Hidden Consequences of Living in a Wormy World: Nematode‐Induced Immune Suppression Facilitates Tuberculosis Invasion in African Buffalo

Most hosts are infected with multiple parasites, and responses of the immune system to co-occurring parasites may influence disease spread. Helminth infection can bias the host immune response toward a T-helper type 2 (Th2) over a type 1 (Th1) response, impairing the host’s ability to control concurrent intracellular microparasite infections and potentially modifying disease dynamics. In humans, immune-mediated interactions between helminths and microparasites can alter host susceptibility to diseases such as HIV, tuberculosis (TB), and malaria. However, the extent to which similar processes operate in natural animal populations and influence disease spread remains unknown.We used cross-sectional, experimental, and genetic studies to show that gastrointestinal nematode infection alters immunity to intracellular microparasites in free-ranging African buffalo (Syncerus caffer). Buffalo that were more resistant to nematode infection had weaker Th1 responses, there was significant genotypic variation in nematode resistance, and anthelminthic treatment enhanced Th1 immunity. Using a disease dynamic model parameterized with empirical data, we found that nematode-induced immune suppression can facilitate the invasion of bovine TB in buffalo. In the absence of nematodes, TB failed to invade the system, illustrating the critical role nematodes may play in disease establishment. Our results suggest that helminths, by influencing the likelihood of microparasite invasion, may influence patterns of disease emergence in the wild

The footprint of recent and strong demographic decline in the genomes of Mangalitza pigs

Altres ajuts: The authors also acknowledge the support of the Spanish Ministry of Economy and Competitivity for the Center of Excellence Severo Ochoa 2016-2019 (SEV-2015-0533) grant awarded to the Centre for Research in Agricultural Genomics (CRAG). Tainã Figueiredo Cardoso was funded with a fellowship from the CAPES Foundation-Coordination of Improvement of Higher Education, Ministry of Education of the Federal Government of Brazil. Thanks also to the CERCA Programme of the Generalitat de Catalunya.The Mangalitza pig breed has suffered strong population reductions due to competition with more productive cosmopolitan breeds. In the current work, we aimed to investigate the effects of this sustained demographic recession on the genomic diversity of Mangalitza pigs. By using the Porcine Single Nucleotid Polymorphism BeadChip, we have characterized the genome-wide diversity of 350 individuals including 45 Red Mangalitza (number of samples; n=20 from Hungary and n=25 from Romania), 37 Blond Mangalitza, 26 Swallow-belly Mangalitza, 48 Blond Mangalitza × Duroc crossbreds, 5 Bazna swine, 143 pigs from the Hampshire, Duroc, Landrace, Large White and Pietrain breeds and 46 wild boars from Romania (n=18) and Hungary (n=28). Performance of a multidimensional scaling plot showed that Landrace, Large White and Pietrain pigs clustered independently from Mangalitza pigs and Romanian and Hungarian wild boars. The number and total length of ROH (runs of homozygosity), as well as FROH coefficients (proportion of the autosomal genome covered ROH) did not show major differences between Mangalitza pigs and other wild and domestic pig populations. However, Romanian and Hungarian Red Mangalitza pigs displayed an increased frequency of very long ROH (>30 Mb) when compared with other porcine breeds. These results indicate that Red Mangalitza pigs underwent recent and strong inbreeding probably as a consequence of severe reductions in census size

Novel coding genetic variants of the GBP1 gene in wild and domestic pigs (Sus scrofa)

The interferon-induced guanylate-binding protein 1 gene (GBP1) plays an important role in host defense against viral, bacterial and protozoan infections. To explore novel genetic variants in this gene, we re-sequenced a 587-bp fragment spanning the exon 2 of the GBP1 gene in a sample panel consisting of 34 wild boars and 59 local domestic pigs from three geographic regions (China, Iberian Peninsula, and Central Europe) and 12 individuals of three commercial breeds (Pietrain, Landrace, and Large White). In a final 543-bp sequence fragment, there were 14 single nucleotide polymorphisms (SNPs), of which five were coding (three novel mutations). A total of 19 haplotypes were reconstructed and most haplotypes were shared by two or more sample groups. Those shared haplotypes revealed a clear signature of genetic introgression from Chinese domestic pigs into European domestic pigs. In addition, there were six haplotypes with frequencies below 1%, but none of them were present in the three commercial breeds (Pietrain, Landrace, and Large White). Although a limited number of individuals and breeds were analyzed, the absence of rare alleles (or haplotypes) in the commercial breeds is an indication that a significant proportion of genetic diversity in domestic species is not present in commercial breeds. This study demonstrated the potential to find sufficient genetic variation for population genetic analyses of demography versus selection, in functional candidate genes of domestic pigs and wild boars worldwide

Hidden Consequences of Living in a Wormy World:Nematode-Induced Immune Suppression Facilitates Tuberculosis Invasion in African Buffalo

Most hosts are infected with multiple parasites, and responses of the immune system to co-occurring parasites may influence disease spread. Helminth infection can bias the host immune response toward a T-helper type 2 (Th2) over a type 1 (Th1) response, impairing the host’s ability to control concurrent intracellular microparasite infections and potentially modifying disease dynamics. In humans, immune-mediated interactions between helminths and microparasites can alter host susceptibility to diseases such as HIV, tuberculosis (TB), and malaria. However, the extent to which similar processes operate in natural animal populations and influence disease spread remains unknown.We used cross-sectional, experimental, and genetic studies to show that gastrointestinal nematode infection alters immunity to intracellular microparasites in free-ranging African buffalo (Syncerus caffer). Buffalo that were more resistant to nematode infection had weaker Th1 responses, there was significant genotypic variation in nematode resistance, and anthelminthic treatment enhanced Th1 immunity. Using a disease dynamic model parameterized with empirical data, we found that nematode-induced immune suppression can facilitate the invasion of bovine TB in buffalo. In the absence of nematodes, TB failed to invade the system, illustrating the critical role nematodes may play in disease establishment. Our results suggest that helminths, by influencing the likelihood of microparasite invasion, may influence patterns of disease emergence in the wild

Genetic Variability and Relationship of Camel (Camelus dromedarius) Populations in Ethiopia as Evidenced by Microsatellites Analysis

AbstractThis study was carried out to assess the genetic diversities and population structure of six camel populations of Ethiopia. Blood samples were collected from 114 camels (17-24 per population) and genotyped using10 camel microsatellite marker loci. The result revealed high genetic diversities in Ethiopian camel populations with average observed and expected heterozygosity, total number of alleles (TNA), mean number of alleles (MNA) and effective number of alleles of 0.55, 0.73,153, 6.8 (0.36) and 4.47(0.23), respectively. Among the 52 private alleles in the six Ethiopian camel populations, 31 of them were occurring at a frequency of ≥5%. It was also found that most of the variations in Ethiopian camels were attributed to within population variation (92%) while 8% was explained by between populations variation. Even though there was high heterozygosity, high inbreeding coefficient was detected in Ethiopian camel populations. From the sex camel populations 34.1, 33.4 and 28.6% alleles of Gelleb, Amibara and Liben camel populations respectively affected by inbreeding. The between population differentiation was (FST=0.11(0.01) indicating moderate population differentiation. The neighbor-joining tree and structure analysis show that the Ethiopian camel populations were clustered into four subgroups. The Afar camels were grouped into two together with the Ethiopian Somali camels (Jigjiga with Mille and Gelleb with Amibara) and the two Ogaden camels (Liben and Hoor) are separated into two subgroups indicating that some of the Afar and the Somali camels were admixed. Therefore, even though high hetrozygosity within population and moderate genetic differentiation between populations were observed, the presence of high inbreeding coefficient may affect hetrozygosity in the overall populations

Sex-Biased Gene Flow Among Elk in the Greater Yellowstone Ecosystem

We quantified patterns of population genetic structure to help understand gene flow among elk populations across the Greater Yellowstone Ecosystem. We sequenced 596 base pairs of the mitochondrial control region of 380 elk from eight populations. Analysis revealed high mitochondrial DNA variation within populations, averaging 13.0 haplotypes with high mean gene diversity (0.85). The genetic differentiation among populations for mitochondrial DNA was relatively high (FST = 0.161; P = 0.001) compared to genetic differentiation for nuclear microsatellite data (FST = 0.002; P = 0.332), which suggested relatively low female gene flow among populations. The estimated ratio of male to female gene flow (mm/mf = 46) was among the highest we have seen reported for large mammals. Genetic distance (for mitochondrial DNA pairwise FST) was not significantly correlated with geographic (Euclidean) distance between populations (Mantel’s r = 0.274, P = 0.168). Large mitochondrial DNA genetic distances (e.g., FST . 0.2) between some of the geographically closest populations (,65 km) suggested behavioral factors and/or landscape features might shape female gene flow patterns. Given the strong sex-biased gene flow, future research and conservation efforts should consider the sexes separately when modeling corridors of gene flow or predicting spread of maternally transmitted diseases. The growing availability of genetic data to compare male vs. female gene flow provides many exciting opportunities to explore the magnitude, causes, and implications of sex-biased gene flow likely to occur in many species

Meta-Analysis of Mitochondrial DNA Reveals Several Population Bottlenecks during Worldwide Migrations of Cattle

Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle from the same location. These findings indicate strong maternal founder effects followed by limited maternal gene flow when new territories are colonized. However, effects of adaptation to new environments may also play a rol

Theileria lestoquardi displays reduced genetic diversity relative to sympatric Theileria annulata in Oman

The Apicomplexan parasites, Theileria lestoquardi and Theileria annulata, the causative agents of theileriosis in small and large ruminants, are widespread in Oman, in areas where cattle, sheep and goats co-graze. Genetic analysis can provide insight into the dynamics of the parasite and the evolutionary relationship between species. Here we identified ten genetic markers (micro- and mini-satellites) spread across the T. lestoquardi genome, and confirmed their species specificity. We then genotyped T. lestoquardi in different regions in Oman. The genetic structures of T. lestoquardi populations were then compared with previously published data, for comparable panels of markers, for sympatric T. annulata isolates. In addition, we examined two antigen genes in T. annulata (Tams1 and Ta9) and their orthologues in T. lestoquardi (Tlms1 and Tl9). The genetic diversity and multiplicity of infection (MOI) were lower in T. lestoquardi (He = 0.64–0.77) than T. annulata (He = 0.83–0.85) in all populations. Very limited genetic differentiation was found among T. lestoquardi and T. annulata populations. In contrast, limited but significant linkage disequilibrium was observed within regional populations of each species. We identified eight T. annulata isolates in small ruminants; the diversity and MOI were lower among ovine/caprine compared to bovine. Sequence diversity of the antigen genes, Tams1 and Ta9 in T. annulata (π = 0.0733 and π = 0.155 respectively), was 10-fold and 3-fold higher than the orthologous Tlms1 and Tl9 in T. lestoquardi (π = 0.006 and π = 0.055, respectively). Despite a comparably high prevalence, T. lestoquardi has lower genetic diversity compared to sympatric T. annulata populations. There was no evidence of differentiation among populations of either species. In comparison to T. lestoquardi, T. annulata has a larger effective population size. While genetic exchange and recombination occur in both parasite species, the extent of diversity, overall, is less for T. lestoquardi. It is, therefore, likely that T. lestoquardi evolved from an ancestor of present day T. annulata and that this occurred either once or on a limited number of occasions

Legacies of domestication, trade and herder mobility shape extant male zebu cattle diversity in South Asia and Africa

All tropically adapted humped cattle (Bos indicus or 'zebu'), descend from a domestication process that took place >8,000 years ago in South Asia. Here we present an intercontinental survey of Y-chromosome diversity and a comprehensive reconstruction of male-lineage zebu cattle history and diversity patterns. Phylogenetic analysis revealed that all the zebu Y-chromosome haplotypes in our dataset group within three different lineages: Y3A, the most predominant and cosmopolitan lineage; Y3B, only observed in West Africa; and Y3C, predominant in South and Northeast India. The divergence times estimated for these three Zebu-specific lineages predate domestication. Coalescent demographic models support either de novo domestication of genetically divergent paternal lineages or more complex process including gene flow between wild and domestic animals. Our data suggest export of varied zebu lineages from domestication centres through time. The almost exclusive presence of Y3A haplotypes in East Africa is consistent with recent cattle restocking in this area. The cryptic presence of Y3B haplotypes in West Africa, found nowhere else, suggests that these haplotypes might represent the oldest zebu lineage introduced to Africa ca. 3,000 B.P. and subsequently replaced in most of the world. The informative ability of Interspersed Multilocus Microsatellites and Y-specific microsatellites to identify genetic structuring in cattle populations is confirmed

LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method

<p>Abstract</p> <p>Background</p> <p>Testing for selection is becoming one of the most important steps in the analysis of multilocus population genetics data sets. Existing applications are difficult to use, leaving many non-trivial, error-prone tasks to the user.</p> <p>Results</p> <p>Here we present LOSITAN, a selection detection workbench based on a well evaluated <it>F</it>_<it>st</it>-outlier detection method. LOSITAN greatly facilitates correct approximation of model parameters (e.g., genome-wide average, neutral <it>F</it>_<it>st</it>), provides data import and export functions, iterative contour smoothing and generation of graphics in a easy to use graphical user interface. LOSITAN is able to use modern multi-core processor architectures by locally parallelizing fdist, reducing computation time by half in current dual core machines and with almost linear performance gains in machines with more cores.</p> <p>Conclusion</p> <p>LOSITAN makes selection detection feasible to a much wider range of users, even for large population genomic datasets, by both providing an easy to use interface and essential functionality to complete the whole selection detection process.</p