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Gathering the seeds of new science

Gathering the seeds of new science
An unopened Joshua tree fruit with seeds behind it. Some aren’t in this nice of a condition. Predation by the moth larvae and other grubs is common (Olivia Turner)

As the Joshua Tree Genome Project kicks off its NSF-funded study of climate adaptation in our favorite spiky desert plants, we’re posting updates on the progress of our work. Today we have a blog post from Olivia Turner, one of four interns with the Chicago Botanic Garden who’re working with JTGP collaborators Lesley DeFalco and Todd Esque to plant thousands of Joshua tree seedlings in experimental common gardens. This post was originally published on the website of the CBG’s internship program.

Hi all! This is Olivia. I am part of a 4 person intern team here on the Mojave Desert, NV working with the USGS on the Joshua Tree Genome Project.

This project is in collaboration with a handful of academic partners from all over the States and our mentors here in Nevada are among the Principle Investigators because they were some of the first scientists to ever investigate the life cycle, reproduction, demography, and the effects of climate change on Joshua trees!

So, why the JTGP?

Joshua trees are an icon of the Mojave, provide food for a large range of desert organisms, and have an incredible relationship with their obligate moth pollinators. Both organisms have a long co-evolutionary history together which is known to result in Joshua tree population differentiation. Given the changes in climate that are projected for the Mojave and surrounding areas, the JT is now also going to be facing selection based on abiotic factors.

Therefore, the Joshua Tree Genome Project was created with the goal of examining the Joshua tree’s local adaptation to climate, with the purpose of exploring the primary source of selection across populations (climate [abiotic] vs. pollinator driven population differentiation [biotic]). This will be done by identify ecophysiological traits that determine seedling tolerance to climate change and the genes that structure these traits (Project Proposal, 2020). Crazy cool! It is a multi-year study and we have the good fortune of being here right at the start. Oh, and of course, this project also involves sequencing, for the first time, the Joshua tree genome.

Our role as CLM interns

A Joshua tree fruit, like a stubby pale green cucumber
Fruit of a Joshua tree (Olivia Turner)

Here at the USGS, we will handle all logistical and practical matters related to the establishment and monitoring of the JTs. This means planting and growing more than 3,000 JTs in our local greenhouse which will then be replanted at four different common garden sites throughout the Mojave. These four sites represent both the extremes and norms of climate existing across the Mojave. We will then have the opportunity to collect preliminary data and even do some experimental work.

These common garden trees will be the subjects in genetic analyses and physiological assessments that will be occurring in later years of the study. The work of the USGS and our role as CLM interns is paramount to the establishment and future success of this amazing project.

Kicking it off

This week (among orientations and wrapping up paperwork) we worked on counting and cleaning Joshua tree seed collected from a multitude of populations and individuals. This counting and sorting of seed is necessary for the next step: planting!

Counting seeds was a great opportunity to see the range of populations we will be working with and the number of individual trees that are a part of this study.

We are so excited to start planting and working in the greenhouse next week-those 3,000 Joshua trees are calling us!

Until next time,

Olivia T.


JTGP collaborator Chris Smith profiled on Tucson.com

Tucson.com, the online edition of the Arizona Daily Star, has a big new profile of Joshua Tree Genome Project collaborator, and now lead PI on the collaborative NSF grant supporting the project, Chris Smith. Smith grew up in Tucson and earned his undergrad degree at the University of Arizona, and the article goes in-depth on his longtime love of desert landscapes and the organisms that make a living in them:

Smith’s early work focused on yucca plants in isolated desert mountain ranges known as “sky islands” and the cactus longhorn beetle, a strange flightless bug that feeds on prickly pear and cholla in northern Mexico and the Southwestern U.S.

Then he met renowned evolutionary biologist Nils Olof Pellmyr, who steered him toward the fascinating bond between Joshua trees and the highly specialized yucca moths that live on them.

(“Olle” Pellmyr, who passed away in 2017, also mentored JTGP collaborators Jim Leebens-Mack and Jeremy Yoder.)


LISTEN: Collaborators Chris Smith and Jeremy Yoder on Nevada Public Radio

Joshua Tree Genome Project collaborators Chris Smith and Jeremy Yoder were on today’s episode of Nevada Public Radio’s “State of Nevada” news show, talking Joshua tree history, natural history, and genomics with host Doug Puppel. You can catch the rebroadcast of the episode tonight at 7pm, or stream the segment on demand on the KNPR website.


The Joshua Tree Genome Project gets big boost with NSF funding

Joshua trees in Tikaboo Valley, Nevada (Jeremy Yoder)

New collaborative grants from the National Science Foundation will support the Joshua Tree Genome Project in studying how one of the most distinctive plants in the Mojave Desert has adapted to the drought and heat of its home range, how extreme desert climates shape the trees’ peculiar relationship with pollen-carrying moths, and how the genetic information within genomes is re-organized over millions of years.

The grants to Willamette University and California State University Northridge, totaling more than $1.5 million, will pay for the assembly of a Joshua tree reference genome and extensive tests of Joshua tree seedlings in experimental gardens. From this, it will be possible to identify genes that help the trees cope with different climate conditions, and pinpoint how different environmental factors have affected their evolution. To conduct the work, the grants will support research experiences for undergraduate students and interns, graduate student thesis projects, and the expansion of a pilot program in which community volunteers across the Mojave learn to map and monitor Joshua tree populations in their own backyards.


Watch JTGP collaborators discuss the project’s progress, and where it’s headed

Last week, Joshua Tree Genome Project collaborators Chris Smith and Jeremy Yoder spoke in a webinar series given by the Joshua Tree National Park Association’s Desert Institute. The talk ended up being a good overview of our plans for the JTGP, as well as an update on the work of assembling a Joshua tree reference genome. So when the Desert Institute posted the video on their YouTube channel, we thought we’d share it here:

Enjoy! And check out the rest of the Desert Institute video catalog, which includes all sorts of great natural history about Joshua Tree National Park and the Mojave Desert.


“Wait, how many branches was that?” — Community monitoring of Joshua trees launches with leadership training

Earlier this month, community members from across the Mojave Desert came together at the Transitions Habitat Conservancy field station in Puma Canyon in the desert hills above Wrightwood, California, with a deceptively simple mission: to figure out how to count Joshua trees.

The volunteer leaders — from the California Native Plants Society, the Mohave Desert Land Trust, and the Transitions Habitat Conservancy — spent the Veteran’s Day weekend at Puma Canyon to learn a protocol for demographic surveys of Joshua tree populations, guided by Willamette University Associate Professor of Biology Chris Smith and his collaborators on the Joshua Tree Genome Project, US Geological Survey ecologist Todd Esque and CSU Northridge Assistant Professor of Biology Jeremy Yoder

USGS ecologist and JTGP collaborator Todd Esque explains how the challenges faced by Joshua tree at different stages of its life cycle. (Photo by Jeremy Yoder.)
USGS ecologist and JTGP collaborator Todd Esque explains the challenges faced by Joshua tree at different stages of its life cycle. (Photo by Jeremy Yoder.)

Seeking Partners For Community Science

Volunteers set out for a survey of trees in Tikaboo Valley, Nevada (Photo: Chris Smith)

Volunteers set out for a survey of trees in Tikaboo Valley, Nevada (Photo: Chris Smith)

The Joshua Tree Genome Project and its partners are excited to announce a new community science program: Mapping Joshua Trees for Climate Change Resilience.

Working with local conservation organizations and teams of community scientists, we will develop a comprehensive map of the current distribution of Joshua trees, and assess population health through on-the-ground demographic surveys. The results of this study will allow us to develop a conservation plan for Joshua trees in the face of climate change. We are currently seeking local leaders from communities across the Mojave Desert to assist us with the project, and will hold a series of training events beginning in November, 2018.

To request more information, or become involved as a community scientist or a conservation leader click here and fill out the registration form.  For more information, keep reading.


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?