Mikhail Plaza uses linkage mapping to put Joshua tree evolution in its genomic place

Mikhail Plaza, MSc.

Earlier today, Master’s student Mikhail Plaza successfully defended his thesis research, in which he built a linkage map for Joshua tree and used it to reexamine data identifying genetic loci that may play a role in local adaptation to climate and to specialized pollinating yucca moths. Mikhail’s project is among the first fruits of the Joshua Tree Genome Project, taking advantage of a new, exceptionally complete draft genome assembly for Yucca jaegeriana, the eastern Joshua tree.

Over the last few years it’s been widely recognized that eastern and western Joshua trees are genetically differentiated, possibly to the point of being separate species, though they continue to hybridize in a narrow zone where they co-occur in central Nevada. The western and eastern tree types are associated with different species of specialized pollinating yucca moths, and differ in floral traits that impact the interaction with those moths — but also in vegetative traits like leaf length, trunk height, and branching architecture, which should not impact pollination but may play a role in adaptation to climate differences between their different ranges. Recent work by Chris Smith’s lab has found single-nucleotide polymorphism (SNP) markers that show signs of divergent natural selection between eastern and western Joshua trees, and determined that these SNPs may also play roles in the development of floral and vegetative traits that differ between the two tree types. However, these SNPs were “anonymous markers” — their placement within the Joshua tree genome was unknown. That meant that it was impossible to know whether they represented many separate genes experiencing divergent selection, or closely linked regions in which selection on one gene might lead to differentiation in nearby regions, a process known as “divergence hitchhiking”.

Mikhail used genome-wide SNP markers collected for a series of Joshua tree seedlings with known parentage — half-sibling families from six “mother” trees — to construct what is known as a linkage map, then re-analyzed the Smith Lab’s data within the framework of that map to find cases in which regions showing signs of divergent selection coincide with loci associated with floral or vegetative traits. Differentially selected regions containing both floral and vegetative loci would be consistent with divergence hitchhiking — and Mikhail’s preliminary results suggest that this has indeed occurred in the evolutionary divergence of eastern and western Joshua tree. Look for a publication reporting his results in the near future, as Mikhail wraps up his work in the lab and gets started in the doctoral program in Plant Biology and Conservation at Northwestern University.

Alby Dang ably defends the Yoder Lab’s first Master’s thesis

Alby Dang, MSc.

Master’s student Alby Dang successfully defended his thesis research, an examination of cooperative dynamics in the Joshua tree/yucca moth mutualism, in a public presentation and meeting with his thesis committee this morning. Alby was the first graduate student to join the Yoder Lab, interviewing for a position in summer 2017 and enrolling the next fall, and he is now the first Master’s graduate from the lab.

In his thesis research, Alby examined the widely held understanding that the evolution of the yucca-yucca moth mutualism has been driven primarily by conflicting interests in the two partner species. Yucca moths lay eggs in yucca flowers before actively pollinating them. The flowers produce no nectar or other rewards, but yucca moth larvae eat the seeds inside fertilized flowers as they develop into fruits. Yuccas have no other pollinators, and the moth larvae eat a small portion of the total seed crop produced by pollination, so the interaction is beneficial — but it may also set up a conflict, in which moths would benefit from laying as many eggs as possible in each pollinated flower, and their host plants would benefit from receiving pollination without sacrificing any seeds to feed moth larvae. Yuccas have been shown to kill off flowers that receive too many pollinator eggs, and it is generally understood that this “sanction” keeps the moths from getting too greedy.

Alby instead considered a way in which yuccas and moths might have an interest in common: a moth that provides better pollination services might produce more seeds in a single fruit, which might support more of her larvae. To test this idea, Alby collected mature fruits from populations of Joshua tree, Yucca brevifolia and Y. jaegeriana, caught pollinator larvae as they exited, and counted the seeds in each fruit. He used genetic marker data to identify larvae whose mothers had visited multiple trees, potentially carrying higher quality “outcross” pollen rather than simply transferring pollen between different flowers on the same tree — and tested the hypothesis that these “mobile moms” helped to produce bigger seed crops that supported more larvae. Look for a formal publication reporting his results in the near future!

The Yoder Lab is officially NSF-funded!

Black Rock Canyon, Joshua Tree National Park

I’m delighted to finally, officially announce that the lab has received funding from the National Science Foundation — for a big, collaborative endeavor we’ve been calling the Joshua Tree Genome Project. Collaborative grants to us here at CSUN and to Chris Smith’s lab at Willamette University, with subawards to collaborators at USGS and the Universities of Alabama and Hawai’i Mānoa will support four years of experiments, fieldwork, and genomic analysis to learn how Joshua trees cope with climate extremes, how their populations might adapt to climate change, and how adaptation to climate has affected the tree’s coevolution with their hyper-specialized pollinators.

Among the big practical outcomes of this funding, for the Yoder Lab, are support for graduate student research stipends and undergraduate research assistants, as well as two years of support for a postdoctoral researcher. The postdoc position will be, I think, exceptionally well suited as a starting point for competitive applications to opportunities like the Smith Fellowship as well — I will be working to start the formal job-search and hiring process this fall, so keep an eye out.

The Yoder Lab at #Evol2019 — where to catch us in Providence this June

(Flickr: Taber Andrew Bain)

The Yoder Lab’s very first group conference will be the Evolution 2019 meeting in Providence, Rhode Island this June. Multiple lab members will be presenting posters with results from fieldwork with Joshua tree and its pollinators, our contribution to the GLUE Project, and some exciting new pollination ecology, among other topics.

I’m particularly excited to be organizing a Spotlight Session for the American Society of Naturalists, on the general topic of mutualisms and how they respond to changing environmental contexts. "Origins, stability, and benefits of interspecific cooperation in a changing world" will take place the afternoon of Sunday, June 23, with nine speakers presenting research on mutualism in study systems as varied as duckweed, leaf-cutter ants, and pure mathematical theory. The full lineup will be

Time Speaker Title
14:30 Jeremy B. Yoder Floral symmetry and the structure of pollination networks
14:45 Sarah Richman Can nectar chemistry alleviate pesticide toxicity in bees?
15:00 Hannah Lindgren What makes a good partner? – Genetic underpinnings of partner quality variation in the model legume-rhizobium mutualism
15:15 Justine Garcia Do symbionts benefit from symbiosis?: fitness of facultative symbionts in host and non-host environments under different contexts
15:45 Coffee Break
16:15 Alexandra Brown The evolution of transmission mode in variable environments
16:30 Liana Burghardt Testing the environment dependence of fitness alignment in the legume-rhizobia symbiosis
16:45 Jason Laurich Mutualism and adaptation in the Lemna minor microbiome
17:00 Lily Khadempour Ant farmers and their fungal crop: coevolution in an ancient agricultural system
17:15 Holly Moeller When bad partners do good: Maintenance of partner quality variation in multispecies mutualism