Viljoen, S. | bioRxiv Science

bioRxiv2025

Urbanization drives genetic erosion and population structure in a historically connected carnivore population

Urbanization is a dominant driver of habitat fragmentation globally, creating small, isolated wildlife populations vulnerable to accelerated genetic drift, reduced genetic diversity, and increased population differentiation. We investigated how urban development affects the genetic composition and structure of caracals (Caracal caracal) in Cape Town, South Africa using microsatellites and mitochondrial DNA sequence data. Sampling across four geographically disparate urban and rural populations revealed contrasting temporal patterns: mitochondrial markers indicated historical genetic connectivity among populations, while microsatellite data demonstrated recent genetic structuring driven primarily by urbanization. An extensively isolated urban population showed reduced allelic richness and pronounced genetic differentiation, reflecting urbanization as a strong barrier to gene flow. Within the isolated urban population, GPS-collared caracals demonstrated a degree of spatial genetic organization, with related individuals maintaining significantly higher home range overlap despite inhabiting a severely fragmented urban landscape. This kin-structured space use occurred despite caracals in the system having large home ranges compressed within a relatively small, isolated environment. Our findings reveal that urbanization has rapidly disrupted gene flow in this otherwise geographically widespread and adaptable carnivore, imposing a sufficient barrier to generate detectable genetic consequences within contemporary timeframes. The contrasting signals from historical versus contemporary molecular markers highlight urbanizations role in fragmenting previously connected populations and demonstrates the value of multi-marker approaches for detecting anthropogenic impacts on wildlife populations. These results underscore urbanizations capacity to rapidly alter population genetic dynamics, even in a highly mobile and adaptable carnivore.

genetics↗

bioRxiv2023

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

Wildlife populations are becoming increasingly fragmented by anthropogenic development. Such 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>1Mb=0.20). Inbreeding primarily manifests as long runs of homozygosity >10Mb, 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 only slightly, 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.

evolutionary biology↗