The Yoder Lab at CSUN is recruiting up to two Master’s students to start in Fall 2022, to develop thesis projects within our ongoing work on the evolutionary genomics of Joshua tree and its coevolution with specialized pollinators.Continue reading
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.
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!
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.
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.
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.
Ideal candidates will have previous research experience, familiarity with the R programming language, and a passion for science. Interested students should contact me at email@example.com 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.