Wednesday, 21 September 2016

Return to the Amazon: lamentable change observed from a 5 year window of absence


I guess I expected to be shocked. The opening of the Interoceanic highway was well underway already 10 years ago. In 2011, my last visit to the Las Piedras River the last connecting dash of the paved road connecting the Atlantic to the Pacific was being drawn: the Billinghurst Bridge over the Madre de Dios River. In 2011, we still had to use the barge to ferry the research group across this wide tributary of the Amazon; while we watched the last steel girders being carefully placed on this architectural achievement. Once completed there would be no weight limit to the vehicles crossing the river; no more barrier to waiting hordes of bulldozers, graders and giant haul trucks.

In 2003 I first travelled up the Las Piedras River with Emma Hume and JJ Duran, a couple who were in the last stage of building their Amazon vision: a small tourist lodge in the heart of the Amazon wilderness. It was journey to biodiversity paradise that would take us 2 days to complete as we zig-zagged our way by boat into near pristine wilderness. In about 2006 the first arterial road from the Interoceanic highway found its way to the Las Piedras River, a road sanctioned by the local community to facilitate the extraction of Brazil nuts from remote and isolated concessions. On my first journey along this road I bounced along on the back of JJs motorbike as we navigated the dusty road all the way to Puerto Maldonado.

In 2011, this road had been much widened, and there were signs of wood extraction from along the road. By this time the end of this road had a name: Puerto Lucerna, and two small huts had been built by families facilitating the extraction of wood and Brazil nuts. The port was now a busy place: people were very happy that they would not have to endure another 2 days by boat to get to Puerto Maldonado: now it was a mere 3 hours with the paved Interoceanic highway.

Now the lines of these roads into the forest have spread further and deeper than the lines on the faces of those I have known during this long time. The weathering of our faces reaches deep to our hearts, as the roads penetrate deep to the heart of a once unspoilt wilderness.

On this journey, again with Biosphere Expeditions, we encountered several logging trucks leaving with giant trees centuries of years old. The Dipteryx micrantha, also known as shihuahuaco or Ironwood, probably sent their first roots into the earth before the arrival of Christopher Columbus on the continent. Some may have been older than Jesus.

The logging booms have followed cycles over the year. In the 80’s and 90’s until the early part of this century, the boom was in mahogany, locally known as Caoba. As this finished, Cedro and Tornillo became the timbers of choice. This wood could be cut into planks in remote locations, made into rafts and floated down the river. Attempts to control the tide of extraction were met by riots and murder. Now, no tree species are safe.

Caoba and Cedro are close to extinct in the region now. While the Ironwood trees were being targeted by charcoal industry five years ago, remote individuals were safe from attention of wood cutters: the wood is too dense and sinks in water. But the arrival of the main road meant big machinery to clear logging roads, and trucks that could carry entire tree trunks to the timber mills in Puerto Maldonado. During my honeymoon of 2007 inadvertently spent at a hotel on the banks of the Madre de Dios River, my wife and I were counting 10-15 trucks a day carrying 1 – 3 trees each. The genocide is now in full swing: over 20 trucks were counted coming out of one arterial road of the Interoceanic highway alone during this journey.

These Ironwood trees are biological keystone species i.e. species important to the survival of many other species across a range of life forms in the rainforest. The fruit are eaten by bats and parrots. They are the preferred nesting trees of Harpy Eagles and Ornate Hawk-Eagles. The trees have natural cavities formed where thick branches have broken off and slowly rotted away over decades or more. In a study of natural nesting sites of the large macaw species, most were recorded from Ironwood.  Aldo Ramirez told me that while most timber harvested in Madre de Dios is illegal, it all leaves the province as legal wood: it is easy to facilitate the paperwork.


Puerto Lucerna on the Las Piedras River is now in 2016 a small village of an estimated 100 people, all of whom have arrived from highlands of Peru in the last five years. A night with a bottle of rum shared with the settlers will soon result in the telling stories of infringements of the law: this is Deadwood (a tv series documenting the gold rush of the wild west) in real life. Satellite imagery documenting deforestation indicates that there are now major land invasions within the surrounding forest, with people setting up small-scale agroforestry schemes. This invasion is occurring principally in two ecotourism concessions adjoining our study site: the mostly absentee concession owners have had no incentive to deal with this. If they did, their lives would be at risk.

The land invasions are following the roads put in by wood cutters. The players behind the wood cutting can only best be described as a mafia style business enterprise. Promises are made of payments to extract wood from concessions that are never made. Big roads are bulldozed through the forest to target tree species, which at this stage include almost any tall, emergent tree species. The Brazil nut concession adjoining our study site has been extensively invaded. Last year the son of the concession owner was killed at Puerto Lucerna. To date, the perpetrators are still at large.

The population of Puerto Maldonado, the capital city of the Madre de Dios department, was around 30 thousand people when I first arrived to the region in 2002. The town was considered safe: girls would walk the dusty streets home late at night unconcerned. In 2003, the first murder that I was aware of occurred, associated with the gold-mine boom just getting going at the time. The town is now a city of an estimated 100 thousand or more. Various villages along the highway are now towns, with parallel population growth. There are now recognised ‘no go’ areas in Puerto Maldonado, a murder having occurred just the week prior to our arrival at a bar across the road from the tourist hotel where I spent the last couple of nights.

In words, I cannot explain or paint the picture of personal pain that I felt each time I came across the jagged stumps of the buttress roots of another Ironwood or Ceiba tree. I think for most us that love the rainforest, the Ceibas are as sacred as the guardian tree felled by the mining corporation in the movie Avatar. The Ceiba is the tree where the pachamama, mother spirit of the Amazon, lives. These enormous trees are now being turned into plywood, a fate more humiliating than royalty turned to slavery. The movie Amazon Gold goes someway to creating these emotions by telling the fate of some of the forest here, with personal stories and music that touches even the hardest soul.

As a conservationist, it is hard to watch this. The desecration of the forest is to me as the desecration of archaeological sites to a historian, or a church to a Christian. But as a biologist I know this cannot continue: the fate of all mankind rests in these forests. They are the sponge that absorbs our carbon; that helps produce our oxygen; that facilitates our rains; that provide medicine, homes and resources to many people. But the many people are becoming too many: this is the root of the problem at the moment in this area: people are flocking here from the overcrowded Andean regions. Down the line, the demands for a western style lifestyle mean we need more soya plantations, more pasture for cattle. The deforestation will not end soon. The countless forms of life that live in these forests, from monkeys to jaguars to orchids, will continue to die.

Is there hope?  

My reason for returning to Las Piedras was to help train Aldo Ramirez, a young biologist I had employed as an assistant to collect data for my PhD project about 8 years earlier. Our mission was to repeat surveys conducted since 2003 to monitor wildlife populations. We also wanted to monitor the local claylick. Aldo is from Puerto Maldonado, brought up on the edge of Lake Sandoval and has an incredible passion for wildlife. His family now runs a homestay ecotourism business. The boom in tourism has seen a proliferation of tourist lodges spring up around Puerto Maldonado, and offer significant employment to many people. On the Las Piedras River an ecotourism concession to the south of where we were based brings in young gap year type students who help with wildlife monitoring. Many conservation organisations are encouraging sustainable forms of agriculture, from cacao to Brazil nuts. But to me now, it seems that for each person like Aldo there are 10 people just wanting to clear a patch of rainforest to live in, or cut down another gigantic tree for the woodcutter mafia. Without creating a sense of urgency regarding this, change will be slow, and our reality is that we may reach a tipping point on the planet whereby the life sustaining systems start to shut down forever within our lifetimes.

I think this macaw was happy to see me again after five years. Wishful thinking I am sure!

Wood is still brought down river from the remote regions by raft



Not all biodiversity is beautiful! But it is still special.



A shotgun is lowered after a shot was fired at macaws at the claylick





Peruvian entomologist Juan Grados once told me every trip he does to the Amazon he discovers a new species of insect



Over 100 macaws were seen during one monitoring period. How these numbers change over the year with the loss of nesting sites remains to be seen.



illegal logging roads

rainforest giants cut down in a matter of hours

remnants of a felled Ceiba
Hope? Conservation research scientists Chris Kirkby, Alan Lee, Catherine Edsell, Aldo Ramirez








Monday, 25 April 2016

2 weeks of ringing

Acacia Pied Barbet stops to smell the Cosmos in our garden


After the Fitz AGM at the beginning of the month (where Peter Ryan said I gave the best talk, yay!) it was back to Blue Hill with Campbell Fleming.

Campbell is just starting his MSc on the topic of the genetics of Cape Sugarbirds.



Basically, we've been interested for a long time on the connectivity of the populations of sugarbirds and other endemics across the biome. The fynbos is a fire driven ecosystem and the birds are very niche specific in what they like: sugarbirds can be abundant in old fynbos, but are absent from young fynbos where the proteas have not yet had a chance to flower. How do the birds deal with this and what are the consequences on their genetics? Are the birds on isolated fynbos mountains e.g. Kammanassie, different from other populations? Are populations being influenced by things we cannot see: e.g. parasites or genetic depression?

In order to answer these questions, we need DNA samples from all over the fynbos biome. Ideally, from several individuals from several sites. I've been collecting samples on an ad-hoc basis over the last year, but with rockjumper and buttonquail demanding a lot of attention, I've never had time to focus on this dynamic set of questions. I'd initially included this study direction in my last research proposal after conversations with Jaqui Bishop, a senior lecturer at UCT, in 2014.

Luckily for me, Phoebe Barnard secured some money to undertake this project at the masters level, and Jaqui Bishop found Campbell to do it. All of this is being supervised by Peter Ryan at the Fitz.

This kind-of relegates me to the role of bird catcher – but I'm fine with that! As you'll see, these 2 weeks took me to some pretty cool places, and I don't have to worry about lab work!

Our week started on the first Sunday of the month, 3 April, and although it was Elena's birthday she agreed to come out with us in the afternoon to help us set up nets. Campbell was after all pretty new at this and needed some help from someone who'd just turned 5! We got off to a good start, with our first birds netted. And so it went...

Monday morning saw a big haul in the Protea repens stands of a range of nectarivores dominated by young Malachite Sunbirds. But we could not stay... we were planning on joining Mark Brown for one of his regular sessions at Nature's Valley. So off we set to Wildspirit Backpackers! Here also we rendezvoused with Carolynne Geary who'd kindly agreed to help us with the setting up of nets, taking down of nets, entering data etc that all goes with the job.



Little did we know that due to an inclemental weather report Mark Brown's session had been cancelled! We found that out on arriving at the rather damp hippy resort that would be home for the next two nights.

Nevertheless, Tuesday morning we decided to get at it anyway, and were rewarded with an acceptable array of birds, this time dominated by Southern Double-Collared Sunbirds. But sugarbirds were few. Daniel Cloete, PhD student looking at pollination affiliations here, had given us some pointers as to where we might find more, and we went to scout out the locations that afternoon: only to be drenched in the process.

Female Olive Bush-shrike

On Wednesday Campbell and I decided to lure some sugarbirds from a patch of fynbos near the backpackers, joined by one of the least hippy backpacker lodgers – an accountant from Germany. Meanwhile, Carolynne had volunteered to mission out to van Staden's where Ben Smit and Jerry Mokgatla were ringing. But again we were low on samples! I think Mark Brown has been training them to be illusive around here :) and so he kindly offered to assist sampling for the rest of the year.

Campbell's team had to move on: I'd over optimistically arranged a ringing session on the Montagu Pass for the Thursday. At least we'd be staying at some up-market accommodation, which was sorely needed as the outdoor shower in the rain had not attracted many users at WildSpirit. Not only that, but Over-The-Mountain also has a cute little restaurant which allowed Carolynne to top up on chocolate cake.

But Thursday was a bit of a black day. The start was late, skies were clear and wind started early. By the time the CapeNature rangers joined us we were ready to close the nets. However, they would let us into a little secret: the wonders of Camferskloof – a paradise of fynbos hidden beyond the hops farms off the Montagu Pass. But... it would have to wait, because again Campbell and I had a scheduled visit: this time Gamkaberg, to see if there were Proteas in bloom and sugarbirds present.

So that afternoon we negotiated the 4x4 trail up the mountain, to find that the Protea repens were in bloom near Oukraal overnight hut, plus sugarbirds and other sunbirds were evident. However, our accommodation was at the base of the mountain, so after setting up some net locations we had to negotiate the rough 4x4 track back down! The researcher accommodation at Gamkaberg is pretty cool – but we'd only be able to catch a few hours sleep before yet again ascending the mountain. Shew. Exhausting. And it would turn out that all that for just 1 sugarbird!

Time to head back to Blue Hill! Although I'd envisaged a day of rest.... Campbell and Carolynne had other plans, and Sunday morning we were netting again! But again clear skies and a stiff breeze so now only 2 sugarbirds! We'd been planning on camping in Welbedacht over the next couple of days, but on the drive back from Gamkaberg we noticed the mountain was on fire. A later inspection would reveal no ancient fynbos left :(. We had to make alternative plans so...





Monday and we were trying our luck on our neighbours farm, but again low capture rates were the theme of the day. At this rate it would take Campbell 100 days of capture just to get his sample of sugarbirds!

Monday saw the arrival of ringers Gert and Koetie Opperman, and with them, a change in luck. They had come to Blue Hill to add the fynbos endemic species to their life lists. Two more mornings with them at locations on Blue Hill saw us reach our goals on Orange-breasted Sunbird. And then we were off to Camferskloof, again.



OT, Outeniqua CapeNature manager, had allowed us to stay at the hikers hut, which is in a state of reconstruction. But it was close to our netting site: and Thursday morning saw us inundated with birds: we had to release many more birds than we would be able to process, and certainly cracked our target for birds for this neck of the woods.
Cape Sugarbird with leucistic (white) feather

CapeNature ranger and interns getting to grips with birds


And as before, then it was Gamkaberg, where this time Tom Barry had helped us organise accommodation at Oukraal, so we would not have to drive the 4x4 route up and down. At Oukraal Tom had also organised for his interns to help out, and so we had company of Nelly and Kirsty in taking data and checking the nets. While our first morning was somewhat subdued as we had set up around the hikers hut, Saturday morning saw us again easily reach our targets with some well placed nets in Protea nerifolia.

But the week was not finished. Saturday night we spent at the Takkieskloof campsite in Riversdal, with a productive Sunday morning, called short by rain. And a shortage of equipment. Sunday afternoon we begged a few extra sample bottles from the Riversdal hospital, and filled those on the Monday morning, with the help of Zoe Woodgate for data entry (and Campbell's lift to Cape Town).

Susprise bird of the day on Garcia Pass: Half-collared Kingfisher


It's taken me most of the week to recover from that expedition: but all in all, we'll call it a success.






Sunday, 27 March 2016

Happy Easter! with an R egg

This morning to entertain my daughter I thought I'd create a colourful egg using the R programming language. I was rather surprised to find that my google searches for any existing code did not reveal anything. Anyway, after a bit of playing around, herewith a token celebration of Easter.

R-easter egg
and the code that made it:

library(plotrix)
plot(c(1.5,8.5), c(0,10), type="n", main="Easter Egg", xlab="bunny", ylab="chocolate")

draw.ellipse(c(5), c(5), c(2),c(5.5),col=c(2))
draw.ellipse(c(5), c(4.9), c(2),c(5),col=c(4))
draw.ellipse(c(5), c(4.8), c(2),c(4.5),col=c(1))
draw.ellipse(c(5), c(4.5), c(2),c(4.5),col=c(1))
draw.ellipse(c(5), c(4.6), c(2),c(4),col=c(3))
draw.ellipse(c(5), c(4.4), c(1.9),c(3.5),col=c(5))
draw.ellipse(c(5), c(4.2), c(1.8),c(3),col=c(6))
draw.ellipse(c(5), c(4), c(1.7),c(2.5),col=c(7))
draw.ellipse(c(5), c(3.8), c(1.6),c(2),col=c(8))
draw.ellipse(c(5), c(3.5), c(1.5),c(1.5),col=c(9))
draw.ellipse(c(5), c(3.5), c(1.2),c(1.2),col=c(10))
draw.ellipse(c(5), c(3.3), c(.5),c(.5),col=c(6))

Thursday, 3 March 2016

Cederberg survey scenes

The Witteberge lie unobtrusively to the south of the N1 highway between the towns of Touws Rivier and Laingsberg. A gravel road that starts just south of Laingsberg runs through these mountains, taking one through some of the Western Capes more spectacular scenery. This 70km stretch of gravel is what I chose to explore on my way to the Cederberg two weeks ago. I had expected lucern fields and pasture, but the landscape is mostly wild upland Karoo, interfacing to Fynbos on the higher ridges. Cape Sugarbirds played amongst the giant Protea laurifolia, while the upper slopes looked perfect for Cape Rockjumpers. Driving into the sunset I made the most of the golden hour:




To break up the drive I spent the night in Touws Rivier, indulging in some atlasing in the morning before the drive north. Later in the day in Matjiesrivier I would rendezvous with the survey team for the week, including veterans Dale Wright, Krista Oswald, Audrey Miller, Michael Leach and Brian Haslett. New to the team was Campbell Fleming, who will be doing research into Cape Sugarbird dispersal and genetics over the next two years. I'd lured him to the Cederberg on promise of samples but had only seen one all day, in a garden in the town of Op-die-berg.

Campbell brings the cheese and wine... gums


CapeNature reserve manager Rika du Plessis had kindly offered us accommodation at her offices at Matjiesrivier, together with the use of rangers for the surveys. With the weather forecast a hot one, we started early in promising habitat near towards Uitkyk pass. While the vegetation had recently burnt and was rather open, within only a few hours in we hit a patch of older fynbos and flushed the first buttonquail to be recorded in the Cederberg (to the best of our knowledge). It was not to be the last.

Yay! Buttonquail! Big thanks to the CapeNature team: Jacques van Rooi, Nicolaas Hanekom, Willem Titus, Craig Bantom, Thomas Wynand Jakobus Veloen


On the Wednesday the survey team headed for old fynbos on the drier Rooi Cederberg, guided by Willem Titus. While we had no luck with our target bird we were able to enjoy some of the Cederberg's fabulous rock art along the way. Our afternoon survey would take us past the Stadsaal archaeological sites with one of the region's most famous rock art scenes: the elephants.

Willem shared incredible stories and added a real personal touch to our adventures in the Cederberg. We would not have seen these paintings without him.


Thursday was to be an epic hike day. We wanted to survey the upland areas, which we knew to be dominated by restios. That survey would take us over the Cederberg past one of South Africa's most spectacular rock formations: the Wolfberg arch. But the hike would be a good one, with a lovely view of a Hottentot Buttonquail on the way off the mountain.

Craig Bantom

Willem captures the scenery. He'd record tracks, spoor and all sorts of information along the route faithfully in his notebook.

Nicolaas took some time out to hack down an invading pine tree. Well Done!

Dale at the Arch

Thomas Wynand puts things in perspective


On Friday the team would split: Dale taking most of the volunteers to Winterhoek, with yet more buttonquails sighted. I would head north past Wuppertal to Heuningvlei after no luck surveying the Truitjieskraal area in the morning. On the way to Heuningvlei I gave a lift to Ryno Veloen, would helped to organise some men from the village and their dogs for a Saturday survey. We tallied 9km of surveys and 15km of hiking before lunch time, but without any luck.

From left to right: Eldrin, Gert, Curtis, Andreas and Ryno.

Eldrin had to take out the sheep before we could survey

While we did not find buttonquail, we did find this quagga-donkey.

All the time I had also been looking for Cape Sugarbirds, feeling guilty for promising some samples for Campbell. Luckily, I finally found a flowering Protea nitida, and spent a busy Sunday morning alone at the nets trapping birds attracted to the flowers. With the mission accomplished it was an overnight stay in Picketberg before Cape Town and meetings Monday morning.

But my week that started 2 Sundays ago is still not over. I drove the 7 hours back to Blue Hill Escape on the Monday evening, and have spent the week ringing with Eben Fourie. Shew.

Again, we are very grateful for the assistance of Rika and the Cederberg and Matjiesrivier rangers. Thank you CapeNature!

Sunday, 7 February 2016

5 Seasons in one week - Eastern Cape Buttonquail Surveys

I've never had my phone turn itself off with the warning message that it was not built to operate at such temperatures. This happened on Monday, when a heat-wave seared the greater Port Elizabeth area. Addo recorded 48 degrees; while our 'cool' fynbos site was 38. Its been a while since I've felt so uncomfortable, with a cold shower the only relief from the heat.

Jerry Mokgatla, Cape Sugarbird Masters student from Polokwane (up north), was happy that it was warmer. It also meant we caught no Cape Sugarbirds at his study site on Lady's Slipper, although we'd set the nets up relatively late, arriving on site at 7.30.

Ben Smit, Jerry's supervisor had joined us for the morning, and was also keen to help out with some Buttonquail surveys. There had been a fire in the area a few years earlier and the veld looked promising. However, our short mission did not result in any success, only the loss of copious amounts of sweat. Ben did find some chameleons to keep us entertained.



Jerry and Ben mimic the birds in their shade seeking behaviour to avoid the high temperatures


Tuesday morning Jerry and I were up on our way to Lady's Slipper at 4am, operating out of Van Staden's wildflower reserve. Weather was overcast, but by the time we got to our ringing site the wind was howling. Opening nets was out of the question. We sat in the car for 2 hours hoping for a break, but none was to be had. There was no sign of any sugarbirds either. We spent the rest of the morning scoping out the Longmore forest in the hope of finding more suitable buttonquail habitat, but without success. In the afternoon we conducted some behavioural observations on sugarbirds as part of Jerry's work to understand how Cape Sugarbird foraging is impacted by temperature. Protea mundii are just starting to put on a show at van Stadens and we had good views of the birds going about their busy social agendas.

Protea nerifolia with rainbow

Protea c susannae

Protea eximia


Wednesday we finally managed to net some sugarbirds – all females and subadults. Ben had been worried about a sex bias towards males, but this session definitely evened out the ratios. However, the session would end early with the arrival of some persistent rain that lasted the rest of the day. A couple of Victorin's Warbler were the highlight of the morning: 




Luckily for me I would not have to spend any more nights in my tent as ECPTA and the wonderful management and staff at Groendal Nature Reserve had laid on the Rooikrantz self-catering cottage. This has to be by far and away the most luxurious accommodation I've stayed in as part of the buttonquail surveys.

On Thursday morning we had the crack team of rangers assembled (and Brian) to help with an ambitious survey of the upland plateaus that form the foothills of the Groot Winterhoek mountains in these parts. We were optimistic since the habitat is basically an extension of what we had been surveying in Baviaanskloof, where we had been very successful with finding Hottentot Buttonquails. After our ascent of 10 Stop Hill (which I was told 3 times in one day is called that for a reason) we reached the plateau with the first veils of rain, which would keep us company for the rest of our 7 km survey.

The first birds up were Common Quail, but shortly after we had a potential buttonquail sighting. And then another buttonquail and another... but now our challenge was not so much if we were seeing buttonquail, but if we were seeing the right one! Hottentot Buttonquail have not been officially recorded this far east before, despite suitable habitat. According to range maps this is were Hottentot Buttonquails end and Black-rumped Buttonquails start. We were in perfect HB habitat: 3 year old, flat fynbos.

10 Stop Hill: you stop 10 times to take photos of the amazing views

Survey conditions were cold and wet

Charlie, Chewbs, Brian, Arthur and Fareni all smiles after a successful survey


It was time to call in the expertise of resident expert ornithologist Ben Smit. Ben is familiar with Black-rumped from KZN, but has yet to officially tick off a Hottentot Buttonquail.

Friday morning finally dawned with balmy weather: temperatures in the 20s and sunny. Ben together with two of his students Nick and Anthony joined us with the rangers (and Brian). Expectations were high as we were basically surveying the adjacent plateau to the one from the previous day. However, 4.5km later and all we'd registered was a Common Quail. Despite being superficially similar from a distance, the plateau had a higher grass component and resulting increased vegetation coverage, despite being the same age in terms of fire recovery time. Really, the habitat was perfect for Black-rumped Buttonquail, but without any.

With a 10 man strong field team, we were pretty confident that what we were looking for wasn't there.


We would like to express our heartfelt gratitude to Khayelihle Ncube for use of the superb Rooikrantz cottage in the Groendal Nature Reserve, Brian Reeves and the ECPTA for organising and paying for everything, and of course the rangers who got their feet very wet during the long surveys across the fynbos plateaus. Also apologies to Ben Smit and the NMMU team for being called out under false promises of a guaranteed Hottentot Buttonquail sighting! Still, this site is very likely the end of suitable habitat and hence the range of our enigmatic endemic, and the data gathered will help us immensely in our modelling of range and habitat suitability.




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