Biology subjects

Bishop, J. M.

Publications and source records attributed to Bishop, J. M..

3 recordsLinked to original sources

bioRxiv2026

Genetic Diversity and Population Structure of the Black-Footed Cat: Insights into Felis's Deadliest Predator

BackgroundBlack-footed cats (Felis nigripes) are one of Africas least studied felines. The population dynamics and demographic history of this solitary species have not been well-described. Reports of ongoing decline of present-day populations resulted in the IUCN Red List categorizing the species as vulnerable to extinction. As populations decline and become isolated from each other, they become susceptible to strong genetic drift and inbreeding, which can lead to the accumulation of deleterious alleles and increased sextinction risk. However, the IUCN cited data deficiencies across the species range as a limitation in this categorization for black-footed cats. In cases where ecological surveys are lacking, range-wide population genomic surveys can improve our understanding of population dynamics. ResultsIn the first genomic study of free-roaming individuals, we sequenced whole genomes of black-footed cats (N=44) from across their distribution. To do so, we incorporated whole genome sequences generated from both modern biological samples and century-old museum specimens. We assembled a highly contiguous reference genome using a combination of PacBio HiFi data and publicly available Hi-C data and investigated the demographic history, population structure, and genetic diversity of wild black-footed cats. We found evidence of historical effective population sizes of [~]11,500 individuals, which is lower than estimates reported in other felid species. Consistent with modest historical population sizes, we found that present-day genome-wide diversity was low ({pi} {approx} 0.0004). However, despite low genetic diversity, we find that black-footed cat genomes do not harbor long runs of homozygosity. Simulation results indicate that low present-day genetic diversity may simply result from modest historical population size. However, other analyses point to evidence of a population contraction in the last 50 generations, which could contribute to future genomic erosion. We also compared genomic variation in populations across the range to evaluate patterns of population structure, finding evidence of higher genetic similarity between individuals in closer geographic proximity. ConclusionOverall, these results provide range-wide information about the demographic history and present-day genetic diversity of an understudied species. Together with analyses of population structure, we speculate that there may be greater connectivity between populations of black-footed cats than previously assumed. Our study underscores the utility of genomic data in providing insights into population dynamics for better conservation management.

evolutionary biology↗

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↗