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Machine Learning Update

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Hartebeest through a dislodged camera-trap cover.

It has been just over a year now since Snapshot Safari was launched. Snapshot Serengeti as the original Zooniverse citizen science camera trap project has remained the flagship project but there are now several other projects under the Safari banner.

 One of the good things about joining forces with all these other projects is that collaboration tends to bring perks that operating on your own doesn’t. For example, different areas of expertise that some of us would just never have thought of, being somewhat far from the mind of field researchers and ecologists.

 I am talking about the computer learning side of things, ML (Machine Learning) in particular. The team behind Snapshot Safari have been working hard on this aspect essentially to help speed up the rate of classification needed now that there is so much data across different projects.

 They have recently engaged a specialist in machine learning at the University of Minnesota who is helping them to develop ML for use with the Snapshot Safari projects.

 The idea is to run an algorithm on the data prior to uploading it to the Zooniverse, this will identify most of the misfire and vegetation only images meaning us volunteers will be left with more of the good stuff, the actual animal images.

 The algorithm has been trained on millions of images from Snapshot Serengeti, now for these latest batches the team have asked the ‘machine’ to predict which species it is seeing, how many and what the behaviour of the animals is. Don’t panic we really are in the early stages and the idea is to compare what it came up with against the actual results from the volunteers whom we already know are pretty darn accurate. The team doesn’t expect great things yet from the ML and doesn’t foresee computers taking over any time soon but it will be interesting to see how the ML goes.

 So, for now things will be continuing as normal, no changes in how you classify or what you do but hopefully there will be fewer blank images with no animals. As the team stresses, they are a looonnng way from machines taking over.

 For those of you who enjoy being part of this developmental side of the project the Safari team will soon be launching a side project called Snapshot Focus. It is designed to also look at how well the ML is at recognising animals in trickier images, especially those with multiple animals. If you feel like helping out as a break from the usual work flow it couldn’t be simpler. All you have to do is answer yes/no as to whether the computer has managed to put a bounding box around every animal in the image.

 Look out for updates from the team over the coming months to learn more about these developments but meanwhile there are still lots of images to classify on Snapshot Serengeti.

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The Lone Lion

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Kalamas and Lakes pride female Photo Credit: KopeLion, Ingela Jansson

 

It seems as though when it comes to lion ecology most of the experts seem to agree that male coalitions are usually the most successful at holding on to females and siring cubs. Certainly when take-overs happen it is usually the coalition with more members that wins the day and lone males find it hard to stand their ground. Numbers seem to count.

Of course that isn’t to say that single males can’t have fun or success. Take Kalamas, a male known to us in the Ngorongoro Conservation Area. He is a nomadic male who wanders far and wide across the area even daring to take trips into the Crater itself, an area that in terms of lions is heavily defended by resident males, competition is very strong there and really not a place for a none resident lone male to be seen.

So what is so different about Kalamas. Well firstly he doesn’t seem concerned about the competition. Earlier this year whilst monitoring the Crater Lion’s Ingela Jansson of KopeLion project spotted a very distinctive dark maned male that she recognised as Kalamas. The last time he had been spotted in the Crater was in November 2015 but this time there he was in full view lounging around mating with one of the Lakes pride females. In the background four contesting males could be heard roaring their presence.

Kalamas ignored them and had the audacity to stay put in the crater with the female for three days before walking back up the steep Crater slope and out onto the open plains of the Ngorongoro Conservation Area where despite being surrounded by Maasai herders and their live stock he managed to stay out of trouble.

A few weeks later however we received a frantic message early one morning to say that Kalamas was sitting out in the open with many herders starting to gather. Fearing some sort of conflict our team rushed to the area, luckily fairly close to headquarters. Once there we could see that people were sensibly keeping a safe distance and approaching by car it was evident that Kalamas had been fighting. He showed deep wounds characteristic of fighting male lions and there was much blood splattered around.
He attempted to stand but couldn’t quite make it and so we feared he may have been fatally injured.

We decided to stay around and monitor the situation; Kalamas just lay there for many hours. As the sun climbed to its midday point kalamas managed to drag himself into the shade of our vehicle where he remained for the rest of the day. Just as we were starting to wonder what on earth to do next, with night fall approaching, Kalamas took us totally by surprise and stood straight up, shook himself gently and, rather shakily started to walk towards the safety of a well treed gully. Satisfied that we had done all we could and that Kalamas would take care of himself we left.

For the next few weeks we monitored his movements and he seemed to lay low, recovering, but you can’t keep a good lion down. Far from learning his lesson about encroaching on other male’s territories he has since been seen in the presence of other females from the Crater rim. His modus operandi seems to be to hang around on the periphery and entice the ladies away for a few days at a time. They just don’t seem to be able to get enough of him. Something about that Jon Snowesque mane of dark shaggy dark hair.

It is an interesting tactic. We ponder whether perhaps mating with pride females belonging to other males in this sneaky way may mean that when (and if) they give birth the resident male is duped into believing that Kalamas’s offspring are their own.
It is certainly a great way for Kalamas to get as many females as possible but not have the burden of looking after any of the offspring.

It is certainly an unusual story and far from the norm. It remains to be seen if Kalamas was at all successful or if the resident males were harder to fool than he imagined. We are looking out for cubs with dark manes though.

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The ladies just love Kalamas Photo Credit: KopeLion, Ingela Jansson

 

 

 

 

Watching For Whisker Spots

I recently met with Meritho, who has to have one of the best jobs in the world; he is paid to watch lions.

Yes it does sound like the dream job, following lions all day, observing their behaviour and trying to identify them but Meritho’s job is not quite the dream it would seem. For various reasons the long running Serengeti Lion Project was put on hold for three years which meant that all the diligently followed lion prides known intimately by researchers have done a lot of growing up, giving birth and dying. Not surprisingly it’s hard to work out who’s who and who belongs to whom.

Meritho has inherited the arduous task of re-establishing the family connections and splits within the Serengeti’s lion prides. Armed with some old scribbled maps and a stack of cards with drawings of lion whisker spots he has to compare each lion he sees with these cards to help him workout just who is still out there in the Serengeti lion society. Of course the camera trap images help a little but only if they capture the perfect close up, in focus image of the lions muzzle showing the spot pattern. In reality its all down to traipsing around the Serengeti looking out for lions and comparing each and every one with the hundreds of hand drawn cards.

 

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I asked Meritho how he tackles this mammoth task. Making a plan is key, he says, with most of the tracking collars non functional you have to think hard where the lions might be and just drive around looking for them.

Ok you can narrow it down a bit as Meritho does by getting up by 5 am, making sure your vehicle is puncture free and stocked with fuel and water and then heading out to try and catch the big cats as they finish up for the night. At this early hour they are often looking for a good spot to spend the day or joining back up with young cubs that have been left somewhere safe whilst mothers where out hunting. All this movement increases his chances of running into lions.

Most of the time Meritho is far from base so eats lunch in the car only returning home around 5:30 as it starts to get dark. Its long hours and most of the time you are either sitting waiting or driving, briefly interspersed with spells actually watching the lions. In return they themselves are often infuriatingly sleepy and won’t lift their heads for you to get good pictures of their whiskers meaning even when you do find lions you cannot always see who they are.

So far he has managed to identify around 150 individual lions and is monitoring around 18 prides. Monitoring lions gives him a sense of pleasure that he is out there doing a scientific job he never dreamt, as a Tanzanian, he would get the chance to do. He says ‘ when I look at where I come from and where I am going as a researcher it brings a lot of value to my life, knowing what research means is one thing but doing research makes me feel like I am contributing something to the world and my home environment’. He is gaining knowledge and experience daily and hopes to continue doing great things within conservation, an inspiration to aspiring local scientists.

It’s great to know that Meritho is out there following the lions again and that the Snapshot Serengeti cameras are still going to be clicking away for sometime to come.

 

Trials and Tribulations

 

Data collection is the back bone of field research work and can sound glamorous and exciting to those who are office bound but I will let you into a little secret, it can be exhausting and frustrating and unrewarding too.

Firstly, you have to remember that researchers often work in remote places and whilst this is amazing it does lead to some logistical nightmares. Take for instance my recent experience. My task was to visit 18 Ilchokuti or lion guardians from KopeLion to collect the data they had recorded during the previous month. Now they are spread out over 1300k2, in itself quite a distance but when you factor in the rough at best, non-existent at worst roads you begin to have an idea of the task. I would be lucky if it didn’t rain, that would only add to the woes. Another thing to remember is that, barring a few lucky people working for high profile organisations, most researchers have to nurse their aged vehicles along, fixing things as you go. This trip wasn’t too bad as we seemed to only suffer from door catches failing so nothing a bit of string or a Leatherman wouldn’t fix. The budgets just never seem to run to decent cars.

Just as I was about to feel smug about the lack of rain hampering our journey it dawned on me that dry conditions held their bad points too. Dust! The fine dust covering some of the landscape here is deadly. It penetrates everything and with a three-day trip planned with no opportunity for a shower, boy does it get tiring. Forget enjoying the scenery as you drive, you mostly feel as if you are in a cloud only with a yellow tinge that makes it hard to breath in place of the fluffy white.

Anyway, I can’t really complain it was a wonderful three days and meeting up with a couple of our guys in the middle of nowhere under a great baobab tree acting as our office for an hour or so was something to make you smile.

 

Data collection Credit: KopeLion

Data collection. Credit: KopeLion

 

 

My colleague, Meritho Katei, over in the Serengeti has an even harder job under similar conditions. I was simply rendezvousing with other people, collecting and issuing data sheets and downloading GPS data. Meritho is trying to pick up on the lion monitoring for the Serengeti Lion project that has been on hold for a while.

His task is to reconnect with the prides of lions previously being followed and studied and to catch up on the family histories. New members need to be identified, files made on them and changes in pride composition noted. He is working with the Snapshot Serengeti camera trap data to see where the prides are hanging out but of course we aren’t quite up to date with the classifying so that’s not the greatest help. Instead he is relying on a lot of kilometres driving, following up on tourist sightings and tracking data and a good set of eyes to track down the prides and observe them.

So as I washed the dust out of my hair, luxuriating in a hot shower after my three day successful, mission accomplished trip, I had to reflect that poor Meritho was in for many months of hard slog catching up with those lions and with the rains coming things are about to get even harder. Good luck Meritho!

 

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Serengeti lion pride

Lion Fight

 

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Photo Credit: Edward Lopatto

 

These incredible images of a major lion turf war have been taken by the team in the Serengeti and come with the fantastic announcement that the long running Serengeti Lion Project is back up and running.

Although the camera-trap aspect of the project has continued without pause, the main work of the Serengeti Lion project  has been on hiatus for the past few years. Now, it is finally being restored and the priority is to sort out who’s who in all the study area prides. Comparing existing id’s and adding new ones is going to take some time.

Looks like these boys are trying to shake up the genes even more. Two coalitions both looking strong have clashed over ownership of prime real estate. The team report that all the males involved looked strong and healthy so this is probably not the definitive battle.

We will have more news for you soon on how the work is going as well as reports from the field, so stay tuned. Meanwhile enjoy these stunning images.

A Team Effort

Snapshot Serengeti has been on the go since 2010 in one form or another and over those years a team of dedicated people has kept it running. The base of the effort is the 225 camera-traps that have been snapping away continuously for that whole period. Of course for that to happen there needs to be researchers and assistants on the ground physically looking after camera-traps, a scientific team who coordinate all data processing and analysis, a management team running the administration of the project  and generous funders to keep everything alive and kicking.

Snapshot Serengeti could also not work without all the thousands of volunteer citizen scientist who generously give their time and energy to classifying all the millions of images, ultimately helping the researchers to answer scientific questions we hope will aid in the conservation of all that we love about the Serengeti.

Here in these blogs we have celebrated all these people but it dawned on me recently that there is one group of people that seem to have been forgotten, our moderators.

Our amazing team at Snapshot Serengeti deserve a special mention. They, like our citizen scientists are volunteers, dedicating their time and expertise for free. Contrary to what some may think they are not part of the scientific team in as far as they are not university students who do the job as part of their studies. No, they are a mixed bunch in terms of back ground and do the job plain and simply because they love the Serengeti and love the project. They spend a huge amount of time online helping other users with their classifications, guiding new users through some of the pit falls they know only too well and sharing their collective knowledge through prompt responses to questions and great information posts helping others with less experience to understand the Serengeti and its wildlife. They also have to deal with the odd, luckily very infrequent, troll which is a thankless task in diplomacy. We are privileged to have such an amazing team and I know that they are greatly appreciated by Snapshot Serengeti’s participants.

So thank you to davidbygott, maricksu and tillydad who have been with us since the beginning and welcome to parsfan and nmw. You Guy’s are the best and Snapshot Serengeti would not be the experience it is without all your help.

 

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Hartebeest through a dislodged camera-trap cover.

Vulture Culture

Lappet-faced vulture

 

Of all the large birds out there on the Serengeti plains the vultures are probably the most recognisable, with their long barely feathered necks and large hooked beaks, you can’t miss them. For a lot of people they are ugly birds and their behaviour makes people shudder, all that frantic plunging of necks inside messy carcasses. Some cultures revere the vulture, instilling magical attributes to them whilst others vilify them.

But the truth is they are just birds with their own unique ecological niche, one that is absolutely essential to the health of the whole ecosystem.

Lets break it down. That neck, well the fact that the whole head and neck is either bare or only lightly feathered is a marvellous adaptation to keeping clean. Yep, not something people generally associate with vultures but they are in fact pretty clean birds. That beak, well it may look like it could kill quite efficiently but it is actually designed to grip hard and rip. Believe me I have been around rescued vultures and felt the effect, there is a lot of power there. A vulture will use its sizable feet to hold a tricky bit of carcase down when trying to tear off a chunk but the real power comes from the strong neck muscles and the powerful beak.

If you look closely at the different species of vulture you will notice that not only is there a difference in size of individual species but in the beak size. There is a hierarchy in vulture etiquette at a fresh carcase. If the dead animal is large and has a tough hide, say a buffalo, the larger species such as lappet-faced will be needed to ‘break in’. Their huge beaks and added bulk allow them to head straight for the good bits where lesser vultures would have to start with the natural openings such as the eyes, mouth and anus. Once the large vultures have broken in, the rabble takes over and fights it out for the good meat, the white-backed and Ruppell’s. Around the peripheries the hooded vultures will be waiting for the chance to snatch up bits of anatomy that are sent flying by over- zealous cousins or to dart in when the carcase looks almost clean to pick off the last bits of flesh in hard to reach places. It is not uncommon to see this species right inside the empty carcase and its slim lined beak is great at cleaning up.

Vultures search for food from the wing. Research has shown that in the Serengeti it is most often the lappet-faced that arrives first despite the numbers of this species being lower than the others. It seems they are extra vigilant or just have better eyes. The descent of this the largest African vulture draws in the other species who can be clued into the find from over 30kms away. It is quite breath taking to see many vultures on rapid descent with wings held inwards, feathers splayed it can also be noisy.

But other than cleaning up unsightly dead things how do vultures help the ecosystem? Like other organisms that consume dead animal matter vultures are immune to a lot of deadly diseases. Their stomachs are filled with very acidic digestive juices which can destroy diseases such as anthrax, cholera and rabies. Most scavengers would not be immune to these types of disease and what’s more, diseases such as anthrax can lay dormant for decades posing an ongoing risk. Of course vultures alone can’t keep the Serengeti disease free but with their ability to fly over 100km a day they do a darn good job of patrolling the plains and keeping them clean.

But outside of protected areas vultures are in decline. In places like South Africa there has always been a value placed on vultures with Sangoma or witchdoctors prescribing vulture heads for people needing to see into the future to answer big life questions. Of course this has modernised, now people purchase vulture heads to see the winning lottery numbers. Vultures are also targeted by poaching gangs who, in an effort not to have their poaching camps discovered, place poison bait to attract and kill the vultures. India, several years ago nearly lost ALL its Gyps vultures. 95% where thought to have died and the main cause discovered to be adverse effects from a drug called diclofenac that was widely given to domestic stock. The drug has since been banned in India but its use as a veterinary drug in Africa is rising causing major concern amongst conservationists. Loss of habitat is also an issue.

We are lucky that the Serengeti is an ecosystem functioning normally with all its facets. You may be lucky to spot, lappet-faced, white-headed, white-backed, Ruppell’s griffon, hooded and Egyptian vultures in our camera trap images. It is quite remarkable to find this type of balance these days and we thank the vultures for their ongoing services.

Living In The Lions Den

 

Snapshot Serengeti is in the limelight again!

A new paper titled “No respect for apex carnivores: Distribution and activity patterns of honey badgers in the Serengeti” has been published by a team from the University of Wisconsin and University of Ljubljana using the Snapshot Serengeti data classified by our citizen scientists.

Honey badgers are surprisingly understudied. Although extremely charismatic the fact that they have large territories, up to 541km2 for an adult male in the Kalahari, and no clear habitat preferences makes it hard to predict where to find and study them.

The Snapshot Serengeti data of course is a dream come true to many researchers enabling them to ask scientific questions without having to wait potentially years to collect data themselves.The team took advantage of the open access data, courtesy of Snapshot Serengeti to look at what they could learn about honey badgers and how they live alongside other predators. Ferocious as they are honey badgers are killed by lion, hyena and leopard and so the team wanted to know whether they avoided areas where these large carnivores were active.

Well it seems that despite ending up as an occasional victim the honey badger is quite happy living alongside the larger carnivores, at least in the Serengeti anyway according to the authors. It appears as if the honey badger actively seeks out the same habitats as the large carnivores. The authors modelled a variety of different explanatory scenarios to see which would be the best fit to explain honey badger distribution across the Serengeti study area. Included where variables such as habitat preference, water availability, cover availability, lion abundance, and leopard abundance. Their best models showed that the presence of all three large carnivores coincided with the presence of honey badgers and that there was also a positive correlation temporally between leopard, hyena and honey badger showing that they use the same habitat at the same time.

It’s interesting stuff. The authors do point out that although the data set was huge there was actually very few incidence of honey badger over the 3 year period covered by their work and so their sample size was small. It does however show just how valuable the data collected by Snapshot Serengeti and the other Snapshot Safari projects can be, if nothing else to give scientists a relatively inexpensive way to explore questions before undertaking more specific research work themselves.

You can read the paper here, although it is not open access unfortunately: https://www.sciencedirect.com/science/article/pii/S1616504717302720

 

These two images illustrate the point nicely, you can clearly see the same camera has captured honey badger and spotted hyena with in 13 days of each other. Interestingly both in day light.

Recap on Snapshot

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Snapshot Serengeti camera-trap image: Topi

Whilst stretching the corners of my brain to think about a new topic to write about in the Snapshot Serengeti blogs it astounds me to realise just how long we have been going for; over 7 years now as Snapshot Serengeti and almost 10 if you include the Serengetilive days.

It is also humbling to know how dedicated our followers are and what support we get from them. Our fun would have been over long ago if the community had not backed us. It has occurred to me that Snapshot Serengeti’s followers do so in differing ways. Those who follow our facebook and twitter pages or WordPress fans who follow us through our blogs may have missed what it is we are up to. So at risk of boring those of you who do know I thought it was about time to reiterate what it is we at Snapshot Serengeti do and how it all works.

Our largest group of followers do so at www.snapshotserengeti.org helping us classify the millions of camera-trap images that are produced by around 225 camera-traps placed in a permanent grid pattern in our study zone in the Serengeti National Park. For continuity’s sake these sites, after an initial bit of trial and error have remained in their fixed spots since they were first chosen by the projects designer, Dr Ali Swanson back in 2010.

Originally the camera-trap grid was set up to answer questions on carnivore interactions specifically if carnivores were avoiding one another spatially and temporally, it soon became apparent that it could be used to pose many more scientific questions amongst them herbivore coexistence and predator prey relationships. The wisdom to leave this permanent window of observance into the lives of the Serengeti animals should lead to many future studies and has spawned many new similar camera-trap projects around the world.

It’s not all about the animals, in fact since teaming with Zooniverse the project has been as much about the advancement of citizen science as anything else. Back in the Serengetilive days there were so few of us taking part that we used to have our names up in a sort of league table of who had classified the most images. Each classified image was labelled by the classifiers name. Now of course there are far too many participants to bother with that kind of thing, besides with multiple people having to agree on each classification it might get messy. The work on developing a robust algorithm that dealt with the uncertainties in each individual classification was so involved it also paved the way for many more projects and several scientific papers.

So what do we ask classifiers to do? Well first you are presented with either a run of 3 images (day time) or 1 image (night time). You are then asked to decide and record what animals are present, numbers of each species, behaviour and whether there are young present or not. It’s pretty straight forward with prompts along the way. If you don’t know what the animal is you simply guess. Yes you read that right, you guess. One thing the developers worked out is that the whole project works better if you cannot skip images. For one thing it avoids all the hard or boring images being left till the end. As each image has to be agreed upon by several classifiers before it is retired this tends to smooth out any miss classifications and research has shown we are around 97% accurate.

If you find something good or something you cannot id and are curious you can add the image to Talk which is the discussion forum. There we have some very dedicated moderators who will help you with your queries.

All in all Snapshot Serengeti is about learning and sharing both for the researchers and for the community of classifiers so if you have been enjoying the facebook posts or reading the blogs but have never had a go classifying get yourself over there to www.snapshotserengeti.org and have a go.

A Spiky Surprise

There is one little animal in Europe that is loved by all, immortalised in children’s books, welcomed by gardeners and flagship of the realisation that our mammal populations may be declining due to our very own actions. Over in the States although not native these same creatures are kept as pets (that’s another story and not such a good one). Although it’s hardly a creature to cuddle or pet they are thought of as very cute, something to do with that snuffling around your garden in dry leaves and, getting all snoozy, having to sleep away the winter in a cosy corner. Yes, I write of the hedgehog.

Now, why, I hear you ask is she writing about a European mammal on a blog about the Serengeti? Well it may come as a surprise to some to find out that there are in fact 18 species of spiny hedgehog found across Europe, Asia and Africa. Six species are present in Africa. The North African hedgehog (Atelerix algirus) extends its range across the Mediterranean belt of North Africa and Iberian Peninsula as well as the Balearic and Canary islands. The long-eared hedgehog (Hemiechinus auritus) touches into Libya and Egypt and the desert hedgehog (Paraechinus aethiopicus) a true Saharan specialist. The last two species are also found through Arabia and Asia. The remaining three species are solely found in Africa; the southern African hedgehog (Atelerix frontalis), Somali hedgehog (Atelerix sclateri) and the four-toed hedgehog (Atelerix albiventris).

The four-toed hedgehog is found across West, Central and East Africa as far as the Zambezi River and so is the species that is found in the Serengeti. As far as I know we have never had a capture event from our camera traps of this enigmatic little creature but please let me know if someone has come across one.

In European culture where woodlands are seen as wildlife havens most people would associate the hedgehog with forests or at the very least the edges of forests and hedgerows where indeed this species is well at home but its African cousins are rather different in their habitat preferences. The four-toed prefers the drier regions and is partial to grasslands and according to The Handbook of the Mammals of the World vol 8 it especially likes overgrazed regions with dense ungulate populations. All that trampled grass and dung supports plenty of insects for it to munch. Well that sounds just like the Serengeti to me!

Although insects make up a large part of the diet they are omnivorous and will eat fungi and fruits as well as other plant matter. A little known fact, they will also kill small vertebrates like frogs, lizards and mice and are known to take on even venomous snakes. Their spines are great protection from the bite of an angry snake.

As formidable as those spines are it is the ability to curl up into a ball that is their true defence. Now they don’t just tuck their heads in and hope for the best, the skin that the spines are attached to is very flexible and is edged by a strong band like muscle that is attached to the forehead. When it is contracted it acts like a drawstring on a bag that holds in the body, head and limbs with the spines closing up the seal. It works remarkably well but inevitably certain animals have learned how to unzip the bag, honey badgers and eagle-owls are amongst those experts in the Serengeti.

As a family hedgehogs are known to perform a bizarre act known as self-anointing. The hedgehog will chew and lick a substance until it has a mouth full of saliva and then with acrobatic contortions it will plaster this saliva all over its body, apparently they do this in a frenzied manor and it is quite hard to distract them once in the process. What is unclear is why they do it. There is no obvious reason. Studies have shown every age group performing self-anointing including nestlings whose eyes have not even opened. They only thing that stands out is that strong smells and tastes seem to trigger the behaviour such as dog or fox urine and a whole host of human made items such as leather, polish or nylon stockings. I am not even going to ask what the scientific research question was when they discovered those three!

So from Mrs Tiggy-Winkle (Beatrix Potter) to sonic the hedgehog we may all be very familiar with this loveable creature but perhaps we don’t know all there is to know. Keep your eyes out for the first Snapshot Serengeti camera-trapping.

 

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Four-toed hedgehog

Image: Author Jkasui, Wikimedia, https://creativecommons.org/licenses/by-sa/3.0/deed.en