Using landscape genomics to investigate evolutionary potential under climate change in a montane meadow-dependent species
David Ackerly, Professor
Integrative Biology
Closed. This professor is continuing with Fall 2023 apprentices on this project; no new apprentices needed for Spring 2024.
Climate change poses special challenges to plant taxa that depend on isolated habitat patches like montane meadows. Opportunities to move and/or adapt may be limited. Evolutionary adaptation requires heritable variation in adaptive traits, which is often low for isolated populations. Non-evolutionary adaptation via phenotypic plasticity depends on individuals’ ability to adjust their physiology to varied environments, but reciprocal transplant studies indicate that local genotypes often suffer reduced fitness when outplanted. Adaptive gene flow and population migration depend on plant propagules’ ability to reach suitable habitat patches amidst an unsuitable matrix. Furthermore, isolated populations often suffer from small effective population size and increased genomic load of fitness-reducing alleles. Recent methodological advances have allowed genomics researchers to estimate the degree of local adaptation among conspecific populations, the frequency of successful movement among localities, and genomic load. These tools hold great potential and could be integrated with species distribution models, which predict broad-scale habitat associations, to produce comprehensive assessments of species’ potential to respond to climate change. However, such integrative studies are scarce, and a knowledge gap remains regarding the climate-relevant evolutionary potential of taxa that depend on isolated habitat patches. Addressing this gap will advance scientific understanding of climate change impacts on biodiversity, and it will help practitioners calibrate management strategies for these vulnerable taxa.
We are studying the landscape genomics and climatic niche of Lemmon’s willow (Salix lemmonii) across the southern Cascade, Sierra Nevada, and San Bernardino mountains to produce an integrated assessment of this species’ climate-relevant evolutionary potential. Often the dominant woody vegetation, S. lemmonii depends on montane meadow habitat, where it is planted frequently in meadow restoration. S. lemmonii forms habitat for endangered wildlife like the Willow Flycatcher (Empidonax traillii), is used culturally by indigenous communities, and guards against streambank erosion and ecohydrological degradation, thereby protecting water resources for people downstream.
The overall approach will follow the recently proposed “FOLDS” model to produce an integrated assessment of Salix lemmonii’s evolutionary potential under climate change. The acronym’s letters denote gene flow, genomic offset, genomic load, dispersal, and species distribution models. Gene flow quantifies the potential for adaptive alleles to move among populations. Genomic offset quantifies the difference between the current frequencies of putative climate-adaptive alleles in a population and the allele frequencies predicted under anticipated future climatic conditions. Genomic load quantifies the prevalence of fitness-reducing alleles. Dispersal quantifies the potential for wholesale population movement under climate change. Species distribution models quantify species-level habitat associations
We have collected Salix lemmonii leaf tissue from 3-6 individuals at 49 montane meadows in National Forests across California’s southern Cascade, Sierra Nevada, and San Bernardino mountains. We are currently extracting DNA from each leaf sample using a modified CTAB method. When DNA extractions are complete, we will follow recently developed ddRADseq library preparation protocols and send the prepared libraries to UC Berkeley’s QB3 facility for genomic sequencing. Bioinformatics and FOLDS analyses will occur in subsequent semesters.
Role: Tasks: Initially, the student’s role will be to assist with DNA extractions. Depending on when extractions are complete, there may subsequently be opportunities to assist with ddRADseq library preparation.
Students should be prepared to commit at least 5 hours per week. It is not necessary to commit to more than 5 hours per week, but opportunities for more hours can easily be arranged.
Learning outcomes: Kyle Rosenblad, the PhD student running the project, will provide hands-on instruction and mentorship. The student will thereby gain technical expertise in using the methods and equipment involved in DNA extraction—a highly transferrable skillset for future studies and employment. Through informal discussions with Kyle, the student will also learn about the ecological and evolutionary concepts underpinning this project and the justifications behind the methods used to test our hypotheses. The student will be welcomed as a member of our lab community, which includes other undergraduates, graduate students, and postdocs. If interested, the student will be invited to attend lab meetings and social events with lab members, although there is absolutely no expectation or requirement in this regard. This will provide opportunities to build the student’s network of peers and mentors. If the student is interested in continuing the mentoring relationship after the conclusion of their involvement with the project, the student can expect Kyle to keep in touch.
Qualifications: None required. Kyle is happy to train you!
Day-to-day supervisor for this project: Kyle Rosenblad, Ph.D. candidate
Hours: to be negotiated
Related website: https://www.ackerlylab.org/
Related website: https://kylerosenblad.org/