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.
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!
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 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.
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…).
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, 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.
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.
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.
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!
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.
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!
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.
Back in October, I wrote about how a grant proposal was turning me into a zombie.
Well, much to my surprise, turns out that my foray into the world of the walking dead was worth the effort. I’ve just heard that the National Science Foundation does, indeed, want to send me to South Africa to carry out this research!
Basically, I’m interested in how the other big carnivores (hyenas, leopards, cheetahs, and wild dogs) manage to live with lions. And I think that one of the keys to their coexistence has to do with how the other carnivores distribute themselves across the landscape to avoid being killed or harassed by lions. Do they avoid huge tracts of land and lose access to the valuable resources within? Or are they able to fine-tune their behavior and still use those areas without getting into trouble?
As you know, I’m using the camera traps to try and figure out these patterns of habitat use by the major carnivores. But that still just tells me what they do in a place (the Serengeti) where there are lions, and I don’t know if the lions are directly causing these patterns. I can’t, for obvious reasons, do an experiment where I take out all the lions and see if the rest of the animals change their behaviors, which would help me identify such a causal relationship.
But in South Africa, there are two virtually identical reserves — they have the same habitat, the same prey animals, and the same carnivores…except that one has lions and one does not. These reserves are right next to each other and surrounded by fencing. So they are pretty much the perfect experimental system where I can actually answer whether or not the patterns we see in predator behavior are caused by lions. What’s even better is that there are already ongoing research projects there that are running camera trap surveys very similar to Snapshot Serengeti. So most of my work will be doing some measurements of the vegetation and working with the researchers in South Africa to compile their data in a way that we can draw these comparisons.
It’s going to be a *lot* of computer work with a *little* bit of getting out into the bush, but the questions are so cool and the ability to effectively isolate the effect of a single top predator (lions) in a natural ecosystem is so rare, that I couldn’t be more excited about it.
Here’s a great post by the BBC about some genetic work that has just been done to shed light on the evolutionary history of lions. Apparently, it’s a bit tricky reconstructing lion history due to the fact that they don’t fossilize particularly well (generally not conducive conditions in lion habitat) and that humans create giant holes in the record by wiping out entire sub-population.
However, from genetic analyses of living lions and museum specimens, these authors have determined that there are two evolutionary groups of lions – those in India and Central/West Africa and those in Eastern/Southern Africa. This happens to have some interesting implications for lion conservation and reintroduction — check out the article!