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An uncommon “common garden”

A Joshua tree seedling in one of the gardens.

Spring in the desert means it’s time to plant Joshua trees. Over the past two weeks, Joshua Tree Genome Project collaborators and US Geological Survey staff led by Lesley DeFalco planted thousands of Joshua tree seedlings in gardens spaced across the Mojave Desert. The seedlings were started in greenhouse conditions last year, from seeds collected in Joshua tree populations growing in different climates across the desert. Seedling Joshua trees are delicate, and we start them gently — first the greenhouse, then planting with tilled soil and generous watering, then months of monitoring and more water, to let them put down roots.

But eventually we’ll step back and let the seedlings face the full stress of the different parts of the Mojave where the gardens are planted. It seems mean, but it’s a gold-standard experimental method to understand a key question that will help us protect the species as climate change ratchets up the heat and drought stress across the desert.


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.


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.


Return to Tikaboo Valley

Sunset over the contact zone (Jeremy Yoder)

We had a whole aisle to ourselves at the Henderson, Nevada, Super Wal-Mart. The shopping list for a month of desert fieldwork with a team of up to twenty filled half a dozen shopping carts — apples and oranges by the five-pound bag, piles of potatoes and pasta and oatmeal, twenty-five dozen eggs, three different kinds of Oreos, dishes and five-gallon water jugs and an extra folding table. We stacked it all in a rental RV, and the next morning we drove north.

For years, JTGP collaborator Chris Smith has organized trips to Tikaboo Valley, a site at the northernmost end of the Mojave Desert where the two species of Joshua tree meet. Over the course of each flowering season, Chris leads a team of Willamette University students, field staff, out-of-town collaborators, and willing volunteers in an ongoing experiment to understand how the trees match two different, highly specialized, pollinator species. Tikaboo provides a natural “common garden” where it’s possible to swap the pollinator species between the two Joshua trees, to see how things work out for all of them.

I drove up from Los Angeles to join Chris and his advance team in setting up camp in advance of the arrival of more than a dozen Willamette students for this week’s spring break. I was sorry to head back before things got properly underway, but I had a couple days to spend with the team scouting for flowering trees — a fine tour of Tikaboo Valley at the very beginning of spring.

Click on the gallery below to scroll through some images of the trip!


How association genetics can find genes that help Joshua trees beat the heat

by JTGadmin 0 Comments

Joshua trees in Tikaboo Valley, Nevada (jby)

This post is by JTGP collaborator Jeremy Yoder, an Assistant Professor in the Department of Biology at California State University, Northridge, who studies ecological and evolutionary genetics.

Since we first launched the Joshua Tree Genome Project, we’ve told you that one big reason we want to sequence a Joshua tree genome is to find genes that are important for adaptation to climate, which could help us makes sure that Joshua trees survive and thrive in a climate-changed future. But we haven’t discussed in detail how we’ll find those climate-adapted genes. The key to that part of the project is association genetics, a method for sifting through the genome to find the parts that contribute to traits we care about.

Figure 1. An example of a “candidate gene” experiment testing whether different diploid genotypes are associated with different trait values, or phenotypes. Points are the phenotypes of individual trees, grouped by their diploid genotypes at a candidate gene; overlaid box plots show that trees with different genotypes differ strongly in their phenotypes. (jby)

To understand how association genetics works, first consider a case in which we already know of a gene that might be important for a particular Joshua tree trait, like height or flower shape or physiological performance — or even just growing in places that are hotter or cooler. To figure out whether different variants in the sequence of our “candidate gene” are related to differences in the trait, we could measure the trait in many trees and then sequence that gene in all of those trees. We would test the hypothesis that the gene shapes the trait by comparing the trait values of trees carrying different variants of the gene sequence. Figure 1 gives an example of what this might look like in a hypothetical case, with tree phenotypes plotted against diploid genotypes at our candidate gene — “homozygous” trees carrying two copies of the G variant have higher phenotype values than homozygous trees carrying two copies of the A variant, and “heterozygous” trees with one copy of each have intermediate phenotypes. In this case, we’d probably conclude that the candidate gene has some effect on the phenotype we decided to measure, because different variants of the gene are associated with significantly different phenotype values.