Archive | November 2013

White Lions of the Timbavati

When I was working in South Africa two years ago, I had the chance to meet a very unusual subspecies of big cat. Following up on a lead from one of my Afrikaner coworkers, I managed to get an up-close and personal encounter with the “white lion”, a rare color mutant of the subspecies Panthera leo krugeri which is found only a few wildlife reserves and parks in southern Africa. This lions used to occur naturally throughout the Timbavati region until they were completely extirpated from the wild through selective trophy hunting. There are now estimated to be less than 300 of these individuals world-wide.

white1

At a reserve where a pride of these lions is maintained, I helped a local veterinarian examine one of these magnificent animals who was suffering from a gastrointestinal aliment. As you can see, the lions are not pure white – they are not albino, but rather leucistic, and this coloration is the result of a recessive gene known as the Chincilla or color inhibitor gene. There is a mutation in an enzyme (tyrosinase) that results in decreased melanin production and inhibits its deposition along the hair shaft. Pigmentation is only found in the very tips. “Whiter” lions are the result of less pigment in the hair shaft, and even the manes and tail tips of the males are pale instead of the typical golden or black. They maintain pigment in their eyes, paws, and lips.

eyes

Interestingly enough, this pale coloration does not seem to inhibit their fitness in the wild. The White Lion Trust has been reintroducing prides of white lions back into their endemic habitat with much success. The goal of the organization has been to conserve this rare phenotype and increase the biodiversity in the Timbavati region. According to their reports, the white lions do not exhibit decreased hunting success and breed successful, producing several cubs over the last few years. Increasing genetic diversity in dwindling wild populations is important for the preservation of the subspecies as a whole. Good luck to the white lion! It was amazing to have a chance to interact with these magnificent animals.

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Happy Thanksgiving

Tomorrow is American Thanksgiving. Whether or not you celebrate Thanksgiving this week, I hope you’re able to spend time with family,

Spend time with family

Spending time with family

hang out with friends,

Hanging out with friends

Hanging out with friends

find some tasty food to eat,

Good eats!

Good eats!

get some rest,

Getting some rest

Getting some rest

and give thanks for the good things in life.

Giving thanks

Giving thanks

And a special thank you from us to you for all the work you’ve put in to classifying animals on Snapshot Serengeti.

Let the analyses begin!

Truth be told, I *have* been working on data analysis from the start. It’s actually one of my favorite parts of research — piecing together the story from all the different puzzle pieces that have been collected over the years.

But right now I am knee-deep in taking a closer look at the camera trap data. Since we have *so* many cameras taking pictures every day I want to look at where the animals are not just overall, but from day to day, hour to hour. I’m not 100% sure what analytical approaches are out there, but my first step is to simply visualize the data. What does it look like?

So I’ve started making animations within the statistical programming software R. Here’s one of my first ones (stay tuned over the holidays for more). Each frame represents a different hour on the 24 hour clock: 0 is midnight, 12 is noon, 23 is 11pm, etc. Each dot is sized proportionally to the number of captures of that species at that site at that time of day. The dots are set to be a little transparent so you can see when sites are hotspots for multiple species. [*note: if the .gif isn’t animating for you in the blog, try clicking on it so it opens in a new tab.]

hourlytestIt’s pretty clear that there are a handful of “naptime hotspots” on the plains. You can bet your boots that those are nice shady trees in the middle of nowhere that the lions really love.

Graduate School

Maybe from time to time you’ve wondered: Who are these scientists running Snapshot Serengeti? How did they get where they are? (And why am I sitting here instead of traipsing across the Serengeti myself?)

Ali and I are both graduate students at the University of Minnesota. What that means is that a while ago (seven years for me!) we filled out an application and wrote some essays for admission to the University of Minnesota’s graduate school — just like you would do for college admissions. The difference is that for graduate school, you also need to identify an advisor — a faculty member who will become both your mentor and your judge — and an area of research that you want to pursue. And while the admissions materials matter, it’s very important that your future advisor want to take you on as a student and that your area of research interest meshes well with hers or his.

In the U.S., you can apply for a Masters program or a Ph.D. program. In some places you can get a Masters on the way to a Ph.D., but that’s not the case at Minnesota. So I applied for the Ph.D., got admitted and started as a Ph.D. student in the fall of 2007. I’m pretty much only going to talk about Ph.D.s from here on out. And I should point out that graduate school systems vary from country to country. I’m just going to talk about how it works in the U.S. because I’m not terribly familiar with what happens in other countries.

For the first 2-3 years in our program, students spend much of their time taking classes. These are mostly higher level classes that assume you already took college-level classes in basic biology, math, etc. I came in with an college degree in computer science, and so a bunch of the classes I took were actually more fundamental ecology and evolution classes so I could get caught up. But many classes are reserved for just graduate students or for grad students plus motivated seniors.

At the same time as taking these classes, students are expected to come up with a research plan to pursue. The first couple years are filled with a lot of anxiety about what exactly to do, and there are plenty of missteps. My first attempt at a research project involved tracking the movement of wildebeest in the Serengeti using satellites and airplane surveys. (Yes, you can see individual wildebeest in Google Earth if you hunt around!) But it turned out not to be a logically or financially feasible project, so I discarded it — after a lot of time and energy investment.

Around the end of the second year and beginning of the third year, grad students in the U.S. take what are called “preliminary” or “comprehensive” exams. These vary from school to school and from department to department. But they usually consist of both a written and oral component. In some places the goal of these exams to to assess whether you know enough about the broad discipline to be allowed to proceed. In other places, the goal is to judge whether or not you’ve put together a reasonable research plan. The program Ali and I are in leans more toward the latter. It requires a written proposal about what you plan to do for research. This proposal is reviewed by several faculty who decide whether it passes or not.

If you pass your written component, you then give a public talk on your proposed research followed by a grueling two to three hour interview with your committee. In our program, students choose their committee members, following a few sets of rules about who can be on it. My committee had five people, including my two advisors. They took turns asking me questions about my proposed research, how I would collect data, analyze it, how I would deal with adversity. The committee then met without me to decide whether I passed or not. (spoiler: I passed)

So, assuming a student passes the preliminary exams, she or he is then considered a “Ph.D. Candidate,” which basically means that all requirements except the actual dissertation itself have been fulfilled. If you’ve ever heard the term “A.B.D.” or “All But Dissertation,” that is what this means. The student got through the first hurdles, but never got a dissertation done (or accepted).

Now it’s time for the research. With luck, persistence, motivation, and lack of confounding factors, a student can do the research and write the dissertation in about three years. Doing research at first is slow because, like learning anything new, you make mistakes. I spent a lot of time gathering data that I’m not going to end up using. Now that I’ve been doing research for a few years, I can better estimate which data is worth collecting and which is not. And so I’m more efficient. While doing research, the student is also reading other people’s related research, and often picking up a side-project or two.

Eventually, the student, together with the advisor(s) and committee members, decides that she or he has done enough research to prove that she or he is a capable professional scientist. All the research gets written up into a massive tome called the dissertation. These days, it’s not uncommon for graduate students in the sciences to write up their dissertation chapters as formal papers that then get published in scientific journals. Sometimes one or more chapters is already published by the time the dissertation is submitted.

When the writing of the dissertation is finished, it gets sent to the committee to read. The student then gives a formal, public talk on the results of the dissertation research, followed by another two to three hour interview with the committee. This time it’s called the “Dissertation Defense,” and the committee asks questions about the research results (and possibly asks the student to fight a snake). The committee then meets without the student and comes up with a decision of whether the student passes or not. There is also often a conditional part of this decision that requires some portion of the dissertation to be revised or added to. So, a decision of “pass, conditional on the following revisions:” is pretty common.

I should mention that while being a grad student has been mostly quite fun, you may not want to drop your day job and run off to academia just yet. There’s the issue of funding. On the plus side, you can acquire funding in the sciences so that you don’t have to take on debt to do your degree (which is not so true in the humanities). Ali and I have both applied for and received fellowships that have allowed us to do most of our graduate program without having to work. But many — maybe most — grad students in the sciences work essentially part-time jobs (20 hours/week) as teaching assistants for faculty. This can really slow down research progress, as well as making some types of research impossible (for example, those that require lengthy trips to the Serengeti). Whether working or on fellowship, students typically gross no more than $30,000 annually, and often less than $25,000, which can be quite reasonable (single person living in a low-cost-of-living area) or prohibitive (person supporting a family living in a high-cost-of-living area). Benefits are pretty much non-existent, with the exception of health coverage, which can range from great (thanks, Minnesota!) to really bad to non-existent.

I mention all this this because I am about to defend my dissertation! In a little less than two weeks I will give a talk, sit down with my committee, and try to convince them I’m a decent scientist. Wish me luck.

Animals aren’t the only thing that’s cool

Crazy week this week, so I just wanted to post a link to this fascinating and hilarious blog post about plant communication. Yup, you heard right. Animals aren’t the only things that communicate: plants do too! But instead of using sound, plants communicate via chemicals.

First, some plants respond to hungry predators (e.g. bugs, mammalian herbivores) by producing bad-tasting or toxic chemicals that stops would-be-munchers in their tracks — this is called and “induced response” or “induced defense” and is pretty well documented in terrestrial plants. But what’s even cooler is that attacked plants might also release chemical signals to “talk” to neighbors — allowing un-munched-on plants to trigger pre-emptive defenses. Originally known as the “talking trees hypothesis,” this interplant communication was first described in the 1980’s — though more recent research suggests that “eavesdropping” might better capture the true nature of the interaction.

The “talking” seaweed Ascophyllum Nodosum, image from: onlyfoods.net

More recently and perhaps even cooler is that plants not only “talk” to each other, but to other animals! The blog post linked above describes an intertidal plant that basically calls in the predators of its predators. When the plant gets munched on, by, say, a snail, it releases a chemical signal that attracts things that eat snails, like crabs.

Crazy, and awesome. Even though I think I’ll stick with studying big furry things, plants are pretty cool.

What makes a vintage year for the Serengeti lions?

### Today’s blog is an excerpt from Craig Packer’s  forthcoming book, “Lions in the Balance: Man-eaters, manes and men with guns”, which will be published by University of Chicago Press in the fall of 2014. ###

When the Italians attempted to conquer Abyssinia in 1887, they provisioned their troops with livestock brought from India, but some of the cattle were infected with the rinderpest virus.  By 1897, the disease had spread south from the Ethiopian plateau to South Africa’s Cape of Good Hope and across to West Africa, killing ninety percent of domestic livestock across the entire continent. Control programs were initiated throughout Africa; by the 1960s rinderpest was restricted to only a few areas, and Serengeti was the last major reservoir in Tanzania.  A cattle-vaccination program around the Serengeti finally eliminated the disease from the wildlife inside the park in 1963.   Liberated from rinderpest, the wildebeest, buffalo, warthog and other ruminant populations grew exponentially until they reached their current plateaus in 1979.

The lion population grew, too, but in a very different pattern.

The lions in the wooded habitat of our study area remained stable from 1966 until 1973 when the population suddenly leapt to a new equilibrium, then remained stable for another ten years before leaping again in 1983.  The ruminant population had nearly tripled between 1966 and 1973; what held back the lions for so long? And what happened in 1973 and 1983?

Our lions endure an annual pattern of feast and famine; the migration brings the wildebeest and zebra within easy reach during the rainier months but sends the herds north to Kenya each dry season.  In normal years, our study lions struggle to persist on warthog and buffalo, but these only sustain the adults – few cubs manage to survive.

The dry season of 1973 was the rainiest in decades, and the unseasonably green grasses attracted the wildebeest and zebra to our woodlands study area more or less continuously until the normal rains returned in November.  Without the usual dry season famine, virtually every cub born in 1973 survived.

These surviving cohorts were large enough to form entirely new prides that could compete successfully against the prevailing social order and redraw the map of lion pride territories.  Tough new gangs squeezed their way into the neighborhood, allowing the lion population to finally rise to a higher post-rinderpest plateau.

The recovering herds not only provided more meat on the hoof, but the wildebeest’s insatiable appetite for grass subsequently modified the habitat in the lions’ favor.  An awful lot of grass was left uneaten when the wildebeest population was held low by rinderpest: grass fires roared through the park each year, burning the young acacia trees to stumps.  But the expanding wildebeest population became the world’s largest lawn service, mowing the grass down to the nubs over thousands of square kilometers – creating fire breaks through much of the park.  By the mid-1970s, less than a quarter of the Serengeti burned each year, and saplings were able to grow unhindered.  Tree recruitment reached a peak in 1980 and persisted for ten years.

Lions need cover to hunt more successfully, and 1983 was the first year with favorable dry-season rainfall in this new improved world for hunting lions.  Once again, the woodland prides recruited large numbers of young – large enough to spawn an expansion of new prides and redraw the map, with more groups packed more tightly than ever before.

The woodlands population crashed during a major disease outbreak in 1994 – lion numbers fell back to levels unseen since the late 1960s.  But in 1999 – the first post-outbreak year with favorable dry season rainfall – the woodland population bounced all the way back up to the same level as in 1983-1993.

On the plains, the population’s initial post-rinderpest spurt occurred sometime after George Schaller’s departure in 1969, reaching a new plateau by 1974 when monitoring of the plains prides resumed.  The plains population remained unchanged until November 1997, when El Niño brought the heaviest rains in forty years.  The grasses on the plains had started growing taller during the early 1990s, and the El Niño floods kept the migration out on the plains for the longest period in decades.  A single year with a more consistent food supply was enough to allow the plains lions to spawn whole new prides in the taller grasses.

As Lenin once said, “Sometimes decades pass and nothing happens; and then sometimes weeks pass and decades happen.”

Thanks to the Snapshot Serengeti camera trap grid, we can now watch the migration respond to year-to-year variations in rainfall.  The next time the lions have a banner year, we will all be able to witness how food on the hoof translates into a baby boom of lucky cubs.

What does the fox say?

By now, you have probably heard of this silly (but hilarious) video that’s been making the rounds of the interwebs lately:

It’s pretty catchy, not just because it’s ridiculous, but because it’s a pretty good question.  I mean, how many of you out there have actually ever heard a fox?

The sounds of the bush are one of the many, many things I miss being back here in civilization. From my slightly sketchy corner of Saint Paul, I hear fire crackers and unmuffled engines roaring. Occasionally I get chattered at by an angry squirrel in the back yard. But that’s about it. Nothing like the otherworldly chorus of the Serengeti savanna that Lucy so beautifully described.

The sounds really are incredible and often unbelievable, and I thought I’d share some of them with you. I couldn’t actually figure out how to upload audio files, so I scoured Youtube for the best audio clips I could find and embedded them as videos here.

Zebras: Nothing like horses, these stripy equids sound something like a braying donkey crossed with a barking dog.

Wildebeest: I believe that somewhere in the annals of Zooniverse blogs, there is an audio or video clip of me doing a wildebeest impression. This is better.

Hyenas: Despite being hell-bent on devouring all of my camera traps, these guys are pretty cool. They have a rather large repertoire of very…unusual…vocalizations that are used to communicate in a number of situations. The whoop, which you hear at 0:05 and 0:55, is a long-distance call often used to rally scattered clan members. The laugh at 2:33 is a sign of nervousness or submission. Similar to human voices, hyena vocalizations are individually recognizable to clan-mates. To learn more about hyena vocalizations, check out this blog by hyena expert and director of Masai Mara’s long-term hyena project, Kay Holekamp.

Lions: And finally, for the best, non-hollywood lion roar, scroll about halfway down through our lion research center’s page. This is what they really sound like.

I’ll take any of these noises over the sounds of the city any day.

George Schaller and the Serengeti Lion

To bring myself up to speed with the fundamentals of lion research in the Serengeti, I have spent the last week or so reading through the classic work The Serengeti Lion: A Study of Predator-Prey Relations, by the reputable George B. Schaller. For a collection of field notes, the book it quite a page-turner. The work covers everything remotely relating to lion biology, from social systems to predation patterns, and manages to capture both the drama of the dynamic Serengeti system and the dusty, hot, sweaty reality of watching big cats sleep for 18 hours a day.

Although the focus of the book is the life of lions, the life of George B. Schaller himself turns out to be just as intriguing. Digging a little into his background, I discovered that Schaller, dubbed the “Megafauna Man” by National Geographic, has undertaken a 50-year career in field biology studying some of the most iconic systems in the world.

Schaller had moved to the Serengeti with his wife and two sons for two years in 1966 to uncover the intricacies of the lives of big cats and their prey. This, however, was not the start of his field career. Back in 1959, when he was a mere 26 years old, Schaller packed up and headed off to Central Africa to study the mountain gorilla. For two years, amidst dodging poachers and eluding Watusi invaders, he uncovered facts about these great apes which helped to dispel common notions about their brutishness and revealed them to be gentle and intelligent animals. His work paved the way for other naturalists, including the well-known Dian Fossey, and led to the creation of Virunga National Park.

In the ‘70s, Schaller worked in both South Asia and South America, studying large mammals including the blue sheep and snow leopards of Nepal and the jaguars, capybaras, and caimans of Brazil. The American novelist and naturalist Peter Matthiessen accompanied Schaller to Nepal and wrote a travelogue on their exploits (The Snow Leopard) that went on to win the 1979 National Book Award. Matthiessen describes Schaller as “one of the finest field biologists of our time. He pioneered the practice of turning regions of field research into wildlife parks and preserves,” a epithet that held true yet again when five years later, the Nepalese government used Schaller’s research to form Shey-Phoksundo National Park.

Following these adventures, Schaller and his wife were given the distinction of being the first westerners invited by China to enter the remote southwest Asian wilderness and research the Giant Panda in its native habitat. As part of this work, Schaller focused on understanding threats to the diminishing panda population and discovered that the primary culprits in their demise were poaching and logging. In his book, The Last Panda, Schaller writes “The panda has no history, only a past. It has come to us in a fragile moment from another time, its obscure life illuminated through the years we tracked it in the forests.” Despite this foreboding prophesy, since Schaller’s work on panda biology, the number of panda in the wild has increased by 45%.

In the 1990s, Schaller worked in Laos, Vietnam, and Tibet studying antelope and in the process discovering and rediscovering several species of mammals including a bovine, a pig, and a type of deer. More recently, he has been collaborating with agencies in Pakistan, Afghanistan, Tajikistan, and China to develop a 20,000-square mile “Peace Park” for the protection of the world’s largest wild sheep species, the Marco Polo sheep.

Over the span of his career, Schaller has made profound contributions to our knowledge about large mammals, both their biology and ecology, and has greatly furthered species conservation in the creation of over 20 parks and preserves throughout the globe. I can highly recommend his writings on the Serengeti Lion, and if you want to delve further into his life and career, his other authored books (there are over 30) include The Year of the Gorilla, The Last Panda, Tibet Wild, and A Naturalist and Other Beasts.

The scourge of Daylight Savings Time

As Ali mentioned, we’re working on figuring out timing issues for all the images in Snapshot Serengeti. Each image has a timestamp embedded in it. And that time is Tanzanian time. You might have noticed that sometimes the time associated with an image doesn’t seem to match the time in the photo — especially a night shot with a day time or a day shot with a night time. We initially shrugged that off, saying that some of the times get messed up when the camera gets attacked by an animal.

But it turns out to be more complicated than that. All the times you see on Snapshot Serengeti — either when you click the rightmost icon below the image on the classify screen, or when you look at a capture in Talk — are on West Greenland (or Brazil) time. Why is that? Well, databases like to try to make things “easy” by converting timezones for you. So when the images got loaded up onto the Zooniverse servers, the Snapshot Serengeti database converted all the times from what it thought was Coordinated Universal Time (UTC) to U.S. Central Time, where both Minneapolis and Chicago are. That would mean subtracting six hours. But since the times are really Tanzanian ones, subtracting six hours sticks us in the middle of the Atlantic Ocean (or in Greenland if we go north or Brazil if we go south).

That wouldn’t be so bad, except for Daylight Savings Time. Tanzania, like everywhere close to the equator, doesn’t bother with it. It doesn’t make sense to mess with your times when sunrise and sunset are pretty much as the same time all year round. However, the ever-helpful database located in the U.S. converted the times as if they experience Daylight Savings Time. So on dates during “standard time,” the Snapshot Serengeti times are off by six hours; subtract six hours to find out the actual time the image was taken. But on dates during daylight savings, the times are off by just five hours.

blackboard

11:35am Tanzanian time. Shown as 4:35pm on Snapshot Serengeti.

And to make things more of a headache for me, those images that got taken during the hour that “disappears” in the spring due to Daylight Savings Time, get tallied as being taken the hour before. This might explain why we get some captures that don’t seem to go together: the images were actually taken an hour apart!

So now I’m focusing on straightening all the timestamps out. And when I do, I’ll ask the Zooniverse developers if we can correct all the times in Snapshot Serengeti so that they’re shown in Tanzanian time. Hopefully we’ll have that all set before Season 7.

By the way, I was able to figure this all out pretty quickly thanks to the awesome blackboard collection that volunteer sisige put together. You can see the actual Tanzanian time on many of the blackboards and confirm that the online time shown below the picture is five or six hours later, depending on the time of year. Many thanks to those of you who tag and comment and put together collections in Talk; what you do is valuable — sometimes in unexpected ways!

Don’t worry!

Deep breath; I promise it will be okay.

By now, many of you have probably seen the one image that haunts your dreams: the backlit photo of the towering acacia that makes the wildebeest in front look tiny, with those two terrible words in big white print across the front — “We’re Done!” Now what are you going to do when you drink your morning coffee?? Need a break from staring at spreadsheets?? Are in desperate need of an African animal fix?? Trust me, I know the feeling.

Deep breath. (And skip to the end if you can’t wait another minute to find out when you can ID Snapshot Serengeti animals again.)

I have to admit that as a scientist using the Snapshot Serengeti data, I’m pretty stoked that Seasons 5 and 6 are done. I’ve been anxiously watching the progress bars inch along, hoping that they’d be done in time for me to incorporate them in my dissertation analyses that I’m finally starting to hash out. Silly me for worrying. You, our Snapshot Serengeti community, have consistently awed us with how quickly you have waded through our mountains of pictures. Remember when we first launched? We put up Seasons 1-3 and thought we’d have a month or so to wait. In three days we were scrambling to put up Season 4. This is not usually the problem that scientists with big datasets have!

Now that Seasons 5 and 6 are done, we’ll download all of the classifications for every single capture event and try to make sense of them using the algorithms that Margaret’s written about here and here. We’ll also need to do a lot of data “cleaning” — fixing errors in the database. Our biggest worry is handling incorrect timestamps — and for whatever reason, when a camera trap gets injured, the time stamps are the first things to malfunction (usually shuttling back to 1970 or into the futuristic 2029).  It’s a big data cleaning problem for us.  First, one of the things we care about is when animals are at different sites, so knowing the time is important. But also, many of the cameras are rendered non-functional for various reasons – meaning that sometimes a site isn’t taking pictures for days or even weeks. To properly analyze the data, we need to line up the number of animal captures with the record of activity, so we know that a record of 0 lions for the week really means 0 lions, and not just that the camera was face down in the mud.

So, we now have a lot of work in front of us. But what about you? First, Season 7 will be on its way soon, and we hope to have it online in early 2014. But that’s so far away! Yes, so in the meanwhile, the Zooniverse team will be “un-retiring” images like they’ve done in previous seasons. This means that we’ll be collecting more classifications on photos that have already been boxed away as “done.” Especially for the really tricky images, this can help us refine the algorithms that turn your classifications into a “correct answer.”

But there are also a whole bunch of awesome new Zooniverse projects out there that we’d encourage you to try in the meanwhile. For example, this fall, Zooniverse launched Plankton Portal, which takes you on a whole different kind of safari. Instead of identifying different gazelles by the white patches on their bums, you identify different species of plankton by their shapes. Although plankton are small, they have big impacts on the system — as the Plankton Portal scientists point out on their new site, “No plankton = No life in the ocean.”

Wherever you choose to spend your time, know that all of us on the science teams are incredibly grateful for your help. We couldn’t do this without you.