The pleasures of slow botanizing


Hiking and botanizing are distinct pleasures. Hiking is the joy of pushing one’s body, of covering long distances, of discovering new landscapes. Botanizing is the opposite. It is the joy of moving slowly, of looking closely, of reading the story of a place, and of relishing the discovery of something beautiful or unexpected. On a recent trip down to Sonora, in northern Mexico, I took the time to slowly and carefully explore a coastal landscape, and was amply rewarded by the stories I found hidden in the landscape.

opuntia nest

Chollas are one of the principal hazards of desert walking, especially at high speed. On a slower meander, they are easy enough to avoid, but beautiful in their improbable forms and sharp armor. Every once in a while a bird finds a way to construct a nest in their branches, making for a well-hidden and well-defended home. Here you can see one of these nests in a hanging chain cholla, Cylindropuntia fulgida (Cactaceae).

randia thurberi

Other plants also have spines, though not as prominent or painful as those of a cholla. On this species the long spines and leaves branch in opposite pairs, giving some clue to its identity. I was flummoxed in the field, despite having a flora, and decided to break open one of the fruits to find out what it might be.

randia thurberi seeds

I was dismayed to find a black sludge inside every fruit, hiding a profusion of small flat seeds. On a whim I tasted the sludge and found it to be one of the least pleasant flavors I’ve yet to encounter. Some help from my friend and better botanist Brad Boyle revealed this to be Randia thurberi (Rubiaceae), the papache. According to some reports the fruit is consumed locally and has a sweet flavor – maybe the ones I found were rotting or molded. A mystery I am not keen to soon resolve.


And my best discovery, hanging low on the branch of a Jatropha (Euphorbiaceae) shrub – an enormous cocoon of the saturniid moth, Rothschildia cincta. I had seen these used before as ankle rattles in ceremonial dances by the Yaqui people, but never knew where they were from. They are marvelously light, smooth, and strong. I only found two in three days of looking.


For me, hiking and botanizing rarely go together. The rhythms are too different, and I like covering ground, so I tend to hike more than to botanize. But the true pleasures of discovering a landscape only come when it is explored with open mind and eyes.

Why is it so hard to detect species interactions?

organ pipe

The western coast of Sonora, México is populated by a fascinating mixture of desert and dry forest species. Here the organ-pipe cactus (Stenocereus thurberi) rises over a landscape dominated by Bursera, Ruellia, Jatropha, and a range of other common shrubs. Do any of these species care about each other? Do they co-occur entirely by chance, or do they actively interact? Presumably they compete for nutrients and water; they may also share pollinators, or require the same seed dispersers, or mutually suffer when one inadvertently attracts herbivores. But does any of this matter when we simply want to predict the distribution of these species?

To answer that question, consider these two contrasting examples from the coast of Sonora.


The first example is from a canyon bottom. A palm (Washingtonia robusta (Arecaceae)) is growing adjacent to a fig tree (Ficus insipida (Moraceae)). But their co-occurrence is probably not due to any direct interaction. They are both here because they share similarly high water requirements. They would both be outcompeted in drier environments or be physiologically unable to survive and reproduce in the open desert. We can safely call this the absence of a direct interaction.


The second example is from a seaside promontory. This is actually not one plant, but two – a Bursera microphylla (Burseraceae) tree, with a hemiparasitic Psittacanthus sonorae (Loranthaceae) rooted onto its branches, happily flowering using stolen water and carbon. In this case the Bursera suffers from the Psittacanthus, and the Psittacanthus cannot live without the Bursera. This is a clear case of a direct interaction.

One of the major goals of ecology is to accurately predict how species will adapt, move or die, as the Earth’s climate begins to change. If species do not interact, the problem is relatively easy; each species can be modeled as independent from all others. But if species do interact, then the problem becomes difficult much more quickly. In these two examples, we know enough about the natural history and physiology of the organisms to determine whether interactions are occurring. But this doesn’t work when the goal is to predict the distribution of all the species on Earth. The problem is that the number of possible pairwise associations between n species is equal to n(n-1)/2. For two species, there is only 1 association to understand. For a thousand species, there are 499,500 possible pairwise associations that need to be understood. These associations provide a lower bound on the number of possible interactions. Too many to ever understand through natural history and expert knowledge.

Back in 2012, my friend Naia Morueta-Holme and I began developing some new statistical approaches to resolve this well-known but unsolved problem. Our idea was that interactions could be determined by subtracting away other confounding factors like shared habitat requirements. We proposed to first build models of species’ broad-scale geographic distributions based on climatic tolerances and predict how likely it was for species to co-occur. We then proposed to compare these co-occurrence scores to how often species did co-occur in small-scale communities. If species were found more often or less often than under the regional climatic expectation, then they were positively or negatively associated with each other. We then further subtracted away any indirect associations between other species. This final association could then hopefully be interpreted as an interaction. We also argued that species associations may exist between pairs of species, but are much more useful in a network context, just as individual friendships are less interesting that an entire social network. This let us identify species that (for example) were hubs in communities, actively attracting or repelling other species.

network framework

Three years later, the framework for doing all this is now published as a shared first-author piece in the journal Ecography as Morueta-Holme, N., Blonder, B., et al., A network approach for inferring species associations from co-occurrence data. I also wrote a free R package, netassoc, that implements the framework.

We used a large dataset of New World plant distributions from the BIEN initiative to explore the framework’s inferences for the trees of the eastern United States. We found that interactions between species are surprisingly rare, and are positive when found. A few species seem to act as key aggregators, like the balsam-fir, Abies balsamea (Pinaceae).
network zoom

And you can see this species does happily co-occur with white cedar (Thuja occidentalis (Cupressaceae)) in this Maine forest!

thuja abies

The framework makes these predictions without needing to know the natural history of every possible pairwise interaction between species. We hope that the approach will provide a useful tool for predicting the future distributions of species under climate change.

It doesn’t work perfectly – the error rates in simulations are higher than we’d like, and small changes in inputs can lead to relatively high uncertainty in predictions. It took three years of simulations and arguments and failures to get this far. At times we thought about giving up and abandoning the whole project. But I’m glad we stuck with it. I think that the ‘easy’ co-occurrence data that the framework uses is inherently very limited. We throw a lot of mathematics at the data, and push the limits as far as they can go. It’s a start.

(The desert photos were taken on a New Year’s trip with two other botanists. As the ecologist Rob Colwell has apocryphally but accurately said, “One botanist, half a walk. Two botanists…quarter of a walk. Three botanists….no walk at all”.)

On the shortest day of the year

On the winter solstice I chased a retreating moon over western Greenland and the Canadian arctic.



On this long westward journey the sun appeared to set two times, and the earth sat in pale twilight glow.


Coastal mountains rose up in the darkness, and sea ice filled the fjords that were not yet frozen.

sea ice


In the stillness of this frozen world, on a transoceanic journey costing less than a percent of my annual income, I thought about how this landscape will appear fifty years from now. It will surely have less ice, and perhaps fewer people will be flying over it. In Paris this year we came to a better climate agreement than many had imagined was possible – but a worse one than we need. We must place immense faith in our countries’ governments to make hard choices in the coming decades if even this weak agreement is to succeed. Will action come? I fear the answer is no. But I desperately hope otherwise.

Hidden treasures of the Macarangas

ant plant 1

A common sight along the roadsides and logging gaps of the lowland forests of Borneo is the slender gray trunk of a sun-loving tree with long, up-curving branches naked except for a few large leaves at the tip. These trees belong to the genus Macaranga, in the Euphorbiaceae family.

ant plant 7

They seem quite unremarkable, but working with them produces a feeling that they are not quite so simple. Most days we would cut down at least a few branches of Macaranga, preparing wood samples, then scanning and pressing leaf samples. In these moments I always felt unsettled, like something was crawling on my skin. And often I had to then flick off a large number of small black ants from my arms and legs and chest, or forcefully tear away the ones that had attached themselves to my skin with their jaws.

ant plant 2

The mystery of where all these ants were coming from was solved when we sawed through a large branch of Macaranga pearsonii.

ant plant 4

It turns out that the stems of this species are hollow. These interior galleries play home to a colony of small black ants. Presumably the ants defend the plant against its enemies, and receive shelter and resources in exchange. I can certainly verify their willingness to defend their home after cutting it in half.

This is a classical ant-plant mutualism. I was later to learn that the ants belong to the genus Crematogaster, and the species here is almost certainly Crematogaster borneensis (see Fiala et al. 1999 for a full treatment of the coevolutionary story). But two mysteries remained to me. First, how did the ants ever leave their hidden fortress worlds? I saw no exits from the thick wood of the branch. And second, what exactly did the ants receive in return for their soldiering?

ant plant 6

The first question was resolved after a bit more exploration. I found that the thick wood of the main branches transitions to thinner branches comprising a set of segments each joined to another where a leaf attached to the stem. In each of these segments was one small hole – just big enough for a single ant’s head to poke through. It is hard for me to imagine the intricate network of paths through the plant that every ant walks, but perhaps a tree is not so different from a set of underground tunnels.

ant plant 5

And the second question was resolved after a closer look at the leaves. At the base of each leaf lamina near the attachment point of the petiole, there were two small circular forms. These were extrafloral nectaries – plant structures that the ants would visit to obtain sugars and so feed themselves. I later learned that the number of extrafloral nectaries per leaf helps to determine the identify of the species.

A formidable and well-fed set of defenses. But some species in Macaranga do more to protect themselves. You may have noticed a red tint around the ants’ gallery in an earlier photograph. This species also exudes a copious bright-red latex. This is a toxic and sticky set of defense compounds meant to mechanically or chemically stop an insect attacker. In only a few seconds a thick and sticky red mess welled up from the stem, almost like blood.

ant plant 3

In most of Euphorbiaceae, this latex produces a strong painful rash for humans – luckily in this species the ants were the worst of it for me. I imagine the situation would be different for a passing caterpillar or beetle.

These Macaranga species are a marvelous example of the coevolution of insects with plants – some positive interactions, as with the ants, and some negative, as with the latex. These interactions have led to the marvelous adaptations of this species’ branches and leaves. It is a dance between species’ forms, played out over millions of years. And it only takes a small amount of careful observing to appreciate.

The things we carry for fieldwork

The experience of field ecology is not as glamorous as one might imagine. Fieldwork is mostly about carrying heavy things into and out of the forest. Curiosity, brilliance, creativity – they are are present, but far less important than sweat and sometimes blood and very rarely tears. Here are a few examples from Malaysia.

carrying 11

Some days are easy – just a light backpack with a notebook, water and a snack.

carrying 6

Other days are harder. Here we are with three gas analyzers, one spectrometer, three tripods, three coolers full of ice, five car batteries, and one computer.

carrying 2

Our vehicle can take for a short way. But in the end, it all goes up into the forest through muddy paths on shoulders and backs.

carrying 10

Some days we carry things out of the forest – here, a Macaranga branch destined for segmentation in our field camp.

carrying 3

Its leaves will be carried back through the forest and into our vehicle –

carrying 7

– and ultimately, with the rest of our gear, back into our field lab. On rainy days the leaves can double as umbrellas.

carrying 8

Some days we carry unintended things, like this leech – a major component of the ‘blood’ part of fieldwork.

carrying 5

Other days we carry equipment for our lab.

carrying 1

And other days we just carry rocks.

carrying 9

It is hard work. But the work is worthwhile. It acquires merit through its challenges. I come to love and understand the forest more deeply through suffering in it. And I appreciate our data ever more when I understand its price.

carrying 4

But sometimes a rest is nice too.

Some thoughts on oil palm

palm oil bar

Palm oil is the villain of Western markets. It appears as an ingredient in all sorts of processed foods, but comes with a bad reputation – environmentally unfriendly at best. Buying only products that don’t include it is nearly impossible, though a growing number of manufacturers are now tapping into a demand for such items. This packaged dinner from Norway, for example, advertises itself as helt uten palmeolje – entirely free of palm oil.

oil free

In the past few years I became increasingly aware of this tension, and began trying to make my own small dietary changes away from palm oil. But I was more following a trend than making choices based on facts, and the realities of oil palm agriculture remained far from my personal experience. That changed this year in Malaysian Borneo, where I have been studying the functional consequences of forest degradation. One of the major causes of forest destruction is replacement by oil palm plantations, and I got the chance to see exactly where our packaged cookies and instant noodles and laundry detergent come from.

sunset palm

Heading into the forest for work each day, I saw whole river basins and mountainsides exposed bare, covered by myriad rows of identical oil palm trees. I saw rigor and pattern imposed on the forest through the bulldozing of long roads and terraces, and imagined the silent hands of the many workers responsible for planting and trimming and fertilizing and harvesting.


The reason for all this effort is the large and heavy bunches of bright-red fruits the tree often produces. These are cut down by hand, then trucked out of the plantation.


Each fruit’s flesh hides a single inner seed, white and oily.


The seeds are then crushed, heated, and leached in an unpleasant-smelling process taking place in refinery facilities (this photo from Costa Rica).


The crude oil is finally sent off in trucks for further refinement or transformation into the products we are so familiar with. It is a long journey from tropical hillside to convenience store display.


My visceral reaction to this production scheme was dismay over the large-scale disturbance it created. I haven’t changed my mind about this, but the controversy over this crop is more nuanced than its bad reputation would suggest.

In Malaysia, palm oil provides about a half million people with jobs, and annual revenue of more than 16 billion dollars, mostly through exports to China and Pakistan. And about 35 percent of growers are smallholders rather than large companies. Many of the people I got to know had relatives who worked in the industry and were very glad for its existence.

jobs (1)

And the crop itself is highly efficient – its yield per hectare is far higher than other oil crops like in this British rapeseed field, and is achieved for much lower fertilizer and pesticide application rates as well.


On the other hand, the crop tends to be planted on land that is directly converted from primary forests with immense value in terms of biodiversity and ecosystem services. More palm oil almost always means more deforestation. These landscapes are often cleared by burning, a process that remains one of the largest contemporary sources of carbon pollution. The heavy smoke-filled air I experienced for days on end in the forest was a direct consequence of land clearance in neighboring Indonesia.


Oil palm plantations, once established, are also often responsible for high nutrient runoff from careless fertilizer application, and for high soil erosion from road construction. Labor on these plantations is sometimes forced.

The crop has major well-recognized problems. But it is not going away. The economic incentives are too great. A crop of oil palm can return anywhere from 4000 to 29000 USD per hectare over a 25 year period, compared to about 10000 USD per hectare for two-rotation logging over the same interval (Fisher et al. 2011). To compare, a cashier job in a big city might pay about 250 USD per month. Mountainsides of oil palm are mountainsides of money.

One option for preventing this land use would be REDD+ programs that provide payments for the carbon storage benefit of not destroying forests. The problem is that a market for carbon doesn’t fully exist yet, and prices are far too low to make this feasible. Current governments are willing to support prices of somewhere around 15 USD per ton of carbon stored, but the yield of oil palm relative to the forest it destroys would require the market to sustain a price of around 50 USD per ton of carbon (Fisher et al. 2011, again). Finding any buyers at this price is highly unlikely in the near future. Put a different way, the opportunity cost of conservation is somewhere around 20000 USD per hectare – and a hectare is not a very large area – only about the size of a single football field.

The alternative solution is to find ways to make oil palm agriculture more sustainable. Efforts like reductions of wasteful fertilizer application and establishment only on land of limited conservation value are a start. This enterprise, Benta Wawasan Sendirian Berhad, located near where I work, is now part of the Roundtable on Sustainable Palm Oil and has self-reported some tentative steps towards these goals. But nearly all the oil palm produced today is still far from any reasonable sustainability standards. Consumer labeling schemes to differentiate different production methods are still in their infancy, and industry definitions of sustainability leave (in my opinion) much to be desired.


Spending long days in the field with endless rows of oil palm on the horizon, it was hard not to think often about the complex issues the crop raises. I still try to avoid buying anything with palm oil as an ingredient – but I now understand much better the biodiversity and land and money and jobs that come into play every time I make that small decision. It is a start.

Something is missing

The dipterocarp forests of Sabah in Malaysian Borneo are home to some of the world’s tallest trees, with some Shorea species reaching over eighty meters in height. This scene, from the lower elevations of the nearly undisturbed Maliau Basin, is what we may imagine when thinking of pristine mature forests – immense cylindrical boles reaching skyward, scattered throughout an open understorey.


But the landscapes of Malaysian Borneo are not all like this one. Some of the country looks hardly like a forest at all. The trees are all gone. Their immense trunks are too attractive and easy a target for logging. Paper, plywood, and the export market for hardwoods supply the demand.


The result is large-scale deforestation. Modern techniques emphasize selective removal of the largest and most valuable trees, and sometimes preserve riverside buffers, but there is no escaping the heavy impact of logging. Steep slopes and easily crumbled soils make the problem worse.

log grabbing

hill loss (1)

Even in selectively logged forests like the one we are working in below, something feels wrong. Some things are missing, and new things appear in their place.

small trees

For me one of the most noticeable differences is the presence of large gaps in the canopy. Forests are naturally dynamic environments where large trees fall and expose sunlit areas in which regeneration occurs. But in these heavily logged forests, the default instead becomes large clearings of dozens of meters, brutally hot, choked by tangles of thorny lianas and spiny palms, sometimes more than two meters deep, only passable by hacking a way through with a parang. The environment is no longer friendly.

logging gap

One of the other most noticeable differences is the sound of the forest. In an undisturbed forest I expect the songs of birds, the calls of monkeys, and the rustling of leaves caused by all other manner of creatures. In a heavily logged forest, the canopy goes silent, but the air comes alive with the heavy rumbling of diesel engines cutting trunks, moving timbers onto tractors, and then hauling them away. A symphony of dust.

loading (1)


Almost eighty percent of land in Sabah has been impacted by high-impact logging or clearing in the last two decades (Bryan et al. 2013), and virgin forest within commercial forest reserves has declined by over 90% since 1970 (McMorrow & Talip 2001). This dramatic loss of forest cover has paralleled the state’s rapid economic development and diversification (timber revenue is largely retained by the state, while oil revenue primarily goes to the Malaysian federal government), and has so potentially played an important role in lifting many out of poverty. Ceasing the economic exploitation of forests would be bad in far different ways than current usage is bad.

Yet at the same time, much of the landscape feels far more like a mining operation than a sustainable forestry operation. Rates of extraction are often too high for the regeneration rates that can be sustained, and the highly disturbed forests that remain will be incapable of producing much economic value for many decades to come. As such, overall timber production has decreased sharply in the past decade (Reynolds et al. 2011). Current conservation efforts and broader implementation of reduced impact logging may help shift the situation towards a more sustainable direction, but I cannot help but wonder if the past decades of industry have done more to steal from the future than to help build it.


In collaboration with the state and the timber industry, much research is being carried out to understand the biological consequences of this disturbance. I play a small part in the BALI / SAFE (Stability of Altered Forest Ecosystems) projects aimed at addressing these questions. These data will provide a factual basis for thinking more carefully about these forests. But only personally experiencing these landscapes can shape how I feel about them. Something is missing, and I hope we will someday find it again.



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