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By Invitation Only: The Next Step in Funding the Joshua Tree Genome Project

Hard at work on the full proposal. (CIS)

Back in January we wrote to you about preparing a proposal for the National Science Foundation. Now, we have some encouraging news to share.

Don’t break out the champagne yet though.

Last month we received the good news that our proposal had been ‘invited for a full proposal’.

As research funding has become more and more competitive, the National Science Foundation has turned to using ‘preliminary proposal’ system. Each January scientists from around the country put together short summaries of their latest and greatest research ideas. From the hundreds of preliminary proposals they receive, about eight dozen (approximately 25%) will be invited to submit a full proposal.

And (drum roll, please!) our proposal was one of the lucky ones invited to prepare a longer form description of our research proposal. So, while the rest of you are out enjoying the summer sun (or hiding from triple digit heat if you live in the Mojave), here at the Joshua tree genome project we’ve been hard at work trying to make the best possible case for our work. In a little less than a week we will send off our full proposal. And then we will wait …

We probably won’t hear a final funding decision until December at the earliest, and statistically, our chances are slim. But, at the moment, our thoughts are occupied with all the things that we will do if we were funded.

Here is a partial list of what we have in mind:

  • Completing, assembling, and annotating the full Joshua tree genome
  • Surveying genetic diversity across the entire range of the Joshua tree
  • Common garden experiments to identify genes involved in climate adaptation
  • An expanded citizen science program with Cal Native Plants
  • Public Lectures at the Desert Institute
  • Research internships for underrepresented minority students
  • Outreach to public school teachers in southern California

It’s a long and ambitious list. We hope that it’s enough to make our work stand out. Wish us luck!


It’s grant proposal season


It was a rainy winter in the Mojave, and it was mighty quiet around the ol’ Joshua Tree Genome Project Page.

But we didn’t just huddle up around the fire.

January means grant proposal deadlines at the National Science Foundation, so while the yucca moths were underground this winter, we were hard at work trying to find funding for the next phase of this project. The generous support we’ve received from donations at Experiment.com and from The Living Desert Zoo, we’ve made huge progress towards assembling the Joshua Tree Genome. However, completing the next stage in the project – identifying the genes involved in adaptation to climate change – is going to be expensive. So, we’re looking to NSF to help us make it happen. Thanks in large part to the work we’ve been able to do so far, that proposal we wrote back in January was interesting enough to NSF for us to be invited to the next round of consideration — look for an update on that part of the process soon.

Research dollars are getting harder and harder to come by as federal spending for basic research has stagnated. So, the competition is fierce, and winning the funding game means we’ve gotta hit it out of the park. I hope what we’ve put together for tomorrow’s deadline is up to the task.

To learn more about the value of basic research check out this great story from the PBS News Hour. It’s an essay by Sheila Patek, a biologist at Duke University who studies, among other things, the biomechanics of mantis shrimp, which use their flimsy forelimbs to punch through tough snail shells. Patek’s work can seem frivolous, but it might also lead to biologically-inspired designs for stronger materials. She says

The nature of discovery is that it is impossible to anticipate what you will find. That is discovery. Discovery-based research is most fruitful when new knowledge is sought for its own sake.

If you agree, maybe phone a friend in Washington to tell her about it?


The Living Desert funds cutting-edge DoveTail technology to assemble the Joshua Tree Genome

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The Joshua tree genome project is excited to announce a new partnership with The Living Desert Zoo and Gardens. Through a very generous gift from The Living Desert, we will use DoveTail Genomics Hi-Rise Technologies to assemble the Joshua Tree Genome.

The genome is the complete set of DNA letters that spell out the ‘instructions’ for how to build an organism. By sequencing the genome of the Joshua tree we hope to be able to understand its evolutionary history, how it’s relationship with yucca moth pollinators originated and evolved over time, and how Joshua trees might adapt to ongoing global climate change.


Ewww-eww! That Smell! Why do Joshua Trees Smell Like that?

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If you’ve ever sat under a flowering Joshua tree on a spring afternoon, you’ve probably noticed a peculiar odor. “What … is … that?”

A little investigation reveals that the odor is coming from the flowers. The smell isn’t bad, exactly. Just odd. And strangely familiar. What does it remind you of? Wild mushrooms? Blue cheese? Windex? Overripe cantaloupe?

Figure 1: The source of the odor: A Joshua tree flower. (William Godsoe)

Figure 1: The source of the odor: A Joshua tree flower. (William Godsoe)

The early American botanist William Trelease described the scent of Joshua Tree Flowers as, “Oppressive” and “intolerable in a room”, but also commented a more positive note that previous descriptions of the odor as “fetid” was “not strictly accurate.”

A paper just published in the American Journal of Botany uses cutting-edge chemistry to unravel the mystery of why Joshua tree flowers smell the way they do. Glenn Svensson, a chemical ecologist at The University of Lund in Sweden, led an international team of scientists, including members Joshua Tree Genome Project, in collecting samples of Joshua tree scent. Using a hacked aquarium pump the team sucked up samples of air around Joshua tree flowers, and collected the odor molecules using some custom-made filters containing a special absorbent.

Figure 2: Sampling scent from a Joshua tree in the Spring Mountains, Nevada. The black pump is connected to hoses that draw air through carbon filters. One filter is placed inside a plastic oven bag containing a Joshua tree inflorescence. The second filter draws in air from the outside, providing an environmental control. (Chris Smith)

Figure 2: Sampling scent from a Joshua tree in the Spring Mountains, Nevada. The black pump is connected to hoses that draw air through carbon filters. One filter is placed inside a plastic oven bag containing a Joshua tree inflorescence. The second filter draws in air from the outside, providing an environmental control. (Chris Smith)

The filters were then taken back to the lab, and analyzed using process called Gas Chromatography Mass Spectroscopy (or GCMS). Gas Chromatography separates the different odor molecules in a long heated column, so that different compounds are retained the column for different lengths of time. Mass spectroscopy ionizes each molecule and produces a “fingerprint” or “mass spectrum” based on its mass and charge. The combination of retention time and mass spectrum data can be used to identify the different molecules contained in the odor mixture.

When Svennson and his team looked at the data from the Joshua trees, they found that up to 80% of the molecules found in Joshua tree’s scent was a complex 8-carbon compound called mushroom alcohol. The technical, less beautiful, name is (R)-1-Octen-3-ol, or pentyl vinyl carbinol.

Figure 3: The chemical structure of Mushroom Alcohol ((R)-1-Octen-3-ol), the primary compound found in Joshua tree scent. (Wikimedia Commons: Ju

Figure 3: The chemical structure of Mushroom Alcohol ((R)-1-Octen-3-ol), the primary compound found in Joshua tree scent. (Wikimedia Commons: Ju)

Mushroom alcohol occurs naturally in many plants and mushrooms, as well as in many foods, including artichokes, wheat bread, and soybeans. At least one other flower is known to emit odors containing mushroom alcohol: the orchid Dracula lefleurii, which mimics mushrooms to attract fly pollinators. Mushroom alcohol is also used commercially as an artificial flavor. The chemical manufacturer Sigma Aldrich describes the flavor as “cheesy, creamy, fishy, green, meaty, mushroomy, earthy, and herbaceous”

So why would a Joshua tree want to smell like a mushroom? The most likely explanation is that odor attracts the yucca moths that pollinate Joshua trees. Many flowers use odor as a way to attract pollinators, and it seems likely that the peculiar odor of the Joshua tree is somehow related to their peculiar pollination biology.

Svensson and his team compared the odor profiles of different species of Joshua trees that are pollinated by different species of moths, and found that they are indeed significantly different from one another. Joshua trees from the eastern Mojave produce less mushroom alcohol and more of another chemical, poetically called (E)-4,8-dimethyl-1,3,7-nonatriene, which is also found in cardamom.

The differences in scent does suggest that odor is important for attracting pollinators but, counter-intuitively, the two different species of yucca moth that pollinate Joshua trees seem to be unable to tell the difference between the different trees; where the two Joshua tree species grow together, the moths get confused and visit both trees equally. Why the flowers differ in their scent, even though the moths can’t seem to tell the difference, remains an evolutionary mystery for the moment.


Getting to the essence of a Joshua tree: DNA extraction

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As we’ve talked about before on this site, the genome is the complete set of DNA letters that spell out the ‘instructions’ for how to build an organism. By sequencing the genome of the Joshua tree we hope to be able to understand its evolutionary history, how it’s relationship with yucca moth pollinators originated and evolved over time, and how Joshua trees might adapt to ongoing global climate change. This summer we started the process of decoding the genome.

Figure 1: Samples of Joshua tree leaves for DNA extraction. (Ramona Flatz)

Figure 1: Samples of Joshua tree leaves for DNA extraction. (Ramona Flatz)



(Photo: Chris Smith)

(Photo: Chris Smith)

Our crowdfunding campaign at Experiment.com concluded last night at midnight, with $10,643 raised — 124% of our original funding goal. That means we’ll have funds for the DNA sequencing we’d wanted to assemble a Joshua tree genome sequence, and some additional funding towards our stretch goal, to develop a gene expression atlas based on that genome sequence. Thanks to every single one of the 325 backers who pledged support, and to everyone who helped spread the word on social media, and to the partner organizations who supported the campaign! We couldn’t have done this without you all.


Let’s stretch!

Can we go higher yet? (Photo and stunt-man: Chris Smith)

Can we go even higher? (Photo and stunt-man: Chris Smith)

We’re unbelievably gratified by the support for our crowdfunding campaign — we’ve won the Experiment.com challenge to recruit the most backers for a project at a liberal arts college, and the bonus from that blew us past our funding goal. But we’ve still got a few days in the campaign, and assembling a genome is a big project. If we had a little more money, there’s more cool work we could do.

That’s where “stretch goals” come in — Experiment allows projects that meet their goals ahead of schedule to propose additional research, and set a new funding goal to support it. We’ve currently raised $10,523 — with about $3,000 more, we’d be able to go beyond assembling a Joshua tree genome sequence, taking the first steps to understand that sequence. We’d do that by building a gene expression atlas.

An assembled genome sequence is really just a long string of DNA nucleotides. What that code actually means — the proteins it codes for, their responses to different environments — is not simple to understand. We can make some headway in understanding a new Joshua tree genome sequence by using what we know about the general structure of protein-coding genes, and comparing genes found that way to other sequenced plant genomes about which more is known, like maize or Arabidopsis thaliana. But that will only get us so far. To really decode the Joshua tree genome, we need to understand what genes are expressed, or turned on, to form different parts of the plant, or to respond to different environmental conditions.

Every cell in a Joshua tree contains the tree’s complete genomic code, but not every gene in that code is expressed in every cell — genes that are important in a leaf cell are not necessarily the same ones that are important in a flower cell, or a root cell. We can take samples of different types of Joshua tree tissue like leaves, flowers, and roots, and specifically sequence the regions of the genome that are active within the cells in those different samples. Doing this will help us identify what parts of the genome actually are protein-coding genes, but it will also tell us something about those genes’ functions — a gene that is strongly expressed in a leaf, but not in flowers or root tissue, is probably important for the specific functions of leaves. Similarly, sequencing expressed genes in leaves from trees experiencing drought stress and trees that aren’t stressed can identify genes that are important for coping with that stress.

So that’s our stretch goal: funding to do the additional sequencing we’d need to target those expressed genes in an array of tissues and maybe more than one environment, too. In total, it’ll bring our project budget to $13,582 — but we’ve already raised enough that all we still need is $3,059. We’ve got five days left in the campaign. Can we do it? If you haven’t pledged your support yet, now’s the time! And if you have, keep spreading the word on Twitter and Facebook.


We won!

(Photo by Jeremy Yoder)

(Photo by Jeremy Yoder)

We’re delighted to announced that we’ve just gotten word that we won the Experiment.com challenge for projects at liberal arts colleges — of all the projects in the competition, ours received the support of the most individual backers. The prize is $2,000 in bonus funding, which we can put towards more of the expenses of sequencing and analysis that go into assembling a reference genome sequence.

We literally could not have done this without the support of over 300 backers, and all the folks who’ve taken an interest in this project and spread the word on social media and by good old word-of-mouth. Many, many thanks. The collaborators are all excited to get underway.


Doing Big Science at a Small School With the Joshua Tree Genome Project

The Joshua Tree Genome project is unusual in a lot of ways. It’s unusual partly because it focuses on such a bizarre and fascinating plant that has a singularly peculiar pollination system. However, it is also unusual because of the research team we’ve assembled. An important part of our team is a group of college students at Willamette University.

Willamette is a small liberal arts college located in Salem, Oregon. There are fewer than 2000 students at Willamette, and its science departments serve only undergraduates: there are no Ph.D. or Master’s students. Willamette is known for excellence in teaching and learning, but it’s not a research-intensive school like the University of California Berkeley or the University of Michigan.

In contrast, a genome project for an organism like Joshua tree – which has a very large genome (3 billion bases) – is a major research undertaking. A genome project is practically the definition of ‘big science.’ When scientists first set out to sequence the human genome, it was a $3 billion project, and it took the US Department of Energy nearly ten years to complete it.

So what is a tiny school like Willamette doing trying to start a genome project?

Part of the answer is that genome sequencing has gotten A LOT easier since the Human Genome Project was started. The advent of Next Generation Sequencing has made it possible to examine hundreds of millions of segments of DNA simultaneously, instead of generating sequence data one or a few fragments at a time. This change in technology has also made the process vastly cheaper. In total, we expect the laboratory procedures for the Joshua Tree Genome to cost around $100,000 – still a great sum, but it’s 30,000 times cheaper than the human genome.

It’s also important to point out that we’re getting a lot of help from scientists at other schools. Jim Leebens-Mack, a professor in Plant Sciences at the University of Georgia, Mike McKain at the Danforth Plant Sciences Center, and Jeremy Yoder at the University of British Columbia each have considerable expertise in different aspects of genome sequencing, assembly, annotation, and analysis. In addition Todd Esque and Lesley DeFaclco, both from the US Geological Survey, have decades of experience in studying the ecology of desert plants and the impacts of climate change.

But the biggest reason that we’re trying to do a big genome project at a small school like Willamette is that it is fundamental to the way we approach science education. Here at the Joshua tree Genome Project, we believe that the best way to learn science is to do science. And the best way for students to do science is through authentic participation in real, cutting-edge research.

Here are some of the students working the lab right now, and what they’ve said about working with Joshua trees.

William (Tad) Cole (WU Class of 2016)

Tad Cole (Photo via Chris Smith)

Tad Cole (Photo via Chris Smith)

“When I transferred to Willamette University from a community college in California, I never expected to be working on Joshua Trees. Back then, I’d have guessed Joshua Trees were some kind of old-growth pine tree.  Nowadays, I find myself immersed in the Joshua Tree-Yucca Moth interaction, writing a thesis on the moths’ pollination and egg-laying behaviors that have been uniquely tailored to the flowers of their spiny hosts. The opportunity to get real-world experience in ecology has become central to my undergraduate education, and has opened my eyes to the possibilities beyond graduation.”

Austin Guimond (WU Class of 2016)

Austin Guimond (Photo via Chris Smith)

Austin Guimond (Photo via Chris Smith)

“Throughout my college career, my most rewarding experience has been participating in hands on research. My time working in the Smith lab has given me a greater understanding and appreciation for the field of evolutionary biology and genetics by participating in work that most undergraduates wouldn’t have the support or funding to do. My current thesis project involves the construction of a chloroplast genome for Yucca brevifolia using illumina next generation shotgun sequencing. Through the construction of the genome, our goal is to gain a greater understanding of the tree’s evolutionary history and to create a more accurate timeline of the trees point of speciation from Yucca jaegeriana.” 

Malia Santos (WU Class of 2016)

Malia Santos (Photo via Chris Smith)

Malia Santos (Photo via Chris Smith)

“Working in the lab I have completed multiple projects that have contributed to current research, attained skills that will pertain to my future, and most importantly gained confidence in myself as a scientist. One of my projects has contributed to determining the effects of climate change on populations of Joshua Trees, where I presented my findings at multiple conferences. My senior thesis is another project that I have been working on that will help to determine the genetic differentiation between populations of Great Bustards (Otis tarda) located in Europe, Mongolia, and Kazakhstan. Alongside my projects I have also germinated over five hundred Joshua Tree seedlings for the lab’s current linkage mapping project.”

Jackson Waite-Himmelwright (WU Class of 2016)

Jackson Waite Himmelwright (Photo via Chris Smith)

Jackson Waite Himmelwright (Photo via Chris Smith)

“Getting to work in the lab and in the field has been the backbone of my college experience. I have hiked around Tikaboo valley and seen tiny black moths climbing all around the flowering heads of Joshua trees. I have had Joshua tree thorns stuck under my skin and fought with insect traps over and over. These amazing experiences along with the countless fascinating discussions I have been a part of because of my involvement in the lab have defined my path through college and my future goals more than any other single aspect of my college experience.”

By contributing to major scientific projects, our students not only learn about the scientific method and master laboratory techniques, they help to create knew knowledge and understanding. And, most of all, the experience is a transformative part of their college experience.

Here at the Joshua Tree Genome Project, we are dedicated to the idea that great science and great teaching go hand-in-hand. We hope you’ll join us in making this idea a reality.


What is the deal with Joshua trees and yucca moths?

Chris Smith examines a cluster of Joshua tree flowers. (Photo: Jeremy Yoder)

Chris Smith examines a cluster of Joshua tree flowers. (Photo: Jeremy Yoder)

One of the strangest things of all about Joshua trees may be the way that they are pollinated.

Many plants attract pollinators with rewards, like sugary nectar, or excess pollen that animal pollinators can eat. A wide variety of insects, birds, and even mammals visit flowers in pursuit of such rewards, incidentally carrying pollen from flower to flower in the process.

Joshua trees, like all yuccas, rely on a different strategy for pollination. Joshua trees produce no nectar and comparatively little pollen. And, instead of attracting a variety of different pollinators, yuccas rely exclusively on a few species of drab moths to assist them with reproduction.

A female yucca moth in the process of laying eggs in a Joshua tree flower. (Photo: Chris Smith)

A female yucca moth in the process of laying eggs in a Joshua tree flower. (Photo: Chris Smith)

These insects, known as yucca moths, are grey, white, or sometimes black, are between one-quarter inch to an inch in size, and at first glance seem entirely unremarkable. However, they have one feature that no other species of moths possess. Surrounding the female yucca moth’s moth is a pair of ‘tentacles’ – long, flexible, coiled appendages. The moths use these tentacle to collect balls of pollen from yucca flowers. The moths then fly to another flower, where they use their tentacles to deposit the pollen onto the floral stigma – the receptive surface where the pollen needs to land in order to fertilize the flower.

Different species of yucca moth use different strategies to get the pollen into the right place. Some moths use a bobbing, pecking behavior, like a child’s drinking bird toy, pushing their tentacles into the stigma to pack the pollen into place. Other species unfurl their tentacle while holding a small batch of pollen and then use their legs and feet to stuff the pollen into the stigma. You can see this in the video below, which shows a female yucca moth inside a cut-open flower, pushing pollen toward the stigma.

Watching the moths’ behavior, it’s hard not to come to the conclusion that the moths are pollinating the plants intentionally. Although it is reasonable to wonder whether moths – not known for their smarts – do anything intentionally, it sure looks like they are trying to pollinate the flowers.

Why would a moth go to so much effort just to pollinate a yucca?

The answer is that the moths are getting something out of the deal. Shortly before they pollinate a flower, the female moths use a needle-like organ called an ‘ovipositor’ to inject their eggs into the developing flower. As the flower matures, it will develop into a fruit and produce seeds. Inside the fruit, the moth’s eggs will hatch into caterpillars that will eat some (but usually not all) of the developing seeds. So, by pollinating the flower, the moth ensures that there will be a nutritious food source for her offspring. And because yucca moths are very reliable pollinators, the trees don’t need to offer ‘bribes’ in the form of nectar, and can get away with producing very little pollen since almost none of it will be wasted.

Things aren’t as simple as they seem.

Although on the surface the relationship between the Joshua tree and yucca moths seems to be very harmonious, a closer look suggests that that it is an uneasy alliance. On multiple occasions yucca moths have developed strategies to ‘cheat’ the system – moths that wait until the yucca has been pollinated by a different species of moth, and then come lay their eggs afterwards without having to do the hard work of pollination themselves. Likewise, there is some evidence that the plants will abort flowers that have too many yucca moth caterpillars (this kills both the caterpillars and the developing seeds, but spares the plant the cost of developing a fruit that will produce few or no viable seeds). Finally, there is some evidence that some species of yucca have evolved changes in the shape of the flower to prevent the moths from laying eggs on the developing seeds.

So what about Joshua trees in particular?

The story of yucca moth pollination in Joshua trees has gotten even more interesting recently. A careful study of the moths that pollinate the Joshua tree revealed that the trees are actually pollinated by two similar, but distinct species. One of the two moths is bigger, and is lighter grey in color. The bigger moth also has a longer ovipositor.

This discovery prompted a closer study of Joshua trees, which showed that trees associated with each of the two different species of moth are actually slightly different from one another. Joshua trees growing in the western Mojave desert, which are pollinated by the larger of the two moth species, tend to be taller and more ‘tree-like’ with a longer trunk. They also have longer leaves. On the other hand, Joshua trees occurring in the eastern Mojave, which are pollinated by the smaller moth, tend be shorter and ‘bush-like’ with lots of branches and shorter leaves. Based on these differences, some botanists have argued that there may actually be two species of Joshua tree: Yucca brevifolia, occurring in the western Mojave and Yucca jaegeriana, occurring in the eastern Mojave. (Preliminary work on the Joshua tree genome suggests that the two tree types are indeed genetically different from one another, but still similar enough that genome sequence data from one species will provide a good starting place for studying the other.)

Examples of Yucca brevifolia and Yucca jaegeriana growing side by side. (Photo: Jeremy Yoder)

Examples of Yucca brevifolia and Yucca jaegeriana growing side by side. (Photo: Jeremy Yoder)

Most interestingly of all, the biggest difference between the trees pollinated by each species of moth is in their flowers, and the biggest difference in flowers is the part of the flower where the moths lay their eggs – the style. Trees pollinated by the larger moth have a longer style, and trees pollinated by the smaller moth have a shorter style. What’s more, if moths accidentally visit the wrong type of tree (which they do sometimes in places where the two trees grow together), the moths are less successful in laying eggs.

All of this leads us to think that the two types of Joshua tree have adapted to the different species of moths. Evolutionary changes in the flowers may have occurred as a way to reduce the number of seeds that get eaten by the moths’ caterpillars. The moths, in turn, may have evolved differences in body size as a way to compensate for the changes in the flowers. This process – changes in one of the organisms causing changes in the other, and vice-versa– is known as ‘coevolution’. Understanding how the genetics of the Joshua tree might have enabled coevolution is one of the questions we hope to answer with a genome sequence.