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Abstract Background While bats are tremendously important to global ecosystems, they have been and continue to be threatened by loss of habitat, food, or roosts, pollution, bat diseases, hunting and killing. Some bat species have also been implicated in the transmission of infectious disease agents to humans. While One Health efforts have been ramped up recently to educate and protect human and bat health, such initiatives have been limited by lack of adequate data on the pathways to ensure their support. For instance, data on the role of bats in supporting different components of human welfare assets would be utilized as a stepping stone to champion conservation campaigns. Unfortunately, these data are limited and efforts to synthesize existing literature have majorly focused on few components human welfare leaving other important aspects. Methods Here, we analyze benefits associated with bats in the context of welfare economics considering all the asset components. We surveyed scientific and gray literature platforms utilizing particular keywords. We then classified these values using integrated approaches to understand different values across human welfare assets of “health,” “material and immaterial assets,” “security or safety” and “social or cultural or spiritual relations”. Results We found 235 papers from different countries indicating that bats play fundamental roles in supporting human welfare. These benefits were more prevalent in Asia and Africa. In terms of the use of bats to support welfare assets, bats were majorly utilized to derive material and immaterial benefits (n = 115), e.g., food and income. This was followed by their use in addressing health challenges (n = 99), e.g., treatment of ailments. There was a similarity in the benefits across different regions and countries. Conclusion These results indicate potential opportunities for strengthening bat conservation programs. We recommend more primary studies to enhance understanding of these benefits as well as their effectiveness in deriving the perceived outcomes.

Abstract The blue wildebeest (Connochaetes taurinus) is a keystone species in savanna ecosystems from southern to eastern Africa, and is well known for its spectacular migrations and locally extreme abundance. In contrast, the black wildebeest (C. gnou) is endemic to southern Africa, barely escaped extinction in the 1900s and is feared to be in danger of genetic swamping from the blue wildebeest. Despite the ecological importance of the wildebeest, there is a lack of understanding of how its unique migratory ecology has affected its gene flow, genetic structure and phylogeography. Here, we analyze whole genomes from 121 blue and 22 black wildebeest across the genus’ range. We find discrete genetic structure consistent with the morphologically defined subspecies. Unexpectedly, our analyses reveal no signs of recent interspecific admixture, but rather a late Pleistocene introgression of black wildebeest into the southern blue wildebeest populations. Finally, we find that migratory blue wildebeest populations exhibit a combination of long-range panmixia, higher genetic diversity and lower inbreeding levels compared to neighboring populations whose migration has recently been disrupted. These findings provide crucial insights into the evolutionary history of the wildebeest, and tangible genetic evidence for the negative effects of anthropogenic activities on highly migratory ungulates.

Abstract Background Rhipicephalus (Boophilus) microplus (Canestrini, 1888), the Asian blue tick, is a highly invasive and adaptable ectoparasite. This tick species has successfully established itself in most regions of the world, with movement of cattle being a major driver for its spread. In the recent past, R. microplus ticks have been reported in three districts of Uganda. Information on its spread and distribution are vital in deepening our understanding of the ecological scenarios that lead to tick persistence and in the formulation of control strategies. This is especially important in the cattle-dense districts. Methods We randomly collected tick specimens from 1,461cattle spread across seven cattle dense districts located in the Central, Karamoja and West Nile regions of Uganda from January to September 2020. The ticks were identified using standard morpho-taxonomic keys and the R. microplus tick species identities were confirmed by sequencing of the ITS2 region, 12S rRNA and 16S rRNA genes and phylogenetic analyses. Results Adult ticks (n = 13,019) were collected from 1,461 cattle. Seventeen tick species were identified based on morpho-taxonomic keys and the majority (47.4%; n=6184) of these were R. appendiculatus. In total, 257 R. microplus ticks were found infesting cattle in 18 study sites in the districts of Amudat, Kaabong, Napak (Karamoja region) and Arua (West Nile region). The identity of R. microplus was confirmed using molecular technics. No R. microplus tick was recorded in the districts of Lyantonde and Nakaseke (Central region). Arua district accounted for 82.1% (n=211) of the R. microplus ticks recorded followed by Napak district at 16.3% (n=42), while Amudat and Kaabong districts accounted for 1.5% (n=4). Rhipicephalus microplus and R. decoloratus co-existed in 6 of the 13 study sites in Arua district, while in another 6 study sites, no R. decoloratus was recorded. In the Karamoja region districts R. decoloratus co-existed with R.microplus. Of the total 618 ticks belonging to four species of the subgenus Boophilus recorded in this study, R. decoloratus accounted for 50.04% (n=334), followed by R. microplus at 41.58% (n=257), R. geigyi at 2.75% (n=17) and R. annulatus at 1.61% (n=10). In the districts of Amudat, Kaabong and Napak, R. decoloratus was more dominant (76.1%; n=179) of the three Rhipicephalus (Boophilus) tick species recorded, followed by R. microplus (19.5%; n=46) and R. geigyi (4.2%; n=10). Contrariwise, R. microplus was more dominant (84%; n=211) in Arua district followed by R. decoloratus (10.7%; n=27), R. annulatus (3.9%; n=10) and R. geigyi (1.1%; n=3). Phylogenetic analyses of the ITS2 region, 12S rRNA and 16S rRNA genes revealed subgrouping of the obtained sequences with the previously published R. microplus sequences from other parts of the world. Conclusion Rhipicephalus microplus ticks were found infesting cattle in four districts of Uganda. The inability to find R. decoloratus, an indigenous tick, from six sites in the district of Arua is suggestive of its replacement by R. microplus. Rhipicephalus microplus negatively affects livestock production, and therefore, there is a need to determine its distribution and to deepen the understanding of the ecological factors that lead to its spread and persistence in an area.

Abstract Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable F ST values, and a recent divergence time (

Abstract Background The cattle industry contributes to Uganda's agricultural output. It faces challenges that include theft and parentage ascertainment. These challenges can benefit from recent molecular genomics and bioinformatics technologies. Objectives We employed genomic analyses to establish potential ownership of a group of nine cattle that were being claimed by two farmers in Uganda. We investigated the genetic relationship of Ugandan cattle with regional indigenous breeds as well as exotic breeds that are currently present in Uganda. In addition, we investigated regions that are likely to be under selection in the Ugandan cattle. Methods Hair samples were collected from seven and two animals from farmers A and B, respectively. They were genotyped for 53,218 Single Nucleotide Polymorphism markers. To establish genetic relationships between the sampled animals, we performed genomic analyses including, principal component analysis (PCA), hierarchical clustering analysis and identity by state/descent. We also performed admixture and runs of homozygosity analyses to assess the ancestry composition and identify regions potentially under selection in Ugandan cattle, respectively. Results The seven animals from Farmer A were genetically close to each other but showed minimal relationship with the disputed animals. The two animals from Farmer B were genetically distant from each other but showed greater similarity to four of the disputed animals. Four of the disputed animals showed great dissimilarity from the animals of both farmers. Comparison of these with the reference breeds revealed minimal European exotic genetic introgression into these animals, but rather high similarity to the Sheko. Results also revealed high homozygosity in the major histocompatibility complex regions. Conclusions Our results demonstrate the use of currently available genomic tools to empirically establish the ownership of cattle; these could be scaled up as a resourceful and viable tool that could be employed to support conflict resolution where reliable livestock identification is unavailable.

The genetic diversity of indigenous chickens, which comprise over 80% of the chicken resources in Uganda, is largely not well-characterized for their genetic contribution. This study assessed the genetic diversity and population structure of the indigenous chicken population in Uganda to serve as an essential component for improvement and conservation strategies. A set of 344 mitochondrial DNA (mtDNA) D-loop sequences among 12 Ugandan chicken populations was evaluated. Twenty-eight polymorphic sites, accounting for 4.26% of the total analyzed loci of 658 bp, defined 32 haplotypes. The haplotype diversity (Hd) was 0.437, with a nucleotide diversity (π) of 0.0169, while the average number of nucleotide differences (k) was 0.576, indicating a population that is moderately genetically diverse. Analysis of molecular variance found 98.39% (ρ < 0.01) of the total sequence variation among the chicken haplotypes within populations, 1.08% (ρ < 0.05) among populations, and 0.75% (ρ > 0.05) among populations within regions. This revealed subtle genetic differentiation among the populations, which appeared to be influenced by population fragmentation, probably due to neutral mutation, random genetic drift, and/or balancing selection. All the haplotypes showed affinity exclusively to the haplogroup-E mtDNA phylogeny, with haplotype UGA01 signaling an ancestral haplotype in Uganda. Neutrality tests Tajima’s D (−2.320) and Fu’s Fs (−51.369), augmented with mismatch distribution to measure signatures of recent historical demographic events, supported a population expansion across the chicken populations. The results show one matrilineal ancestry of Ugandan chickens from a lineage widespread throughout the world that began in the Indian subcontinent. The lack of phylogeographic signals is consistent with recent expansion events with extensive within-country genetic intermixing among haplotypes. Thus, the findings in this study hold the potential to guide conservation strategies and breeding programs in Uganda, given that higher genetic diversity comes from within the chicken population.

Abstract Background Crimean-Congo haemorrhagic fever (CCHF) is a tick-borne viral infection, characterized by haemorrhagic fever in humans and transient asymptomatic infection in animals. It is an emerging human health threat causing sporadic outbreaks in Uganda. We conducted a detailed outbreak investigation in the animal population following the death from CCHF of a 42-year-old male cattle trader in Lyantonde district, Uganda. This was to ascertain the extent of CCHF virus (CCHFV) circulation among cattle and goats and to identify affected farms and ongoing increased environmental risk for future human infections. Methods We collected blood and tick samples from 117 cattle and 93 goats, and tested these for anti-CCHFV antibodies and antigen using an enzyme-linked immunosorbent assay (ELISA), quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and target enrichment next generation sequencing. Results CCHFV-specific IgG antibodies were detected in 110/117 (94.0%) cattle and 83/93 (89.3%) goats. Animal seropositivity was independently associated with female animals (AOR = 9.42, P = 0.002), and animals reared under a pastoral animal production system (AOR = 6.02, P = 0.019] were more likely to be seropositive than tethered or communally grazed animals. CCHFV was detected by sequencing in Rhipicephalus appendiculatus ticks but not in domestic animals. Conclusion This investigation demonstrated very high seroprevalence of CCHFV antibodies in both cattle and goats in farms associated with a human case of CCHF in Lyantonde. Therefore, building surveillance programs for CCHF around farms in this area and the Ugandan cattle corridor is indicated, in order to identify opportunities for case prevention and control. Graphical Abstract

In 2007, an outbreak of African swine fever (ASF), a deadly disease of domestic swine and wild boar caused by the African swine fever virus (ASFV), occurred in Georgia and has since spread globally. Historically, ASFV was classified into 25 different genotypes. However, a newly proposed system recategorized all ASFV isolates into 6 genotypes exclusively using the predicted protein sequences of p72. However, ASFV has a large genome that encodes between 150–200 genes, and classifications using a single gene are insufficient and misleading, as strains encoding an identical p72 often have significant mutations in other areas of the genome. We present here a new classification of ASFV based on comparisons performed considering the entire encoded proteome. A curated database consisting of the protein sequences predicted to be encoded by 220 reannotated ASFV genomes was analyzed for similarity between homologous protein sequences. Weights were applied to the protein identity matrices and averaged to generate a genome-genome identity matrix that was then analyzed by an unsupervised machine learning algorithm, DBSCAN, to separate the genomes into distinct clusters. We conclude that all available ASFV genomes can be classified into 7 distinct biotypes.

The African swine fever virus (ASFV) is currently causing a world-wide pandemic of a highly lethal disease in domestic swine and wild boar. Currently, recombinant ASF live-attenuated vaccines based on a genotype II virus strain are commercially available in Vietnam. With 25 reported ASFV genotypes in the literature, it is important to understand the molecular basis and usefulness of ASFV genotyping, as well as the true significance of genotypes in the epidemiology, transmission, evolution, control, and prevention of ASFV. Historically, genotyping of ASFV was used for the epidemiological tracking of the disease and was based on the analysis of small fragments that represent less than 1% of the viral genome. The predominant method for genotyping ASFV relies on the sequencing of a fragment within the gene encoding the structural p72 protein. Genotype assignment has been accomplished through automated phylogenetic trees or by comparing the target sequence to the most closely related genotyped p72 gene. To evaluate its appropriateness for the classification of genotypes by p72, we reanalyzed all available genomic data for ASFV. We conclude that the majority of p72-based genotypes, when initially created, were neither identified under any specific methodological criteria nor correctly compared with the already existing ASFV genotypes. Based on our analysis of the p72 protein sequences, we propose that the current twenty-five genotypes, created exclusively based on the p72 sequence, should be reduced to only six genotypes. To help differentiate between the new and old genotype classification systems, we propose that Arabic numerals (1, 2, 8, 9, 15, and 23) be used instead of the previously used Roman numerals. Furthermore, we discuss the usefulness of genotyping ASFV isolates based only on the p72 gene sequence.

The potential of pine pollen (PP) to masculinize sexually undifferentiated Nile tilapia was evaluated by feeding graded levels of PP (0.08–3.20 g kg-1 basal diet) to triplicate groups of three-day-old Nile tilapia for 28 days. Masculinization and associated differences in growth were compared to fish individuals fed the same basal diet with no PP (CT; negative control) and with 0.06 g 17α-methyltestosterone (MT) kg-1 basal diet (positive control). Both PP and MT treatments significantly skewed the expected 50:50 (male: female) ratio towards more male individuals. Notably, MT and 1.28 g PP kg-1 of diet produced a significantly high proportion of males (89.2 ± 2.2% and 80.0 ± 2.9% respectively), compared to 50.8 ± 2.2% in the CT treatment (P

African swine fever (ASF) is a high-consequence transboundary hemorrhagic fever of swine. It continues to spread across the globe causing socio-economic issues and threatening food security and biodiversity. In 2020, Nigeria reported a major ASF outbreak, killing close to half a million pigs. Based on the partial sequences of the genes B646L (p72) and E183L (p54), the virus responsible for the outbreak was identified as an African swine fever virus (ASFV) p72 genotype II. Here, we report further characterization of ASFV RV502, one of the isolates obtained during the outbreak. The whole genome sequence of this virus revealed a deletion of 6535 bp between the nucleotide positions 11,760–18,295 of the genome, and an apparent reverse complement duplication of the 5′ end of the genome at the 3′ end. Phylogenetically, ASFV RV502 clustered together with ASFV MAL/19/Karonga and ASFV Tanzania/Rukwa/2017/1 suggesting that the virus responsible for the 2020 outbreak in Nigeria has a South-eastern African origin.

Abstract Background The need for enhancing the productivity of fisheries in Africa triggered the introduction of non-native fish, causing dramatic changes to local species. In East Africa, the extensive translocation of Nile tilapia (Oreochromis niloticus) is one of the major factors in this respect. Using 40 microsatellite loci with SSR-GBS techniques, we amplified a total of 664 individuals to investigate the genetic structure of O. niloticus from East Africa in comparison to Ethiopian and Burkina Faso populations. Results All three African regions were characterized by independent gene-pools, however, the Ethiopian population from Lake Tana was genetically more divergent (Fst = 2.1) than expected suggesting that it might be a different sub-species. In East Africa, the genetic structure was congruent with both geographical location and anthropogenic activities (Isolation By Distance for East Africa, R2 = 0.67 and Uganda, R2 = 0.24). O. niloticus from Lake Turkana (Kenya) was isolated, while in Uganda, despite populations being rather similar to each other, two main natural catchments were able to be defined. We show that these two groups contributed to the gene-pool of different non-native populations. Moreover, admixture and possible hybridization with other tilapiine species may have contributed to the genetic divergence found in some populations such as Lake Victoria. We detected other factors that might be affecting Nile tilapia genetic variation. For example, most of the populations have gone through a reduction in genetic diversity, which can be a consequence of bottleneck (G-W,

Bushmeat hunting and consumption, although widely utilized as necessary supplement to household income and nutrition in many regions, presents threats to public health and wildlife conservation efforts. In northern Uganda, consumption of bats and primates, two wildlife groups often implicated in zoonotic disease emergence, is not widely culturally accepted; however, these species are reported by hunters to often be hunted and sold as culturally desirable species, like antelope and warthog. To investigate the prevalence of market bushmeat misidentifiction, we collected 229 bushmeat samples from 23 communities adjacent to Murchison Falls National Park. Reported species was recorded on acquisition for each sample. PCR targeting mammalian cyt b and 12 s rRNA genes and sequencing were performed to identify samples to the lowest taxonomic unit using NCBI BLAST. Overall, 27.9% (61/219) of samples had disparate results between species reported and BLAST analysis. Thirty-four species were identified, with the most frequent wildlife being waterbuck (31.5%), warthog (13.7%), and black rat (5.9%). These data reveal a public health risk for bushmeat consumers in northern Uganda as they cannot assess species-related risk when purchasing bushmeat and take appropriate precautions against zoonotic pathogen exposure. These data also provide insight into regional hunter prey preference and market preference of local community members which may inform conservation strategy in the region.

In many Ugandan rural communities, pigs are generally kept under traditional smallholder systems without basic biosecurity measures in place. In some instances, these systems are at the livestock-wildlife interface, as it is the case in Nwoya district, which is bordered by Murchison Falls National Park (MFNP). This pig system has potential for the maintenance and transmission of pathogens like African swine fever (ASF) between different herds, and also with wild pigs (warthogs and bushpigs). In this paper, we describe the spatial and temporal pattern of the movements of free ranging domestic pigs in a rural setting in Northern Uganda where ASF is endemic. We also determine their use of habitat to highlight the potential interaction hotspots between domestic pigs and between domestic and wild pig populations. We fitted 10 free-ranging domestic pigs owned by different homesteads with GPS harnesses during rainy and dry seasons. The pig home range, daily distance, activity pattern and habitat use were calculated. Our results show that the maximum area covered (MCP 100%) by the pigs varied between 35,965 and 475,077 m2. The core area varied from 1,317 to 50,769 m2. The pigs' home ranges were significantly bigger during the dry season than during the rainy season (Wilcoxon test, W = 22, p = 0.04). The mean full day (24 h) distance was longer in the dry season than in the rainy season (Student test, t = 2.7, p = 0.03). The pigs were mostly located within their own homestead, but they also used other homesteads, grass and crop fields. This study highlights that free-ranging domestic pigs may cover a wide area, especially during the dry season. Interestingly, the home range of pigs from different herds may overlap with areas used by wild pigs which share crops and other resources in this area. This study provides insights into a better understanding of the potential for spread of diseases such as ASF at small-scale and can be used to raise awareness of such risks and to better target implementation of preventive measures.

Rudimentary non-market-oriented pig rearing systems have been implicated in the persistence of Taenia solium cysticercosis, an endemic disease of high public health concern in Uganda. We investigated the seroprevalence and key predisposing factors of the disease in Moyo and Lira, two pig-producing districts in Northern Uganda. Cross-sectional serosurveys were conducted in 428 pig farms (Moyo, 262; Lira, 166). Farmers kept on average two adult pigs per herd. Tethering was a common practice in rural areas; free-ranging less so. Confinement of pigs in pens was characteristic of periurban farming systems. Pigs were mainly fed crop residues and forages in the rainy season, and swill and crop residues in the dry season. The majority of farmers of the survey were women (55%) above 45 years old, and 51% of farmers had attained primary school education. A total of 723 pig serum samples were collected, 403 in Moyo, and 320 in Lira. They were analyzed for Taenia spp. antigens using B158C11A10/B60H8A4 Antigen-ELISA. The overall animal seroprevalence of Taenia spp. serum antigen was 10.4% (95% confidence interval [CI]: 4.9–17.6), with 13.2% (95% CI: 7.1– 21.2) the highest in Moyo vs 6.9% (95% CI: 2.9–13.9) in Lira. The herd-level seroprevalence was estimated at 13.7% (95% CI: 9.8–18.5) in Moyo and 11.4% (95% CI: 7.0–17.2) in Lira. Out of 12 explanatory variables assessed for association with the observed seroprevalence, only the district of origin was significant (p = 0.01). Pigs originating from Lira were a protective factor against Taenia spp. cysticercosis (odds ratio: 0.54). These findings highlight the urgent need for an awareness campaign with prevention and control measures to minimize the risk of transmission to pork consumers in these districts.

Bushpigs (Potamochoerus larvatus) are considered a nuisance to farmers because of their crop raiding habits. Through their incursions into farmlands, they may interact with free-ranging domestic pigs and potentially cause transmission of infectious diseases such as African Swine Fever (ASF). The role of the bushpig in the epidemiology of ASF is poorly known and one of the gaps of knowledge is precisely the nature of interaction between bushpigs and domestic pigs. Thus, in this study, we investigated the frequency of bushpig visits to crop fields in rural communities where ASF is endemic, at the edge of a wildlife protected area in northwestern Uganda, to better understand the potential for interaction and disease transmission. We used three methods (questionnaires, camera traps, and observations for tracks) to assess bushpig visits to farmland. These methods were implemented concurrently in 28 farms during rainy and dry seasons. The results obtained by each of the three methods were analyzed by generalized linear mixed models. Potential risk factors including crop type, season, and landscape characteristics related to bushpig ecology were tested as explanatory variables. A generalized linear model and the Kendall test were used to compare the results and consistency of the frequency values obtained by the three methods. A high percentage (75%) of interviewed farmers reported visits from bushpigs in 29.6% of assessed crops (n = 145), and a frequency of 0.014 +/−0.05 visits per night was obtained through camera-trapping. Bushpig tracks were detected in 36% of sessions of observation. Cassava (Manihot esculenta) and groundnut (Arachis hypogaea L.) crop fields were the most visited, and these visits were more common during the rainy than the dry season. Distances from crop sites to the boundary of the protected area and to the river also influenced visit frequency. Camera-trapping was the least sensitive method while questionnaires and track observations presented consistent and complementary results to characterize spatial and temporal visits of bushpig into the crop fields. Evidence from our study shows that when used in combination, these methods can provide useful data to improve our understanding of the interactions between bushpigs and domestic pigs at the wildlife-domestic interface.

The potential impact of future climate change on fruit fly species distribution was assessed in Uganda using two general circulation models (HADCM and CCCMA) and two future predicted CO2 emission scenarios (A2 and B2), under both full and no species dispersal modes. Future ranges were overall projected to decline by 25.4% by year 2050. Under full-dispersal, D. ciliatus > C. cosyra > B. invadens ranges were predicted to increase, while the rest are likely to decrease. In the no-dispersal scenario, a significant average decrease in size of niches is predicted. Range losses are predicted higher under B2 than A2. Future niches will likely shift to northern Uganda. The results should assist in the development of climate change adaptive pest management strategies.

East Coast fever (ECF) is a fatal sickness affecting cattle populations of eastern, central, and southern Africa. The disease is transmitted by the tick Rhipicephalus appendiculatus, and caused by the protozoan Theileria parva parva, which invades host lymphocytes and promotes their clonal expansion. Importantly, indigenous cattle show tolerance to infection in ECF-endemically stable areas. Here, the putative genetic bases underlying ECF-tolerance were investigated using molecular data and epidemiological information from 823 indigenous cattle from Uganda. Vector distribution and host infection risk were estimated over the study area and subsequently tested as triggers of local adaptation by means of landscape genomics analysis. We identified 41 and seven candidate adaptive loci for tick resistance and infection tolerance, respectively. Among the genes associated with the candidate adaptive loci are PRKG1 and SLA2. PRKG1 was already described as associated with tick resistance in indigenous South African cattle, due to its role into inflammatory response. SLA2 is part of the regulatory pathways involved into lymphocytes' proliferation. Additionally, local ancestry analysis suggested the zebuine origin of the genomic region candidate for tick resistance.

The genetic diversity of African pigs, whether domestic or wild has not been widely studied and there is very limited published information available. Available data suggests that African domestic pigs originate from different domestication centers as opposed to international commercial breeds. We evaluated two domestic pig populations in Western Kenya, in order to characterize the genetic diversity, breed composition and admixture of the pigs in an area known to be endemic for African swine fever (ASF). One of the reasons for characterizing these specific populations is the fact that a proportion of indigenous pigs have tested ASF virus (ASFv) positive but do not present with clinical symptoms of disease indicating some form of tolerance to infection. Pigs were genotyped using either the porcine SNP60 or SNP80 chip. Village pigs were sourced from Busia and Homabay counties in Kenya. Because bush pigs (Potamochoerus larvatus) and warthogs (Phacochoerus spp.) are known to be tolerant to ASFv infection (exhibiting no clinical symptoms despite infection), they were included in the study to assess whether domestic pigs have similar genomic signatures. Additionally, samples representing European wild boar and international commercial breeds were included as references, given their potential contribution to the genetic make-up of the target domestic populations. The data indicate that village pigs in Busia are a non-homogenous admixed population with significant introgression of genes from international commercial breeds. Pigs from Homabay by contrast, represent a homogenous population with a "local indigenous' composition that is distinct from the international breeds, and clusters more closely with the European wild boar than African wild pigs. Interestingly, village pigs from Busia that tested negative by PCR for ASFv genotype IX, had significantly higher local ancestry (>54%) compared to those testing positive, which contained more commercial breed gene introgression. This may have implication for breed selection and utilization in ASF endemic areas. A genome wide scan detected several regions under preferential selection with signatures for pigs from Busia and Homabay being very distinct. Additionally, there was no similarity in specific genes under selection between the wild pigs and domestic pigs despite having some broad areas under similar selection signatures. These results provide a basis to explore possible genetic determinants underlying tolerance to infection by ASFv genotypes and suggests multiple pathways for genetically mediated ASFv tolerance given the diversity of selection signatures observed among the populations studied.

Abstract Background Glossina fuscipes fuscipes is the main vector of African Trypanosomiasis affecting both humans and livestock in Uganda. The human disease (sleeping sickness) manifests itself in two forms: acute and chronic. The Lake Victoria basin in Uganda has the acute form and a history of tsetse re-emergence despite concerted efforts to control tsetse. The government of Uganda has targeted the basin for tsetse eradication. To provide empirical data for this initiative, we screened tsetse flies from the basin for genetic variation at the mitochondrial DNA cytochrome oxidase II (mtDNA COII) gene with the goal of investigating genetic diversity and gene flow among tsetse, tsetse demographic history; and compare these results with results from a previous study based on microsatellite loci data in the same area. Methods We collected 429 Gff tsetse fly samples from 14 localities in the entire Ugandan portion of the Lake Victoria coast, covering 40,000 km2. We performed genetic analyses on them and added data collected for 56 Gff individuals from 4 additional sampling sites in the basin. The 529pb partial mitochondrial DNA cytochrome oxidase II (mtDNA COII) sequences totaling 485 were analysed for genetic differentiation, structuring and demographic history. The results were compared with findings from a previous study based on microsatellite loci data from the basin. Results The differences within sampling sites explained a significant proportion of the genetic variation. We found three very closely related mtDNA population clusters, which co-occurred in multiple sites. Although Φ ST (0 – 0.592; P

Abstract Background Non-clinical Theileria parva infection among indigenous cattle occurs upon recovery from primary disease during the first year of life. Continuous exposure to infection through contaminated tick infestations with absence of clinical disease gives rise to endemic stability. Endemic stable populations may become sources of infection if contaminated tick vectors are shared with susceptible exotic cattle. This study aimed at establishing a nationwide distribution of non-clinical T. parva infection among indigenous cattle populations to inform novel control strategies. Methods The occurrence of non-clinical T. parva infection among apparently healthy 925 indigenous cattle from 209 herds spread out in 10 agro-ecological zones (AEZs) was determined using a nested PCR assay. The influence of AEZ, breed, sex, age and farmers’ ranking of ECF importance were interrogated for influence of non-clinical parasite occurrence. Results The overall prevalence of non-clinical T. parva infection was 30% (278/925). A gradual increase of non-clinical T. parva infection was observed ranging from 17% (95% CI: 0.03 – 0.23) to 43% (95% CI: 0.3 – 0.55) in the North Eastern Savannah Grasslands (NESG) to the Western Highland Ranges (WHR) respectively. A similarly associated 18% (95% CI: 0.07 – 0.28) and 35% (95% CI: 0.3 – 0.39) non-clinical parasite prevalence was observed among the East African shorthorn Zebu (EASZ) and Ankole cattle respectively. Average herd level non-clinical T. parva prevalence was 28%, ranging from zero to 100%. The likelihood of non-clinical T. parva infection was 35.5% greater in the western highlands compared to the northeastern semi-arid AEZs. Conclusions Non-clinical T. parva occurs countrywide, structured along patterns of AEZ and breed gradients. These findings may guide policy formulation, deployment of integrated control strategies and local cattle improvement programs.

Nile perch establishment in novel ranges in East Africa is one of the most successful freshwater invasion stories in the recent history. Itbecame ecologically dominant and well established in several lakes in the Lake Victoria Region in a period of less than 5 decades. Geneticdiversity of both introduced and native populations were assessed and patterns compared in order to establish the genetic consequences oftheir introductions. Genetic variation was surveyed at both the mitochondrial control region (CR) and at nine microsatellite loci. A total of 527 Nile perch fish were sampled from 5 East African lakes: native source populations were examined from lakes Albert and Turkana while introduced populations were sampled from lakes Kyoga, Nabugabo and Victoria. Both types of markers revealed higher average geneticdiversity for invasive species (HE = 0.70, h = 0.81) than for native source populations (HE = 0.66, h = 0.69). Both populations scoredrelatively higher than the average for freshwater fishes (HE = 0.62). Both native and introduced populations had 2 underlying geneticgroupings in similar proportions as revealed by the STRUCTURE program. The high genetic diversity was most probably a consequence ofhigher numbers of propagules than outlined by official records of introductions. Use of high number of individuals at stocking is probably the reason for apparently minimized ‘founder effects’ of Nile perch in the introduced ranges. The two underling populations revealed through genetic analysis may be representatives of the two subspecies of Nile perch previously reported in other studies. Implications to the management of this fishery in the East African region is that with the relatively high genetic diversity, the species could be sustainably exploited if it were effectively managed. In addition, further studies of the life histories and other attributes of the two genetic groupings of Nile perch in the region are recommended, as they may require different management plans.

African swine fever (ASF) is a highly contagious, lethal and economically devastating haemorrhagic disease of domestic pigs. Insights into the dynamics and scale of virus transmission can be obtained from estimates of the basic reproduction number (R0). We estimate R0 for ASF virus in small holder, free-range pig production system in Gulu, Uganda. The estimation was based on data collected from outbreaks that affected 43 villages (out of the 289 villages with an overall pig population of 26,570) between April 2010 and November 2011. A total of 211 outbreaks met the criteria for inclusion in the study. Three methods were used, specifically; (i) GIS- based identification of the nearest infectious neighbour based on the Euclidean distance between outbreaks, (ii) epidemic doubling time, and (iii) a compartmental susceptible-infectious (SI) model. For implementation of the SI model, three approaches were used namely; curve fitting (CF), a linear regression model (LRM) and the SI/N proportion. The R0 estimates from the nearest infectious neighbour and epidemic doubling time methods were 3.24 and 1.63 respectively. Estimates from the SI-based method were 1.58 for the CF approach, 1.90 for the LRM, and 1.77 for the SI/N proportion. Since all these values were above one, they predict the observed persistence of the virus in the population. We hypothesize that the observed variation in the estimates is a consequence of the data used. Higher resolution and temporally better defined data would likely reduce this variation. This is the first estimate of R0 for ASFV in a free range smallholder pig keeping system in sub-Saharan Africa and highlights the requirement for more efficient application of available disease control measures.