Biodiversity: the Blog

Why are there so many species and what are we going to do about it?

From Arizona to the Amazon

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I usually study population dynamics in the upper Sonoran Desert near Tucson, but since I am still entering data from last summer’s fieldwork and analyzing it, I took my laptop down to Brazil for nearly a month. While I’m here, I also get to climb massive trees and learn about the questions and methods used by Scott Saleska’s lab to better understand the future of the Amazon under climate change.

Climate models predict wildly different things about how the Amazon Rainforest will respond to a new climate, but all agree that whatever happens will have a big effect on the rest of the world’s climate. There is a lot of carbon stored in these trees, and if they release that to the atmosphere through dying or burning, it will accelerate global warming. On the other hand, if they grow bigger and faster, they might actually buffer the climate by taking up more carbon dioxide.

One problem is that no one really knows how these trees respond to changes in the climate. Our best understanding, captured in mathematical models, predict that drought would cause the forest to die back, looking barer and browner. Yet during recent droughts, the forest appeared to green up! Was it because the forest is light limited and fewer clouds meant more light for the plants to  grow? Would that response continue if the drought continue?

It turns out that in a very diverse forest like the Amazon, no one really knows how the leaves behave. Unlike in, say, New Hampshire, where trees all put out buds around the same time and then lose their leaves around the same time, this forest appears evergreen. Since leaves don’t live forever, we might assume trees replace their leaves. But how often? All at once, or on a sort of rolling basis? Regularly, or in response to some environmental signal? Tree species might behave very differently – after all, some grow fast in response to forest gaps, while others grow slowly in the shade of larger trees until they reach the canopy. So how similar are their leaf lifespans and replacement strategies? These answers are pretty difficult to answer, especially because walking up to a tree whose lowest branches are over 100 feet in the air makes it very difficult to look at their flowers – or even their leaves.

Fortunately, with improved arbor techniques, climbers can now safely access much more of the canopy to measure and tag individual leaves. Imaging and remote sensing might be calibrated to in the future provide an even faster way to measure leaf age and species identification. I’m enjoying learning both techniques for measuring leaf traits and leaf demography as well as for climbing into the canopies. And I’m especially enjoying thinking about a completely different set of scientific questions: questions about movement of water and carbon through a whole ecosystem, instead of competition, predation, and population dynamics.


Grad student Neill Prohaska shows the lab's newest member some equipment.

Grad student Neill Prohaska shows the lab’s newest member some equipment.

Alejandro learning to climb an access line into a 40m high canopy.

Alejandro learning to climb an access line into a 40m high canopy.


One instrument tower has stairs for easy access.

One instrument tower has stairs for easy access.

Neill at the top of the walk-up tower, looking out over the canopy of the Tapajos National Forest. I was surprised how diverse the canopy structure was.

Neill at the top of the walk-up tower, looking out over the canopy of the Tapajos National Forest. I was surprised how diverse the canopy structure was.

The other tower, which measures the carbon flux of the forest, must be climbed like a ladder, wearing a harness.

The other tower, which measures the carbon flux of the forest, must be climbed like a ladder, wearing a harness.

Written by pacificsummer

July 26, 2014 at 11:52 am

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What does wilderness mean to you?

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Where does the grassland end and the pinion-juniper forest begin? Looks simple from back here, but hike to the first juniper you find, and there is still an awful lot of grass....

Where does the grassland end and the pinion-juniper forest begin? Looks simple from back here, but hike to the first juniper you find, and there is still an awful lot of grass….

Drawing lines is hard. In a variable and idiosyncratic world, our tendency is to lump ideas or places into groups. We learn in preschool to categorize, to delineate, and later to characterize and describe those categories. This leaves us frustrated when we look closer at where those lines should be, and they become difficult to draw.

Very frustrated.

Last week, I posted about Dave Bertelsen, who has recorded flowering plants along a five mile section of trail ascending the Santa Catalina Mountains for nearly 30 years. The vegetation’s structure, species identity, and density looks very different at an elevation of 8,000 feet than at 5,000 feet, which looks different than plants at 3,000 feet. Biologists commonly recognize these as different “communities,” “biomes,” or “assemblages” of plants, but when you hike from 2,500 feet up to 6,000 feet, you realize it is hard to draw a line between them on the ground. It makes perfect sense when you think of each individual species responding to the temperature, moisture, soil, competition from other plants, and herbivory from animals, but it makes generalization more difficult.

Another line that becomes difficult to draw when you think about it too hard is which areas to ask the US Congress to designate “Wilderness.” That designation is the highest legal protection against housing developments, mining, and other activities that would change the character of a place. We probably each have an idea of what wilderness looks like, and what activities are compatible with wilderness. But those ideas may vary from person to person in ways that seem subtle when viewed as an abstract national policy, but can be very important when that line touches a place you love.

Earlier this week I attended a meeting of the Southern Arizona Climbers’ Coalition. I had been meaning to join them for nearly a year, when they first formed. After all, I didn’t just move to Arizona for grad school. My list of potential advisors was strictly within a few hours of decent rock climbing. At this meeting, I had been invited to give a short presentation on the ecology of the region, and I used it as an opportunity to ask what ecology should be included if you had only two pages in a guide book. Being down in the weeds, it can be hard to see the big picture of the desert and Sky Islands, even from the top of a six pitch crag. Thanks to the folks who responded to that question – if you have an opinion, especially if you’re new to the area – please email me or leave a comment on this post!

Almost more valuable than those comments were the conversations I had about ongoing land management issues. Climbers enjoy and value wilderness, I suspect more than much of the general public. The recent shift of land management agencies toward prohibiting safe and practical rock climbing in areas being managed for wilderness character changes the way the increasingly large segment of the public uses the land. It also puts the climbing community in the very awkward position of somehow opposing wilderness designations. Of course we want to protect the landscape from mines, off road vehicles, and other large impacts. But it seems ludicrous to lump rock climbing in with mining and road creating, especially when a majority of climbers practice Leave No Trace ethics (though not as many as I wish would). Many of us have worked or volunteered with, or for, or been members of organizations like The Wilderness Society, which are promoting more wilderness designations.

I definitely see rock climbing in the traditional style (trad climbing) being consistent with wilderness character. Typically (these days) anchors and gear are primarily removed, with the possible exception of webbing used to rappel off the top of the climb, which eventually fades and disintegrates – eventually, not fast, but still eventually. One of the earliest North American pioneers of rock climbing, John Muir, who was also a wilderness advocate and started the Sierra Club, would have agreed, I think, though he likely would be astounded at our safety technology today. Maybe, like many old climbing hardmen, he would be contemptuous, too, but I like to think his vision, compassion, attention to detail, and evidence based values would have won him over to the freedom of climbing having a place, even in wilderness. Judiciously, of course, and with climbing ethics firmly in mind.

But what about sport climbing, in which metal bolts are drilled into the rock, usually requiring a mechanized drill, and left for following climbers to use? Those bolts also need to be replaced periodically that practically for the safety of the climbers. These bolts are rarely visible except right next to a crag (and sometimes maddeningly invisible to a climber on the route), so they are unlikely to heavily impact the wilderness experience of nonclimbers. Rock climbers who want a pure experience, a true pathfinding adventure without metal cairns, may not appreciate their presence, although my understanding of climbing ethics is to not place bolts where finding alternative protection is actually possible. This is definitely not a cut and dried area – especially when you consider drilling in metal rap anchors at the top of a popular trad route to make the descent safer (or possible).

Should leaving any gear or drilling bolts be allowed in areas where we want to preserve wilderness character? Wilderness is, after all, an important legal protection for areas that we would like to keep climbing against threats like mining that would completely remove access. If even wheelbarrows are prohibited, can exceptions be made for mechanized equipment like drills? Actually – what about cameras and wristwatches and smartphones? Are only mechanized things that interact with the landscape prohibited? That touch something other than the person? Where do you draw that line?

Somewhere like Cochise Stronghold, a backcountry area whose rugged terrain practically protects itself from offroad vehicles and even off train mountain bikes, certainly includes rock climbing in its wilderness character. Anecdotal evidence from climbers there suggest that a few humans climbing the rocks slowly and awkwardly (okay, some of us more slowly and awkwardly than others) does little to strike fear into the hearts of nearby animals. Anecdotal, to be sure. And does the short term presence of a drill’s racket increase that disturbance? By how much? (I am currently writing a paper on how the ecology of fear affects biodiversity, and I would love to collect more rigorous empirical data on the effects of climbers.)

I had a good series of conversations with other members of SACC following the meeting about other access issues related to ecological and species specific concerns. One of my greatest frustrations as a recent college graduate back in D.C. dealing with gigantic policy concerns and disagreements between close allies in environmental issues was my lack of expertise. Besides the lack of climbing in the Washington area, that was a major factor in driving me to pursue a Ph.D. in a basic science department.

It’s been nearly five years to the day since I packed my mountain bike and clothes into a station wagon, and drove three days to Arizona and begin a Ph.D. in Ecology and Evolutionary Biology. Although I had spent the previous 18 months working on federal environmental policy, I chose a basic science department, rather than one dedicated to solving immediate and applied issues. This even despite the fact that the 6 months prior to my position in D.C., I had worked for BLM in Nevada, and before that for a lab studying the effects of an invasive plant. My entire post-college professional experience was in solving pressing environmental problems, and I walked into a department where that training was not particularly valued, and instead the focus was on what questions would move the state of human knowledge forward. Perhaps a naive choice, but perhaps wise. After all, I had been glad that as an undergraduate, I focused on a degree in Biology (Scripps being a small liberal arts college, we had no differentiation possible within that major at the time) rather than an attractive interdisciplinary major in Environment, Economics, and Politics.

I’m not done with my PhD yet. I’m still writing and revising drafts of papers for publication, some of which will eventually become my dissertation. It feels like a long slog sometimes. An exciting and endlessly fascinating slog, but nevertheless long.

I may be still slogging the long slog, slog by slog, but it felt good at that meeting to offer my background in ecological theory, local field work, and access to current scientific literature to contribute to the conversation between climbers and land managers. I came away with ideas for new topics I want to research in my spare time (ha).

I would say it felt spooky for my former world of negotiating differences in environmental allies to collide with my current research and climbing worlds in so personal a way, but I’m actually more surprised it hasn’t happened sooner.

Written by pacificsummer

July 12, 2014 at 12:54 pm

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Summer stress

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What I'm placing behind my ear is no tropical flower: that is the rind of a saguaro fruit, burst open to reveal the deliciousness inside! Behind me, most shrubs like the ocotillo are leafless. Thanks to Elena Martin for the photo.

What I’m placing behind my ear is no tropical flower: that is the rind of a saguaro fruit, burst open to reveal the deliciousness inside! Behind me, most shrubs like the ocotillo are leafless. Thanks to Elena Martin for the photo.

The news (and some photos on Facebook) would have me believe the summer is all about sitting on the beach, enjoying a fast paced book. But my last three summers in the Sonoran Desert have been a race against time to census seedlings as they pop up and quickly die following the patchy monsoon thunderstorms. The seasons have been full of long days in the hundred degree plus heat, and dreaming of seedlings again in my sleep.

Actually, the monsoons that just began may have brought a silent sigh of relief from many dry and browning plants in the region. The long, arid early summer was finally over. June can be a miserable time of year, made bearable by the fact that candy falls out of the sky. Saguaro fruits (Carnegiea gigantea) ripen and split open during June, revealing the sugary flesh surrounding thousands of seeds the size of poppy seeds. Those the white winged doves fail to eat off the cactus fall to the ground, where, if we are lucky, we find them before the coyotes, javelinas, or ants. As they dry in the sun, they reach a sticky, chewy, very sweet consistency, broken by the bitter crunch of the seeds. A little like a date or a fig, maybe. Mostly it tastes like a saguaro.

A few species seemed to jump the gun on the monsoons. During a season when most stems are brown and the only leaves that dare show themselves whither reticently, the limberbush (Jatropha cardiophylla) in the Santa Catalinas started to put out small leaves and even to bloom, a full two weeks before the monsoon rains arrived! I observed them myself on a hike up the Finger Rock Trail with naturalist David Bertelsen and environmental science teacher Elena Martin on June 27. In this unpredictable region, with its patchy storms and fickle promise of rain, why spend the energy and the water to make flowers prior to the storms hitting? Where had the plant held on to this reserve of moisture? Was it to get the jump on all the other plants when the rain finally hit? Do limberbush in other canyons, and other mountain ranges have this same phenology? Do they always in the Catalinas?

Dave is one of the few people who could may actually be able to answer that final question, by checking his notes. Nearly 30 years ago, he set out to hike the Finger Rock Trail weekly for 20 years, all the way from Tucson to the top of Mount Kimball, and record all flowering species and which section of the trail they appeared in. The result is a rich data set of phenology (the seasonal timing of events) of the flowering plants along that trail, which climbs thousands of feet in elevation. He has published several papers on this data, along with Theresa Crimmins and Mike Crimmins. I was astounded that he had a vision right from the start of the degree of dedication and the amount of time he planned to continue. It was a bold vision, especially for someone who was working a full time job – and not a research job.

Speaking of working full time at a job outside of academia and even scientific research, we had a conversation along the way about the term “citizen scientist.” To me, that term evokes the National Guard’s advertising campaigns for “citizen soldiers,” individuals who have a high degree of training and professionalism in their military duties, even while not being full time employed as such. But Dave hears it differently: he wonders why the “citizen” need be there at all. It implies that scientists are a class apart, excluding the general public, instead of being accessible to anyone pursuing answers through rigorous use of the scientific method. Charles Darwin, for example, was not a professional scientist, but made great contributions to scientific fields. Albert Einstein was employed full time at a patent office while he developed much of the early theory of relativity. Dave suggested the term “naturalist” has a less diminutive connotation for people studying nature without an official posting to do so.

After our hike, I was reading through the final entries in the field journals kept by students on the field course I recently helped teach. One of the final questions posed by the main instructor was, “What research project would you want to go spend an additional three weeks studying?”

Forget three weeks, I thought. Be bold like the Jatropha. Start now, and in 20 years, you’ll have the jump on the others, you’ll have that data set.

Written by pacificsummer

July 6, 2014 at 10:39 pm

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“What is hiking in Arizona like?”

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That question was posed this last weekend by a woman from Chicago as we hiked through the conifer forests high above Boulder, Colorado. I had traveled to the Rocky Mountains for the weekend to meet up with my parents, my sister, and her boyfriend, to enjoy the longest day of the year from a high vantage point. As often happens in the mountains, we made a new friend on the trail.


It’s a good question, though. What is hiking in Arizona like? A month ago, I was serving as the teaching assistant for a field ecology course for the University of Arizona. We explored some of the reasons why the geology, flora, and fauna of the Sonoran Desert is so diverse and dramatic. That diversity means hiking in Arizona can be like many different things.

The classic image of Tucson or Phoenix is that of the giant saguaro cactus (Carnegiei gigantea) and bare ground. It is true that hiking around Tucson involves a lot of dry washes, loose rock, thorny and spiky plants, and venomous animals. This time of year, it is beastly hot even near sunrise and sunset, with little relief.


But southern Arizona is dotted with mountain ranges between the wide basins of desert. The change in elevation creates distinctive changes in the temperature and moisture conditions, and support isolated islands of distinct biological communities. Travel only a little higher in elevation, say, to the foothills of the Santa Rita, Patagonia, or Dragoon Mountains, and you will find a grassy savannah like view dotted with trees. Some students were so close to expecting a lion or elephant to emerge from behind the tall grass that their Facebook photos convinced friends back home they had taken an African safari.


Travel higher into the mountains, and they become steeper. The mesquites (Prosopis spp.) are replaced by oaks (Quercus spp.), which turn over into pines (Pinus spp) and eventually even quaking aspens (Populus tremuloides). These elevations, slopes, and forests feel not so different from hiking in Colorado. The gathering thunderclouds on the solstice even felt like the monsoon we are waiting for in Tucson.


 Many Tucsonans have noticed this on their annual trek up Mount Lemmon to see real life snow on the one or two days the clouds dump up there each winter. (I hear it used to be more frequent, but not in my five year experience.) But why are the mountains here, and why do the plants and animals change with elevation?

These questions have captivated ecologists for more than 100 years, since the Carnegie Desert Laboratory was founded at the top of Tucson’s centrally located Tumamoc Hill. Well known ecologists have recorded the change in vegetation in the sky islands surrounding the lab, using the corresponding gradients of temperature and precipitation to theorize about their role in determining plant assemblages.

The short answer is that long, long ago, tectonic plates collided, created stretching forces in the Earth’s crust that led to volcanoes popping up throughout the region (perhaps more on the geologic story in a future post). During the Ice Age, the plant life of the region probably looked like the the tops of our mountains do today (perhaps more of this coming, too) – except with woolly mammoths and other megafauna trampling them (and watch for more of this)! As the climate warmed, those species either could not survive in the hotter, drier environment, or were excluded from the area by species that found an advantage in hotter, drier conditions that migrated north from tropical regions (more of this definitely coming in a future post). The process of adiabatic cooling creates colder but also moister conditions at the tops of these mountains (more on this later).

You can learn more about sky islands and hiking in Arizona from Brusca and Moore’s new book, A Natural History of the Santa Catalina Mountains.

Hiking in Arizona is like, well, like hiking in Mexico. Like hiking Canada. Like hiking in Europe, or in Africa. Why it is like hiking in so many different places inspires questions about geology, chemistry, physics, molecular biology, ecology, and other scientific disciplines.

Written by pacificsummer

June 23, 2014 at 7:46 pm

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Focus on the Sonoran Desert: Fiddler crabs

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As we head deeper into the most miserable of the Sonoran Desert’s five seasons, lend me your eyeballs (and your ears) and let me renew your interest in this unique region.

For the past 3 weeks, I served as a graduate teaching assistant for University of Arizona’s field course on the Sonoran Desert. At the same time, I was drafting and revising a manuscript with collaborators for a special journal issue on species interactions in the region. It has been a fantastic time to step back from my narrower research questions to consider the broader context of the environment in which interactions occur.

Let me say first of all that the five seasons of the Sonoran Desert include summer monsoons, autumn, winter, spring, and the arid foresummer. Guess which one we are experiencing now in Tucson!

The key to much of the moisture and diversity in this subtropical, semi-arid region is the Gulf of California (also known as the Sea of Cortez). It is home to a unique endemic porpoise which that may soon be extinct, a strong fishing culture that is slowly learning to fish more sustainably, inspiring researchers and educators at CEDO Intercultural, and a literary and ecological legacy from the trip that John Steinbeck and his friend Ed Ricketts took in the 1940’s. It is also the home to several species of fiddler crabs, which provide endless entertainment and substantial numbers ready volunteers for research projects on their behavior, morphology, and density.

Inspired by the “True Facts” videos posted by zefrank1 on YouTube that make animal diversity approachable and entertaining, we put together a tribute to those videos based on my shaky, low quality footage of fiddler crabs in the estuary:

Additional note: Stay tuned for Biosphere 2‘s renovations emphasizing the regional importance of the desert sea!

Written by pacificsummer

June 7, 2014 at 3:33 pm


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Recently, I decided I needed to know how many seeds a paloverde tree drops during the period from May-June when it produces copious (and delicious) pods. However, virtually anything that eats in the Sonoran Desert seems to eat these paloverde seeds. So I need to design a seed trap that allows seeds to fall into it, but does not allow animals to eat the seeds before I return.

I first thought five gallon buckets would be pretty resistant to javelinas and pocket mice, but quickly realized the Harris’s antelope squirrel has no problem boinging in and out of them. My next try was to extend the bucket with a squirrel baffle type cone. This had the added benefit of increased diameter of seed collection, but the decided detriment of acting like a sail on gusty days. Even with all the heavy rocks I could find piled in the bottom, the prototype blew over ten minutes after I set it up.

However, I was rewarded for leaving my camera out with my first ever video of a bobcat! He or she wandered by late in the afternoon, and returned a few days later at dusk. Check it out:

PS Thanks Prohaskas for letting me try out my seed traps behind your house!

Written by pacificsummer

May 14, 2014 at 8:28 pm

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What happens in the dark forest while you sleep?

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The UA Science: Sky School, a residential science program in multidisciplinary science, is housed at the summit of Tucson’s nearest Sky Island, in an old military base converted to an astronomical observatory. One of the buildings on site, the old enlisted barracks (it was only men up there back then), is condemned and boarded up. No one to my knowledge has been inside in a decade. It is very, very dark if you walk past it on a moonless night to set out a wildlife camera. (I sing to myself if I’m alone.)

Ten days ago, I was up at Sky School with a group of middle schoolers, and walking past the enlisted barracks in the night, we saw a light on in a downstairs window!

I don’t know if some electrical system went haywire, someone had broken in, or the ghosts were out in full force in anticipation of the full moon (this was two days before the lunar eclipse). One week later, I passed by in the dark, and the light was off. Spooky.

Lots of things happen outside while we sleep. Some of them we will never know about. Some of them we lack the olfactory or other senses to detect. But if you could see in infrared like a snake, or echolocation like a bat, or even hear like a fox, here is what you would have seen in a clearing between the telescopes at the summit of Mt. Lemmon last Friday night:


Written by pacificsummer

April 20, 2014 at 1:21 pm


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