Phylogenetic analysis of canine distemper virus in South African wildlife

<div><p>Canine distemper virus (CDV) causes a severe contagious disease in a broad range of hosts. This is the first study to genetically characterise CDV strains from four different wildlife species in South Africa. The phylogenetic diversity of CDV is examined, using the haemagglutinin gene. The South African wildlife CDV isolates showed a high degree of similarity to CDV in South African domestic dogs. Phylogenetic analyses confirmed the presence of 12 geographical lineages with CDV strains from South African wildlife falling within the Southern African lineage. The study reveals two possible co-circulating sub-genotypes corresponding to the northern and southern regions of South Africa respectively. CDV strains from the non-canid species were distinct, but similar to CDV isolates from domestic dog and wild canids. Residues at amino acid sites of the SLAM binding region support the notion that CDV strains encoding 519I / 549H are better adapted to non-canid species than canid species. The amino acids present at site 530 are conserved regardless of host species. Strains from South African wild carnivores showed no difference between host species with all strains presenting 530N. All non-canid strains in this study presented the combination 519I/549H. No evidence of host adaptation or lineage grouping was observed for the Nectin-4 binding region. Further studies should include CDV strains isolated from various hosts from a wider geographical range in South Africa.</p></div

Assessing introgressive hybridization in roan antelope (Hippotragus equinus):Lessons from South Africa

Biological diversity is being lost at unprecedented rates, with genetic admixture and introgression presenting major threats to biodiversity. Our ability to accurately identify introgression is critical to manage species, obtain insights into evolutionary processes, and ultimately contribute to the Aichi Targets developed under the Convention on Biological Diversity. The current study concerns roan antelope, the second largest antelope in Africa. Despite their large size, these antelope are sensitive to habitat disturbance and interspecific competition, leading to the species being listed as Least Concern but with decreasing population trends, and as extinct over parts of its range. Molecular research identified the presence of two evolutionary significant units across their sub-Saharan range, corresponding to a West African lineage and a second larger group which includes animals from East, Central and Southern Africa. Within South Africa, one of the remaining bastions with increasing population sizes, there are a number of West African roan antelope populations on private farms, and concerns are that these animals hybridize with roan that naturally occur in the southern African region. We used a suite of 27 microsatellite markers to conduct admixture analysis. Our results indicate evidence of hybridization, with our developed tests using a simulated dataset being able to accurately identify F1, F2 and non-admixed individuals at threshold values of qi > 0.80 and qi > 0.85. However, further backcrosses were not always detectable with backcrossed-Western roan individuals (46.7-60%), backcrossed-East, Central and Southern African roan individuals (28.3-45%) and double backcrossed (83.3-98.3%) being incorrectly classified as non-admixed. Our study is the first to confirm ongoing hybridization in this within this iconic African antelope, and we provide recommendations for the future conservation and management of this species

Broad-scale genetic assessment of Southern Ground-Hornbills (Bucorvus leadbeateri) to inform population management.

The Southern Ground-hornbill (SGH) (Bucorvus leadbeateri) is considered an umbrella species for biodiversity conservation in savannah biomes since they require large territories and significant protection measures that help to conserve a wide range of biodiversity with similar savanna and grassland requirements. Declines of the species are attributed to low reproductive rates coupled with multiple anthropogenic threats, including secondary poisoning, and persecution. Little is known about connectivity and population structure of SGH populations in Africa, south of the equator. Knowledge of population differentiation is needed to ensure that targeted conservation management plans can be implemented to slow population declines and ensure survival of the species. To inform a long-term conservation strategy, we investigated the broad-scale population structure of Southern Ground-hornbill across their sub-equatorial range. Our study based on 16 microsatellite loci identified moderate variation (average of 5.889 alleles per locus and a mean observed heterozygosity of 0.546) similar to other long-lived avian species. In contrast, mitochondrial DNA sequences analysis identified low diversity (Hd = 0.3313, π = 0.0015). A Bayesian assignment approach, principal component analysis, analysis of molecular variance and phylogenetic analysis identified weak to moderate population structuring across long distances and mitochondrial data showed a shallow phylogeny. Restriction to long-distance dispersal was detected that could not be attributed to isolation by distance, suggesting that other factors, such as their dispersal biology, are shaping the observed genetic differentiation. Although our study does not support the designation of populations as independent conservation units, we advocate that population management should continue to follow the Precautionary Principle (mixing founders from the same range state, rather than allowing mixing of founders from the extremes of the range) until there is scientific certainty. Following further research, if no independent conservation units are detected, then the global captive population can contribute to reintroductions across the range. In the wild, populations at the edge of the species range may need additional management strategies and gene flow should be promoted between neighbouring populations

Diversity of selected toll-like receptor genes in cheetahs (Acinonyx jubatus) and African leopards (Panthera pardus pardus).

BackgroundThe growing world population amplifies the anthropogenic impact on wildlife globally. With shrinking habitats, wild populations are being pushed to co-exist in close proximity to humans, leading to an increased threat of infectious disease. Therefore, understanding the immune system of a species is key to assess its resilience in a changing environment. The innate immunity system (IIS) is the body’s first line of defense against pathogens. High variability in IIS-genes, such as the toll-like receptor (TLR) genes, appears to be associated with resistance to infectious diseases. However, few studies have investigated diversity in TLR genes in non-model organisms and drawn conclusions for the conservation of vulnerable species. Large predators are threatened globally, and their populations increasingly have been declining over the last decades. Big cats, such as leopards (Panthera pardus) and cheetahs (Acinonyx jubatus) are no exception to this trend and are listed as ‘vulnerable’ by the International Union for Conservation of Nature (IUCN) including several subspecies, e.g., A. j. venaticus and P. p. melas, that already face extinction. To better understand vulnerability in terms of immune genetic diversity in the two sympatric occurring species, we compared selected TLR genes (TLR2, TLR4, TLR6 and TLR8) between modern African leopards (P. p. pardus) and Southern African cheetahs (A. j. jubatus). ResultsOur study supports the previously detected high genetic diversity in African leopards and confirms genetic impoverishment in Southern African cheetahs. Despite notable differences, both species share some haplotypic similarities in the investigated TLRs. Moreover, our historic cheetah samples from all five subspecies showed levels of genetic diversity comparable to modern African leopards. By including historic cheetahs and samples from all known subspecies, we put the observed IIS diversity into an evolutionary context.ConclusionThe genetic diversity in the investigated TLR genes in modern Southern African cheetahs and in historic cheetahs is low compared to African leopards. However, according to previous studies, the low immune genetic diversity might not yet affect the health of this cheetah subspecies. Compared to historic cheetah data and other subspecies, a more recent population decline might explain the observed genetic impoverishment of TLR genes in modern Southern African cheetahs.<br/

Phylogenetic analysis of canine distemper virus in South African wildlife

Canine distemper virus (CDV) causes a severe contagious disease in a broad range of hosts. This is the first study to genetically characterise CDV strains from four different wildlife species in South Africa. The phylogenetic diversity of CDV is examined, using the haemagglutinin gene. The South African wildlife CDV isolates showed a high degree of similarity to CDV in South African domestic dogs. Phylogenetic analyses confirmed the presence of 12 geographical lineages with CDV strains from South African wildlife falling within the Southern African lineage. The study reveals two possible co-circulating sub-genotypes corresponding to the northern and southern regions of South Africa respectively. CDV strains from the non-canid species were distinct, but similar to CDV isolates from domestic dog and wild canids. Residues at amino acid sites of the SLAM binding region support the notion that CDV strains encoding 519I / 549H are better adapted to non-canid species than canid species. The amino acids present at site 530 are conserved regardless of host species. Strains from South African wild carnivores showed no difference between host species with all strains presenting 530N. All non-canid strains in this study presented the combination 519I/549H. No evidence of host adaptation or lineage grouping was observed for the Nectin-4 binding region. Further studies should include CDV strains isolated from various hosts from a wider geographical range in South Africa.S1 Table. H gene sequence isolates used in determining the phylogenetic relationship of canine distemper virus. The accession number, host species, year and country of origin (when available) are indicated for each strain. South African strains isolated for this study indicated with asterisk ( ).S2 Table. Residues at amino acid sites of the SLAM and nectin-4 cell binding regions on the canine distemper virus H-protein, arranged in geographical lineages and host species (domestic dog, wild canid and non-canid). The accession number, host species, year and country of origin are indicated for each strain. South African strains isolated for this study indicated with asterisk ( ). Identical amino acids are indicated with a dash (-), varying amino acids are indicated by single letter amino acid codes.http://www.plosone.orgam2019Veterinary Tropical Disease