The influence of gene flow on population viability in an isolated urban caracal population.

Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated populations often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences of urbanization in a caracal (Caracal caracal) population that has become isolated in the Cape Peninsula region of the City of Cape Town, South Africa, and is thought to number ~50 individuals. We document low levels of migration into the population over the past ~75 years, with an estimated rate of 1.3 effective migrants per generation. As a consequence of this isolation and small population size, levels of inbreeding are elevated in the contemporary Cape Peninsula population (mean FROH = 0.20). Inbreeding primarily manifests as long runs of homozygosity >10 Mb, consistent with the effects of isolation due to the rapid recent growth of Cape Town. To explore how reduced migration and elevated inbreeding may impact future population dynamics, we parameterized an eco-evolutionary simulation model. We find that if migration rates do not change in the future, the population is expected to decline, though with a low projected risk of extinction. However, if migration rates decline or anthropogenic mortality rates increase, the potential risk of extinction is greatly elevated. To avert a population decline, we suggest that translocating migrants into the Cape Peninsula to initiate a genetic rescue may be warranted in the near future. Our analysis highlights the utility of genomic datasets coupled with computational simulation models for investigating the influence of gene flow on population viability.

Molecular detection of tick-borne pathogens in caracals (Caracal caracal) living in human-modified landscapes of South Africa.

BACKGROUND: Wild carnivores living alongside humans and domestic animals are vulnerable to changes in the infectious disease dynamics in their populations. The aims of this study were to determine the prevalence and diversity of selected tick-borne pathogens (TBPs) of veterinary and/or zoonotic concern in wild populations of caracals (Caracal caracal) occurring in human-modified landscapes in South Africa. Using molecular techniques, we screened 57 caracal blood samples for infection by rickettsial bacteria and piroplasms in three regions of South Africa: rangeland in the Central Karoo (n = 27) and Namaqualand (n = 14) as well as the urban edge of the Cape Peninsula (n = 16) of South Africa. To characterise pathogen identity, we sequenced the 18S rRNA and 16S rRNA genes from positive samples and analysed sequences within a phylogenetic framework. We also examine the diversity of potential tick vectors. RESULTS: All individuals tested were infected with at least one tick-borne pathogen. Pathogens included Hepatozoon felis, Babesia felis, Babesia leo and a potentially novel Babesia species. An Anaplasma species previously described in South African domestic dogs was also found in 88% of urban edge caracals. Higher rates of co-infection characterised urban edge caracals (81% vs 15% and 0% in the two rangeland populations), as well as a greater incidence of mixed infections. Host attached tick species include Haemaphysalis elliptica, an important pathogen vector among carnivore hosts. CONCLUSIONS: This study confirms the occurrence of previously undocumented tick-borne pathogens infecting free-ranging caracals in human-modified landscapes. We identify clear differences in the pathogen profiles among our study populations and discuss the likely health costs to caracals living adjacent to urban areas.

Widespread anticoagulant poison exposure in predators in a rapidly growing South African city.

Anticoagulant rodenticides (ARs) are used worldwide to control rodent populations. ARs bioaccumulate across trophic levels and threaten non-target wildlife. We investigated the prevalence of AR exposure in seven predator species in the rapidly developing Greater Cape Town region of South Africa - a mosaic of natural, urban, and agricultural areas within a global biodiversity hotspot. We focused sampling on caracals (Caracal caracal, n = 28) as part of a larger caracal ecology study, but also opportunistically sampled Cape Clawless otters (Aonyx capensis, n = 9), large-spotted genets (Genetta tigrina, n = 4), honey badger (Mellivora capensis, n = 1), water mongoose (Atilax paludinosus, n = 1), small gray mongoose (Galerella pulverulenta, n = 1), and Cape Eagle owl (Bubo capensis, n = 1). We tested livers from all species, and blood from ten caracals, for eight AR compounds to assess prevalence and amount of exposure for each compound. We used generalized linear models to test spatial, demographic, and seasonal risk factors for ten measures of AR exposure in caracals. We detected at least one of the four most toxic AR compounds in six species. Exposure was high for caracals (92%) and all species combined (81%). For caracals, proximity to vineyards was the most important AR exposure risk factor. Vineyards in Cape Town do not use ARs to protect their vines but do host commercial hospitality structures where ARs are used. Vineyards may thus link caracals that forage within vineyards to the rat poisons used in and around their commercial structures. Residue levels were unexpected in large-spotted genets and Cape Clawless otters, suggesting invertebrate vectors. ARs may present a cryptic threat to populations already vulnerable to increasing habitat loss, vehicle collisions, poachers and fire. Targeted mitigation should include a mix of environmentally responsible policies that reduce AR use, particularly in areas near wildlife habitat.