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Plant physiology, the key to understanding how Joshua trees could adapt to a warming world

Karolina Heyduk is a postdoctoral researcher at the University of Georgia, and a co-PI on the Joshua Tree Genome Project. Karolina studies comparative genomics and the physiology of photosynthesis (Karolina Heyduck)

This is a post by JTGP collaborator Karolina Heyduck, a postdoctoral researcher at the University of Georgia.

Our Joshua tree proposal has been submitted to the National Science Foundation! Now we wait to hear if we’re granted to green light to study sources of adaptation in these remarkable desert species.

So what does “adaptation” mean anyway?

Adaptation refers to the process by which species over time acquire traits that allow them to succeed in a given habitat. A habitat includes both biotic elements – herbivores, pollinators, and pathogens – as well as abiotic phenomena like water availability, nutrients, light intensity, and temperature. Our research team is interested in both aspects. We suspect both pollinators and environment (temperature and water availability) are playing a role in Joshua tree speciation and adaptation, but we hope to test this with help from the NSF. Plant species that have become especially adapted to their environment didn’t arise in a single generation; instead, over many years, plants have passed down traits to their offspring that allowed these species to survive and thrive in tough conditions. However, when these abiotic environments change quickly – for example, due to climate change – plants may not be able to adapt fast enough, especially if they are long-lived with many years between generations.

For Joshua tree, which can live over 100 years, adapting to their changing climate will be critical to their survival. Joshua trees are already showing signs of trouble (check out this National Geographic article on them), and the Mojave is only expected to become warmer, forcing Joshua trees to either adapt or die. Currently Joshua trees are found across both high elevation (cooler) and lower elevation (warmer habitats). In both of those elevational levels, we also find Joshua trees in drier and wetter habitats. We might hypothesize that those Joshua trees already found in the hottest and driest habitats might survive best in the future, but we simply do not know. One big goal of our NSF grant will be to screen populations from different habitat types for traits that will help them succeed in the changing Mojave. But how do we do that?

We will measure chlorophyll fluorescence with a fluorometer to determine photosynthetic efficiency and overall plant stress. (Wikimedia Commons: Felipe Jo)

Our first step will be to collect seeds from different populations across both high/low elevations and with varying degrees of rainfall. We will grow these seedlings and plant them in gardens across the Mojave desert. Once they stabilize, we begin screening them for a long list of characteristics relating to water use efficiency and photosynthesis – two huge traits when it comes to desert survival. Water use efficiency refers to how much water a plant loses for every molecule of CO2 is gains. Plants take in CO2 through their open stomata, tiny pores on the surface of the leaf, but stomata also allow water vapor to escape from the leaves. This loss of water to the atmosphere is important for plants to pull water from the soil, forming a suction force like when you drink from a straw, but too much water loss in the desert can be deadly. Plants can minimize water loss by closing stomata, but this must be balanced by the need to take in atmospheric CO2 for sugar production. Photosynthesis is also important for plant survival, but can be impaired by extreme temperatures and a lack of water (Figure 1).

Measuring these traits will take us a while, and can only be done with the help of both undergraduate students and citizen scientists. Once we’re done measuring our traits of interest, we can begin to determine which Joshua tree populations are most flexible – and therefore might be the quickest to adapt – to changing environmental conditions. Understanding how Joshua tree physiology interacts with their habitat is critical for our understanding of how to help this magnificent species persist into the future


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

by JTGadmin 0 Comments

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.


Getting to the essence of a Joshua tree: DNA extraction

by JTGadmin 0 Comments

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.


Keep the momentum going!

Thanks to all of the folks who have pledged their support for our crowdfunding campaign! We’ve had a very exciting first week. We’re more than 1/3 of the way to our fundraising goal, and are pulling ahead in the competition for the most donors, with 59 backers this week.

One of the challenges for crowdfunding, however, is to keep the momentum going after the initial excitement wears off. That nest egg has to be nurtured if it is ever going to take flight. So, we need your help in spreading the word about the project. Please help us reach more people by inviting your friends to like our Facebook page and tweet about the project using @JTGenome.

Also, check out our Experiment.com project page for news about the campaign. We’ll be posting updates over the next week. You can also subscribe on our website to receive email announcements each time our blog here is updated, using the form under “Subscribe by E-mail” in the sidebar.

(Chris Smith)

(Chris Smith)


We’re sequencing the genome of Joshua tree, but we need your help

(Photo: Chris Smith)

(Photo: Chris Smith)

The Joshua Tree Genome Project officially launches today, with a crowdfunding campaign to sequence the genome of one of the most iconic plants in the American southwest. People who love science, Joshua trees, and the Mojave Desert can help finance the development of a Joshua tree genome sequence through Experiment.com.

Why sequence the Joshua tree genome? A reference genome would help answer many important questions about the evolutionary history of this iconic desert species, and about how best to ensure that it survives in a world reshaped by human activity. A sequenced genome will let us:

Discover genes adapted to desert environments. The Mojave Desert contains some of the hottest and driest regions of North America. To survive these inhospitable environments, Joshua trees have an array of physiological and morphological adaptations, from a thick, waxy cuticle on their the leaves, to reduced stomate size and specialized water storage cells. Sequencing the Joshua tree genome will help us find the genes that create these traits, and identify variation in those genes that may allow some Joshua trees to better warmer, drier climates.

Understand the evolution of mutualism. Like all yuccas, Joshua trees rely on highly specialized moths, called yucca moths, to move their pollen from plant to plant. Female moths actively collect and distribute pollen after laying their eggs in Joshua tree flowers; and their larvae eat some of the seeds that develop in the pollinated flower. The moths’ exceptionally reliable pollination service compensates for the loss of a few seeds, and Joshua tree flowers exhibit a suit of adaptations that promote active moth pollination while preventing moth larvae from eating too many seeds. Sequencing of a Joshua tree genome would pave the way to identify genes that contribute to these co-evolved adaptations, and help understand how they have changed over time.

Plan for Joshua tree’s future. Ensuring that Joshua trees will persist into the future means preserving not only the plants themselves, but also the genetic variation that will allow them to adapt to changing climates and environments. We will use a landscape genomics approach to measure the total amount of genetic variation in different populations, and estimate genetic differentiation between populations. This information will let us identify populations of Joshua tree with the greatest potential to adapt to future environmental changes, and give these areas the highest priority for conservation.

Reveal processes of genome evolution. Like all members of the Agavoideae, Joshua trees have a bi-modal karyotype, thought to have resulted from an ancient allopolyploidy event — the combination of two whole genomes by hybridization between species. Sequencing the Joshua tree genome will reveal how genome evolution proceeds following polyploidization events, including the extent of genomic rearrangements among chromosomes of different ancestries, and processes that contribute to diploidization.

The Joshua Tree Genome Project is a collaboration of ecologists, evolutionary biologists, and geneticists, with the support of major Mojave Desert conservation organizations. You can help sequence a Joshua tree genome by donating to the Project through our Experiment.com campaign, and by spreading the word on Twitter and on Facebook.