The ∼ ∼ ∼ ∼ 500 species of the cichlid fish species flock of Lake Victoria, East Africa, have evolved in a record-setting 100 000 years and represent one of the largest adaptive radiations. We examined the population structure of the endangered cichlid species Xystichromis phytophagus from Lake Kanyaboli, a satellite lake to Lake Victoria in the Kenyan Yala wetlands. Two sets of molecular markers were analysed -sequences of the mitochondrial control region as well as six microsatellite loci -and revealed surprisingly high levels of genetic variability in this species. Mitochondrial DNA sequences failed to detect population structuring among the three sample populations. A model-based population assignment test based on microsatellite data revealed that the three populations most probably aggregate into a larger panmictic population. However, values of population pairwise F ST indicated moderate levels of genetic differentiation for one population. Eleven distinct mitochondrial haplotypes were found among 205 specimens of X. phytophagus , a relatively high number compared to the total number of 54 haplotypes that were recovered from hundreds of specimens of the entire cichlid species flock of Lake Victoria. Most of the X. phytophagus mitochondrial DNA haplotypes were absent from the main Lake Victoria, corroborating the putative importance of satellite lakes as refugia for haplochromine cichlids that went extinct from the main lake in the last decades and possibly during the Late Pleistocene desiccation of Lake Victoria.
The introduction of invasive Nile tilapia (Oreochromis niloticus), and the rapacious predator Nile perch (Lates niloticus), into Lake Victoria resulted in a decline in population sizes, genetic diversity and even extirpation of native species which were previously the mainstay of local fisheries. However, remnant populations of native fish species, including tilapia, still persist in satellite lakes around Lake Victoria where they may coexist with O. niloticus. In this study we assessed population genetic structure, diversity, and integrity of the native critically endangered Singidia tilapia (O. esculentus) in its refugial populations in the Yala swamp, Kenya, and contrasted this diversity with populations of the invasive tilapia O. niloticus in satellite lakes (Kanyaboli, Namboyo and Sare) and Lake Victoria. Based on mtDNA control region sequences and eight nuclear microsatellite loci, we did not detect any mtDNA introgression between the native and the invasive species in Lakes Kanyaboli and Namboyo, but did find low levels of nuclear admixture, primarily from O. niloticus to O. esculentus. Some genetic signal of O. esculentus in O. niloticus was found in Lake Sare, where O. esculentus is not found, suggesting it has recently been extirpated by the O. niloticus invasion. In both species, populations in the satellite lakes are significantly genetically isolated from each other, with private mtDNA haplotypes and microsatellite alleles. For O. niloticus, genetic diversity in satellite lakes was similar to that found in Lake Victoria. Our data imply a low frequency of immigration exchange between the two populations of O. esculentus and we suggest that the populations of this endangered species and important fisheries resource should be conserved separately in Lakes Kanyaboli and Namboyo and with high priority.
ABSTRACT. African catfish, Clarias gariepinus, is an important species in aquaculture and fisheries in Kenya. Mitochondrial D-loop control region was used to determine genetic variation and population structure in samples of C. gariepinus from 10 sites including five natural populations (Lakes Victoria (LVG), Kanyaboli (LKG), Turkana (LTA), Baringo (LBA) and Jipe (LJP), and five farms (Sangoro Aquaculture Center (SAN), Sagana Aquaculture Centre (SAG), University of Eldoret Fish Farm (UoE), Kibos Fish Farm (KIB), and Wakhungu Fish Farm (WKU)) in Kenya. Similarly, samples from eight localities (four natural populations: LVG/LKG, LTA, LBA, and four farmed: SAN, SAG, KIB, UoE) were genotyped using six microsatellite DNA loci. For the D-loop control region, samples from natural sites exhibited higher numbers of haplotypes and haplotype diversities compared to farmed samples, and 88.2% of haplotypes were private. All except LJP and LTA shared haplotypes, and the highest number of shared haplotypes (8) was detected in KIB. The 68 haplotypes we found in 268 individuals grouped into five phylogenetic clades: LVG/LKG, LTA, LBA, LJP and SAG. Haplotypes of farmed C. gariepinus mostly have haplotypes typical of LVG/LKG, and some shared haplotypes of the LBA population. Microsatellite analysis showed farmed samples have higher numbers of alleles than natural samples, but higher observed and expected heterozygosity levels were found in samples of natural Belg. J. Zool. 147 (2): 105-127 (2017) 106 populations. Fifteen pair-wise comparisons had significantly different FST values. All samples were in Hardy-Weinberg equilibrium. Samples from the eight localities grouped into four genetic clusters (LVG/ LKG, LTA, LBA and SAG), indicating genetically distinct populations, which should be considered for aquaculture and conservation.
Lake Kanyaboli, an isolated satellite lake of Lake Victoria, has been suggested as a potential refugium for haplochromine cichlids that have gone extinct in the main basin of Lake Victoria. Mitochondrial DNA (mtDNA) molecular markers, as well as feeding ecology studies, were employed in this study to re-evaluate the evolutionary and ecological significance of six common Lake Kanyaboli haplochromines. The mtDNA marker revealed high genetic variability within four of the six haplochromine cichlids. Five haplotypes were discerned in Astatoreochromis alluaudi (n = 27), seven in Lipochromis maxillaris (n = 29), five in Astatotilapia nubila (n = 12) and 11 in the endangered Xystichromis phytophagus (n = 205). A haplotype genealogy suggests that Lake Kanyaboli harbours mtDNA haplotypes that could have been lost or not sampled in Lake Victoria, or could have arisen in situ. Lipochromis maxillaris appears to have undergone a recent demographic expansion. The pairwise F ST s indicated that only the comparison between X. phytophagus and A. nubila led to a nonsignificant F ST value. All other comparisons were significant at the 0.01 level, indicating the genetic distinctiveness of the haplochromines in the satellite lake. This could suggest that the lake harbours 'pure' relict populations of the haplochromines and therefore that Lake Kanyaboli can be considered a 'genetic reservoir'. Gut content analysis of the six haplochromine species revealed that eight different food items were consumed. No single species fed exclusively on a single food item, but certain food items contributed higher proportions of the fish diet for each fish species. Resource partitioning therefore could be discerned within this haplochromine community. Thus, Lake Kanyaboli and similar satellite lakes provide an opportunity for conservation of both genetic and trophic diversity threatened by introduction of exotics in the Lake Victoria basin. Lake Kanyaboli should be recognized and conserved as important evolutionary significant units for Lake Victoria region haplochromine species.
Summary Approximately 850 bp of the mitochondrial control region was used to assess the genetic diversity, population structure and demographic expansion of the endangered cyprinid Barbus altianalis, a species known to be potamodramous in the Lake Victoria drainage system. The 196 samples taken from the four main rivers draining the Lake Victoria catchment (Nzoia, Yala, Nyando and Sondu–Miriu) yielded 49 mitochondrial DNA haplotypes; 83.7% thereof were private haplotypes restricted to particular rivers. The overall mean haplotype diversity was high (0.93663 ± 0.008) and ranged between 0.566 (Sondu – Miriu) and 0.944 (Nzoia). The overall mean nucleotide diversity was low (0.01322 ± 0.00141), ranging from 0.0342 (Sondu – Miriu) to 0.0267 (Nzoia). Population differentiation tests revealed strong and highly significant (P ≤ 0.001) segregation of populations in the four river basins. FST values among the four river‐based populations ranged from 0.05202 to 0.44352. The samples formed two main haplotype networks based on a 95% parsimony criterion, each exhibiting a strong signature of past population expansion. The smaller network was restricted to the River Nzoia, whereas the larger network contained representatives from all four rivers; within this the central haplotypes were found in more than one river, whereas the peripheral haplotypes tended to be river‐specific. The degree of population differentiation and the number of river‐specific haplotypes are too high to be explained by recent anthropogenic impacts alone and suggest that the species has probably existed in the Lake Victoria catchment as two populations: the now ‘extinct’ migratory population and the extant river restricted non‐migratory populations.
In order to improve the conservation and sustainable utilization of the African catfish Clarias gariepinus of the Yala Swamp in Kenya, genetic diversity and population structure of Lakes Kanyaboli and Namboyo populations of the species were studied using DNA sequences of the mitochondrial D-loop control region. Genetic diversity inferred as haplotype and nucleotide diversities and number of singletons and shared haplotypes was higher in the Lake Kanyaboli population (LKG) than the Lake Namboyo population (LNG) of C. gariepinus. Thirty-one haplotypes were inferred, of which 25 (80·6%) were private or singletons, while only six (19·4%) haplotypes were shared between LKG and LNG. Both populations were differentiated, with F value that was significantly different from zero (P < 0·05). Two clusters were inferred both from the maximum likelihood tree and the spanning networks of phylogenetic relationships of haplotypes. Mismatch distribution for total sample was multi-modal but individually, distributions were uni-modal in LKG, but multimodal in LNG. The mean ± s.d. raggedness index for both populations was 0·085 ± 0·098 and not significantly different from zero (P > 0·05). Individual raggedness indices were 0·015 and 0·154 for LKG and LNG respectively. Fu's F was negative for both populations, with LKG recording -14·871, while LNG had -2·565, significantly different from zero for LKG (P < 0·05), but the value for LNG was not significant (P > 0·05). Tajima's D was negative for both populations, with LKG recording -1·734, while LNG had -1·136. Standardized square differences (SSD) were 0·001 for LKG and 0·048 for LNG and non-significant between them (P > 0·05). Values between all populations were also not significantly different (P > 0·05), mean ± s.d. SSD 0·025 ± 0·033.
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