GIS team blog
Welcome to Kew's GIS team blog. Here you will find information about the Geographic Information Science (GIS) Unit and its staff. We'll be posting updates on new developments in the field and our projects, also our thoughts and musings!
If you follow the work of Kew’s Geographic Information Science (GIS) unit you will be aware of the Sampled Red List Index (SRLI) project for plants. We even won an award from the Species Survival Commission for our efforts! I’d like to bring you up-to-date with what has been happening with the project and where things are heading.
Firstly, a quick reminder about what we are doing. We’re monitoring a set of plant species from all over the world in order to find out how endangered plants are faring and how that is changing over time. You should think of it a bit like a barometer indicating change, telling us whether things are getting better or worse for the world's plants. We presented the results of our first assessment in 2010 and showed that 1 in 5 plants are at risk, which got a lot of attention.
Cover of the 2012 SRLI report
We’re now a team of 6 people and were planning the next stages of the project - there are a lot of species and much work to be done.
The 2010 assessment marked the baseline of our barometer and we need to take a health check on plants again to see how they are doing.
Herbarium specimens need to be searched and scoured, and field teams will be going on discovery expeditions to hopefully find some of these really rare species.
Opportunistic collection of SRLI species during the drive north to Ambilobe, Madagascar
SRLI in Madagascar
Madagascar has a high number of SRLI species and excellent networks with Kew so it was the ideal country to test our methods and rediscover some of the species on our list. We work closely with local botanists and experts in the field, as they are vital in identifying species from difficult specimens.
Some SRLI species collected in Madagascar
During the 3 weeks in Madagascar, we managed to find 25 SRLI species, including numerous threatened species such as the Vulnerable orchid Sobennikoffia poissoniana.
We also found the only cycad known from Madagascar - Cycas thouarsii (Least Concern). While the species seems to be doing well at some of the locations, we also came across a site where most of the individuals had either been removed (most likely for the horticultural trade) or burned.
We were also fortunate enough to come across much wildlife during our expeditions such as the beautiful Indri (Endangered), numerous chameleons and many snakes.
Here's a snap of the SRLI Kew Madagascar field team with GIS's Maiko Lutz and Steve Bachman second and third from the left, with local specialists
Making use of citizen science
For the next phase of the project we will mobilise a global network of local botanists, botanic gardens and conservationists to establish an international, broad-based monitoring scheme. But we don’t only intend to use traditional data gathering methods as they can be slow and resource-heavy. We believe that existing projects (such as iNaturalist) and the new idea of the ‘citizen scientist’ may play an important role in the future of the SRLI for Plants project.
The first phase of the project gave us a snapshot of the status of biodiversity, using dried herbarium specimens and literature sources. However, to truly understand the changing status of the world’s biodiversity, targeted fieldwork is essential to update this information.
- Maiko -
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When people consider a trip to Peru, the first places they might think to visit are the Andes and Machu Picchu or the vast Amazon tropical rainforest - they rarely venture to the sites along the dry coast. I have to admit, I was one of those people. On my first journey to Peru I promptly made my way to Cuzco and trekked up to Machu Picchu with all the other tourists. So when I was told that the GIS team destination was the desert coast of Peru to find a lush and diverse ecosystem in the desert, I admit that I was a bit sceptical.
We were going in search of the Lomas, an extremely fragile ecosystem whose sole source of water is a coastal fog called Garúa, formed from cool, moist air driven up from the Humboldt Current pushing over the mountains of the coastal desert. These ecosystems span the coast of Peru and Chile in locations optimally combining moisture and elevation. Working alongside Peru’s SERNANP parks service and with the appropriate permits, our ultimate destination was the San Fernando Reserve, located on the coast of the Ica Region, approximately 30 kilometres southwest of Nazca.
We really did not know what to expect and a quick survey of some satellite images appeared to be giving little away.
GoogleEarth map of the Reservada San Fernando, Ica Province (Courtesy of GoogleEarth)
As we entered the reserve we started to see signs of life. The first area of vegetation we encountered was dominated by plants of the genus Tillandsia. What is incredible about these plants is that radio carbon samples indicate this system of vegetation is ancient (over 36,000 years old). We are only just beginning a journey to understand how the Tillandsia vegetation has apparently existed in the same place for millennia, surviving for much of the year without fog in a rainless world.
A Tillandsia plant
We continued over the last ridge towards the coast and discovered an area composed of a range of plant families, with the cacti, mallows (Malvaceae), legumes(leguminosae) and daisies (compositae or asteraceae) families predominating, and the whole area scattered with lilac flowering Nolanas (from the Solanaceae family).
Some of the beautiful flowers of the Lomas: A. Cactaceae family, B. Leguminosae family, C. Compositae family, D. Solanaceae family
Within this sandy landscape dotted with colourful flowers we made a base for five days.
The GIS team camping in the Reservada San Fernando
The Lomas is truly an amazing ecosystem, existing in a climate of extremes both of temperature and moisture. It was a challenge to start the day in temperatures reaching 30° C and ending the day at 15°C after the fog had rolled onto the hills.
View of sand dune transect within the Reservada San Fernando
We followed a 7 kilometre transect, varying 1,000 meters in elevation and descending the great sandy hills to sea level. Twenty plots were surveyed for species cover and 72 herbarium specimens were collected, many of them from species found nowhere else on earth. Herbarium specimens are small carefully selected bits of plants which, when pressed and dried, are vital to help conservation. They are the basic botanical scientific evidence, standing testament in the herbariums (plant libraries) of Peru and world. The samples are labelled with the GPS coordinates of where they are found.
The plants of the Lomas have adapted to capture the condensed water from the Garúa fog. It was clear that the key to finding the Lomas is timing - the plants in the Lomas flourish throughout October and November when the fog is at its most abundant, but, as in Chile’s flowering desert, some years are better than others. The diversity of plants flowering at this time of year is overwhelming, as each species must get through its whole annual cycle in just a few months, and produce seed for the next year.
Selection of flowers from the Lomas
Plants on the brink
The plants of the Lomas face a life of hardship, as the extreme variations in both temperature and moisture have required adaptations to survive. Sadly, humans impose even greater challenges, from mining and pipelines, to tourists recklessly driving through the Lomas on massive recreational dune buggies. The Lomas vegetation is now in danger at the hands of such anthropogenic pressures.
Sand dune buggies used by tourists in Huacachina
In addition to these activities, the threat from climate change may pose even greater challenges, particularly as it brings about significant changes to the climate regime that these plants depend upon for survival. Many Lomas around Lima have already been completely lost due to unregulated urban expansion. However, thanks to the present Peruvian government’s foresight, Lomas protection is being extended. But protection can only happen with wide collaboration and ecological research. The conservation of the Lomas has never been so urgent, and we need to act fast, before these secret worlds are lost forever.
- Amanda -
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The end of paper maps?
Paper maps have always been an essential component of botanical fieldwork. Prior to the trip they can be used for planning purposes like helping to define target areas for fieldwork, identify potential obstacles, plan road trips and, of course, whilst in the field they provide an essential navigation tool.
However the days of the paper map may be numbered as digital mapping goes mobile. Over the last year the GIS team have been testing out new mapping software on smart phones and seeing how effective they are in the field. One of the most promising products we’ve seen is called Locus Map and it is available for devices using the Android operating system. We put Locus Map to the test during several recent field trips and here is the verdict:
So what is Locus Map?
Locus Map is an application or ‘app’ that can be used on smart phones. Specifically, it can be used on the Android operating system, so is not available on Microsoft or Apple. On the simplest level, Locus Map puts a map on your phone and, of course, the great thing about smart phones these days is that they usually have an integrated Global Positioning System (GPS) receiver. So, if your GPS is on and you start up the app you will see exactly where you are and where you are going.
The extensive array of options are too numerous to review entirely so we’ll give a brief overview of some of the main features that we found useful:
Waypoints and tracks
Anyone familiar with using a GPS device will be at home with the waypoints and tracks options on Locus. You can record, pause and stop a tracklog and numerous settings allow you to control the way the track is recorded e.g. minimum distance between points and various style options. You can even allow Google’s MyTracks to take over recording.
The basic ‘Add point’ feature is the same as a standard waypoint. You have numerous options to customise how this is displayed on the map e.g. symbols and colours and you can group these into different categories or layers e.g. new observations for trees or good places to camp! When adding the point you can set the location in numerous ways e.g. GPS co-ordinates (most likely), but you may wish to add a waypoint some distance away from your exact location e.g. a vegetation patch in the distance, and this can be done by selecting the location using the cross-hairs on the map. There are notes fields to add additional pieces of information and even the ability to add you own custom fields, something most standalone GPS devices do not have. With the smartphone you also have the advantage of being able to enter text rapidly using the many text options including predictive text tools such as SwiftKey. Finally, it is worth pointing out that there is an ‘Add Photo point’ feature which is exactly the same as the add point feature described above, but with a photo.
As you would expect, all the standard navigational tools are built in. The compass can be used to guide you to a point of interest or a waypoint. A neat feature I found myself using a lot is ‘Guide to’ which allows you to choose a point on the map and it will show you direction and distance from that point. There is also a ‘Show view’ option which indicates the direction of view - simple, but very handy.
Having a good GPS is one thing, but looking at a dot in the middle of a white screen doesn’t help you a great deal. We need to have context in the form of base maps to help us understand where we are. Many smartphone mapping tools provide these base maps e.g. Google Maps, but they are downloaded to the phone so they incur data charges as you roam. When taking your phone abroad you are likely to incur significant data charges as your phone downloads more map tiles when you move around. The way to overcome this problem is to download an entire map before your trip so that it can be viewed even if you are offline.
There are two main types of map you might want to download: a vector map with points, lines and polygons (e.g. cities, road/rivers and lakes/vegetation patches etc.) or raster maps, which are usually satellite images. These help to provide context and highlight interesting features that you may want to visit. Locus provides some nice links to standard vector and raster basemaps that can be easily downloaded and made visible in your map viewer. Switching layers is very easy using the Maps icon.
Offline maps is also a way to get your own data visible on the phone. On a recent trip to Ethiopia for example, Jenny from the GIS team prepared a model of Coffea arabica distribution and imported this into Locus so that in the field, when she found coffea populations, she could see what the value of the model was at that site. Note that in some cases you may need to transform your data in order to get it into the right format. We use a package called MAPC2MAPC to help with that process.
Locus Map showing wild Coffea arabica occurrence records and the underlying species distribution model
Locus is extremely versatile in terms of file format options thereby making the movement of data on and off your device extremely easy. Prior to our trip to Madagascar in June this year I converted data from our BRAHMS database to KML format and then loaded that directly into Locus, thereby giving us all the locations of specimens that we wanted to visit. (see map below)
Adding your own data to Locus Map is easy. Here you can see the green dots that represent existing herbarium collections and the red dots represent the new collections we made on the recent trip. A satellite image is used as the basemap.
As with most apps nowadays there is a free and pro version. So what do you get with the paid pro version? Well one thing you won’t get if you go pro is advertisements, but aside from that it is mostly the removal of limitations in some of the features.
Locus Map in action in Peru. Here we are trying to get to the enclosed patch of woodland illustrating use of the ‘Guide to’ feature
- Smart and clean user interface and very easy to use
- Great feature list
- Good developer support - constant updates and improvements
- Customisable right sidebar - add only the features you regularly use to help keep your interface clean
- Links to other mapping systems e.g. save your tracks directly to Google ‘My Tracks’
- The wide array of options means it is occasionally hard to find certain features
- Pro paid version is needed to ensure there are no limitations on all features
- Some ‘add-on’ apps needed to enable certain features e.g. Bluetooth support
In our opinion Locus Map is proving to be far and away the most useful mobile mapping app we have discovered to date. The app is stable and user friendly and has proven to be a real asset for fieldwork. If you have found something better let us know!
- Steve -
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Day 4 - 22nd March
We were woken this morning by the loudly insistent call to prayer from loudspeakers installed in the courtyard of the compound where we've stayed. I'm feeling a lot better today after a bit of unsettled tum. Aaron emerged looking rather pale and skipped the breakfast we took at the local cafe. Today we headed into the mountainous forests in the Shako area. The forests around here are managed but still diverse. It was a steep climb away from the road and exhausting in the dry heat of the morning. We climbed fairly high and made some plot surveys. The coffee plants were sparse in this area and had already finished their flowering. After the survey we enjoyed a tranquil moment's rest as we sat listening to the sounds of the forest - the chirp of insects and the calls of birds and monkeys. Curiously, there are aspects of this forest that remind me of a British woodland on a hot, hot July day; brambles that catch and tear as we struggle through the undergrowth; the fiery sting of nettles; and a familiar mustiness of mossy bark, dead leaves and warm earth.
Steeply sloping Afromontane forest (Image: Paul Little)
Back to the car again and our colleague, Dr Tadesse, diverts us to a local village to try some of the rich, dark honey made in the forest and for which this region is famous. The locals stare curiously at us as Dr Tadesse barters for the honey and we cannot help but look about us with equal fascination. The locals still depend heavily on the forest and it is with some surprise that I note the smartly dressed fellow standing nearby in a shirt and waistcoat is carrying not a walking stick, but a spear!
Dr Tadesse tries the region’s famous dark forest honey (Image: Paul Little)
We go on to the next town where we pause again to meet one of Dr Tadesse's contacts. Everyone's exhausted and, with Aaron unwell, it's decided to halt here rather than press on to Bonga. We enjoy a glass of mango juice with lime and it's sooo good! Like no other fruit smoothie I've ever tasted! Jenny and I indulge in another. The hotel we've stopped at is luxurious with running water, electricity and (oh joy!) hot showers. One really comes to appreciate things taken for granted at home. We have the afternoon free now and I use it as an opportunity to do some bathroom laundry. It's as well that we stopped, for out of nowhere comes a sudden storm with lightning and heavy rain. I was glad to be under a hot shower rather than out in such an African squall! However, I'm sure there'll be plenty more opportunities to experience the local weather...
Day 5 - 23rd March
We sit outside for breakfast and enjoy the variety of birds to be seen. Sunbird, hadada ibis, common bulbul, as well as scavenging kites and a vulture. We leave the CoffeeLand Hotel in Bonga at 8am. We cross the Gojeb river which divides the regions of Kafa and Jimma. The area consists of moist Afromontane mosaic shading into farmland and humid savanna woodland. We stop to survey a plot in Belete forest where we find a fallen coffee tree with one remaining coffee cherry.
A solitary cherry of Coffea arabica (Image: Paul Little)
Later we find a splendid specimen in its typical habitat, so I take some time to get good pictures. All in all, however, the wild coffee trees are pretty sparse here. We are followed by a local woodsman who carries with him an axe fashioned from a steel blade fastened to a roughly polished handle, which still has the shape of the tree branch it was made from. He helps lead us to the coffee trees and a small neat plantation within the forest. Back in Jimma again and we return to our previous hotel. My room on the third floor overlooks a construction site. Concrete pillars jut skyward and, on hearing a plaintive cry, I glance up to find two kites levelly regarding me. These magnificent creatures are a nuisance here, like pigeons and crows. It's our mess that draws them.
Day 6 - 24th March
Today is a road day. We travel by road to Awasa (Hawassa). I was up by dawn and took some footage from the balcony of the sunrise and some morning activity. Jenny is keen to see hippos so we make a short diversion to a pool where they are reported to be active. Clearly the hippos had seen us coming for by the time we arrived they had all snuck away and hidden behind trees and bushes. We traverse the highlands before descending steeply into a hot river valley. I settle on a technique for shooting out of the car window without conspicuously rubber-necking like a demented tourist. I set the lens to mid aperture, shutter to 1000/s, and leave the lens focused at its hyperfocal distance. Resting the camera levelly on my arm I watch the world fly by and just press the button when passing something happening. The whole day is spent on the road. The hour before sunset is called the golden hour and it happens just as we drop down from the highlands and into the Ethiopian Rift Valley. The landscape is bathed in the richest golden light I have seen. The people by the road are radiant and I can't help but snatch dozens of pictures as we drive along.
So many moments of everyday life beg to be captured as we pass by... (Image: Paul Little)
In the approaching dusk we see a huge African storm sweep down the valley; a giant mushroom standing on its column of water, flashes of electrical discharge flickering through the cloud. The light quickly fades and now we pay the penalty of the roadworks and diversions. Ethiopian roads are best avoided after dark. We still have an hour and a half to our destination. Even the best tarmaced roads are fraught with hazards. There are no pavements and people and mule carts don't carry lights. Faced with the dazzling headlights of oncoming traffic our driver has little more than intuition, a quick flick of full beam and toot of horn to ensure our side of the road is clear. More than once a cartful of faces beam happily back at our headlights as I involuntarily stretch for a brake pedal.
Day 7 - 25th March
We are in the town of Awasa by Lake Awasa. We had stayed in a smart hotel following the long journey of the day before. Running water and a relished hot shower. On the way to the next survey locality we stop into one of the smart hotel resorts in order to see the lake shore. We are approaching the easternmost leg of the expedition and we film a little dialogue here. The lake teems with different species of birds and as I take pictures from the shore I look down to see a palm-sized rock bobbing in the water. The pumice comes from the volcanic floor of the rift valley.
A fisherman on Lake Awasa punts his Tankwa, a papyrus reed boat (Image: Paul Little)
We head south along the highway towards the Kenyan border and pass trees laden with huge black birds. The marabou storks glare coldly down as we pass beneath. Dr Tadesse points out a plush compound, Villa Alpha, former home of the late, renowned African artist Afewerk Tekle.
We stop in Dilla for lunch. We film ourselves trying the region's distinctive Yirga Chefe coffee. Another potent brew, slightly caramel with fruity, citric notes, and a creeping lockjaw finish. A young lad taps at the window until we relent and buy a bunch of ripe bananas for an extortionate 10 bir. They're half the size of Tesco's but twice the flavour. We pass through Dilla and along a highland ridge to Yirga Chefe. This east side of the rift valley is influenced by a different weather system to Yayu and Jimma. Here the weather originates in the Indian Ocean and, perhaps as a consequence, the coffee plants here look significantly different to those we saw before, with noticeably smaller flowers and thicker, firmer leaves. As we climb the ridge we drive through a small town whose dusty roads lined with wooden houses look not unlike an old Wild West town. The children here are particularly delighted to see us ferengi and fling themselves alarmingly at our hurtling 4x4 waving frantically and shouting, "YoiYoiYoi!"
Back at the hotel, as we settle to sleep, a storm breaks over the town and after an hour or so the streets are awash. By morning it's as though nothing had happened. The deep roadside storm drains serve their purpose well.
- Paul -
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Day 1 - 19th March
Late start due to prolonged and random breakfast and we hit rush hour as a consequence. We pick up our driver and leave Addis heading for Jimma. As we make our way further from the city, the tin-roofed shacks give way to more traditional thatched and mud-walled huts. Saw my first wild baboons by the road near Welkite. There was a distinct temperature difference as we descended from the cool heights to the dry valleys. As the day wore on, we entered hilly terrain dissected with numerous valleys and dry river beds. Among the valley trees of the plains, numerous nests of the weaver bird dangled and danced like grassy Christmas baubles. The valleys were comparatively lush and lined with trees: acacia, eucalyptus, figs, palm and false banana (Ensete ventricosum). We stopped for lunch in Seka, at a cafe where I enjoyed my first taste of strong Ethiopian coffee - thick and black as pitch. I've been learning my coffee descriptives: this one had been thoroughly brewed and was smokey and nutty with citrus notes, finishing on a blend of palpitations, shakes and mild seizure.
An Ethiopian Jebana (coffee pot) is heated against charcoal and frequently topped up (Image: Paul Little)
Day 2 - 20th March
Awoke at sunrise to find it still puzzlingly dark, the reason revealing itself with flashes of lightning and a crescendo of rain on the hotel's metal roof. Skipping breakfast we hastily bundle into our truck and set out for Yayu. We soon find ourselves travelling though coffee plantations which are remarkably biodiverse, with many species growing under the shade of various native trees.
Ethiopian coffee plantations can be remarkably biodiverse, many species growing under the shade of various native trees (Image: Paul Little)
The forest was occasionally punctuated by shiny, corrugated metal processing stations. Already people are going about their business. A boy does press-ups over a ditch as monkeys gaze down from their tree. We pass a long procession of children clutching their books on their way to school. So many little scenarios flash past before I can even raise a camera. I sit back and soak it all in. By 8am we've ascended to over 2000 m above sea level, beyond the range of coffee. This all accords pleasingly with the satellite data our GIS specialist Jenny has brought along. At last, in Bedele, we pause for breakfast. The others opted for scrambled egg but I venture the local option. It's a delicious mix of beans and spicy sauce with scrambled egg. It's scooped up with torn-off chunks of bread, a tricky challenge when it's polite to only use one's right hand. We find a roadside cafe where we stop for coffee.
A characteristic coffee processing station, constructed from corrugated metal (Image: Paul Little)
Day 3 - 21st March
We stop at a gleaming, corrugated metal compound inside which is a coffee processing plant. The overseer knows our partner, Dr Tadesse, and is very obliging in showing us about the facility. He goes to great efforts in starting up the coffee mill so that I am able to film the milling process. The milling machine is a huge, roaring mechanism of spinning belts and wheels and not a safety rail to be seen. I clamber over it as I try to record the various stages of the process, intensely aware of my dangling camera strap. I film the coffee beans going in, through and out of the fearsome contraption.
"The coffee milling machine is a huge roaring mechanism of spinning belts and wheels..." (Image: Paul Little)
The young lads operating it take great delight in demonstrating how they can haul a sack of close on 70 kg onto their backs and carry it to the store. Outside on the veranda some 30 or so women patiently pick through the beans, discarding any bad ones. They giggle and turn away whenever I point my camera towards them. Out in the yard three youths shuffle back and forth through an expanse of beans, turning them with their feet to dry in the sun. They walk together with their arms over each others' shoulders like old friends sharing confidences. This is something I see quite often on the street here. Men happily strolling along hand-in-hand or arm-in-arm in a way we British would interpret as decidedly romantic! Not so. Merely a rather sweet Ethiopian expression of friendship.
"Three youths shuffle back and forth through an expanse of beans, turning them with their feet to dry in the sun.." (Image: Paul Little)
We travelled for 30 km or so before pulling over for a brief survey of the local coffee plants, and found ourselves in some wonderful managed, moist, afro-montaine forest. Our first discovery was a magnificent false banana (Ensete ventricosum) about 5 years old and 5 metres high.
A magnificent false banana (Image: Paul Little)
Then a mighty old buttressed tree (Schefflera abyssinica). This led us on to a lovely, mature, wild coffee plant (Coffea arabica) in a perfect setting to be photographed, so I spent some time on it whilst the others made a plot survey nearby.
Wild Coffea arabica near Metu (Image: Paul Little)
Coming back to the car, there was a clear boundary of deforestation. For lunch we stopped in the nearby town. My stomach was in no mood for spicy tibb, but I was able to snaffle most of the potato portion without the others complaining. Skipping coffee for a cold Pepsi brought a welcome sugar boost. Leaving the town we passed a traditional round thatched hut sporting a shiny white satellite dish. Now I'm hoping to pass another with my camera ready. We've been steadily gaining altitude up to a height of 2300 m. Farmers in this area surround their properties with fences of euphorbia and grow crops of enset, a relative of the banana.
We stopped briefly to photograph a Lily of the Nile (Zantedeschia aethiopica) and were approached by some boys selling green peaches. Not yet ripe, they were delicious all the same.
- Paul -
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About the GIS team
Kew was one of the first botanic gardens to have a dedicated Geographic Information Science (GIS) Unit. This was officially established in 1998 with the mission to ‘provide an interface for Kew's plant diversity research, presenting data and producing tools to underpin surveys and inventories, conservation and environmental monitoring’.
More than ever, GIS is part of our lives from GPS devices in smart phones to the latest satellite images in Google Earth. We use GIS techniques to support Kew’s science and conservation and most importantly, we like maps too! We are going to use this blog to tell you about the projects we are involved in and the new technology and techniques we are investigating. Make sure you subscribe to the GIS unit blog feed to keep up-to-date with all things GIS.
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