View from the canopy, a rainforest lagoon, and the smallest monkey in the world

The Yasuni rainforest is a wonderland for a biologist. It jostles for position as the world’s most biodiverse place with other sites in the Peruvian and Bolivian Amazon, and Andean lowlands. It is home to hundreds of amphibian, reptile, bird and mammal species, over 1000 species of tree, and thousands and thousands of insects. Enigmatic large cats, anaconda, pink river dolphins, ten primate species, bird species ranging from the enormous harpy eagle to tiny hummingbirds, and untold undiscovered species are all here. A visit is a chance to maybe catch a glimpse of some of these, but it all depends on luck. Like stepping into a tropical greenhouse at a botanic garden, it envelops you in humidity and the smell of vegetation, but with a glorious cacophony of insect, bird and frog calls. A hundred shades of green hide almost all animal life to the untrained eye, but with time the animals become easier to see. The noise in the canopy that you initially confuse with leaves in the wind alerts you to monkeys, the forest floor becomes alive with camouflaged frogs and insects, and butterflies dance across your path. Birds are easier to hear than to see, but a hummingbird may pause, hovering inches from your face, as it zips along it’s flight path, and the croak of a macaw means you can catch a flash of red as it flies over the canopy far above. Your eyes become trained to notice movement, and with time you see more and more.

We arrived for a week at Tiputini Biodiversity Station – just across the river from Yasuni National Park proper – full of anticipation. We knew all these species were all around us (and with camera trapping projects run by the station, it is sometimes unnerving to realise just how close some of these species regularly are), but it would be mostly down to luck, combined with the infinite skill and knowledge of our guide, Jose, that would determine what we would see.

We started in the canopy, high above the forest floor, at dawn on our first morning. We set off in the gloomy pre-dawn light, straining to see the trail and not trip over any tree roots. Jose immediately spotted a tiny, perfectly camouflaged frog, by the side of the trail, which set the tone for the following days as he repeatedly spotted birds and animals that were invisible to us. The canopy platform was 45 metres off the ground, in the vast branches of an enormous tree, themselves part of a complex ecosystem supporting bromeliads and climbing plants, birds, insects, and amphibians. To reach it, we climbed a metal tower, which became slightly more nerve-wracking with every flight of stairs. It was a cloudy day, so rather than sunrise we watched the light change and the forest wake up.

Ecuador (176)

Ecuador (175)

We soon spotted two gangly spider monkeys making their way between the tree tops, some distance away and beneath us. One, after reaching a new palm, re-caught a frond of the previous one while suspended by its tail, making a bridge for the smaller monkey to climb across. Scarlet macaws circled the tower in a spectacular flypast. A hummingbird visited the epiphyte flowers, colourful paradise and opal-crowned tanagers were busy in the tree canopy above us, and a lizard froze and changed colour under our gaze. We spotted a many banded aracari, a puffbird, a bare throated fruit crow, and vultures hunched among bare branches in the distance.

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Back on the ground, we caught sight of our first primate species, the rare and endemic golden-mantled tamarin.

© Flickr user lowjumpingfrog

After a huge lunch and a siesta, we were back on the trails, this time on a slow walk to a lagoon. On the way there we crept quietly off the trail – with Jose whispering instructions – and stood beneath a tree, craning our necks. The inhabitants we were looking for were pygmy marmosets, the smallest monkey in the world. After a short while, a tiny, scrabbling gremlin skittered down the trunk.

Photo by Jim Wolfe

Photo by Jim Wolfe

The pygmy marmosets feed by chewing through the bark of the tree, and lapping up the sap. The tree was covered in pits.  (This video is of the same species, but was filmed by a lodge in Peru)


Further along the trail we saw dusky titi monkeys, woolly monkeys, and monk saki monkeys, bringing the first day’s total to six species of primate.

The lagoon itself was ringed by palms, the lower couple of metres of which were muddy from the high water during the rainy season. We paddled quietly across the water in a canoe. Hoatzins, a prehistoric dinosaur of a bird, huffed and crashed about in the branches, and caciques whirred about, noisily building their hanging nests. We also spotted an anaconda, motionless, under some low hanging branches. The most biodiverse place on earth was living up to its reputation.

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Whereas the first morning was spent observing the forest wake up from above, the second found us in a boat, travelling downstream on the Tiputini river. We were heading for a parrot clay lick, a part of the river bank where flocks of parrots congregate each day, to get vital minerals from the soil. boat tiputini

As we rounded a bend in the river we came across a submerged tapir, which lumbered up and out of the water, and disappeared up the bank. Kingfishers, disturbed by the boat engine, seemed to lead the way, pausing on a branch ahead of us only to take off again as we got close. Turtles plopped into the water, and night herons stood guard at the water’s edge. Once in position, we watched as parrots gathered in the cecropia trees above the lick, and eventually, after much noisy chatter, they descended and continued to excavate a small cave out of the bank. Once or twice they were spooked by something, a huge flock rising and circling before returning to eat some more.

On our way back, the boat slowed, and Jose gestured that he had seen something in the water. We were then led a merry dance by three pink river dolphins, noses and fins appearing behind us, then in front of us, but never alongside the boat.

Later that evening we were on the river again, scouring the banks with a huge spotlight, looking for reflected eye-shine of caiman. The jungle at night feels like a different world, and it was cool and breezy on the boat, watching nightjars, and alert for animals on the riverbank. Then it was to bed, to be quickly lulled to sleep by the rhythmic chirps, whirrs, pips, buzzes and croaks of insects and frogs in the absolute darkness. This recording gives a taste of the Amazonian night time soundscape.


The best commute in the world, and searching for a subflava in a gold mine

One of the main questions we were investigating was the importance of rivers in structuring populations of our chosen antbird species (the Peruvian warbling antbird Hypocnemis peruviana, yellow-breasted warbling antbird H. subflava, and the chestnut-tailed antbird Myrmeciza hemimelaena). In other words, how connected are individuals on one side of a river with those on the other? Are they equally likely to mate with those on near and far sides of a river? And if there are river effects, do these differ between species, depending on their ecology and behaviour? (These are questions at a local scale, that form part of broader questions relating to the diversification of Amazonian birds; more background information about the project is given in an earlier post.)

It is possible to look at population connectedness by using genetic analysis of blood samples. In a technique analogous to DNA fingerprinting, individual patterns of genetic markers can be described for each bird. Instead of using these to work out the relationship between two birds, the distribution of markers within a whole population can be assessed. Clusters in the data reflect groups of individuals that are more closely related to each other than to other groups. These clusters can then be matched with their geographical location, and if they fall on opposite sides of a river, then this would suggest that the river is a barrier to gene-flow (interbreeding) between populations.

Our analyses are still not complete, so the final part of the story is not yet known, but all this meant that we needed to cross the river to collect samples. Instead of setting off into the forest in the morning, we would descend the 250 stairs from the high upland terra firme, down to the riverbank. We’d scramble into a boat, and if the engine started quickly, we’d be on our way in the dawn twilight, watching the sky change colour, and the mist rise from the river. It was only a short journey down river, either 10 minutes to the village of Boca Amigos, or 20 minutes to a satellite station belonging to CICRA, known as CM1. But it was a beautiful way to travel to ‘work’, one that I never failed to appreciate, and one that was always different depending on the weather and light.

Boca Amigos is a small village, home to a handful of families, with most houses also seeming to double as a shop or bar. There’s a small school, and a football pitch, as can be found in every Peruvian community no matter how small. We’d arrive before many people were up, and would quietly walk between the houses to reach the trails into the forest beyond.

The journey to Boca, and our exploration of the surrounding forest, also brought home one of the less beautiful aspects of life in the Amazon: gold mining. We would pass mining dredges on our way downriver (in fact we could hear them, generators running late into the night, from CICRA).

The price of gold keeps on rising, and the opportunity to make a decent living in the jungle by mining gold continues to attract migrants, particularly from the Andes. The work is tough and relentless, but profitable. It results in huge mounds of gravel, deforestation, and leaves behind desolate expanses of bare ground, and pits filled with polluted water.

The cheapest and easiest way to extract gold is to use mercury. Mercury is therefore being constantly washed into the river, entering the forest ecosystem and food chain, and is likely to be having a terrible effect not only on the forest species but also on human health. The whole issue of mining is complex and controversial: the needs of people and the protection and conservation of the rainforest requires a careful balance, which has not yet been reached. It is an issue right across Amazonia. Although the blue-tarpaulin covered mining camps that we walked through behind Boca were small-scale, some mining operations have an impact on a much greater scale, and anyone who has flown between Cusco and Puerto Maldonado will have seen a huge scar in the otherwise mostly unbroken rainforest canopy.

Mist-netting around a gold mine was not something I had expected when I set off for Peru. It was shocking to see the devastation of the mines. We would climb over huge felled trees, and navigate around the pits, trying to hear our species singing above the noise of the generators.

We found birds adjacent to the mines, and were defecated on from a great height by a group of howler monkeys who objected to our presence, so jungle life continues in the adjacent forest. This gave some hope that once abandoned, the mines could be reclaimed by the forest. But I have no idea how long it will take for all traces of the mines to be gone, as the ground has not simply been cleared, but excavated, and the effects of mercury – invisible and far-reaching – are likely to persist for much longer. Working there also gave us a more personal perspective on the whole situation. We exchanged buenos dias with miners as they were preparing their breakfast, bemused at the site of us with our microphones and mist-netting gear, and they came to our rescue when our boat engine wouldn’t start. It is easy to say that the mining should be stopped – and heartbreaking to learn about the extent of the destruction across Peru and beyond – but is not easy to achieve, especially whilst also ensuring the livelihoods of those who currently depend on it. A much more in-depth and eloquent report on gold mining can be found on the Smithsonian magazine website, and an award-winning new film, Amazon Gold, documents the destruction of the Peruvian rainforest for gold. The trailer below is well worth a look.

Zen and the art of outwitting a small bird

A working day started soon after 4am, so we could be at our chosen spot by sunrise. In the dark, I would scan the floor for dangerous creatures, shake any more from my clothes, and tip my boots upside down just to make sure before putting them on. Despite my fears of spiders, snakes, scorpions, cockroaches, centipedes…I think I only ever found a frog, in a boot, once.

I’d meet my field assistant in the comedor, and we’d quietly go through our morning routine, filling water bottles, stocking up on breakfast snacks, and then assembling the various bits and pieces we needed in the field: a toolbox full of needles, tubes of ethanol, capillary tubes, bird rings, rulers, and scales, speakers, mp3 players, mistnets, bird bags, bamboo poles, machetes, microphone and sound recorder.

Setting off into the forest, the low light – if any at all – would turn to almost complete darkness as we entered the trail system and walked under the canopy. It took a while for the light to reach us through the trees, so we made our way by the light of our headtorches, which would catch the blue shine of spiders’ eyes on the forest floor.

It felt exciting to head off into the forest while many were still asleep at the station, seeing the first of the new jungle day, and enjoying the sound of the nightshift merge into the dayshift. It also meant we got to walk face first into all the spiders’ webs that had been constructed across the trails over night. We’d walk waving a stick or machete in front of us to catch the webs first.

Rainforest sunrise

We were out to find three particular species of bird. All three are antbirds, small, insectivorous birds that lives in the understorey of the forest. One species, the chestnut-tailed antbird (Myrmeciza hemimelaena) barely gets above the ground, zipping between dense tangles of vegetation half a metre off the forest floor. The other two are usually found between 1–4 metres off the ground; one, the yellow-breasted warbling antbird (Hypocnemis subflava) has a tendency to be found in bamboo patches, while the other, the Peruvian warbling antbird (Hypocnemis peruviana) is usually in the broad-leaf forest matrix. Finding them was easy, because they are all highly territorial, defending their patch of forest against intruders. We could mimic an intruder, by playing the song of each species on our speakers, prompting an angry, defensive bird to head in our direction. Generally, this would bring both male and female birds towards us, as they defend their territories together as a pair, and sing duets to do so. The challenge once we knew where they were was to work out where to put a mist-net with the highest chance of them flying into it.

A mist-net between two bamboo poles, supported by orange cord

The trick was to anticipate which branches or tangles of vegetation would be most appealing to the birds, and the route they might take from one to another, and to put the net between them. Sometimes the trail itself was suitable, other times we’d need to clear enough space to fit the 12 metre long net. We’d loop it onto two bamboo poles, pull it taught, and tie the poles to suitable trees nearby. The net extended from the ground up to almost 4 metres, and consisted of 4 parallel pockets running the length of the net. It was hard to see, and if positioned out of the light would be almost invisible, to us as well as the birds (and on one occasion a furious large Amazonian squirrel that thrashed about until it thrashed itself free). The speakers would be placed on the ground in the middle of the net, with the appropriate song playing on a loop. When a bird flew into the net, it would fall into the pocket just beneath it, unhurt but slightly tangled. We’d keep a close eye on the net and quickly extract a bird once it was caught. It would be put into a small cloth bag until we were ready to process it a few minutes later.

Bird bags on our machetes

So that we would know if we saw, or caught, the same bird again, we put small rings on their legs – one metal ring with a unique number, and then three coloured rings in a unique combination. I’d measure the length of the wing, tarsus, beak, and weigh the bird, as well as take a couple of drops of blood from the vein under the wing for genetic analysis. Within a few minutes the birds would be released back into its territory.

Taking a blood sample from a chestnut-tailed antbird. Photo credit: Frances Buerkens

But it wasn’t always so simple, and we must have spent many hours watching birds come towards the net, fly over it, stay just next to it, and not fly into it. There was nothing we could do but watch, and will the bird to fly where we wanted it to. Sometimes we’d re-position the net and try again, sometimes it would be so close for so long that we couldn’t give up, but sometimes the birds were just not going to fall for our tricks. Add to that a swarm of ants, a nest of tiny ticks, bamboo spikes or wasps and a day in the field was often a lesson in patience and calm. We’d head back for lunch in the heat of the day, brandishing hard-won blood samples, the forest quite different to how it had felt at dawn, anticipating cold showers, ‘clean’ clothes, and tasty food.

Ants all over my binoculars

Why are there so many birds?

The main question behind my PhD research is why, and how, are there so many species in the Amazon rainforest. There really is a ridiculous number of species. Hundreds of bird and tree species can be found at single sites, dwarfing the numbers found in whole countries in Europe for example. The Amazon is not alone in being highly biodiverse, many tropical regions harbour vast numbers, but the Amazon and Andean lowlands have the greatest number found anywhere on earth.

It is mind boggling to try and grasp the magnitude of the diversity: whereas you’d be lucky to see one or two dozen bird species in your garden at home, in the rainforest hundreds of birds live in the same patch of forest. Many have had their minds boggled trying to work out why it is that diversity increases as you travel from the poles to the equator. And more still have concentrated on tropical rainforests, enthralled by the conundrum of so many species evolving in the first place, and then being able to coexist.

The particular hypothesis I am interested in is one that has roots in the earliest explorations of Amazonia. Alfred Russel Wallace, now celebrated for his insights into the theory of natural selection, set out in 1848, at 25 years old, to explore the Amazon rainforest. He noticed that some species were found on one side of a river, but never the other. The rivers themselves seemed to be the boundary, the limit of a species’ range. Since then numerous biologists have explored the extent to which rivers may limit species ranges, and more crucially, the extent to which they actually drive speciation (the evolution of two new species from one) or simply limit the distribution of species that have evolved elsewhere.

Chestnut-tailed antbird.
Photo credit: Will Minehart

My PhD tried to unravel a tiny fraction of the story, by looking at how populations of different species are structured across rivers. I was in Peru to get blood samples from my study species, so I could work out from genetic analyses the extent to which populations on opposite riverbanks were connected with each other. If rivers are barriers between populations, meaning that birds on one side very rarely mate with birds on the other, then with a great deal of time, these populations may evolve to become distinct species. The rest of my time was spent behind a desk back home, looking at hundreds of bird range distribution maps, and how they related to the many rivers that run through the Amazon basin.

Birds may seem a daft choice for investigating the ‘river barrier hypothesis’, as they have wings. But many tropical birds are surprisingly bad at flying across open spaces such as rivers. My study species the antbirds prefer to stay in the dark dense understorey, and therefore are some of the most likely to be affected by river barriers.

Although my research questions focus on the evolution of Amazonian diversity, they are part of a much broader set of questions trying to get at the root of how and why species evolve into new species. These PhD students studying coral ecosystems are dealing with the same evolutionary questions, and do a great job of explaining their research. They also convey a little of the frustration in carrying out field and lab work:

This is quite unrelated except as another brilliant example of creative science communication, prizewinning no less, by my talented colleagues at the EGI. Original music by Stuart Noah and choreography by Cedric Tan, with a cast of PhD students…