Evolution of Labeo victorianus predates the Pleistocene desiccation of Lake Victoria: evidence from mitochondrial DNA sequence variation

Geological data show that Lake Victoria dried out some 15 000 years ago. These data suggest that the entire faunal diversity within the lake has evolved since this time. However, mitochondrial DNA sequence diversity in the endemic cyprinid fish, Labeo victorianus, was high (24 haplotypes in 38 individuals; percentage sequence divergence of 0.74%), suggesting that the evolution of this species predates this Late Pleistocene climatological event. This finding is consistent with what has been reported earlier for cichlid fishes in the lake

Population morphological variation of the Nile perch (Lates niloticus, L. 1758), of East African Lakes and their associated waters

In this study an attempt was made to determine whether there are morphological variations associated with the different geographical populations of the Nile perch of East Africa. Analyses of the levels of morphological differentiation based on morphological characterisation and variation were carried out. The study was based on 864 Nile perch sampled from 25 different locations from different Lakes in the region and 10 morphological characters. Also determined were the length – weight relationships and condition factor of sampled Nile perch. The log transformed data of all sampled Nile perch were subjected to multivariate analysis, using ‘PAST’ statistical software. Findings showed that peduncle form and size, of all the variables used in this study, contributed most to the variance. The analysis clustered the Nile perch into two groups, which were found to be as characterised by earlier morphological description of this species and most probably are representatives of two distinct taxa of Nile perch in the East African waters. The LWRs and condition factor conformed to the fish isometric growth formula W = aLb with the value for the pooled data being W = 0.6664L0.3264. The existence of 2 morphs agrees with earlier taxonomists (Harrison, 1991; Ribbink, 1987; Bwathondi, 1985; Holden, 1967) who proposed that Nile perch exists in two populations – a bigger shallow water dwelling morph and a smaller deep open water dwelling morph. This calls for identification and mapping of the 2 populations in the different waters of East Africa that may require application of different management regimes.Keywords: Nile perch, taxa, morphological variation, East Africa

Evolution of Labeo victorianus predates the Pleistocene desiccation of Lake Victoria: evidence from mitochondrial DNA sequence variation

Geological data show that Lake Victoria dried out some 15 000 years ago. These data suggest that the entire faunal diversity within the lake has evolved since this time. However, mitochondrial DNA sequence diversity in the endemic cyprinid fish, Labeo victorianus, was high (24 haplotypes in 38 individuals; percentage sequence divergence of 0.74%), suggesting that the evolution of this species predates this Late Pleistocene climatological event. This finding is consistent with what has been reported earlier for cichlid fishes in the lake

East African pigs have a complex Indian, Far Eastern and Western ancestry

In this study, we have characterized the mitochondrial diversity of 81 swine from Uganda. Median-joining network analysis of D-loop sequences from these individuals and others characterized in previous studies allowed us to determine that Ugandan pigs cluster with populations from the West (Europe/North Africa), Far East and India. In addition, partial sequencing of the Y-chromosome UTY locus in 18 Ugandan domestic pigs revealed the segregation of a single HY1 lineage that has a cosmopolitan distribution. A Western and Far Eastern ancestry for East African pigs had been already reported, but this is the first study demonstrating an additional contribution from the Indian porcine gene pool. This result is consistent with the high frequency of zebuine alleles in cattle from East Africa. The geographic coordinates of East Africa, at the crossroads of many trading routes that, through the ages, linked Europe, Africa and Asia, might explain the rich and complex genetic heritage of livestock native to this area.We are greatly indebted to the Swedish International Development Agency (Sida) under the framework of Sida-Mak Bilateral Research Support Programme Phase 3 to the Post Doc program at the Directorate of Graduate and Research Training for the financial support (Grant No. 75007369, Swedish Research Links, contract number 348-2011-7380).Peer reviewe

Analysis of B. taurus and B. indicus admixture in Uganda as revealed by the Illumina BovineSNP50 Genotyping BeadChip

The NextGen project investigates disease resistance in indigenous Ugandan cattle. Since population structure and stratification may produce biased results, We have investigated the genomic structure of sampled animals genotyped with the BovineSNP50 Genotyping Beadchip. A total of 788 animals from 9 populations belonging to Ankole (crossbred between B. indicus and B. taurus), Zebu and Ankole-Zebu crosses have been sampled in 52 grid cells throughout the country (Table 1). We merged this data whit other 400 Italian Holstein Cattle, genotyped in the framework of SELMOL project to seek for a likely introgression of European B. taurus. The data were filtered with the following exclusion criteria: MAF < 0.01, genotype call rate (SNPs) < 0.95, genotype call rate (Animals) < 0.95. The resulting working dataset were composed of 43494 SNPs and 1188 animals. Hidden genetic structures were investigated by a Bayesian clustering approach with the ADMIXTURE software (Novembre et al. 2010). The software Admixture identified four ancestral genomic components. Three of them likely correspond to European taurine, African indicine and African taurine components (Figure 2). The fourth has a still unidentified origin (Yellow, Figure 2d). Most Ugandan individuals investigated have a remarkable level of admixture. Overall, about 20% of the Zebu genome is of African taurine origin, confirming previous data on the foundation of African Zebu. The European taurine (Blue, Figure 2) is a minor component of African genomes, rare in Zebu and evenly distributed in Ankole, other taurine subgroups and Ankole- Zebu crosses. Indicine and taurine components show a clear geographical structure, the former being predominant in north-eastern Uganda, and the latter in the south-west. Holstein Fresian introgression is spread mostly in south-western Uganda, while the fourth component is located in restricted geographical area in the East (Figure 3). The Ugandan cattle population is a complex admixture of African taurine (green in Figure 2) and zebuine (red) genomes, with a minor component of European origin (blue) and a rare but relevant contribution (yellow) from a still unidentified source. This complexity is to be accounted for in the following GWAS and selection signatures analyses planned within the NextGen project

Genetic and antigenic variation of the bovine tick-borne pathogen Theileria parva in the Great Lakes region of Central Africa

BACKGROUND : Theileria parva causes East Coast fever (ECF), one of the most economically important tick-borne diseases of cattle in sub-Saharan Africa. A live immunisation approach using the infection and treatment method (ITM) provides a strong long-term strain-restricted immunity. However, it typically induces a tick-transmissible carrier state in cattle and may lead to spread of antigenically distinct parasites. Thus, understanding the genetic composition of T. parva is needed prior to the use of the ITM vaccine in new areas. This study examined the sequence diversity and the evolutionary and biogeographical dynamics of T. parva within the African Great Lakes region to better understand the epidemiology of ECF and to assure vaccine safety. Genetic analyses were performed using sequences of two antigencoding genes, Tp1 and Tp2, generated among 119 T. parva samples collected from cattle in four agro-ecological zones of DRC and Burundi. RESULTS : The results provided evidence of nucleotide and amino acid polymorphisms in both antigens, resulting in 11 and 10 distinct nucleotide alleles, that predicted 6 and 9 protein variants in Tp1 and Tp2, respectively. Theileria parva samples showed high variation within populations and a moderate biogeographical sub-structuring due to the widespread major genotypes. The diversity was greater in samples from lowlands and midlands areas compared to those from highlands and other African countries. The evolutionary dynamics modelling revealed a signal of selective evolution which was not preferentially detected within the epitope-coding regions, suggesting that the observed polymorphism could be more related to gene flow rather than recent host immune-based selection. Most alleles isolated in the Great Lakes region were closely related to the components of the trivalent Muguga vaccine. CONCLUSIONS : Our findings suggest that the extensive sequence diversity of T. parva and its biogeographical distribution mainly depend on host migration and agro-ecological conditions driving tick population dynamics. Such patterns are likely to contribute to the epidemic and unstable endemic situations of ECF in the region. However, the fact that ubiquitous alleles are genetically similar to the components of the Muguga vaccine together with the limited geographical clustering may justify testing the existing trivalent vaccine for cross-immunity in the region.Additional file 1: Table S1. Cattle blood sample distribution across agroecological zones.Additional file 2: Table S2. Nucleotide and amino acid sequences of Tp1 and Tp2 antigen epitopes from T. parva Muguga reference sequence.Additional file 3: Table S3. Characteristics of 119 T. parva samples obtained from cattle in different agro-ecological zones (AEZs) of The Democratic Republic of Congo and Burundi.Additional file 4: Figure S1. Multiple sequence alignment of the 11 Tp1 gene alleles obtained in this study.Additional file 5: Table S4. Estimates of evolutionary divergence between gene alleles for Tp1 and Tp2, using proportion nucleotide distance.Additional file 6: Table S5. Tp1 and Tp2 genes alleles with their corresponding antigen variants.Additional file 7: Table S6. Amino acid variants of Tp1 and Tp2 CD8+ T cell target epitopes of T. parva from DRC and Burundi.Additional file 8: Figure S2. Multiple sequence alignment of the 10 Tp2 gene alleles obtained in this study.Additional file 9: Table S7. Distribution of Tp1 gene alleles of T. parva from cattle and buffalo in the sub-Saharan region of Africa.Additional file 10: Table S8. Distribution of Tp2 gene alleles of T. parva from cattle and buffalo in the sub-Saharan region of Africa.Additional file 11: Figure S3. Neighbor-joining tree showing phylogenetic relationships among 48 Tp1 gene alleles described in Africa.Additional file 12: Figure S4. Phylogenetic tree showing the relationships among concatenated Tp1 and Tp2 nucleotide sequences of 93 T. parva samples from cattle in DRC and Burundi.This study is part of the PhD work supported by the University of Namur (UNamur, Belgium) through the UNamur-CERUNA institutional PhD grant awarded to GSA for bioinformatic analyses, interpretation of data and manuscript write up in Belgium. The laboratory aspects (molecular biology analysis) of the project were supported by the BecA-ILRI Hub through the Africa Biosciences Challenge Fund (ABCF) programme. The ABCF Programme is funded by the Australian Department for Foreign Affairs and Trade (DFAT) through the BecA-CSIRO partnership; the Syngenta Foundation for Sustainable Agriculture (SFSA); the Bill & Melinda Gates Foundation (BMGF); the UK Department for International Development (DFID); and the Swedish International Development Cooperation Agency (Sida). The ABCF Fellowship awarded to GAS was funded by BMGF grant (OPP1075938). Sample collection, field equipment and preliminary sample processing were supported through the “Theileria” project co-funded to the Université Evangélique en Afrique (UEA) by the Agence Universitaire de la Francophonie (AUF) and the Communauté Economique des Pays des Grands Lacs (CEPGL). The International Foundation for Science (IFS, Stockholm, Sweden) supported the individual scholarship awarded to GSA (grant no. IFS-92890CA3) for field work and part of field equipment to the “Theileria” project.http://www.parasitesandvectors.comam2020Veterinary Tropical Disease

Correlated Genetic and Ecological Diversification in a Widespread Southern African Horseshoe Bat

The analysis of molecular data within a historical biogeographical framework, coupled with ecological characteristics can provide insight into the processes driving diversification. Here we assess the genetic and ecological diversity within a widespread horseshoe bat Rhinolophus clivosus sensu lato with specific emphasis on the southern African representatives which, although not currently recognized, were previously described as a separate species R. geoffroyi comprising four subspecies. Sequence divergence estimates of the mtDNA control region show that the southern African representatives of R. clivosus s.l. are as distinct from samples further north in Africa than they are from R. ferrumequinum, the sister-species to R. clivosus. Within South Africa, five genetically supported geographic groups exist and these groups are corroborated by echolocation and wing morphology data. The groups loosely correspond to the distributions of the previously defined subspecies and Maxent modelling shows a strong correlation between the detected groups and ecoregions. Based on molecular clock calibrations, it is evident that climatic cycling and related vegetation changes during the Quaternary may have facilitated diversification both genetically and ecologically