What lies beneath


What do you see on this alpine slope? What you don’t see may be as important as what you do. You might see a rocky substrate with a very sparse cover of plants, all apparently similar. A few grasses and sedges, several asters, and a few other stragglers from other families. They are all short and small, with similar traits reflecting adaptations to the short snow-free growing season. Does anything distinguish them? How can they all coexist next to each other?


The answer may lie in the things you don’t see – in what lies beneath the surface of the soil. Species may coexist when niche differences between them are large enough. Although aboveground differences are minimal, belowground differences may not be. I decided to dig some holes to find out whether these species’ root systems were equally similar.

baldy site photo 76

Consider the example of this buckwheat, Eriogonum umbellatum var. aureum. This individual is about ten centimeters wide and just two centimeters tall. You, like me, might expect it to have a comparably small root system that would be easily extricated.

roots 1

Unfortunately for me the soil here is a primarily comprised of a blue-gray slate. The surface is a loose gravel, but within a few centimeters of digging, the soil becomes loose rocks, and after a few more centimeters becomes solid rock, only occasionally with a fracture plane present. Soil is a generous description. Yet somehow the plants manage to grow in this matrix, and their roots manage to slip into cracks or themselves make new ones. Digging is a precarious affair where rocks must be carefully removed, and fragile roots must be traced until they disappear into subterranean nothingness. Here you can see the beginning of an extraction operation, with a Phacelia hastata plant also emerging from the soil.

roots 2

It turns out that this diminutive plant has an impressively large root system, not only covering a wide area but also plunging deep into the rock. What you see here isn’t even the entire root system – I lost the deepest root into a crack that I was not able to fracture with my digging tools. Here you can see my collection effort back in the lab.

roots 4

And it also turns out that not every species has this same extensive root system. Here is a grass species I brought back to the lab, Achnatherum lettermanii. In this case I dissected it into leaves, stems, roots, and dead tissue. You can see here that the roots are much shorter and smaller – a marked contrast to the buckwheat.

roots 3

In the end I was able to unearth the full root systems of over seventy plants. The diversity was impressive, and may help to explain why so many species coexist despite such apparent aboveground niche similarity.

We ecologists rarely explore plants’ root systems. They are time-consuming and difficult to dig up. Measuring them often comes at the price of killing the plant. The whole plant measurements I took would be nearly impossible for a large tropical tree, with its roots hopelessly tangled amongst those of its neighbors. But sometimes these extra efforts and costs are worthwhile. They show us things we could not see any other way.

Getting to work

My commute to work this summer takes three hours each day. Most people have shorter journeys, but I don’t spend mine driving a car, riding a bus, or sitting in traffic.


I walk. A mile and a half of road, then two and a half miles of mountain, climbing from 9500′ to 11600′.

This is the route. Home is in the valley on the left.


And here is my office. There are no walls, no chairs, no windows – but neither are there
cubicles or computer screens. There is no dress code and there are no time-sheets. I get my exercise along the way.


My commute, beautiful as it looks, is not always perfect. It is a steep and sweaty journey, and all of my equipment must be carried up each day on my back. Some days I am tired, and some days I am sick, but the route does not get shorter or easier.


Some days there is heavy rain, and the journey is a cold, muddy, and slippery mess, with fieldwork requiring waterproof paper and frozen fingers. Unless there is thunder, every day is a work day.


I do spend most of my year at a real desk analyzing data, writing papers, having meetings, doing labwork, and thinking. But my favorite times of the year are during the summer field season, where happiness and health are easily within reach. Most of us are constrained year-round to jobs in cities, jobs indoors, hours spent on highways and bus stations. My work, though physically hard, is a choice, and not one on which my subsistence depends. I feel lucky to have escaped.

I do wish that more of our cities could be designed to promote healthier and happier lives (as the architect and planner Jan Gehl has eloquently argued in his book Cities for People – and then also been invited to implement in several major metropolises). But I am glad to stay away from cities, at least for now. There is too much beauty in the mountains.


Marmots, copper, and hot sauce


Usually I like seeing marmots. They represent everything I like about the high country out here. But recently our relationship has gotten much worse. The problem happened at 8:28:57 AM on July 1st, when a marmot bit through the sensor cable of the solar radiation probe for my weather station. I had left the cables weakly armored after the early-season installation and was planning to replace the armor with something stronger immediately. I got around to doing it just a day or two too late to avoid providing a breakfast for this rodent.


Finding the cables and mounting posts gnawed at was more than little disappointing. It meant I had to pull the entire set of instruments off the mountain for repairs.


Back in the lab, I found five or six places where the cables for various instruments had been nibbled, and three where it was chewed clear through. I cut away the problematic sections, stripped each cable and then all of its data lines, re-soldered the connections, heat-shrinked the joint, then waterproofed the repair job and patched the external wrapping.


And then I did what I should have done in June. I bought several meters of braided tin-plated copper sheathing and carefully enclosed each cable. It was hard enough to cut through the sheathing with metal shears, so I wasn’t very worried about teeth.


Then, back up the mountain with the weather station, the sheathing, the computer, and an assortment of tools in a backpack, plus one secret weapon.


Habanero hot sauce. We secured all the sheathing with metal wire, leaving very little to chew on – but just to be extra safe, we covered all the lines with the spiciest sauce I could buy. I don’t think anyone will want to even lick the station now.

hot sauce

My summer student, incidentally, was curious about how the hot sauce would taste on an apple. He discovered the answer shortly thereafter: it tastes awful. A culinary lesson for him, and an important lesson on protecting equipment for me. I’m glad to see our weather station back up and running, taking important data for the rest of the summer growing season and the beginning of the coming winter.

The local wildlife

Living the middle of a national forest in the Rockies means that there is more wildlife in and around my house than you might expect. Here a few of the regular visitors.


First, here is a deer mouse (Peromyscus maniculatus) that moved in when the snowpack was still melting. It found a supply of packing materials and would regularly rock-climb over the stone backing to the wood stove to bring supplies back to its nest. I had no idea that mice were such good climbers.

Second, here is a predator that likely solved my mouse problem a few weeks later. This fox (Vulpes vulpes) has a family of five kits, and regularly passes by my cabin at all hours of the day, usually with several dead rodents in its mouth.


And third, here is a rodent large enough to not be seriously concerned about fox predation – a golden marmot (Marmota flaviventris). This one lives under the cabin across from mine and has a fondness for eating dandelions (Taraxacum spp.).

dandelion 1

dandelion 2

dandelion 3

No mountain lion sightings yet, but plenty of scat in the mountains – it is a wonderful feeling to know that there is so much life all around our small human existences.

chased off the mountain

Learning from a mustard

arabidopsis 3

Ask a molecular biologist about their favorite plant and they will likely answer with Arabidopsis thaliana. This mustard-family species is an excellent resource for evolutionary biology because of the wide range of genetic and genomic resources available for it. As a result it has become a model organism for plants in the same way that zebrafish are for human diseases.

For an ecologist who prefers to be in the field rather than in the lab, Arabidopsis is not a very inspiring organism. It is a small weedy-looking thing that completes its entire life cycle in about a month. Compared to the grandeur of a redwood or the beauty of an alpine primrose or the mysterious clonal lifestyle of an aspen, it has little to offer. Nevertheless, a few years back, I found myself embarking on a study with this species in collaboration with several Arabidopsis experts. Why?

The answer is that it is a marvelous system for experimenting on plant phenotypes and for then interpreting these experiments in an evolutionary context. Without too much trouble one can generate a range of individuals with known mutations causing known phenotypes, or with natural phenotypes representative of growth in very different environments worldwide. Arabidopsis is a tool.

I was interested in a question about leaf carbon economics. Leaves generally fall along a spectrum from ‘fast’ to ‘slow’ (Wright et al. Nature 2004), with some species having fast-photosynthesizing but cheap and low-lifespan leaves and others with slow-photosynthesizing but expensive an high-lifespan leaves. Why should carbon economics in plant leaves be restricted along this one-dimensional strategy axis? A number of theories have been proposed to explain this pattern, including some that I have helped to develop. But these theories had never been compared to each other using the same dataset because each required one to measure very different predictor variables. Knowing which (if any) theory was consistent with reality would help us understand the basis of this fundamental economic fact about plants.

arabidopsis 1

And so – Arabidopsis. It grows quickly, which makes it suitable for lab work. It can be forced into a range of phenotypes based on multiple approaches (recombinant inbred lines, near isogenic lines, natural ecotypes, knockout mutants). These phenotypes can then be traced back to known genetic changes. We decided to measure a range of economic and predictor variables in a wide set of Arabidopsis genotypes.

arabidopsis 2

I had little expertise or interest in growing the plants, but was lucky to work with an excellent French group of scientists who were already growing and phenotyping the species. Their previous work already showed that these phenotypes are associated with leaf economic trait variation (Vasseur et al. Ecology Letters 2012). They had developed an automated platform to go from seed to spreadsheet with a minimum of human intervention. I visited this facility last year and was highly impressed by its capability. Nearly everything is computer-controlled.

arabidopsis 4

One of the things we ourselves measured was the minor vein density of different genotypes – this variables characterizes the leaf’s vascular system (which transports water and sugar). A few theories (e.g. Blonder et al. Ecology Letters 2011) we developed suggest that this variable is a strong predictor of leaf economic traits. We also measured several other predictors including leaf dry matter content, a variable important to another theory (Shipley et al. Ecology 2006). And then we put it all in a statistical model to see which theories would survive the data.


The answer, surprisingly, was that very few theories were consistent with data. We found that minor vein density might play an important role (via its influence on an unmeasured but real variable), and that this vein density did seem to vary across genotypes in a way consistent with it playing a causal role. But ultimately, we were left with something of a mystery. We need more and better theory – reality is still too complex. I personally think that leaf venation networks do play an important role in leaf economics (but see a recent study in tropical forests – Li et al. Ecology Letters 2015) but in a way that is more complex than we first proposed.

You can read our study in Annals of Botany Plants (link, pdf). It took more than a few years to go from idea to publication, but I’m proud to see this finally out.

One of the wonderful things about science is changing one’s mind because of new data. Even if those data comes from an unremarkable small mustard plant.

arabidopsis 5

Krummholz: life at the edge

How extreme can environments be before life can no longer hold on? The quaking aspen (Populus tremuloides) trees I study seem to cope well with all sorts of extremes – they are found as far north as boreal Canada and as far south as Mexico. Normally when I see an average aspen clone, it looks happy and healthy, as in this subalpine Colorado meadow.

low elevation

But averages are boring. The interesting biology happens at the extremes. We’re interested in carbon economics, and want to understand if aspen clones in very extreme environments are almost at the point of negative carbon economics, where more carbon is lost through respiration than is gained through photosynthesis. So off we went in search of a very unhappy aspen clone – myself and a post-baccalaureate student in charge of this project named Richard.


A few years ago I climbed Mt. Bellview, the brown peak in the background, and recalled seeing some very small trees growing near its summit. So off we went to find them, and then measure them.


About 1500′ of scrambling later, Richard and I found ourselves on a dry scree field, covered in small and sharp rocks. Shifting these rocks revealed bedrock just a few centimeters down. Yet somehow, more than a few aspens were growing out of this substrate.

find aspens

They didn’t look very happy. In good conditions, aspens will grow easily ten meters high, with lush dark green leaves; here, each stem was no more than knee-high, with small and tortured looking stems. This kind of vegetation is typical of alpine krummholz where plants are exposed to extreme temperature and wind. The plants have no choice but to hunker down.

aspen roots

The slope was loose, but we measured some aspects of growth rate, and then installed light-loggers in the trees’ upper branches.

leaf length

light loggers

In a few weeks we’ll climb the mountain again, this time with a portable gas analyzer able to measure photosynthetic rates in these plants. By merging these measurements with the growth rate and light data we are now collecting, Richard will be able to understand how well these plants are growing at this upper elevational extreme. To me it doesn’t look like that great of a place to live – we were happy to downclimb the slope and head home – but maybe the aspens see it differently. We’ll find out soon.

bellview bottom

Knowing when to go


For the past few days I have been testing an infrared camera for a study on temperature variation across environments. My assistant and I have been carrying approximately fifteen thousand dollars’ worth of non-waterproof equipment into the mountains to make some preliminary analyses. This gets interesting when the sun disappears, then wind picks up, the view across the valley changes quickly from blue sky to heavy dark clouds, and thunder echoes among the peaks.


It’s hard to know what to do in these scenarios. Taking instruments up a peak requires extensive preparation and hard physical work, and it is a waste to give up and go home too early. But tarrying too long means the risk of heavy rain, or worse – a lightning strike.

Sometimes a storm passes easily, leaving blue skies behind.


But other times, clouds descend, and the storm is everywhere.


Today I decided the risk wasn’t worth it, so we hastily packed our gear and rushed down the slope away from the storm, accompanied by the sounds of thunder. As we reached home, the sky cleared and then the storm was gone. We gambled – and lost – and then went back to work in the sun.


I don’t know if one can ever know perfectly when to go, and when to stay. But we probably still made the safe decision. The risk on any one day is low, but the cumulative risk over hundreds or thousands of days in the field is high. Better to live to do science another day!



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