Archive | May 2013

Update on Season 5

In short, delay.  😦

In long, we’ve processed all the images and are uploading them onto the Zooniverse servers. However, it’s taking a long time. A really long time. Since Season 4, the Minnesota Supercomputer Institute (MSI) has switched over to a new system, and it seems like the upload time from this new system is painfully slow. We’ve uploaded over 25% of the images, but it’s taken a couple days uploading non-stop. So best estimate is mid to late next week for when they’ll all be uploaded. We’re trying to coordinate with the staff at MSI to see if they can increase upload speeds for us, but no guarantees.

(Man, I wish we had some images of turtles or snails or sloths or something from Serengeti… Wait! I know what’s slow — stationary, actually.)

Waiting…

Meanwhile, you can read a guest blog post that I wrote over at Dynamic Ecology. Dynamic Ecology is read by ecologists, so my blog post introduces the concept of citizen science (and Snapshot Serengeti, of course) to professional ecologists who may not be very familiar with it. One question that comes up in the comments is: can you do citizen science if you don’t have cool, awesome animals? Like, what if you have flies or worms or plankton instead? I think the answer is yes. But feel free to give your perspectives in the comments there, too.

Not on the A-List

I’m working on an analysis that compares the classifications of volunteers at Snapshot Serengeti with the classifications of experts for several thousand images from Season 4. This analysis will do two things. First, it will give us an idea of how good (or bad) our simple vote-counting method is for figuring out species in pictures. Second, it will allow us to see if more complicated systems for combining the volunteer data work any better. (Hopefully I’ll have something interesting to say about it next week.)

Right now I’m curating the expert classifications. I’ve allowed the experts to classify an image as “impossible,” which, I know, is totally unfair, since Snapshot Serengeti volunteers don’t get that option. But we all recognize that for some images, it really isn’t possible to figure out what the species is — either because it’s too close or too far or too off the side of the image or too blurry or …. The goal is that whatever our combining method is, it should be able to figure out “impossible” images by combining the non-“impossible” classifications of volunteers. We’ll see if we can do it.

Another challenge that I’m just running into is that our data set of several thousand images contains a duiker. A what? A common duiker, also known as a bush duiker:

Common duiker

You’ve probably noticed that “duiker” is not on the list of animals we provide. While the common duiker is widespread, it’s not commonly seen in the Serengeti, being small and active mainly at night. So we forgot to include it on the list. (Sorry about that.)

The result is that it’s technically impossible for volunteers to properly classify this image. Which means that it’s unlikely that we’ll be able to come up with the correct species identification when we combine volunteer classifications. (Interested in what the votes were for this image? 10 reedbuck, 6 dik dik, and 1 each of bushbuck, wildebeest(!), and impala.)

The duiker is not the only animal that’s popped up unexpectedly since we put together the animal list and launched the site. I never expected we’d catch a bat on film:

Bat

Our friends over at Bat Detective tell us that the glare on the face makes it impossible to truly identify, but they did confirm that it’s a large, insect-eating bat. Anyway, how to classify it? It’s not a bird. It’s not a rodent. And we didn’t allow for an “other” category.

I also didn’t think we’d see insects or spiders.

Spider

Moths fly by, ticks appear on mammal bodies, spiders spin webs in front of the camera and even ants have been seen walking on nearby branches. Again, how should they be classified?

And here’s one more uncommon antelope that we’ve seen:

Steenbok

It’s a steenbok, again not commonly seen in Serengeti. And so we forgot to put it on the list. (Sorry.)

Luckily, all these animals we missed from the list are rare enough in our data that when we analyze thousands of images, the small error in species identification won’t matter much. But it’s good to know that these rarely seen animals are there. When Season 5 comes out (soon!), if you run into anything you think isn’t on our list, please comment in Talk with a hash-tag, so we can make a note of these rarities. Thanks!

“Home” — the one without the wildlife

It’s hard to believe that I’m really and truly done with the Serengeti. It’s strange to not have a veranda to sit on, and watch the elles or giraffes munch on our trees; see the eyeshine of hyenas lurking in the shadows, hoping for a bite of our dinner. The only wildlife I’ve seen in the last week is squirrels. As entertaining as they are, it’s just not quite the same.

Nonetheless, it’s good to be “home.” It’s funny the things you take for granted when you live here. As an idea, I’ve made a list of just some of the things I’ve done in the past week that I hadn’t done in at least 5 months:

  • gone to a farmer’s market
  • run (oh the pain)
  • gone to the kickboxing gym (even more pain)
  • brushed my teeth with tap water (!)
  • drunk tap water (The strangest thing to get used to)
  • had a shower. With hot, running water.
  • eaten fresh, water packed mozzarella (I really do love food)
  • drunk an IPA (and beer. There’s no such thing as good beer in Serengeti.)
  • bought clothes
  • put clothes in a washing machine
  • driven on the right side of the road (This is surprisingly hard to get used to.)
  • put dishes in a dishwasher
  • had hot water come out of the tap
  • sat on a leather sofa
  • eaten baby spinach
  • eaten ice cream
  • watched something on YouTube (I still can’t believe how fast the internet is!)
  • driven a car with power steering
  • used a microwave
  • used a toaster
  • listened to the radio
  • checked my mail (that is NOT a pretty sight after 5 months…)

The list could go on, especially when it comes to food. But perhaps the most significant thing about this trip home is that, well, I’m here for good. Or as good as “for good” gets in grad school. I’m here, in Minnesota, until I finish my dissertation. What that means is that the next 12 months will be spent furiously analyzing the Snapshot Serengeti data to understand lion/hyena/cheetah/leopard/wild dog interactions, presenting at conferences, writing papers, searching for post-doc positions, and ultimately defending the last 5 (soon to be 6) years of research to a committee of UMN faculty members. It’s terrifying! Way scarier than spitting cobras, getting stuck in the mud, or having lions roaring right outside the car window…at least in my opinion.

Good News Bad News

So there’s good news and there’s bad news. Which would you like first? Good news?

The good news is that the pictures from Season 5 are being processed at the Minnesota Supercomputer Institute right this minute. There are about 900,000 images total, so it will take a few days to process them all. (What are we doing? We’re resizing them, extracting the place and time they were taken, and grouping those that need it into groups of 3.) Then we’ll need to upload them to Zooniverse’s servers. That might take another day or so. If everything goes without a hitch (fingers crossed), we’ll be ready to unleash Season 5 by the end of next week! (So for those of you who wanted some warning, this is your warning. Clear you schedules. Get your work done early. Set up an ‘away’ message on your email…)

Sneak Preview of Season 5 (July to December 2012)

Sneak Preview of Season 5 (July to December 2012)

The other news is bad, I’m afraid. We just found out that the grant proposal we wrote to the National Science Foundation back in January got turned down. Our grant would have funded Snapshot Serengeti and the Serengeti Lion Project for another five years, and included money for scientists to continue to analyze all the data you’ve been generating by identifying animals in the Snapshot Serengeti images.

Our proposal was reviewed by three other scientists independently and then talked about by a group of scientists who had our proposal and the three reviews to look at. Our three reviews varied. One person thought that our proposal was the most exciting project s/he had read yet this year. But the others were a bit concerned about exactly how we would analyze the data. This proposal was a “pre-proposal,” meaning that we only had a few pages to explain what we wanted to do, how we would do it, why it’s important, and the broader impact we would have. I guess we didn’t manage to get in enough of the “how” for these reviewers.

We were all taken by surprise by the rejection. The Lion Research Center has been reliably funded by the National Science Foundation for decades. But things are changing. Firstly, this “pre-proposal” system is new; it’s only in its second year. And everyone — both proposal writers and proposal reviewers — are still figuring out what exactly should go in the new shorter pre-proposals. And secondly, the Sequester is still in place, so the National Science Foundation has less money to give out this coming year than usual.

In any case, we’re now regrouping to come up with a new funding plan. We’ll be able to apply again to the National Science Foundation in January 2014 to fund camera trapping starting in 2015. And we’ve got several papers that we plan to write in the next six months using Snapshot Serengeti data that we’ll be able to point to to show reviewers that we can properly analyze the data. Meanwhile, we’re going to try to keep the cameras rolling by looking for other funding sources to cover our year-long funding gap. Suggestions welcome.

Detecting the right number of animals

This past spring, four seniors in the University of Minnesota’s Department of Fisheries, Wildlife, and Conservation Biology took a class called “Analysis of Populations,” taught by Professor Todd Arnold. Layne Warner, Samantha Helle, Rachel Leuthard, and Jessica Bass decided to use Snapshot Serengeti data for their major project in the course.

Their main question was to ask whether the Snapshot Serengeti images are giving us good information about the number of animals in each picture. If you’ve been reading the blog for a while, you know that I’ve been exploring whether it’s possible to correctly identify the species in each picture, but I haven’t yet looked at how well we do with the actual number of animals. So I’m really excited about their project and their results.

Since the semester is winding up, I thought we’d try something that some other Zooniverse projects have done: a video chat*. So here I am talking with Layne, Samantha, and Rachel (Jessica couldn’t make it) about their project. And Ali just got back to Minnesota from Serengeti, so she joined in, too.

Here are examples of the four types of covariates (i.e. potential problems) that the team looked at: Herd, Distance, Period, Vegetation

Herd: animals are hard to count because they are in groups

Herd

Distance: animals are hard to count because they are very close to or very far from the camera

Distance

Period: animals are hard to count because of the time of day

Period

Vegetation: animals are hard to count because of surrounding vegetation

Vegetation

 

* This was our first foray into video, so please excuse the wobbly camera and audio problems. We’ll try to do better next time…

Goodbye party

My last field season is drawing to a close. I’ve spent two and a half of the last four years living in Serengeti, and as much as I’ve missed my life in Minnesota, I can’t believe I’m really leaving Tanzania. Things have been a little hectic, so here I’m just posting some photos from my going away party.

party1

Pre-party. Fabio is prepared.

cooking

Cooking!

Winlady, who helps us with cleaning the house during the week, made delicious chapatis and pilau – a traditional spicy Tanzanian rice & meat dish. If I had any idea she was such a good cook, I’d have been bugging her for pilau every week!

dinner1

The Swedish stick game. We throw sticks…at other sticks…it’s actually kind of awesome. (Hey, we have to entertain ourselves out here…)

stickgame1

Sticks!

stickgame2

And then we had a visiting rhino beetle.

rhinobug2

rhino bug.

Tom, a post-doc with the Savanna Dynamics research project, found me a going away present in the nearest town (Mugumu, ~ 3 hours away).

shirt1

Oh the things you can get secondhand in Mugumu

I will miss this place.

helenali1

fire1

All in the name of science

Today’s guest blogger is Lucy Hughes. Lucy lived and worked on a private nature reserve in South Africa for four years, carrying out field research that included a camera-trap study into the reserve’s leopard population and twice monthly bird surveys for Cape Town University’s Birds in Reserves Project (BIRP).black-divider

Arrhhh, that really hurts! A three inch thorn had just penetrated my, admittedly inadequate, footwear and was stuck deep in the sole of my foot. Thorns are a serious hazard of camera trap placement in the South African bushveld where plants with thorns or hooks seem to make up about 90% of species.

My colleague Michelle ran back to the landy to get a first aid kit whilst I set about extracting the thorn, there seemed to be an awful lot of blood. I watched the path eagerly for Michelle’s return but as she got near she seemed to slow down and as she opened her mouth to speak I knew exactly what she was going to say. “Luce, if it’s not too painful, what about spreading your blood around a bit?”

Callous as it may seem it wasn’t a bad idea. We had been having trouble with capturing clear night shots of leopards. They always seem to be in a hurry and the shots we had were often blurry making it impossible to id the individuals. We needed a way to get the leopards to pause for a second or two in shot of the camera trap.

M2E1L0-15R354B449

We had been advised that scent was the answer and were experimenting with various different ones and now it seemed human blood was to be the next test. I dutifully hobbled out in front of the camera and scraped my bleeding foot around on a nice flat rock Michelle had procured, wondering about the sensibleness of using human blood as bait for a predator. My slight discomfort was all in the name of science.

In the end it didn’t work, It rained a couple of nights later and my efforts where washed away. We never did find the perfect scent.  We were told that tinned sardines worked wonders as well as catnip and perfume. We tried them all. It seems our cats where immune to these. The only thing that stopped them in their tracks was the scent of other leopards. I did learn however that the scent of tinned sardines was particularly interesting to giraffe of all animals. My method was to bury a plastic cup up to its rim in sand and put a blob of sardines in the cup. Now you would have thought that giraffe would have walked on by but as the picture below testifies, giraffe just have to take a closer look. You always learn something new!

M2E53L205-204R371B323

Complex Landscapes

This past week I’ve been reworking a paper about a study with Anna Mosser and Craig. The study asks the question: How did lions come to live in groups? It doesn’t seem like group-living in lions would be something you would spend much time thinking about – until you realize that lions are the only cat that regularly lives in groups. What’s special about lions?

Craig’s work over the past decades has shown that seemingly intuitive ideas about why lions form groups are wrong. Lions don’t form groups in order to hunt more efficiently. Lions don’t form groups to cooperatively nurse their young. Lions don’t form groups to protect young against aggressive outsiders. Instead, it appears that the primary purpose of lion groups is to defend territories against other groups of lions.

So territorial defense appears to be the key to group living in lions. But is territorial defense the only thing that matters? That’s what we set out to investigate. We created a computer model that simulates a bunch of lions living on a landscape. The model is a simplification of what happens in real life, but it contains some essential aspects of lion living.

First, we have complex landscapes. Previous research suggests that group territoriality is more likely in complex landscapes because there are highly desirable areas that are worth defending. If you had a landscape where everything was more or less the same, then you wouldn’t need to fight your neighbor over some small patch of it; you could just wander off and find your own patch that would be more-or-less the same quality as your neighbor’s.

Second, we have various behaviors that we can turn on or off in our simulated lions. For example, we can tell them that they can live together in a territory, but they can’t cooperate to defend it. We can also tell them whether or not they can live in a territory with their parents when they grow up. And we can tell them whether they’re allowed to make their territory bigger if they recruit more lions into their group.

By manipulating the types of landscapes and the various behaviors, we explored how often our simulated lions formed groups. Our results suggest that while territorial defense is important, it’s also important to have complex landscapes with high-value real estate. If the landscape isn’t very complex, then it’s easy enough to find an area to set up a territory without fighting for it. And if the landscape is complex, but doesn’t have any areas with high value, then there’s nothing worth fighting for or defending. It’s also important that lions be able to pass their valuable territories on to their offspring, for without inheritance, the benefits of all that fighting and defending are gone in a generation.

Lions evolved on the savannas of East Africa, where the landscape is complex with patchy areas of high value (near where rivers come together, for example). Humans did too. It’s possible that the same sorts of savanna landscapes that shaped group living and territorial defense for lions did so for people, as well.

Our simulation model

The simulation model. White areas are high-value real-estate, while black areas are low-value. Red shapes show where lions have formed a group territory, while blue shapes show where there’s a territory defended by just a single lion.

Big, Mean, & Nasty

Slide1

I recently gave a talk at the Arusha-based Interpretive Guide Society – a really cool group of people interested in learning more about the natural history of Tanzania’s places and animals. I’ve taken a few clips from the presentation that describe in a bit more detail how lions bully their competitors.

Looking at the photos above (all nabbed from the internet), how many of you would like to be a wild dog? A leopard? A cheetah? There’s no doubt about it – lions are big, and mean and nasty. If you are any other carnivore species in the Serengeti – or across Africa, lions chase you, steal your food, even kill you. So what do you do? How do you survive? That’s essentially what my dissertation seeks to answer. How smaller “large carnivores” – hyenas, leopards, cheetahs, and wild dogs — live with lions. Under what circumstances do they persist? Under what circumstances do they decline or even disappear?

There are a handful of ways in which these species interact, but what I’m most interested in is aggression and it’s repercussions. As the above pictures suggest, lions tend to dominate aggressive interactions.

Slide2

The relationship between lions and hyenas is one that has wormed its way into the public psyche through nature documentaries such as “Eternal Enemies.” While such movies play up the frequency of such interactions, they certainly do happen. Lions not only kill a number of hyenas, but steal their hard-won kills. Dispel any notion of lions as some noble hunter — they in fact steal a lot of their food from other carnivores. In fact, research from Kay Holekamp’s group in Masaai Mara  indicates that lions can suppress hyena populations just because they steal food from them! It’s actually a similar story for wild dogs – lions kill wild dogs too, but since wild dogs expend so much energy hunting, that if lions steal just a small fraction of the food that wild dogs catch, wild dogs simply cannot recover. They would have to hunt for more hours than there are in a day to make up for this caloric loss.

It doesn’t stop there. We don’t know how much food lions steal from cheetahs or leopards. We also don’t know how often lions kill leopards, but lions kill cheetah cubs left and right. Studies from Serengeti indicate that lions may be responsible for up to 57% of cheetah cub mortality!

Slide3

So how do hyenas, wild dogs, leopards, and cheetahs survive? Well, that’s what I’m trying to figure out. But what I can tell you is that not all of these smaller carnivores sit back and take their beating quietly. Take hyenas. They’re about 1/3 the size of a lion, but they live in groups. Big groups. Much bigger groups than lions. And if there are no male lions around, if hyenas have strength in numbers, they can steal food from female lions, and even kill their cubs. While leopards don’t live in groups, they can easily kill (and eat!) a lion cub that has been hidden while mom is away hunting.

Unfortunately, what we don’t know is whether this reciprocal aggression by leopards and hyenas has any measurable affect on lion populations, and whether it’s this aggression that allows hyenas and leopards to coexist with lions. The cameras behind Snapshot Serengeti will provide the first-ever map of leopard and hyena distributions within the long-term lion study area – by comparing lion reproductive success (which we know from >45 years of watching individually identified animals) to leopard and hyena distributions, we can see if lions do better or worse in areas with lots of hyenas or leopards – and whether this is due to getting less food or producing fewer cubs.

Slide4

What about cheetahs and wild dogs? Even though wild dogs, like hyenas, live in groups, there’s no evidence that this helps them defend themselves or their kills against lions. And cheetahs, well, there’s no record of them killing lion cubs, but who knows?

So how do these guys live with lions? To be honest, wild dogs don’t tend to do very well in places with lots of lions. In fact, it’s generally believed that wild dogs have failed to recolonize Serengeti, despite living *just* a few km from the border, because lion populations are so high. For a long time, researchers and conservationists believed that cheetahs also couldn’t survive in places with lots of lions – but that perception is beginning to change, due, in part, to data coming in from Snapshot Serengeti! It seems that cheetahs not only do just fine in reserves with lots of lions, but use the same areas within the park as lions do. I have a sneaking suspicion that how cheetahs use the habitat with respect to lions, how they avoid encountering lions even though they’re in the same places, holds the key to their success. Avoidance, combined with habitat that makes avoidance possible (read: not the short grass Serengeti plains you see below).

Slide5

I’ll write more about avoidance and habitat another day. In fact, I’m currently revising a paper for a peer-reviewed journal that addresses how cheetahs and wild dogs differ in the ways they avoid lions – if accepted, it will be the first appearance of Snapshot Serengeti data in the scientific literature! I’ll keep you posted…

Data-palooza

You might remember the Kibumbu pride from their rather gruesome encounter with a leopard. But probably not – that was a long time ago.

They now have a new claim to fame. As of April 22, 2013, the Kibumbu lions became the first Serengeti pride to bear a GPS collar. GPS collars are cool, but if you are a nerd like me, and trying to calibrate 225 camera traps against the known reality of animal movements, GPS collars are really [expletive deleted] cool.

IMG_0839

Daniel collaring a study lion

With regular old radio-collars, we have to get out in the field, driving (seemingly aimlessly to bystanders) in circles on hills until we get a signal in the direction of a given lion pride. With 26 prides being monitored now, we get to each pride about once a week. But with GPS collars, the data comes to US. On it’s own. EVERY HOUR. I can tell you where the lions are without ever leaving my hyena-chewed, baboom-mangled armchair. Data of this richness are simply impossible to get otherwise. I tried a few “all-night follows” – trying to serve as a living GPS collar. Trying to figure out why, when lions are lurking 300 meters from a camera trap, they don’t appear in it. I usually fall asleep by 9pm.  Apparently I don’t make a very good GPS collar.

You might wonder why on earth we don’t have 26 GPS collars, instead of 1. Unfortunately, they are expensive (read >$5,500 a pop), and the battery life doesn’t last as long as regular old VHF collars, meaning we would have to dart lions more often – which is a stress that we like to minimize. But Ingela Janssen had an extra collar from her conservation work in the Ngorongoro Conservation Area, and the chance of calibrating camera trap captures against hourly lion movements was too good to pass up!

Here’s the first map of Kibumbu’s movements. The first position came in at 6pm on April 22, and the last was recorded on the 23rd at 9pm. Since lions are nocturnal, we take one position every hour from 6pm to 7am, and then one position during the day (at noon). You can see from the lines that lions can move quite a ways without actually getting very far.

KB_firstMap

Kibumbu’s first GPS recorded movements

And here’s their latest map.

And the last few weeks...

And the last few weeks…

I realize that these graphics don’t give you any sense of where in the study area the lions are.  Until I figure out how to work some really cool magic with Google Earth, here’s a map of where the cameras are. You can see from Kibumbu’s maps that they are hanging out along a (sometimes dry) river – the Ngare Nanyuki – which I’ve circled in red on this camera layout map.

Slide1

Camera Traps – Ngare Nanyuki River circled

The GPS collar won’t show up until Season 6 camera photos — but it looks a bit different from our normal collars with two big lumps instead of one:

GPScollar

Vectronic GPS collar – stock image

So keep your eyes peeled!