Host genetics and haemoparasite diversity in the common warthog (Phacochoerus africanus) from South Africa

Abstract

The common warthog (Phacochoerus africanus) was initially confined to the northern provinces of South Africa; however, in recent decades, they have expanded southwards, with an extralimital range now encompassing most of the country. These expansions are primarily through their natural dispersal ability and translocations into southern conservation areas. However, the degree to which these populations are connected and South African warthogs' genetic structure and diversity is not yet known. Previous studies on warthog genetics have been continent-wide; however, they have not included warthogs from South Africa. We aimed to address this gap by sequencing 92 mitochondrial DNA (mtDNA) and 23 Sex-determining region Y (SRY) gene sequences from significant populations across the warthog’s traditional and extra-limital range. The mtDNA sequences defined 17 haplotypes, whereas the SRY gene defined only one haplotype. Haplotype network analysis revealed a structure reflecting the southward expansion through natural dispersal and recorded translocations. Overall haplotype diversity (Hd) ranged from 0.38 to 0.83, with southern population centres (Addo Elephant National Park Hd=0.38, and Mokala National Park Hd= 0.41) representing the lower end of the range, likely reflecting a founder effect from the initial translocated groups. When combined with continent-wide data, the South African population was confirmed to be an extension of the previously defined southern clade, reflecting the southward expansion of the species from East Africa. The secondary aim of this study was to evaluate the prevalence and diversity of three haemoparastic bacterial genera, namely Anaplasma, Bartonella and Mycoplasma, in warthogs (Phacochoerus africanus) in the Kruger National Park (KNP). Molecular estimates of infection rates for these three genera were determined from DNA extracts from 100 EDTA blood samples using a variety of PCR assays. For Anaplasma, assays targeting the 16S rRNA, citrate synthase (gltA) and the heat-shock operon (groESL) genes were utilised. These assays and subsequent nucleotide sequencing confirmed that 50% (50/100) of warthogs were Anaplasma-positive, with juveniles displaying a significantly higher infection rate (15/18; 83.3%) than adults (35/82; 42,68%). Phylogenetic analyses of individual and concatenated gene datasets confirmed that the Anaplasma species in warthogs is closely related to a novel species detected in Ornithodoros soft ticks from Zambia. Bartonella screening utilised six published assays targeting the riboflavin synthase (ribC), gamma subunit of NADH dehydrogenase (nuoG), and the RNA polymerase beta-subunit (rpoB), citrate synthase (gltA) and filamenting temperature-sensitive mutant Z (ftsZ) gene regions. Despite this broad range of targets, no Bartonella DNA was detected in any samples, suggesting either an absence or very low level of this bacterial genus in warthogs in the KNP. Lastly, samples were screened for Mycoplasma DNA with PCR assays targeting three gene regions, namely 16S rRNA, ribonuclease P (RNase P) and 23S rRNA. Mycoplasma was confirmed in 60/100 (60%) samples through amplification and sequencing of at least one of the three targets. Nucleotide sequencing and phylogenetic analyses of individual and concatenated gene targets confirmed Mycoplasma strains fall within the Mycoplasma parvum-M. suis clade, with one variant, sister to M. parvum, likely representing a novel species. This study on the genetic structure and haemoparasitic diversity in the common warthog highlights both how their expanding distribution, through dispersal and human-mediated translocation, is reflected in their genetic structure and how a significant South African population hosts two potentially pathogenic bacterial genera, Anaplasma and Mycoplasma.