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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.

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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Africa is experiencing extensive biodiversity loss due to rapid changes in the environment, where natural resources constitute the main instrument for socioeconomic development and a mainstay source of livelihoods for an increasing population. Lack of data and information deficiency on biodiversity, but also budget constraints and insufficient financial and technical capacity, impede sound policy design and effective implementation of conservation and management measures. The problem is further exacerbated by the lack of harmonized indicators and databases to assess conservation needs and monitor biodiversity losses. We review challenges with biodiversity data (availability, quality, usability and database access) as a key limiting factor that impacts funding and governance. We also evaluate the drivers of both ecosystems change and biodiversity loss as a central piece of knowledge to develop and implement effective policies. While the continent focuses more on the latter, we argue that the two are complementary in shaping restoration and management solutions. We thus underscore the importance of establishing monitoring programmes focusing on biodiversity–ecosystem linkages in order to inform evidence-based decisions in ecosystem conservation and restoration in Africa. This article is part of the theme issue ‘Detecting and attributing the causes of biodiversity change: needs, gaps and solutions’.

Determining the genetic characteristics of natural fish stocks is useful for conservation and aquaculture programs. For African catfish, Clarias gariepinus, genetic characterization could help identify populations suitable as brood stock for culture, and those in need of conservation. This study determined the genetic diversity, population structure, and demographic history of C. gariepinus from Lakes Victoria (LV), Kenyatta (LKE), Kamnarok (LKA), and Rivers Nyando (NR), Tana (TR) and Sosiani (SR) in Kenya. Using 128 DNA sequences of D‐loop control region, 34 haplotypes were recovered, of which 79.4% were singletons. Only 7 haplotypes were shared between sites, implying little gene flow between sites. Number of haplotypes was highest in LKE and NR populations and lowest in SR. Haplotype diversity was highest in LV, and lowest in SR, while, nucleotide diversity was highest in LKA and lowest in LV. Phylogenetic analyses revealed five clusters: Lakes Victoria, Kamnarok and Kenyatta, and Rivers Tana and Nyando, from both maximum likelihood tree and minimum spanning network. This, together with significant FST values among the sites imply population differentiation. Mismatch distributions were multi‐modal in LKA, LKE, NR and TR, signifying demographic equilibria. Neutrality tests Tajima`s D values for the sampled populations were negative and significantly different, suggesting stable populations. These results show the existence of genetically distinct populations of C. gariepinus that require spatially explicit management actions such as reducing fishing pressure, pollution, minimizing habitat destruction and fragmentation for sustainable utilisation of stocks.