Blog post archive

Welcome to the No Free Lunches blog! These posts follow the work of Gabriella Leighton, a PhD student at UCT, working with the Urban Caracal Project to understand how urbanisation affects the foraging ecology of Cape Town caracals. For the original personal blog visit: Here is an archive of previous posts:

Trip report: Spanish adventures in ecotoxicology

Original post:

The caracal samples finally arrived on the 10th May 2019! I was so relieved when Pablo (the fantastic lab technician at IREC) handed me the box. We immediately unpacked the samples and set to testing the  clean-up methods we’d been practicing on three caracal samples. Looking at the results of these tests we found the recoveries of compounds worked best with the more traditional, cheaper sulphuric acid clean-up method.

The caracal blood samples, which had been liquid to start with, had been solidified into “morcilla” (Spanish blood pudding) by the time they got to us! We had had to add ethanol and exposure to extreme heat as part of the requirements of the Spanish Ministry of Agriculture’s import permit. This meant rather than pipetting anything, we had to weigh the blood to 0.5g per sample for extraction. However, we soon realised these recoveries were not good enough and had to increase this to 1g to improve detection. Over the next weeks we used an n-hexane extraction followed by a sulphuric-acid clean-up method to obtain extracts of caracal blood and fat tissue. In total, I tested 69 blood and 25 fat samples for organochlorine pollutant (e.g. DDT and PCBs) exposure. The fat content of the samples was estimated using gravimetry (i.e. weighing the empty tube and then weighing it again after the sample extraction when the fat residue in it had dried, and then calculating the difference) to give the results per lipid weight.

While in the process of doing these extractions, there was a slight hiccup. We had planned to run samples in the Gas Chromatography with Electron Capture Detector (GC-ECD) system as we extracted them. But in the very first sample of our very first run the sulphuric acid was not completely removed from the sample extract, which damaged the column of the GC-ECD system. It was quite a face-palm moment, as not only was the machine broken but we couldn’t even see any results at all because the first sample killed everything. We had to order a new column, which took several days to arrive and to install and recalibrate. Once the GC-ECD system was functional, we ran the extracts again with relevant pesticide standards for calibration (something rather arbitrarily called “Pesticide Mix 13″), which took five days to complete. When looking at the chromatographs (i.e. the graph produced by the GC that shows peaks of compounds over time; the compounds can be identified by looking at the time at which they were made, called the ‘”retention time”) we found several large peaks in many of the samples that were not identified by GC-ECD. These peaks may represent polybrominated diphenyl ethers (PBDEs, organic compounds containing bromine that are used widely as flame retardants) in the samples that were not present in our internal standard but may also have been cholesterol or similar large compounds. We did identify peaks of the organochlorines that were in our internal standard: the most important being DDT and it’s metabolite DDE, and several PCBs (PCB138, 153 and 180; the number refers to the number of chlorines and the position of those chlorines in the compound). In order to confirm the identification of both these unknown peaks and known peaks we will have to run the extracts again using GC-Mass Spectrometry (MS) . Once the organochlorine testing is complete, the same sample extracts are to be used to test for PBDEs (which I’m very excited about). This will only take place when the IREC obtains the equipment for Inductively Coupled Plasma Mass Spectrometry (ICP-MS) in late Spanish summer, probably in October.

When the extractions were complete, I also started the acid digestions necessary for testing for the presence and concentrations of heavy metals in the blood samples. While we didn’t initially plan to do this, I’m really pleased we can include this analysis, as heavy metals are a critical component to pollution in urban areas. The method uses temperature-controlled microwave heating of the lyophilised (i.e. freeze dried) sample with nitric acid and hydrogen peroxide for determination of metals by spectroscopic methods. This testing will also take place when the ICP-MS equipment arrives, which will allow the simultaneous testing of multiple heavy metals together.

While at my short stay at IREC I tried my best to get involved in some other projects: I assisted in the necropsy of a weasel; I donated blood to a tick-borne diseases project; I helped in a project on monitoring European swallow nests, and assisted in a project ringing and sampling European quails. I also travelled to Elche on the east coast of Spain in the province of Alicante to assist in a European eagle owl monitoring project. We checked on four nests with fledgling owls and retrieved camera traps previously set up to monitor diet. At IREC I met other researchers working on similar projects on Spanish wildlife: vultures, Egyptian mongoose, Eurasian otter, Iberian lynx, wild boar, European rabbits and least weasels. I also got to experience some of Spain’s natural areas, such as the Cabañeros National Park near Toledo, and Cabo de Gata-Níjar Natural Park in Almería. On the 16th May I presented my PhD research and my plans for the data I was collecting to the IREC. I was informed that the talk was to be filmed and lived-streamed for those not able to attend in person. This was a terrifying prospect for me, as I’m not only camera-shy, but also hugely intimidated by public speaking. I later discovered that this was a first attempt for UCLM and they’d never tried live-streaming anything before. Nevertheless, the talk was quite successful, with about 15 people connecting to watch remotely in addition to approximately 20 people who attended in person. Despite my fears, I realised this was a good opportunity to share my ideas with the institute and I received many enthusiastic questions both immediately after the talk but also in the weeks afterwards. I found that everyone I met was very interested in the research taking place in South Africa, the kinds of wildlife conservation issues we have to tackle and how this differed from most places in Europe. I also realised that there is relatively little ecotoxicology work being done on South African wildlife compared to most European countries, and I hope that my visit will have catalysed more collaboration and increased focus in this really fascinating (to me) and important field.

The preliminary data has been sent to me since my return to South Africa and I am in the process of summarising and analysing them. Once I’ve looked at the basic patterns, I’m planning to model the concentrations with several environmental covariates (e.g. proportion wetland or agricultural cover in caracal home range, protected area status, transformer density), as well as sex, age and various bloodwork variables to identify patterns of contamination with land use type and between demographic groups and physiological condition. I’m so enthusiastic about this dataset that I’m going to be hard-pressed to focus on getting work done on my other chapters! I really enjoyed everything about this first experience of ecotoxicology research: the labwork was rewarding, the people were amazing, the equipment was impressive, and the results promise to be very interesting! This (too-)short stay in Spain gave me the opportunity to broaden my horizons in not only in terms of academic networking and witnessing the scale and type of science taking place in Europe, but also arming me with a new skillset and data that will undoubtably strengthen my thesis conclusions.

Note: this text is a modified version of an international travel report originally written for the University of Cape Town’s Postgraduate Funding Office because I received a Smartt Memorial Scholarship for the short stay at UCLM/IREC in Ciudad Real, Spain. The testing of caracal samples was funded with a grant from the Table Mountain Fund.

Urban Caracal Project goes to Spain!

Last year my supervisors and I worked hard on securing funding to get my samples tested for exposure to environmental pollutants. In June 2018 we were delighted to hear we got it! The Table Mountain Fund granted us the full funding for the testing… However, I still needed to arrange my own personal funding in order for me to go over to the lab and assist in the analysis and learn the methods (as well as meet the ecotoxicology experts from the EU). In April 2019 I was hugely relieved and excited when I got funding from the University of Cape Town, which would allow me to take part in an international collaboration at an institution in Spain which specialises in this kind of analysis.

I eagerly booked my flights and there was a lot of frantic preparation, as I had to organise permits from both the South African and Spanish sides in order to get the samples there. There are a fair few regulations around moving animal samples (mine were mostly blood and some fat samples) between countries. We needed a CITES export permit from CapeNature (caracal are an Appendix II species) in addition to an import permit from the Spanish Ministry of Agriculture. We struggled a little to get information about how to store the samples for transport, which led to some last-minute late nights putting samples into new tubes and making sure I had the right volumes of blood for analysis and had used the correct pathogen inactivation method. Before I left I also had to get the samples endorsed by CapeNature, which involved a physical inspection.

After some delays, the samples are now in Amsterdam! I have already been in Ciudad Real, Spain for a week. The week before I attended an EU workshop in Madrid on rodenticides in raptors which I found very informative and interesting. I got to meet many respected researchers working on toxicology around Europe and learnt a lot not only about pesticide testing but also the decision-making process for large-scale, international projects. Since then, I’ve been settling in at the Instituto de Investigación de Recursos Cinegeticos (IREC) and, with the help of very experienced lab technicians, I have been deciding which compound extraction method to use when my samples do get here.

There are several methods of sample preparation, specifically in the extract clean-up stage. I am particularly interested in testing for persistent organic pollutants (POPs), including PCBs and DDT/DDE. We have tried three methods of clean-up: using sulphuric acid with a sodium sulphate filter, or with a aluminium nitride filter, or using Florisil (synthetic magnesium silicate) with a sodium sulphate filter. This has also given me an opportunity to familiarise myself with the lab equipment and methods before we start on my samples. So far, it’s been a huge learning curve, and one of the biggest challenges is my lack of Spanish! With a bit of effort and hand-waving from both sides I am managing to understand most things, however, and I’m hoping to learn some of the language while I’m here. I’ll find out the results from the clean-up tests once the practice samples we used have been analysed by Gas Chromatography – Electron Capture Detector (GC-ECD). Now just to wait for my samples to arrive!

Starting that stable isotope stuff (finally)

I’m excited to say that I’ve managed to get going on my third chapter’s data collection! We’re planning to use stable isotope analysis (SIA) to explore longer-term, integrative trends in Cape Peninsula caracal feeding ecology. Essentially what this means for me is that I’m spending a lot of time with minuscule pieces of hair (again). Who knew that’s what I would spend the majority of my thesis data collection phase doing?! Good times.

Isotopes are variants of a particular chemical element which differ in neutron number, and therefore have different masses, which makes them useful tools to ecologists. They’ve been used to study diet in lots of different ecosystems, both aquatic and terrestrial. Simply put, carbon isotope ratios can give an indication of the type of plant in the food web (C3 vs C4 – there are mainly C4 plants in urban areas), and nitrogen isotope ratios indicate trophic level (how high up the food web the animal sits). I’d like to look at how this changes over an urbanisation gradient (i.e. north to south on the Cape Peninsula). You can also look at interesting things like niche width and diet overlap between different groups or populations. Anyway, back to the hair… In order to look at foraging I’m analysing the carbon and nitrogen isotope ratios in the hair of caracals (and I’ll do this for their two most common prey items too – Guinea fowl and Otomys or vlei rat). To do this the hair needed to be degreased (i.e. cleaned of any oils and dirt). This required taking a small bunch of hairs from an individual caracal and washing them in an Eppendorf tube with a mixture of chloroform, methanol and distilled water (in a ratio of 2:1:0.8 in case anyone wanted to try it. But always use chloroform in a fume hood. Safety first, kids). Then I removed the solvent and rinsed the hair with distilled water a few times and dried it in an oven.

Once dried I then packed up all my nice clean samples and made my way over to the other side of campus to the Archeometry lab were I spent some days measuring tiny, tiny quantities (0.35-0.5mg) of hair into small tin capsules which go into the mass spectrometer (which measures the relative abundance of isotopes in a given sample). Well, the weighing was relatively quick, it was getting the hairs into the capsule and folding it without them flying out that was the time-consuming part. The stable isotope compositions are expressed in terms of delta values (δ) in permil (‰), i.e. parts per thousand differences from a standard. They express the proportion of an isotope that is in a sample. So, in addition to the hair I also had to weigh out the same amount of three standards that are commonly used for hair: sucrose, Merck gel and Valine. I never thought I’d be glad to be measuring out individual sugar grains.

Back in 2016 an Honours student analysed most of the captured caracal samples, so luckily all I had to add to the database was the remaining captures, some mortalities, a few Karoo samples and a bunch of Namaqualand samples. This amounted to 45 samples, which wasn’t too bad. It should be interesting to see the differences between the four populations (Cape Peninsula, the greater Cape Town area, Karoo and Namaqualand) and I’m so tempted to get into playing around with the data. But I better finish writing up my first two chapters first!

URBIO Conference 2018

Last week I attended the 10th International URBIO conference that was conveniently held in Woodstock, Cape Town. My supervisors Laurel Serieys and Justin O’Riain were also in attendance, and it was great to have such a strong iCWild contingent there. URBIO (International Network for Urban Biodiversity and Design) describe themselves as “an open worldwide network of educators, scientists, government officials, and practitioners that promote the design and management of sustainable cities.” The theme this year was Urban Biodiversity and Food Security, and this meant talks and posters relating to urban sustainability, design and management, urban ecology, policy, food security and urban agriculture, and human dimensions and conservation.

While there were a fair few “pure” ecology talks, I doubt they imagined a talk on caracalfood security when they dreamt up the theme! Nevertheless, my abstract was accepted and I presented in the afternoon on Wednesday the 12th September. I spoke about our ideas around the Cape Peninsula potentially representing an “ecological trap”, with attractive abundant prey drawing caracals into greater risk of mortality through obvious causes, like car collisions, but also through cryptic causes, like exposure to environmental toxicants (we are particularly interested in anticoagulant rodenticides, DDT and PCBs). We have already tested three species of predators on the Cape Peninsula for rodenticides (caracal, Cape clawless otter and large-spotted genet), and all three show exposure to a range of different compounds. I know from the diet results that this exposure isn’t from introduced rodents (e.g. Rattus norvegicus), but is more likely from consuming predators that do consume those rodents. We’ve found caracals feeding on large-spotted genet, Cape grey mongoose, raptors and snakes – all possible secondary or tertiary sources of toxicants.

Next steps are to look into the patterns in DDT and PCB exposure. We hope to send our samples to a Spanish lab (at UCLM) in the near future. Then I can look at patterns of toxicant exposure and the diet data (e.g. proportion predators consumed), home range characteristics (e.g. proportion urban area) and health measures from blood-work.

On the Friday 14th September Laurel presented her results on caracal persistence in a dynamic landscape. The preliminary habitat selection models are showing that as a highly mobile species moving in a closed system on the isolated Cape Peninsula caracals persist through very broad selectivity. They seem to be able to adapt to most landscapes and rapid changes they face.

I was very impressed with the international crowd. There were Swiss, American, Japanese, Icelandic, Australian, Indian, Ugandan, Malawian, Kenyan, Columbian and Israeli delegates… to name a few I remember. It was valuable to get such diverse perspectives on urban topics – from academics, but also urban planners, landscape designers, NGOs and conservation managers.

Along with stimulating talks on everything from invasive plants to urban pollinators to urban planning and the biotic homogenisation debate, there was absolutely delicious food (all vegetarian!) in a Green Star rated location at the Double Tree Hotel. The keynote talks were varied. I really enjoyed the one by Lief Peterson on the “hidden economy” of traditional healing and wild-harvested medicine around Cape Town, as well as Timon McPhearson’s talk on urban nature-based solutions for resilience in the Anthropocene, where he focused on the issue of urban heat.

URBIO 2018 was definitely a worthwhile experience for me. I met some really interesting people from all over the world, had some engaging conversations and now have a lot to think about, and certainly a lot of papers to hunt down and read!

The big ‘upgrade’

It looks like I’ll be working on urban caracals for a bit longer! As my project developed my supervisors and I made the decision, about 6 months ago, that it had the scope to be upgraded to a PhD.

I knew I wanted to do my doctorate but I needed to decide whether I wanted to carry on looking at caracal diet or start on a completely new project. I resolved that the caracals were too interesting to pass up on – not only as a species, but also in their persistence in such an urbanised area. I wasn’t going to find such an exciting combination of cool cats and urban ecology in any other place! Plus, the Urban Caracal Project has collected such an incredible dataset with which to work, it enables me to explore so many questions.

Over the last few months we’ve been working on how to grow my current thesis, and have decided to add two new data chapters. The focus is still on foraging ecology, but now I’ll be looking at diet using another relatively new method which employs stable isotopes. Additionally, I’ll be looking at possible consequences of an urban diet by exploring if exposure to various pollutants could have adverse health effects on caracals. I’ve been doing a fair amount of reading and preparation, and finally gave my upgrade presentation last week! It was a really long time coming (I had originally planned to do it much earlier in the year), but I’m pleased with how everything came together, and I feel the proposal was strengthened by the development of several ideas over the last few weeks.

I’m excited by how these new aspects of isotopic enrichment and ecotoxicology enhance my thesis, and make it much more interesting to me on a personal level. We’re exploring core ideas around urban caracal foraging from several different angles using several different methods. We want to know how caracal compare with other urban medium-sized carnivores (i.e. “mesocarnivores”) – do they avoid, adapt to, or exploit urban resources?

Already, the caracals are showing really interesting patterns which we will be investigating more closely with spatial models – a real learning curve for me! So far we have seen that adult males have much larger home ranges than females or juveniles, and are taking more urban prey. They are also hunting closer to the urban edge, at lower elevation and on gentler slopes. Is this putting them more at risk? Are they more likely to be affected by poisons ingested through contaminated prey?

I’m excited to see what the new samples (fur isotopes and concentrations of pollutants in different tissues) will reveal to us! I’m sure we’ll start to piece together quite a comprehensive understanding of how caracals are managing to adapt to “life on the edge”.

There are so many parties involved in this work; it astounds me. It may sound clichéd, but I’m grateful to all of them for the part they’ve played in making my dream of working on such an amazing project for my doctorate a reality!

SAWMA symposium 2017

This year the South African Wildlife Management Association symposium was held in the Western Cape, at Goudini Spa in the Boland. This was great for the Urban Caracal Project, as it was a short drive from Cape Town.

I presented some of the early diet results and spoke about some of the management implications. These included the relatively low consumption of carnivores, which includes domestic cats (at only 2% of all feeding events). This is important because a lot of Cape Town residents are really worried about the risk of caracal predation on their pets. We can now see this is in fact not a big issue, and can be fully addressed simply by managing pets, especially those on the urban edge. I also mentioned routes of secondary rodenticide (i.e. rat poison) exposure. We now know that introduced rodents (house mice and rats) make up a tiny proportion of diet. But we also know that most of the Cape Town caracals are exposed to several different anticoagulant rodenticide compounds. So where are they being exposed? It might be that this exposure comes from the other carnivores that they eat (e.g. genets and mongoose), which are eating introduced rodents, and possibly even the poisons themselves. Preliminary testing has shown that these species have even higher levels of poison exposure than the caracals, so this may well be the case. But further investigation would be needed to know for sure. Lastly, my talk would have been incomplete if I didn’t mention penguin predation. The situation at Boulder’s Beach has received a lot of media attention recently. But it isn’t really new, just newly discovered. Predators are a natural part of the Cape Peninsula system and land-based penguin colony management may have to include more intensive protective measures. It was interesting to hear Dr Lauren Waller’s (CapeNature) perspective on this in her presentation the next day, where her focus was the Stony Point colony. Joleen Broadfield (UCP field manager) then gave a super interesting talk about the threats to survival of Cape Town caracals. The main cause of mortality seems to be car collisions, but when considering the collared cats, disease and poisons are also important threats.

The conference presentations were all of a high standard this year, and we all got great insight into conservation efforts all over southern Africa, but also some input from keynote speakers from Australia and the UK. It was great to share ideas with fellow carnivore researchers – special mention to Marine Drouilly of the Karoo Predator Project who won a prize for her PhD talk! Check out her awesome work! The venue was also great, with it’s hot springs, mountain scenery and paths through stunning fynbos spring flowers.

Impressions: hair identification

Another milestone reached: all the identifications are done! Of course, there are still some elusive kills and scat which I’ll never be 100% sure on, but not from lack of trying. The last step for identifying species once all other methods had failed was looking at hair cuticle scale patterns. This requires making an impression of the outside of the hair. In the old (and non-vegetarian) days, people used gelatine, but I just used clear nail polish, which works just as well. You place the hair into some (slightly dried) polish and, once dried, pull it off and examine the impression left behind under a microscope. The process also requires subsampling the hair from the scat beforehand (I used a numbered grid and a random number generator), and washing the hair in solvents to clean them of natural oils and dirt. This may all sound easy, but a lot of it requires dealing with individual hairs. I can tell you there is a particular kind of agony in trying to place a single, minuscule mouse hair into wet-but-not-too-wet nail polish, let alone trying to pull it out again.

Surprisingly (to me) different species actually have pretty different scale patterns under magnification. I made some reference slides for myself of the species unlikely to be in the keys and guides I used, like grey squirrel and domestic dog. I took a few quick photos through the microscope with my phone:

One of the guides I used was written by Hillary Keogh in 1985 (fetchingly entitled A photographic reference system based on the cuticular scale patterns and groove of the hair of 44 species of southern African Cricetidae and Muridae), and I fortuitously managed to get hold of her original slides some time ago. She describes southern vlei rat (Otomys irroratus) hair as “Covered with lanceolate-pectinate scales. Almost petal at start of base… pattern gradually flattens out to become an irregular waved mosaic pattern.” Accompanying this helpful text was a terrible quality black and white photo of something I assumed was meant to be the hair. After struggling for some time, I suddenly realised I actually had in my possession the very slide the hair I was squinting at was on. From there on, it got easier. Contrary to that photo, Otomys hair is very distinctive, so I could move through a bunch of the samples I wanted to check quite quickly.

For the most part, my guesses based on macroscopic structure of the hair were correct. But I’m glad I could confirm them; I made a few corrections and sometimes found more than one type of hair present. In total I checked 84 samples which means I’m now finished! I must admit I vastly underestimated how long it would take to get here. Now the real fun (read: panic) begins… data cleaning and analysis in preparation for SAWMA 2017 next week!

Of mice and museums

The past week has seen me back at the Iziko South African museum in Company’s Garden in town. It was a rat-run, pun intended. In my previous trips I was working with Graham Avery on identifying bird and larger mammal bones. This time around I met with his wife, Margaret Avery, who is an expert on micromammals (this includes rodents) and specifically studies the Cenozoic period. What this means is that Margaret is very good at recognising very small mammal species by looking at their teeth and cranial bones. The couple has been working for the museum for a long time and they are now emeritus associates. Despite ongoing renovations and constant moving of offices and collections in the museum building, we managed to book the lab for two days last week and one day this week – just before and after the big storm hit Cape Town!

What I’ve been learning over the last few months is that there are some really interesting micromammals right here on the Cape Peninsula. By far the most common in my samples have been African vlei rats, which belong to a genus called Otomys. What I didn’t realise is that there are several species of Otomys in this area. The two species we’ve found so far in the scat samples are Otomys irroratus (this comes up a lot) and Otomys saundersiae (aka Otomys karoensis), which co-occur in the Fynbos biome of the Western Cape. Otomys irroratus is associated with mesic grasslands, but according to Margaret the smaller O. saundersiae can be found in rockier, higher altitude areas. These species are exclusively herbivorous, mainly eating grasses.  Interestingly, they aren’t typical rodents in that they usually only produce one or two offspring at a time, which are born precocial, erupted incisors at the ready.

Rhabdomys pumilio, or the four-striped grass mouse, is another fairly common small rodent player in the Cape Town caracal diet so far. There have also been some remains of incredibly tiny African pygmy mice (Mus minutoides), grey climbing mice (Dendromus melanotis), Namaqua rock mice (Micaelamys namaquensis), African marsh rats (Dasymys incomtus) and brown rats (Rattus norvegicus). The latter species is closely associated with cities, yet we have found only a few instances of it becoming dinner. Even more surprisingly, we did not find any remains of house mice (Mus musculus). It is the most numerous species of the genus Mus globally, although originating in northern India, as they have spread with humans all over the world. House mouse phylogenies have even been used to reconstruct early human movements. Given that they are very common in urban areas, as they live in houses, I would have thought we would see them in the caracals’ diet.

Bigger rodents like grey squirrels (Sciurus carolinensis) and mole-rats have also featured. The Cape mole-rat (Georychus capensis) is quite distinctive, with russet-coloured fur and a silvery-white underbelly. Like most mole-rats they live in underground tunnels, rarely emerging to the surface, and they are nocturnal. However, unlike some other species, they are solitary, except when raising young, and are extremely aggressive to intruders. My discovery of the Cape dune mole-rat (Bathyergus suillus) in a scat was confirmed by Margaret, and we found quite a few more samples containing evidence of this species. I was very interested when we found some gerbil teeth! The Cape gerbil (Gerbilliscus afra) is a nocturnal rodent endemic to the Western and Northern Cape, South Africa and is found in sandy soils in which they dig complex tunnels. Despite its adorable appearance, it is often considered a pest during population explosions, as it is well adapted to agricultural fields. It’s fascinating to consider that this species has persisted while surrounded by such built-up areas.

We found quite a few non-rodent micromammals too. So far there have been three species of shrew: the reddish-gray musk shrew (Crocidura cyanea), greater red musk shrew (Crocidura flavescens) and the lesser dwarf shrew (Suncus varilla). We have also found a few instances of golden moles – which were further identified as the Cape golden mole (Chrysochloris asiatica). This is an insectivorous mammal with short, iridescent fur, no external eyes and large digging claws, which is widespread in south western South Africa. Its populations are not in decline and it seems to adapt easily to urban areas, and has become the bane of many gardeners.

While going through all the samples, I made sure to group those scats found in the same GPS cluster – just to check whether the remains belonged to the same individual or not. Margaret can tell this by looking at left and right-sided bones (especially jaws) and the number of upper and lower teeth. It seems like the caracals like to snack on more than one of these smaller prey items at the a time, as most of the scat had several individuals or several species present in one sample.

The broader patterns in the scat and kill data are beginning to emerge. Once I have all the identifications done (there are still a few that need to be done purely on the basis of microscopic hair scale patterns), I’ll begin to analyse the data properly, but for now I can see that most of the prey base is made up of wild species, rather than introduced ones. While I can’t say much about prey preference because I don’t have records of prey abundance for micromammals on the Cape Peninsula, it is still interesting to see that the caracals aren’t necessarily focusing on synanthropic (i.e. human-associated) prey. The southern cats nearer to Cape Point seem to eat more birds (especially Cape cormorant), while rodents make up the bulk of the diet for the northern and Noordhoek wetland caracals. So far, it also looks like female caracals take more avian prey than males do.

I found my time at the museum engaging – it’s wonderful being able to work with people who are so dedicated, knowledgeable and enthusiastic in their field. I’ve learnt plenty and I’m very grateful to the Avery’s for all their help, which has yielded some very interesting findings!

When predator becomes urban caracal prey

I’ve been sorting out the caracal kills database over the last few weeks, filling in missing information and looking through photos of kills that never made it to the freezer for closer inspection. It can be tricky identifying a half-eaten prey item when you have it right in front of you, but this becomes much more challenging when all you have is a blurry photo. Around 80% of the kills are birds, so usually this involves identifying feathers. For the most part the feathers are pretty easy: unmistakable spotty and black for guinea fowl, or greenish, brown and white with fluffy barred down for Egyptian goose. I breathe a sigh of relief when I see these. However, there have been some really difficult feathers to figure out, and quite a few frustrating ones which I’m pretty sure we’ll never get. Investigating the diet of a cat that seemingly eats anything, in a city with all sorts of introduced animals means that its hard to rule out even the strangest prey candidates. Along with domestic cats, goats and sheep, there have also been peacocks, domestic chickens, geese and ducks…

Some of the most fascinating cases concern birds of prey. Its intriguing to consider that the tables can be turned and the hunter becomes hunted. The first case of this I came across was the Rock Kestrel (Falco rupicolus), unexpectedly revealed as a late evening snack for Protea (TMC24), one of the southern Peninsula females. Luckily, these feathers were collected so we could look at them carefully. This species is known to breed in the Cape Point area, occurs widely in many southern African countries and is common in South Africa, particularly, as the name suggests, in mountainous or rocky areas. They are known to hunt in open areas, and pounce on their prey from the ground, and take a variety of species, from rodents to rock pigeons to reptiles and insects.

I then heard of another case of hunter turned prey in Wilderness, South Africa at the end of last year: a Black-headed Heron successfully nabbing a vlei rat, only to be taken by a caracal a few seconds later. This amazing scene played out in front of Kelsey Green’s camera lens, resulting in some amazing photos. So it’s very possible that this Rock Kestrel was distracted enough in its own hunting endeavour to fall prey to a hungry caracal.

Since then, I have discovered some more instances of raptor-cide. The next was an opportunistic kill found in the Noordhoek wetlands. Sadly, the only evidence I had was some photos of a mangled carcass taken in very dappled light, with the feathers fairly obscured by leaves. I could tell that the feathers and head belonged to a bird of prey, I just couldn’t be sure as to which one. So I sent them to Jessleena Suri, who has been fantastic in helping me identify bird kills in the past. She also has an interest in urban ecology, as well as ornithology, and has plenty of experience with this kind of thing, as she did her Masters on urban Black Sparrowhawk (Accipiter melanoleucus) diet in Cape Town. That project has some really interesting results. She rose to the challenge, and managed to pin down the unfortunate bird as a juvenile Jackal Buzzard (Buteo rufofuscus). This species is much larger than a Rock Kestrel, and the juveniles look quite different from the adults, as they are mainly brown above and rufous brown below and on the tail feathers. It can be quite problematic differentiating buzzards, but I’m pretty confident in this identification.

The last case I found while going through some more photos taken at clusters. I wasn’t given much to go on, as the (single) photo was blurry and the feathers were covered by vegetation, but once again I could see I was looking at something different. After some consultation with Campbell Fleming, a professional birder (and convenient office-mate), and a useful feather quiz by Faansie Peacock (see Question 3), I’m pretty sure these belong to a Spotted Eagle Owl (Bubo africanus). This species is much more commonly found in urban areas, like Tokai where these feathers were discovered, than the Cape Eagle Owl (Bubo capensis). This kill was made by one of the juvenile male caracals, Strandloper (TMC21), perhaps getting experimental with his meal choice.

These cases highlight to me that nothing is ever certain, especially in this urban jungle! You could very easily be hovering at top of your food chain and the next day be caracal cuisine.

“Oh look, another cape cormorant”: some trips to the museum

The last few weeks have been spent preparing samples for further identification by bone. This involved carefully sorting through each cleaned and dried scat sample to pick out the hard bits (i.e. bones, teeth, claws and nails) and package them separately. This makes it easier for comparison to reference skeletal material. Next, I decided to reorganise the samples according to prey group by date: rodents (the large majority!), other mammals, birds and reptiles. With all my samples neatly packed and organised they were ready for a trip to the museum!

I was very excited to have (finally) organised a meeting with Graham Avery, a retired museum curator and archaeozoologist at Iziko Museums of South Africa. He has expertise in identifying southern African bird bones, as well as larger mammals. With his little dog Suzy for company, we quickly got to work looking through my bird samples, using his impressive collection of reference bird skeletons. Each reference specimen has been carefully cleaned, each bone neatly labeled and placed into a brown cardboard box.

The trick is comparing a broken piece of mangled bone from the scat to a bone from the reference collection – which sometimes takes a while to find! Graham is remarkably good at this. If a bone is diagnostic, even if it’s just a fragment, we can narrow it down to a specific bird group and very often to a specific species. The best samples are those with a bit of coracoid, quadrate, furcula, tarsometatarsus or humerus.

Sometimes the sample resembles “rice crispies” (as Graham puts it), but quite often there was something identifiable. Often, we just have to use what we can get… Claws can be quite informative:

Sometimes there’s evidence of the caracal feeding on the bones:

And sometimes we have to look at a few different pieces. This gets tricky when there’s more than one species in the sample.

In the beginning we had a nice variety of birds: Cape francolin, Egyptian goose, guinea fowl, yellow billed duck and a gull here and there. However, as we started getting to the Cape Point area samples, things got a little less varied and a lot more predictable very fast. Things is, the caracals only really eat cormorants down there. Which would have been fine, except that all those samples were grouped together. So we had to look at 88 cape cormorant samples. Consecutively.

Fortunately, things have become a bit more interesting now that we’ve moved onto what I labeled as “unknown” and the larger mammals. We’re still working on those, and I’m really loving finally getting some confirmed identifications! It’s such a relief after staring at these samples for so long. The next step is to meet with Graham’s wife Margaret Avery who is the go-to expert on southern African micro-mammal cranial bones and teeth. I know most of the samples will be vlei rat, but I’m super interested to see which other species of rodents we’re going to find.

Two charismatic caracals' favourite snacks

First, to introduce the main cat characters. Protea is one of the adult female caracals and the 24th cat to be captured on the project. Her territory stretches along the white, sandy beaches on the wild, west coast from the Cape of Good Hope lighthouse through to Kommetjie, which she uses as a highway to travel from one hunting spot to the next. The UCP intern team have been following her movements closely, as she is one of the few females collared, as well as one of the few cats collared in the southern part of the Cape Peninsula. Titan is another interesting southern Peninsula character. As his name suggests, he's the biggest caracal captured, weighing in at 16kg (more than double Protea's mass!), and traveling pretty impressive distances usually on the eastern coast from Simon's Town down to around Dias beach.

Through ongoing effort scat and prey remains have been found at GPS clusters, and prey items identified, and these lend important data for the caracal diet analysis. Indeed, the data on these two cats have revealed some interesting results on what they like to eat, but most importantly that they don't seem to be very fussy eaters! Some of the most common prey items are Egyptian geese; these are Protea's favourite by far!  Other frequent items on her menu are sacred ibis, various gull species, and cape and white-breasted cormorants. Cape cormorants are a common breeding resident near Cape Point, but are an endemic species that is classified as endangered due to recent rapid declines.

Protea's feeding site remains include a few large spotted genets and grysbok, and the scat analysis so far shows she likes cape grey mongoose, and the occasional domestic cat.

The rest of her prey items are an assortment of birds: little egret, yellow-billed duck and cape francolin come up fairly regularly.

Of course, it's always exciting when unexpected prey items are found. Two notable species that became lunch are a rock kestrel, a species known to breed around the Cape Point area, and a sandwich tern, which is especially common along the coast in summer. Protea continues her finer taste for endangered birds in her partiality for African penguin. These seabirds are sometimes recorded off the west coast, presumably commuting to the nearby breeding colony at Boulders Beach in Simon's Town on the eastern side, which must be when she is able to catch them.

The value of scat analysis is that it reveals the small prey items often overlooked in other methods, probably because they are eaten whole! The scat analysis tells us that Protea likes to snack on smaller prey too... shrews and vlei rats feature often, and sometimes snake scales are also found.

Titan's diet is pretty similar, but a little less varied. He loves cape cormorant, and has certainly eaten a lot of them! The scat confirms this penchant for cormorant and also reveals that he occasionally goes for a rock hyrax (a.k.a. dassie), doesn't turn his nose up at vlei rats, striped mice and shrews, and also likes the salty taste of African penguin. One of the most amazing findings in Titan's scat were distinctive black and white quills! Yes, he's fierce enough to take on a crested porcupine.

A few more caracal lunches, and some mystery claws!

Ongoing student protests at UCT have really slowed things down, as many of my student volunteers have been unable to come to campus. It has been a very tumultuous time, with anxiety levels high. As a result I have not managed to process many samples. Nevertheless, there have been a few interesting ones!

One of the most intriguing samples was this one:

Mystery sample

Mystery sample

The fluffy grey hair looked rodent-like, but the bones were fairly robust, with a large vertebra. The strangest part was the huge claws! They couldn’t be from a cat, as they weren’t hooked enough, they were too large to be from a squirrel, rat, genet or mongoose, and they didn’t quite look like bird claws. I was at a loss…

After asking around and getting a few different suggestions for what this mystery prey item might be, I got a final say from Woody Cotterill, who has an interest and expertise in small mammals. Woody came to the lab to take a look at some of my samples and give some advice on how to go about identifying prey items.

Taking one look at the sample in the petri dish he said “It’s definitely Bathyergus.” Some quick Googling revealed that the prey item was most likely a Cape dune mole rat. This species is not only endemic to South Africa (i.e. its found only here), but its also the biggest of all the mole rats! I managed to get my hands on a taxidermic specimen, and was very surprised by how large it was. Roughly chihuahua-sized! But with much more impressive claws.

Now that I’m focusing more on prey identification, the detective work of the project has begun. My focus at the moment is to pull together a reference library to help me find out what these caracals are eating – not just from the scat but also from the kill remains found in the field. This involves looking at hair under a microscope, so I’m collecting hair from all potential prey items. I’ll also be using teeth and claws, as well as feathers for the birds. While the majority of samples will be the usual favourites on the menu, I’m sure there’ll be a whole lot more mysteries to solve.

Appreciation post

This project has challenged me in many ways so far, not least because I took it on so late in the year. I feel under constant time pressure with so much to catch up on and get done. Thankfully, I have a team of wonderful student volunteers who are passionate about carnivore biology and conservation! They have helped so much with processing my samples in their breaks between lectures and practicals, fitting it all into their busy schedules. So thanks guys!

The people who have helped me out so far are: Alveena Aziz, Caton Schutte, Clara Steyn, Dayna Hegarty, Kaelin Stemmet, Katherine Chaplin, Kyra McKellar, Lindsay Powell, Megan Pockalny, Michelle Pretorius, Shakirah Rylan, Tara van Ryneveld and Vivienne Coetzee. Thanks also go to some of the UCP interns who have become involved.

Gabi Leighton

SAWMA symposium 2016

I was fortunate enough to attend the annual South African Wildlife Management Association symposium in Tzaneen, Limpopo last month.

I presented some of the preliminary findings on the Cape Town caracals’ diet, focusing on the differences between two methods (kills found at GPS clusters and scat). We had to make a poster and also give a 5 minute speed-presentation of our work.

This was a really valuable few days of interesting talks and people. Very glad that I went and was super pleased to win the prize for the best student poster!

Preview of the poster I presented at the symposium

Preview of the poster I presented at the symposium

I think the next symposium will be in the Western Cape, so hopefully I can go again, and this time do a longer talk about my work!

Gabi Leighton

Some (very) preliminary diet findings

Here are a few of the more interesting prey items found in the scat analysis so far. Most of the samples contain mammalian prey items (i.e. composed mainly of hair), and of those, most seem to be rodent. I still need to go through all those with hair and look at cross-sections under the microscope to identify the species (or at least to genus level). Nevertheless, these are the more exciting ones:

Hope you enjoy the photos!

Gabi Leighton

Caracal diet field trips

I was lucky enough to join in on some field work action earlier this year… This involves setting traps to catch the cats (much trickier than it sounds!) and investigating GPS clusters (i.e. points where the cats have been hanging out for a while) to find evidence of kills and scat, which I’m using for my diet analysis.

No such thing as a free caracal lunch

This is just a brief introduction to the caracal diet aspect of the Urban Caracal Project, which will also be documented here.

I’m an MSc Biological Sciences student in my first year of study at the University of Cape Town. My research aim is to investigate the diet of caracal (aka “rooikat”) living and hunting in the urban spaces of Cape Town, South Africa. These elusive yet adaptable medium-sized cats have managed to persist in a city with an increasingly hardening urban edge; using greenbelts, empty land as well as natural areas. The latter is mostly land forming part of the Table Mountain National Park (TMNP).

Most citizens of Cape Town are surprised to hear that caracals live in such close proximity, perhaps illustrating how good they are at going unseen! As can be seen on this website, a lot of really exciting work is being done to study the effects that urbanisation is having on these cats, from movement patterns and gene flow to rodenticide and disease exposure. My project is a small part of this larger ongoing research effort and will investigate their diet. However, I’m hoping to make it a bit more interesting for myself by putting the dietary data in a spatial context, linking what they choose to eat, where they choose to eat it and how this is influenced by urbanisation. We expect that while there might be easy pickings near the urban edge, this may draw caracals closer to the risks of the big city… There ain’t no such thing as a free lunch!

Gabi Leighton