Methods
Summary
Meeting our research objectives starts with the humane capture of the caracals for the collection of biological samples and fitting with radio-collars to collect GPS data.
Caracal capture
We use cage traps, which are the safest method to capture medium-sized wild cats. We place traps in areas where we observe signs of caracal activity, but also minimal human activity. Caracals are lured into traps with visual and scent attractants inside the cages. To reduce stress during the capture and handling process, traps are placed in areas sheltered from wind and sun, and protected with vegetation. Traps are checked a minimum of four times daily and are not active during extreme weather patterns (rain, cold, or heat). Once a caracal is captured, we immediately call a veterinarian to assist with the drugging and handling of the caracal. We anesthetize the caracals on site so they are never removed from their natural habitat. They are anesthetized for approximately one hour, during which time we collect biological samples and radio-collar each animal. Once the animals have safely recovered from the anesthetizing drugs, we release them at their site of capture. Using these methods, the caracals are never removed from their natural environment.
After radio-collaring and sample collection, we use the following methods to address four key objectives:
1. Assess the effects of extreme isolation by urbanization on the behavioural ecology of caracals. A minimum of thirty caracals will be radio-collared in Table Mountain National Park to collect movement data. We have already radio-collared 23 caracals. We will use the GPS-location data collected with the radio-collars to investigate habitat preference (i.e., What kind of vegetation do they prefer? Where do they hunt, rest, find prey, or have kittens?). We will also assess patterns of avoidance (i.e., Do they try to minimize road crossings? Does electric fencing, urban development, or areas that have recently burned in fires affect their movements?).
Radio-collars will collect exact GPS locations every 3-hours that we will use to estimate home range size, overlap, and habitat use over time (e.g., LoCoH home ranges). These data will be used to answer the questions listed above. We will also collect extremely fine-scale data (data collected every 20-minutes for 36 hours every 10 days). These data will be used for diet studies and to assess potential movement corridors within the fragmented landscape. We will separately analyze 3-hour and 20-minute GPS data to address our different questions. However, we will use similar methods with each data type. We will use a mixture resource and step selection function models to assess the patterns of preference vs. disturbance. See the pre-analysis section below for more information about our analyses using these models.
2. Investigate genetic signatures of isolation and urbanization on multiple types of genetic markers. The urban Cape Town is likely a long-term absolute barrier to gene flow between populations within and outside of the city. The important consequence of this isolation may be may be profound genetic drift (random processes that lead to loss of genetic variation) and inbreeding driving the loss of genetic diversity in the urban Cape Peninsula population. We will conduct fine-scale genetic assessment across the genome of each caracal using low-coverage sequencing methods. Using these data, we will contrast genetic variation at genomic regions that can inform us about population processes (i.e., neutral markers) such as population declines, inbreeding, and genetic similarities and differences between populations. We will make comparisons in these different genetic indices among the isolated Cape Town population and 3 populations in areas with high degrees of habitat connectivity in the Western and Northern Cape for which samples have already been collected. We will also measure gene flow (genetic exchange) between the isolated Cape Town population, and populations outside of the city to assess degree of genetic isolation of the population.
Additionally, we will also assess genetic variation at the major histocompatibility complex (MHC), a gene family considered the paradigm for the study of the ability of populations to respond to changing environments. For urban wildlife populations with increased disease risk that can lead to precipitous population declines, the study of immune genes can reveal information about the adaptive potential of populations threatened by disease. We will sequence a MHC Class II gene (DRB1) to evaluate variation responsible for immune defense against extracellular diseases (i.e., pathogens). We will examine the effects of isolation by urbanization in shaping MHC variation that is critical to immune genetic health and defense against novel diseases.
3. Investigate the role of the epigenome in facilitating caracal adaptation to urbanization. Epigenetic changes regulate genome activity independent of DNA sequence. The most studied epigenetic mechanism is DNA methylation of CpG sites in the DNA sequence. CpG sites are usually clustered in gene regulatory regions and their methylation, or de-methylation, can result in changed gene expression patterns. In vertebrates, numerous studies have linked anthropogenic environmental stressors (i.e,. exposure to common pollutants) to detrimental epigenetic changes in multiple tissue types. However, DNA methylation may also function to increase phenotypic variation, facilitating adaptive response and act as an evolutionary buffer to rapid environmental change. Using blood samples, we will explore differential DNA methylation patterns across the isolated Cape Peninsula population, and populations outside of the city that are not isolated. We will also compare genomic variation as discussed above in #2 with measures of methylation diversity between each population to test whether greater methylation diversity in the urban population will compensate for low genetic variation.
4. Effects urbanization on health, and threats to survival. We are collecting blood samples at the time of capture that will be used for health assessments, and have already collected data for more than 20 caracals. We will also use samples to test for exposure to, or infection with, common feline and canine diseases that could influence survival, for which we have collected samples for more than 30 caracals already. We are opportunistically collecting dead caracals found in our study area, and have collected more than 25 dead caracals within the last year. We will perform autopsies to assess individual health and cause of death (i.e., vehicle collision, pesticide exposure, disease). We will collect tissue and blood samples that will enhance our genetic and disease survey sample size. We will also collect organ samples that can be used for pesticide exposure testing.
Challenges
We have overcome numerous challenges already, demonstrating our ability to take these challenges head on! We have worked with a piecemeal shoe-string budget, as is the nature of any project of this type. However, by reaching out to the local community, we've turned this into a grassroots effort, and community members with a variety of expertise have pulled through to help us in may ways. For example, we have community members that help fix equipment in disrepair after years of use on other projects. Working in the field, we have become savvy about navigating the mountains while staying safe in an area where crime is frequent. We have reached out to colleagues to help sponsor some of our laboratory testing. Overall, through asking for help in a variety of ways, and prioritizing public outreach, we are managing a project that has been very successful to date and is already yielding fascinating results.
Protocols
This project has not yet shared any protocols.