region and the insertion patterns of short interspersed elements (SINEs) of 759 individuals. We show that sympatric forms are genetically differentiated in 4 of 6 cases, but we also found apparent weakening of the genetic differentiation in areas with turbid water. We estimated the timings of population expansion and species divergence to coincide with the refilling of the lake at the Pleistocene/Holocene boundary. We also found that estimates can be altered significantly by the choice of the shape of the molecular clock. If we employ the nonlinear clock model of evolutionary rates in which the rates are higher towards the recent, the population expansion was dated at around the event of desiccation of the lake ca. 17,000 YBP. Thus, we succeeded in clarifying the species and population structure of closely related Lake Victoria cichlids and in showing the importance of applying appropriate clock calibrations in elucidating recent evolutionary events. (C) 2009 Elsevier B.V. All rights reserved

Genetic Structure of Pelagic and Littoral Cichlid Fishes from Lake Victoria

<div><p>The approximately 700 species of cichlids found in Lake Victoria in East Africa are thought to have evolved over a short period of time, and they represent one of the largest known examples of adaptive radiation. To understand the processes that are driving this spectacular radiation, we must determine the present genetic structure of these species and elucidate how this structure relates to the ecological conditions that caused their adaptation. We analyzed the genetic structure of two pelagic and seven littoral species sampled from the southeast area of Lake Victoria using sequences from the mtDNA control region and 12 microsatellite loci as markers. Using a Bayesian model-based clustering method to analyze the microsatellite data, we separated these nine species into four groups: one group composed of pelagic species and another three groups composed mainly of rocky-shore species. Furthermore, we found significant levels of genetic variation between species within each group at both marker loci using analysis of molecular variance (AMOVA), although the nine species often shared mtDNA haplotypes. We also found significant levels of genetic variation between populations within species. These results suggest that initial groupings, some of which appear to have been related to habitat differences, as well as divergence between species within groups took place among the cichlid species of Lake Victoria.</p></div

Patterns of genomic differentiation between two Lake Victoria cichlid species, Haplochromis pyrrhocephalus and H. sp. ‘macula’

Abstract Background The molecular basis of the incipient stage of speciation is still poorly understood. Cichlid fish species in Lake Victoria are a prime example of recent speciation events and a suitable system to study the adaptation and reproductive isolation of species. Results Here, we report the pattern of genomic differentiation between two Lake Victoria cichlid species collected in sympatry, Haplochromis pyrrhocephalus and H. sp. ‘macula,’ based on the pooled genome sequences of 20 individuals of each species. Despite their ecological differences, population genomics analyses demonstrate that the two species are very close to a single panmictic population due to extensive gene flow. However, we identified 21 highly differentiated short genomic regions with fixed nucleotide differences. At least 15 of these regions contained genes with predicted roles in adaptation and reproductive isolation, such as visual adaptation, circadian clock, developmental processes, adaptation to hypoxia, and sexual selection. The nonsynonymous fixed differences in one of these genes, LWS, were reported as substitutions causing shift in absorption spectra of LWS pigments. Fixed differences were found in the promoter regions of four other differentially expressed genes, indicating that these substitutions may alter gene expression levels. Conclusions These diverged short genomic regions may have contributed to the differentiation of two ecologically different species. Moreover, the origins of adaptive variants within the differentiated regions predate the geological formation of Lake Victoria; thus Lake Victoria cichlid species diversified via selection on standing genetic variation

Results of AMOVA at mitochondrial and nuclear loci.

<p>Results of AMOVA at mitochondrial and nuclear loci.</p

The relationships between geographical distance and genetic differentiation.

<p>Pane A: mitochondrial. Panel B: nuclear microsatellite loci.</p

Numbers of individuals typed and sequenced in each species.

a<p>P: pelagic, V: vegetation zone, R: rocky-shore.</p

Haplotype network of the mitochondrial control region.

<p>Different species are represented by different colors. <i>H. (Y.) pyrrhocephalus</i> and <i>H. (Y.) laparogramma</i> are pelagic. <i>L. rufus</i> lives in the vegetation zone and the remainig species live in rocky shores. The size of the the circle shows the number of the samples having the haplotype.</p

Sampling locations of the cichlids.

<p>Different species are represented by different symbols as indicated in Panel B. Panel A: Lake Victoria. Panel B: the sourhtern part of Lake Victoria. Panel C: Mwanza Gulf.</p