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Joshua Tree Genome Project PIs offer field research experience this spring

Chris Smith explains the survey protocol to volunteer leaders. (Photo by Jeremy Yoder.)
Chris Smith explains the survey protocol to volunteer leaders. (Photo by Jeremy Yoder.)

The Departments of Biology at Willamette University and California State University Northridge are pleased to announce a unique field course opportunity for undergraduates in the biological sciences and allied fields: Field Research in Desert Evolutionary Ecology. Professors Christopher (Chris) Smith (WU) and Jeremy Yoder (CSUN) will lead a two week class from Monday, May 22 to Friday, June 2, focused on the population ecology of the Joshua tree, an archetypical species of the Mojave Desert that is threatened with extinction due to climate change. Working from the Zzyzx Desert Studies Center in Baker, California, students will participate in primary research on the population ecology of Joshua trees, will learn surveying and data analysis techniques, and will complete focused research projects culminating in a research symposium. Click through for more details, and a formal course description.


New publication: Conservation challenges and solutions for the Mojave Desert

Burned Joshua trees at the site of the 2020 Cima Dome fire in Mojave National Preserve (Flickr, jby)

The Mojave Desert, home to our favorite woody monocot (Joshua tree), encompasses some of the largest tracts of undeveloped land in the continental United States. That wilderness is under increasing pressure from suburban sprawl as climate change threatens to make its desert landscapes even less hospitable to the thousands of unique native plant and animal species that call it home. At the same time, the Mojave is prime territory for solar and wind energy facilities that can help us slow and stop climate change. A new perspective article in the journal Biological Conservation led by Joshua Tree Genome Project co-PI Chris Smith enumerates the challenges faced by Mojave Desert communities — human and otherwise — and the trade-offs necessary to protect Mojave biodiversity in the 21st Century

With Joshua tree as a recurring case study, we attempt to lay out a general plan for identifying and prioritizing populations of threatened Mojave species that have the best chance of surviving into a climate-changed future. We discuss the challenges of defining species’ current and future geographical distributions, assessing populations’ demographic health, and identifying and quantifying genetic variation that can support adaptation to projected climate change. We also find a lot of opportunity to resolve apparent conflicts between renewable energy development and conservation of Mojave wilderness — with appropriate input from residents and other stakeholders, it should be possible to balance the need to protect the desert’s biological treasures as we build the infrastructure needed to save them from the global threat of climate change.

The full paper is available to read without a subscription via this sharing link through January 20, 2023.


Field season 2021 is already testing our Joshua trees’ limits

A fieldwork update from JTGP collaborator Karolina Heyduk, a plant physiologist and Assistant Professor at the University of Hawai’i Mānoa.

There’s heat, and then there’s Nevada’s 105°F heat that is so dry your skin feels like it should audibly sizzle when you step outside. That’s the kind of heat the Joshua Tree project’s team members found themselves in early June when we all met in the desert to collect some preliminary data for our NSF award. We’re about a year into the project; seeds of Joshua trees were started back in 2020, seedlings were out-planted earlier this spring, and now we’re giving them a year to acclimate to their common gardens before we assess the level to which local adaptation is playing a role in shaping the demography, population structure, and long-term success of this iconic desert species. 

We all met outside of Las Vegas, Nevada, where JTGP scientists Dr. Lesley DeFalco and Dr. Todd Esque, both with the USGS, are based. Todd and Lesley have led the development of our common garden experiments and manage the day-to-day operations of the gardens. Earlier this spring Todd and Lesley led a massive effort, assisted by a small army of USGS researchers, to get the seedlings started and planted in the gardens. The four common gardens are spread across the Mojave and have been planted with Joshua trees (Yucca brevifolia and Yucca jaegeriana) from populations that have different home environments. The seedlings are only a few inches tall, but already we can see differences in “garden effects” – that is, seedlings in the hottest garden are growing much more slowly than those in a wetter, more northerly garden. While we definitely could see garden effects, it’s too early to tell if plants from different populations are faring better in different gardens. That’ll be what we hope to discover with the data we will collect next year in the summer of 2022.


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.)