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.

Queer meetup at #Evol2019 — “Outgroup” goes official

For years at the Evolution meetings there’s been a meetup of lesbian, gay, bi, and trans attendees — going back at least to the 90s. It’s called “Outgroup”, for the obvious phylogenetic double-entendre, and it’s operated largely unofficially. Someone would post a time and location during the meetings, over a lunch break or at a handy pub after an evening poster session, and folks would converge to chat and share a meal or a round of drinks. I was involved in that organization, such as it was, at several of the meetings I’ve attended since 2005, and it was always a nice social time in the midst of the conference.

Here’s a logo I worked up for Outgroup, back in the day

At last year’s big joint meeting at Montpellier, things got more official, with the participating scientific societies providing some budget for a meetup at a bar near the convention center. This year for Providence 2019, we’re continuing that move with the “LGBTQ and Allies Mixer and Happy Hour” — right on the program after the third poster session, on Monday the 24th. The plan is that we’ll meet up in the conference center rotunda at 7pm, during the poster session, and I’ll have some additional drink tickets to pass out for attendees; after the poster session closes at 8pm, we’ll adjourn to some other location. There look to be some good options within walking distance of the conference center. (And if anyone has more specific suggestions, I’d be happy to hear them!)

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

Graduate students: Present in an Evolution 2019 spotlight session

Blue on Eriogonum compositum (jby)

I’m excited to be organizing a spotlight session for the American Society of Naturalists at this year’s Evolution 2019 meeting in Providence, and I have a talk slot available for a graduate student working on mutualistic species interactions.

The session title will be “Origins, stability, and benefits of interspecific cooperation in a changing world”. I’m looking for presentations of recent research on the ecology, evolution, and coevolution of mutualists, especially ways in which the stability and benefits of mutualism change in different environments, or ways in which mutualists help each other weather environmental stresses. The speaker lineup includes folks at all career stages working with evolutionary theory and a wide range of empirical systems.

Speaking in this session counts as your one allotted presentation for Evolution 2019. I’m also sorry to report that there is no support for the session — speakers are still responsible for their own travel, lodging, and conference registration.

To apply, please e-mail me at jeremy.yoder@csun.edu with a brief description of what you’re likely to present. (I don’t need a formal title or an abstract at this time, but if you have them handy, it’ll help.) To ensure consideration, please apply by Friday, 25 January 2019. Thanks!

Earn a Master’s in the Yoder Lab at CSUN

A Joshua tree flower in closeup.

My lab at California State University, Northridge, is open for Master’s students enrolling for the 2018-19 school year. I’m building a research program focused on the coevolution of interacting species, particularly how mutualists shape each others’ genomic diversity, and how interactions between species can help or hinder adaptation to abiotic factors like climate. You should join!

Why the Yoder Lab?

You should come to work with me if you’re interested in the evolution and coevolution of interacting species, and if you’re excited to do fieldwork in the desert, execute experiments in the greenhouse, collect and crunch population genomic data, model evolutionary processes with differential equations and computer simulations — or maybe to do several of those things. The lab is just getting started with an array of projects, and in some cases my collaborators or I have preliminary data waiting for the right person to tackle it. My startup funding includes support for graduate student stipends to cover up to a year of your time doing thesis research, and I’ll work with incoming students to identify and apply for external support such as the National Science Foundation Graduate Student Research Fellowship.

Why a Master’s degree?

If you’re considering a research career in biology, most of the discussion and advice you’ve read has probably been focused on Ph.D. programs. The Ph.D. is a “terminal degree,” and if you want to become a university professor, you’ll have to earn one. But there are good reasons that you might prefer to earn a Master’s. First, you want to try research and study before committing to a Ph.D. Research for a Master’s degree typically takes two years, while for a Ph.D. it’s more like five, and often six. If you’re not sure you want to make that commitment, doing a Master’s is a good way to see whether you like research and the academic work environment. Second, you want to work in science, but not as research faculty. Depending on the specific focus of your research, a Master’s in biology can be good preparation for jobs in conservation, at government research labs or regulatory agencies, or in research technician positions in academia and the private sector.

Why CSUN?

CSUN is an excellent place to earn a Master’s in Biology. We’ve got a big, collegial Department of Biology with faculty specializing in everything from marine biology to molecular genetics, and a great ecology and evolutionary biology group. The department has a good record of preparing Master’s students for Ph.D. programs, if that’s what you choose to do, and CSUN was recently recognized by Nature as a Rising Institution for Research. Our campus in the San Fernando Valley is surrounded by natural habitats ranging from coastal chaparral to the Mojave Desert and montane woodlands, and it’s within commuting distance from much of greater Los Angeles, including Santa Monica and Hollywood.

On top of all this, CSUN has significant structural advantages. Biology departments that offer both Master’s and Ph.D. programs can often short-change the Master’s side, with curriculum requirements that are poorly calibrated for a short, focused course of study. CSUN’s graduate program is constructed with Master’s students in mind, and they receive the full attention of their thesis advisors. On the other hand, departments that offer only Master’s degrees often have limited financial support for graduate students, expecting them to work a second job or take on student loans — but CSUN offers teaching assistant positions and an array of other fellowship and scholarship opportunities, including support specifically for students from groups underrepresented in science.

Apply today

Ideal candidates will have previous research experience, familiarity with the R programming language, and a passion for science. Interested students should contact me at jeremy.yoder@csun.edu with a description of your research interests, any previous research experience, and your career goals. Include a CV, if possible, and contact information for at least two references. You can learn more about my research on the Lab’s projects page, through my scientific publications, or in this recent podcast interview. Formal applications to the CSUN graduate program in biology require GRE scores and transcripts, and are due February 15. The Yoder Lab values diversity, and members of groups under-represented in ecology and evolutionary biology are especially encouraged to apply.

PI Jeremy Yoder on the Slightly Evolved podcast

The latest episode of the Slightly Evolved podcast features an interview with me — starting from host Toby Fountain’s traditional question about his guests’ first published research paper, it ends up being a walk through most of my career, from how I got to graduate school to my plans for the new lab here at CSUN. Oh, and also Star Trek. Of course there was going to be Star Trek.

You can listen to the interview, and past episodes of Slightly Evolved, on Soundcloud, check it out (and subscribe!) on iTunes, or stream it in the embedded player below.

—Jeremy

Postdoctoral research with the Yoder Lab

Medicago truncatula plants in a climate-controlled growth chamber.

In addition to recruiting graduate students, the Yoder Lab is open to postdoctoral researchers interested in coevolution and ecological genomics. I don’t currently have funding designated to support postdocs, but I’m eager to work with prospective postdoctoral researchers to apply for independent funding through one of the opportunities listed below, or another of your choosing.

Continue reading

Graduate student (MSci) opportunities in the Yoder Lab

A Joshua tree flower in closeup.

The Yoder Lab at California State University Northridge seeks exceptional, motivated candidates for the M.S. program in Biology. The lab opens in fall 2017 to study the coevolution of interacting species, particularly how mutualists shape each others’ genomic diversity, and how interactions between species can help or hinder adaptation to abiotic factors like climate.

Our research particularly focuses on the yucca-yucca moth brood pollination mutualism and the legume-rhizobium nitrogen fixation symbiosis, using population genetics and genomics, phylogenetics, ecological fieldwork and greenhouse experiments, and both mathematical and simulation-based modeling. Planned projects include population genomic study of adaptation to extreme climates and specialized polliantors by Joshua tree (Yucca brevifolia and Y. jaegeriana) and experiments to study climate adaptation in barrel medick (Medicago truncatula). Students will be encouraged to develop independent projects with these or other local systems.

CSUN and the Department of Biology offer graduate student support in the form of teaching assistantships and a variety of fellowships and aid programs. Research assistantships for up to one year of the two-year Master’s program will also be available through startup funding, and students will work with the PI to identify and apply for external support such as the National Science Foundation Graduate Student Research Fellowship.

CSUN is in the San Fernando Valley in Los Angeles, surrounded by natural habitats ranging from coastal chaparral to the Mojave Desert and montane woodlands, and within a short commute of Santa Monica and Hollywood. CSUN was recently recognized by Nature as one of the top 25 Rising Institutions for Research in North America, and the Biology department has a reputation for turning out excellent Master’s students who often continue on to top-tier Ph.D. programs. The Yoder Lab is part of the Ecology & Evolution program, and our research offers connections to the department’s other programs in Molecular, Cellular, and Physiological Biology, Marine Biology, Microbiology, and Genetics and Developmental Biology.

Ideal candidates will have previous research experience, familiarity with the R programming language, and a passion for science. Interested students should contact PI Jeremy Yoder at jbyoder@gmail.com. In your email, please describe your research interests, any previous research experience, and your career goals. Include a CV, if possible. Formal applications require GRE scores and transcripts, and are due February 15, though exceptions may be possible. The Yoder Lab values diversity, and members of groups under-represented in ecology and evolutionary biology are especially encouraged to apply.