Archive | Research RSS for this section

Wander over to Wildebeest Watch!

Wildebeest Watch Home

Can’t get enough of these gnarly gnus? Head on over to our new spinoff project, Wildebeest Watch!

In collaboration with Dr Andrew Berdhal from the Santa Fe Institute, and Dr Allison Shaw at the University of Minnesota, we are taking a closer look at what the wildebeest are doing in the Snapshot Serengeti images to try and better understand the details of the world’s largest mammal migration.

Every year, 1.3 million wildebeest chase the rain and fresh grass growth down from the northern edge of the ecosystem down to the short grass plains in the southeast. We have a broad-scale understanding of where they are moving across the landscape, but don’t understand how they make these detailed decisions of where and when to move on a moment-to-moment basis. Wildebeest as individuals aren’t known for being particularly smart — so we want to know how they use the “wisdom of the crowd” to make herd-level decisions that get them where they need to go.

So while you’re waiting for more photos of lions, hyenas, and other sharp-toothed beasts, why not wander over to Wildebeest Watch to help us understand the collective social behavior of these countless critters?

Curbing Idealistic Images and CDV for the Sake of Lion Conservancy

Meredith: Our brilliant team of Snapshot Serengeti undergraduate volunteers at the University of Minnesota are perhaps even more on top of the lion literature than I am! This week, we have a guest post from one such student, Clayton Mazur, describing some recent work of Dr. Packer’s on lion disease spread in Serengeti Park. This post is a synopsis of a scientific paper that can be accessed in full here


I propose we play a word-association game. I will offer a word and you think of what comes to mind. “Africa.” Did you imagine Mt. Kilimanjaro, or the towering, lush rain-forests of the Congo? “Wildlife.” Did you envision the sprawling savannas of Tanzania, home to hundreds of thousands of migrating wildebeest? If so, I would bet that your savanna also included the enigma of Africa: the African lion. Was he a graceful figure standing upon Pride Rock looking out over his kingdom? Perhaps he was laying in the shade, his dark mane flowing in the breeze as he waits for the females to return with a kill. I would argue that elegant images such as these are what come to mind for the majority the public. The portrayals of lions in the media- from Lion King to the MGM Lion- support this notion.  As elegant as these images are, reality is less than elegant for the lions living in Serengeti National Park in Tanzania, Africa.

African lions have unique social structures that help them brave the tough conditions of the savanna. Lions live in families called prides; one to two male lions rule a pride. The roles of female and male lions within a single pride are vastly different.  While females hunt, raise the cubs, and reproduce, male lions defend the pride from attack by other predators such as hyenas. Living in a large family group offers lions protection, but it also comes with costs. One cost is that females need to supply a large number of individuals with enough food for survival. Female lions coordinate hunts whereby they stalk prey and then give chase, but this technique only yields about 26% success. The low success rate forces large prides to split or starve.  Perhaps a more interesting difficulty of living in a large pride is the spread of disease within lion populations. As Dr. Craig Packer has found, disease prevalence is a threat to the current lion population.

A fatal disease that persists in the carnivores of Serengeti National Park is Canine Distemper Virus (CDV). CDV infects a range of carnivores, from dolphins to rodents and even some primates. The viral infection causes encephalitis, pneumonia, anorexia and eventually, death. You may be familiar with CDV if you own a dog, for many owners in the US vaccinate their dogs for CDV. In Serengeti National Park, where local villages cannot afford to vaccinate their dogs, CDV is a conservation concern for African Lions who contract CDV from domestic dogs. To try to remedy the concern, an intense vaccination regime started in 2003. Packer and colleagues attempted to characterize the progression of CDV in both domestic dogs and African Lions. Their goal was to determine if domestic dogs were responsible for the infections observed in African Lions. The team also wanted to determine if the 2003 vaccination program had any effect at reducing CDV in the domestic dogs and/or African Lions.

The scientists worked with blood plasma collected from both domestic dogs (obtained from 1992-2012) and from African lions (obtained from 1984-2012).  After collecting the blood samples, the team ran serological tests to detect for the presence of the CDV virus in individual dogs or lions. Using a Bayesian model, the scientists then calculated the probability that an individual lion or dog would contract CDV in one year. The scientists also used sensitivity models to determine the extent at which domestic dogs transmit CDV to lions. From the results of these models, the scientists were able to comment on the fate of the lions with regard to CDV.

The research team drew results by interpretation of the two models. They found that CDV had persisted in the populations of both dogs and lions for more than 25 years. Outbreaks of CDV occurred in 1981, possibly in 1976, and in 1993. Not only do these results suggest a historic presence of the fatal disease in the national park, the dynamics of each outbreak of the disease was unique. The scientists found that the year in which CDV infected the most dogs differed from the year in which CDV infected the most lions. The researchers proposed that this pattern identified domestic dogs as initial vectors for CDV in the park. After a 1994 outbreak in the lion population, the dynamics of the outbreaks become more disjoint. The disjointed dynamics between the domestic dog and lion populations suggest that after 1994, infections cycled through the dog population and the lion population separately. However, the spread of CDV between dogs and lions was not eliminated after 1994.

With domestic dogs established as an initial vector of CDV, the scientists wanted to know transmission rates between domestic dogs and lions. Again, they used a sensitivity model to predict this factor. The scientists found that domestic dogs were ten times more likely to spread CDV to lions than lions were to spread CDV to domestic dogs. With such a high prevalence of CDV in the domestic dog population and the tendency for CDV to spread from dog to lion, the effects of the 2003 vaccination effort were an important factor to analyze for the conservation of the Serengeti National Park lions. The scientists first analyzed the effects of the vaccine on the domestic dog population. Before 2003, there had been very sparse vaccination in villages surrounding Serengeti National Park. As was expected, this vaccination effort did little to curb CDV infection in either lions or domestic dogs. It was not until after 2003 when all villages to the east of Serengeti National Park and all villages within 10 km to the west of Serengeti National Park vaccinated their dogs against CDV did there exist a decrease (~5%) in CDV infections.

With CDV slightly decreased in domestic dogs due to the vaccination effort, was there a similar decrease in CDV infections in the lion populations?  Unfortunately, the sample size of lion serum that the scientists could obtain was not enough to comment on the updated magnitude of dog-lion CDV transmission. Overall, the scientists determined that CDV was still able to cycle in the lion population with very little reduction in the prevalence of the disease. However, not all is hopeless for the lion populations of Serengeti National Park. Dr. Packer’s team suggests that direct vaccination of lions may be more effective at preventing the disease. Additionally, the team suggests that advances in serological techniques would allow for increased accuracy when researching episodic diseases, such as CDV. Implementation of safe vaccines coupled with more accurate serological tests could minimize the effects of CDV outbreaks and ensure the health of the Serengeti lions.

As evident from the work of Dr. Packer and colleagues, there are threats to the conservation of the lion populations of Serengeti National Park. Not only do prides run the risk of individuals starving to death, splitting, and human-lion conflict, disease is another risk factor of living in a pride. Yet, these prides, these perfect families, come to mind when the public thinks about lions. Idealistic images of cubs play fighting or suckling from their mother are important for generating interest and compassion for African lions. One can be content with the image of the brave, courageous, elegant male lion standing on Pride Rock overlooking his kingdom, but one must simultaneously recognize the reality of the lion’s plight. Only then will conservation for lions be truly feasible.

Getting Good Data, Part II (of many)

Okay, so by now you’ve heard dozens and dozens of times that you guys produce really good data: your aggregated answers are 97% correct overall (see here and here and here). But we also know that not all images are equally easy. More specifically, not all species are equally easy. It’s a lot easier to identify a giraffe or zebra than it is to decide between an aardwolf and striped hyena.

The plot below shows the different error rates for each species. Note that error comes in two forms. You can have a “false negative” which means you miss a species given that it’s truly there. And then you can have a “false positive,” in which you report a species as being there when it really isn’t. Error is a proportion from 0 to 1.

Species specific error rates.

Species specific error rates.

We calculated this by comparing the consensus data to the gold standard dataset that Margaret collated last year. Note that at the bottom of the chart there are a handful of species that don’t have any values for false negatives. That’s because, for statistical reasons, we could only calculate false negative error rates from completely randomly sampled images, and those species are so rare that they didn’t appear in the gold standard dataset. But for false positives, we could randomly sample images from any consensus classification – so I gathered a bunch of images that had been identified as these rare species and checked them to calculate false positive rates.

Now, if a species has really low rates of false negatives and really low rates of false positives, then it’s one people are really good at identifying all the time. Note that in general, species have pretty low rates of both types of error. Furthermore, species with lower rates of false negatives have higher rates of false positives. There aren’t really any species with high rates of both types of error. Take rhinos, for example: folks often identify a rhino when it’s not actually there, but never miss a rhino if it is there.

Also: we see that rare species are just generally harder to identify correctly than common species. The plot below shows the same false negative and false positive error rates plotted against the total number of pictures for every species. Even though there is some noise, those lines reflect  significant trends: in general, the more pictures of an animal, the more often folks get it right!

Error rates vs. species commonness, measured by the total number of pictures of that species

Error rates vs. species commonness, measured by the total number of pictures of that species

This makes intuitive sense. It’s really hard to get a good “search image” for something you never see. But also folks are especially excited to see something rare. You can see this if you search the talk pages for “rhino” or “zorilla.” Both of these have high false positive rates, meaning people say it’s a rhino or zorilla when it’s really not. Thus, most of the images that show up tagged as these really rare creatures aren’t.

But that’s okay for the science. Because recall that we can assess how confident we are in an answer based on the evenness score, fraction support, and fraction blanks. Because such critters are so rare, we want to be really sure that those IDs are right — but because those animals are so rare, and because you have high levels of agreement on the vast majority of images, it makes it really easy to review any “uncertain” image that’s been ID’d as a rare species.

Pretty cool, huh?

The How To Guide for Getting Field Experience

The Minnesota winter has finally come upon us and time is passing exasperatingly slowly, waiting to hear back from funding sources, plowing through homework, cleaning up data, and mostly daydreaming about heading back to Serengeti. Perhaps the dread of spending the next semester in the cold is stirring undergraduates into action, but I’ve been contacted by numerous students recently inquiring about something near and dear to my heart: field experience and how to get it.

Field work is what makes biology for me – I don’t think I could get by without that glimmer of hope, the promise of going out and getting dirty and experiencing ecology in the raw. The summers of my own undergraduate career and the two years before I entered graduate school were spent almost entirely out in the bush: measuring fishes and catching snakes and doing pretty much whatever kind of work I could come across that would let me mess around doing science in the great outdoors.


“Doing Science” in the Great Outdoors

I lived for that work, but I can’t claim that it’s entirely glamorous. You won’t be picking up a brand new Ferrari any time soon, that’s for sure. My first field jobs could barely be called sustenance living, but after a few years of experience, I was picking up jobs that came with fancy, real-person benefits (oooh, like Dental).

And then there’s that whole “in the field” thing to consider — in all its glorious, treacherous, beautiful and exhausting majesty. I’ve been on field jobs where people have suffered through dengue and malaria, contracted parasites, twisted limbs, narrowly avoided encounters with venous snakes (on an almost daily basis), and quite literally passed out from exhaustion in the middle of the wilderness. “Sweat, blood, and tears” sums it up quite nicely. You’re stuck with the same old crew for weeks, or even months, on end, often with limited amenities. If isolation is not your thing, perhaps second thoughts may be in order. Also take into account the facilities you’ll be living in. I’ve been overwhelmed by the relative “luxury” of some field stations (electricity! food that isn’t rice and beans!), and enjoyed the struggle of situations at the opposite end of the spectrum (cold showers are good for you, and you didn’t need to check that Facebook this month anyway…).


Just another day at work


Which isn’t to sell any aspect of fieldwork short. Doing fieldwork is an absolutely wonderful way to get your butt outdoors, see the world, enjoy nature, and it does wonders preparing you for a career in science. Techniques I’ve learned and people I’ve met along the way have been invaluable when it came to getting new jobs and heading back to school. I feel far more prepared to do my own research after having participated in such a diversity of projects. Plus, you get to be your down David Attenborough and live the things you’ve only ever seen on Nature documentaries or in the zoo. It’s a well worth-while experience.

So, the important part: where to find the job.


For those still in an undergrad program looking for a summer position, the NSF Research Experiences for Undergraduates (REUs) are definitely the first place to hit up (NSF REU; NSF for BIOLOGY). These are great paying positions that are geared specifically towards getting you involved in your own research. I completed two REUs during my undergrad, spending one summer working in Panama studying developmental plasticity in Red-eyed tree frogs and another on the island of Puerto Rico filming the territorial behaviors of Anolis lizards. These experiences are wonderful because you are highly involved with the lab you work in, you get to meet and interact with a large body of scientists from various disciplines, and if you’re designing your own project, get invaluable input into the process of constructing an experiment. For me, both of my REU projects resulted in publications – an important factor for applying for graduate school.


List servs are beautiful, beautiful things, because job applications find their own way into your inbox and sit there waiting for you to read them. They’re also a great place to join in on scientific discussion and share ideas, articles, and even research equipment. Some of my favorite list-servs are:

  • ECOLOG-L: Run by the Ecological Society of America
  • MARMAM: For researchers working with marine mammals
  • MAMMAL-L: I believe this was set up by the American Society of Mammologists?

You can probably tell that I’m a bit biased towards mammal work, but ECOLOG runs job advertisements from everything ranging from forest ecology to herps and fishes through to hyena biology in Kenya.



Biology job boards are the next place I turn when looking for the next field position. These update fairly regularly, so keep checking up on them:

  • Texas A&M biology: My absolute favorite – there are some really fantastic research opportunities that make their way to the Texas A&M job board
  • ConBio: Run by the Society for Conservation Biology
  • Primates: For those interested specifically in primates
  • AZA (Zoos):  If the field isn’t quite for you, but you’re still gung ho about working with animals, be sure to check out what’s going on at the zoos
  • USAjobs: Government jobs are some of the better-paying gigs in the biology business

Find the job applications is, like most things in life, just the first step in a Process. Next come the cover letters, the applications themselves, scrounging up enough references and actually getting them to submit letters for you on time (often, the most difficult part). But hopefully this provides as starting point for those ready to get out there and do some science.

Cheetahs rocking the boat…again!

Cheetahs, it seems, just can’t stop shattering everything we believed to be true about them.

Scientists have long believed that lions (and hyenas to some extent) threaten cheetah conservation efforts —  in large part because they kill so many cheetah cubs. But last year, researchers from South Africa revealed that lions probably don’t kill as many cheetah cubs as folks previously believed. And shortly after that, our research showed that regardless of the amount of lion-inflicted cheetah cub mortality, cheetahs do just fine around large lion populations.

Just last month, another story broke that shakes up how we think about cheetahs. It turns out that not only are cheetahs not as vulnerable to killing by lions, but they cheetahs aren’t nearly as vulnerable to non-lethal bullying either. It was thought that because cheetahs couldn’t fight back against lions – or hyenas – they lost a lot of their hard-earned kills to these ruthless scavengers. (Yes, both lions and hyenas do steal food from each other and from cheetahs.) We knew that wild dogs expend so much energy hunting that they can’t afford to lose even moderate levels of food, and assumed that cheetahs were similarly vulnerable. But, as a recent study from Bostwana and South Africa found out, they aren’t.  It turns out that despite being super fast, cheetahs don’t expend all that much energy chasing down their prey. Researchers estimate that cheetahs could lose a full 50% of their kills to lions and hyenas, and still get all the calories they need!

All in all, it’s beginning to look a lot like the biggest threats to cheetahs aren’t lions and hyenas. Instead, availability of denning sites (as suggested by our research) and human destruction of habitat that forces cheetahs to travel far and wide in search of prey (suggested by this most recent study) are probably much, much greater threats to their survival.


Tidbits on wild dogs

One of our long-time Snapshot Serengeti members (thanks Reid!) sent me this NY Times article on African wild dogs. As you know, we don’t have wild dogs in the study area (though keep your eyes peeled! TANAPA did reintroduce them into the western corridor the other year, and I keep hoping we’ll catch one traveling through our grid).

But I am very interested in how dogs interact with the larger carnivore community. And these animals are just *so* cool – incredibly energetic and full of nerve. Watching a small group of dogs defend their kill against a hunting party of hyenas was one of the highlights of my trip to South Africa in June.

Photo by Ingela Jansson

Photo by Ingela Jansson

The article points out that wild dogs may fare better when lions fare worse (which I’ve reported on here) — and that raises some questions about questions about how to target conservation efforts. Do we have to choose between which species to protect? I’d say “not necessarily.” My dissertation research suggests that although dogs fare worse in small reserves with lions, there are places where wild dogs seem to do just fine. Selous Game Reserve (TZ) and Kruger National Park (SA), for example – big areas that have complex habitat structures. So the answer to protecting the entire carnivore guild may lie in larger, diverse reserves.

There are currently efforts in place to do create a protected area the size of Sweden that spans five southern & east African countries. If successful, according to the NY Times, the Kavango-Zambezi Transfrontier Conservation Area will be the largest terrestrial protected area in the world. Now that’s something to celebrate.

Nyala are way prettier than impala

I’m in South Africa, getting a feel for the ongoing Panthera camera trapping surveys, collating data, falling madly in love with the country and South African bush, and scheming for how I need to find a way to come back.

Things are a bit of a whirlwind, but so far I am amazed and excited about the amount of monitoring that many of the small private and state-run reserves have been doing. There is an extraordinary amount of information that has been collected over the last decade on how all of the top predators move and live across these parks. There are parks with and without lions. Parks with and without hyenas. With and without wild dogs. Some parks are big and some are small. Some are very thickly treed, others are somewhat open. (Note that one thing I discovered very quickly is that pretty much all South African habitat, even the grassland, would equate to “woodland” in the Serengeti. So…”open” is a relative term.)

The amount of data here is enough to get any science nerd’s heart a flutter. But I am trying to focus on what is out the window instead of what’s on the computer for now. I’ve only a few days in South Africa, and endless time to analyze the data.

In the meanwhile, I thought I’d share one of my new favorite animals: the nyala.

These cousins to the waterbuck we capture in camera on Serengeti, and you can see it a bit in their pretty faces. But these animals are far more stunning than anything I’ve ever seen in Serengeti. The females are small and sport bright white stripes on their red fur, and the males have these  incredible “manes” that run down the undersides of their necks and to their bellies. They are pretty awesome. As is everything I’ve experienced in South Africa so far. Yep, definitely need to find a way back!

More results!

As I’m writing up my dissertation (ahh!), I’ve been geeking out with graphs and statistics (and the beloved/hated stats program R). I thought I’d share a cool little tidbit.

Full disclosure: this is just a bit of an expansion on something I posted back in March about how well the camera traps reflect known densities. Basically, as camera traps become more popular, researchers are increasingly looking for simple analytical techniques that can allow them to rapidly process data. Using the raw number of photographs or animals counted is pretty straightforward, but is risky because not all animals are equally “detectable”: some animals behave in ways that make them more likely to be seen than other animals. There are a lot of more complex methods out there to deal with these detectability issues, and they work really well — but they are really complex and take a long time to work out. So there’s a fair amount of ongoing debate about whether or not raw capture rates should ever be used even for quick and dirty rapid assessments of an area.

Since the Serengeti has a lot of other long term monitoring, we were able to compare camera trap capture rates (# of photographs weighted by group size) to actual population sizes for 17 different herbivores. Now, it’s not perfect — the “known” population sizes reflect herbivore numbers in the whole park, and we only cover a small fraction of the park. But from the graph below, you’ll see we did pretty well.


Actual herbivore densities (as estimated from long-term monitoring) are given on the x-axis, and the # photographic captures from our camera survey are on the y-axis. Each species is in a different color (migratory animals are in gray-scale). Some of the species had multiple population estimates produced from different monitoring projects — those are represented by all the smaller dots, and connected by a line for each species. We took the average population estimate for each species (bigger dots).

We see a very strong positive relationship between our photos and actual population sizes: we get more photos for species that are more abundant. Which is good! Really good! The dashed line shows the relationship between our capture rates and actual densities for all species. We wanted to make sure, however, that this relationship wasn’t totally dependent on the huge influx of wildebeest and zebra and gazelle — so we ran the same analysis without them. The black line shows that relationship. It’s still there, it’s still strong, and it’s still statistically significant.

Now, the relationship isn’t perfect. Some species fall above the line, and some below the line. For example, reedbuck and topi fall below the line – meaning that given how many topi really live in Serengeti, we should have gotten more pictures. This might be because topi mostly live in the northern and western parts of Serengeti, so we’re just capturing the edge of their range. And reedbuck? This might be a detectability issue — they tend to hide in thickets and so might not pass in front of cameras as often as animals that wander a little more actively.

Ultimately, however, we see that the cameras do a good overall job of catching more photos of more abundant species. Even though it’s not perfect, it seems that raw capture rates give us a pretty good quick look at a system.

Lions and cheetahs and dogs, oh my! (final installment)

I’ve written a handful of posts (here and here and here) about how lions are big and mean and nasty…and about how even though they are nasty enough to keep wild dog populations in check, they don’t seem to be suppressing cheetah numbers.

Well, now that research is officially out! It’s just been accepted by the Journal of Animal Ecology and is available here. Virginia Morrell over at ScienceNews did a nice summary of the story and it’s conservation implications here.

One dissertation chapter down, just two more to go!




A different way to see the world

I posted a little while ago about the applications of remote sensing technology in biological research. Here’s a TED talk by one of the authors of the South African study I mentioned with some fascinating visuals showing the level of detail these technologies can reveal to us. While the talk starts off flying you through a “lion’s-eye” view of hunting terrain, Greg Asner goes on to reveal some of the other ecological and conservation implications of these technologies and how they can help us do things from finding illegal goldmines and documenting species composition in the Amazon to tracking habitat changes by elephants and fire back in Africa.



Get every new post delivered to your Inbox.

Join 5,340 other followers