About

Erika Zavaleta is a former Faculty Co-Director and an HHMI Professor of Ecology and Evolutionary Biology at UC Santa Cruz. Her role involves leadership in ecological and evolutionary research, contributing to the academic community through her expertise in these fields. The page indicates her involvement in conservation and ecological scholarship, highlighting her significant contributions to the university's conservation efforts and academic programs.

Research topics

• Sociology
• Political Science
• Mathematics
• Ecology
• Medicine
• Social Science
• Biology
• Law
• Psychology
• Environmental ethics
• Gender studies
• Mathematics education
• Demography

Selected publications

• Adapting species risk assessments to a changing climate: the underestimated vulnerability of foundational trees

  DRYAD · 2026-03-26

  datasetOpen accessSenior author

  This dataset supports a systematic review and risk assessment of 27 endemic and near-endemic California tree species under projected climate change. It comprises two supplementary tables. Table S1 contains 52 records of species distribution model (SDM) outputs drawn from the published literature, organized by species and source study. For each record, the table includes the species' Latin and common names, the citation, climate models and emissions scenarios used, the type of distribution data (presence-absence), baseline period and year, and projected percent contraction in climatically suitable habitat at mid-century (~2055), end-of-century (~2100), and ~2125 time horizons, reported as low and high estimates. Projected values are standardized to common reference years to enable cross-study comparison. Table S2 provides species-level summary data for all 27 focal species, including total range area (km²), the proportion of range occurring within California, mean projected habitat loss and area of persistence across time horizons and estimate ranges, a demographic change score synthesizing field-observed responses to climate change, and climate risk scores corresponding to IUCN Red List Criteria A3 and B1. Risk scores are reported both across all studies and separately for a focal subset (Rose et al. 2023).

  PublisherDOI

• Identifying adaptive variation in spatially structured populations using low-coverage whole-genome sequencing data

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-21

  articleOpen access

  Successful implementation of evolutionary management programs to rescue climatically threatened species requires identification of adaptive genetic variation. Although current genotype-environment association methods have been successful in identifying adaptive variation, they can be improved in two important aspects. First, most existing methods do not account for genotype uncertainty in widely available low-coverage whole-genome sequencing data. Researchers often restrict analysis to loci for which genotypes can be inferred reliably or call the most probable genotype, allowing the use of traditional genotype-based methods, such as BayeScEnv and Bayenv. However, discarding data and false genotype calls increases the uncertainty in estimates of genetic variation and introduces systematic biases. Second, most methods use phenomenological approaches, such as logistic regression, to partition estimated genetic variation into adaptive and non-adaptive components. Consequently, current approaches may inadvertently fail to account for evolutionary processes, such as migration-selection balance. Structured migration between climatically disparate locations can produce deviations from a smooth S-shape response curve, which can be difficult to accommodate using generalized linear regression models. To overcome these challenges, we developed a method that accounts for genotype uncertainty in sequencing data and propagates this uncertainty to inform the parameters of a model of evolution. A key feature of this evolutionary model is that it mechanistically describes how genetic variation arises from joint interactions between local adaptation, structured migration, mutation, and drift. We apply our approach to analyze multiple synthetic datasets and a real dataset of North American rosy-finches (3.7 million SNPs), a high-alpine, climatically threatened clade of bird species.

  PublisherOA PDFDOI

• Co-limitation by stable, dynamic and directional habitat features shapes climate vulnerability in an alpine specialist

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-11

  articleOpen accessSenior author

  Abstract Alpine ecosystems are among the most climate sensitive on Earth, yet logistical challenges and detection biases often impede robust assessment of alpine dependent species. We investigated habitat associations and density patterns of the Sierra Nevada subspecies of the Gray-crowned Rosy-Finch ( Leucosticte tephrocotis dawsoni ), an alpine obligate and regional endemic, over five breeding seasons from 2018 to 2022 using hierarchical distance sampling and mark–recapture distance sampling to explicitly account for imperfect detection and spatial heterogeneity. Density estimates tracked annual snowpack variation, ranging from 4.77 individuals/km² in a low snow year to 12.08 individuals/km² in a high snow year. Abundance was highest near persistent snow patches that provide foraging habitat and near cliffs that provide nesting substrate, and declined sharply above approximately 10% woody cover, with densities approaching zero beyond approximately 25%, indicating a steep ecological threshold. In contrast, the proportion of surveyed blocks with detections remained relatively stable across years. Together, these patterns indicate a three timescale co-limitation framework in which breeding habitat is shaped by static features (cliffs), dynamic annual drivers (snowpack), and longer-term directional change (woody encroachment). By linking population density to climate sensitive habitat features, this study provides a high-resolution abundance-based baseline for long term monitoring and offers a framework for evaluating climate vulnerability in alpine and other resource-limited systems. Open Research Statement Data necessary to replicate the analyses and results presented in this manuscript will be archived in the Dryad Digital Repository upon acceptance, with no embargo on the material. The R code associated with this manuscript is not novel. All analyses use publicly available packages and functions without modification, including mrds (v2.3.0), unmarked (v1.2.5), tidyverse (v2.0.0), MuMIn (v1.47.5), and standard ggplot2 visualization tools. All code is properly cited within the manuscript and publicly available through CRAN. Complete analysis scripts will be archived in Dryad alongside the data upon acceptance to facilitate full reproducibility of results.

  PublisherOA PDFDOI

• Climate change impacts on California's foundational trees: demographic shifts are already underway

  DRYAD · 2026-04-13

  datasetOpen access

  This dataset supports a scoping review of peer-reviewed and grey literature (1971–2023) on climate change impacts on 31 endemic and near-endemic foundational tree species in California. The dataset consists of three tables. Table S1 is a comprehensive bibliography of literature consulted for each species, organized by common name, scientific name, publication title, and full APA citation. Table S2 summarizes, for each species, the number of available range projection studies and spatio-temporal demographic analyses, along with species range areas within and outside California. Table S3 synthesizes the results of demographic studies for each species, recording the direction of change in recruitment, mortality, and density in response to water availability and temperature, as reported across individual studies. These data can be used to assess the state of climate change research on California's foundational tree species, identify research gaps, and support conservation planning and prioritization. No legal or ethical restrictions apply to reuse of this dataset.

  PublisherDOI

• Adapting Species Risk Assessments to a Changing Climate: The Underestimated Vulnerability of Foundational Trees

  Global Change Biology · 2026-04-01

  articleOpen accessSenior author

  Climate change is one of the top threats to biodiversity. However, many species risk assessment frameworks, including the globally authoritative International Union for Conservation of Nature Red List, do not consistently and comprehensively incorporate loss of climatically suitable habitat into listing or threat categorization decisions. Using California's foundational, endemic and near-endemic trees as an exemplary set of high biodiversity and cultural value species (N = 27), we reviewed and synthesized the literature on species' model-projected changes in suitable habitat, and on field-observed spatial and temporal demographic responses to climate change. We demonstrate multiple approaches to using this existing literature to integrate climate threats into species risk assessments, with a focus on the Red List criteria. Over the next century, our focal species are projected to lose between half and three-quarters of their existing suitable habitat, which would lead to substantial impacts on ecosystem structure and function in forests, woodlands and savannas. Overall, species are more vulnerable than is reflected by their current Red List status. Even under conservative estimates of climate change impacts, two-thirds of our focal species could now meet the Red List A3 Criterion for Endangered or Critically Endangered status, because of projected loss of climatically suitable habitat (a six-fold increase). We also found a positive relationship between species' model-projected risk and observed demographic responses to climate change, indicating that in many cases, projected responses are already evident on the ground. To inform conservation prioritization, we visualized the geographic patterns of species' suitable habitat loss using heatmaps. Our results illustrate the need to revise species risk assessments in light of climate change to better align research and conservation priorities with species' vulnerability. They also highlight the conservation needs of currently widespread but high climate-risk species, and the regional threats to ecosystem structure and function from foundational species loss.

  PublisherDOI

• <scp>ESA</scp> 2024 Meeting Review: Belonging and Identity in Ecology

  Bulletin of the Ecological Society of America · 2025-01-22

  articleOpen accessSenior author

  Discipline-based education research has become increasingly important within ecology. Each year, the annual Ecological Society of America (ESA) meeting hosts sessions and workshops centered around teaching and learning in ecology. Much of this research has focused on student outcomes related to knowledge, conceptual understanding, and skill-building, as well as how instructors can support the development of these outcomes (e.g., Klemow et al. 2019, Prevost et al. 2019, Smith et al. 2019). However, there is a need to better understand how we can support the development of affective (feelings and emotions) outcomes in undergraduate ecology education (Ward et al. 2021, Shinbrot et al. 2022). Sense of belonging has been shown to contribute positively to students' mental health and well-being (Pittman and Richmond 2008, Kennedy and Tuckman 2013, Gummadam et al. 2016), academic achievement and motivation (Freeman et al. 2007, Zumbrunn et al. 2014, Wilson et al. 2015), and institution-level retention (Finn 1989, Tinto 1993, 2017, Hausmann et al. 2009), and it is pivotal for supporting students underrepresented in STEM disciplines (e.g., Estrada et al. 2016, Hernandez et al. 2013, Hurtado and Carter 1997, Marshall and Thatcher 2020, O'Brien et al. 2020, Rainey et al. 2018). Sense of belonging refers to the feeling of being valued, included, and accepted (Goodenow 1993). In the context of ecology, research shows that students who experience a low sense of belonging are less likely to want to pursue graduate studies in the discipline (O'Brien et al. 2020). Further, African American students in ecology experience a lower sense of belonging than their white peers (O'Brien et al. 2020), making this an important issue related to increasing equity in ecology. This meeting review summarizes an ESA 2024 organized oral session focused on emerging research and practice about belonging in ecology education. In this session, speakers from different types of institutions, career levels, and disciplines presented an array of education research studies and cases of undergraduate programs, field courses, and research experiences that aim to support belonging. Below, we review the session's talks and provide recommendations for future research studying affective outcomes in ecology. Natasha Woods, Maria Miriti: The Undergraduate Network for Increasing Diversity of Ecologists (UNIDE) is a Research Coordination Network funded by the National Science Foundation, with a mission-centered on promoting diversity in ecology and environmental (EE) disciplines. Elevating the perspectives of underrepresented students is integral to the mission of UNIDE. This network includes a Student Advisory Board (SAB) composed of diverse students across the United States and Puerto Rico. The primary role of the SAB is to ensure student perspectives are at the forefront of UNIDE's initiatives. The SAB created a Student Support Network to build an online community for students of color to reduce isolation and increase retention of these students in EE disciplines. UNIDE created a pedagogy working group consisting of educators and ecologists from around the U.S. who are focused on developing and disseminating a curriculum that promotes social belonging and greater inclusion of underrepresented students in EE education. This effort is built from UNIDE's earlier work that sought to understand the relationship between identity and the motivation to pursue EE. The SAB has been working with the pedagogy working group to review syllabi and has presented at conferences to address gaps they have experienced in their EE programs. The SAB has helped refine understanding of racial barriers and retention and inclusion in ecology. For example, students have shared how small group activities can actually reduce a sense of belonging for minoritized students due to the reluctance of other students to partner with them. Through all these initiatives, UNIDE aims to cultivate a more inclusive and diverse community within ecology and environmental sciences, with students at the forefront of its efforts. James Vonesh, Daniel Carr, Rodney Dyer, Andrew Parent, Emily Philpott, Christina Spohn, Samuel Albert, Laurel Dent: A sense of belonging is crucial for student well-being, retention, and academic success. Belonging fosters effective teamwork, a skill essential for achievement in academic and professional settings. Field courses, a cornerstone of ecological training, offer a unique opportunity to cultivate belonging and teamwork. However, STEM instructors often lack the pedagogical training to intentionally foster these outcomes in field settings, leading to inconsistent and unmeasured results. Traditional assessment methods, such as end-of-course surveys and anecdotal observations, often fail to capture the nuances of these complex learning experiences. In contrast, outdoor experiential education emphasizes belonging and group dynamics. Integrating this expertise into STEM field courses can enhance student experiences. This paper presented a case study where STEM departments collaborated with their university's outdoor program to incorporate experiential education activities into a five-week field course. These activities focused on building connections between students, increasing comfort and self-efficacy in the field, and providing a framework for understanding and assessing group dynamics. To capture the dynamic nature of student experiences, we utilized a novel assessment tool: the Footprints on the James (FoTJ) eJournal app. The FoTJ eJournal app allows for real-time, longitudinal tracking of student perceptions of belonging, participation, and teamwork. This innovative app provides a platform for students to record their feelings and experiences throughout the field course, offering valuable insights into the evolution of group dynamics. Our findings highlight the potential of integrating outdoor experiential learning principles into STEM field courses to build belonging and teamwork. Outdoor experiential activities were very positively associated with these outcomes. Reflections suggest belonging and teamwork increase through time but also reveal finer-scale patterns that traditional assessment would miss. Belonging became more consistent through time and exhibited dynamics likely associated with the specific conditions or activities of that day. The sense of teamwork initially increased rapidly but then plateaued. This nuanced assessment, enabled by the FOTJ eJournal, allowed for a deeper understanding of group dynamics, identification of individuals needing support, and improvement of future field programs. Furthermore, collaborations between STEM departments and outdoor programs offer a practical and broadly applicable approach to enhancing field-based STEM education by increasing capacity, improving risk management, and ultimately, achieving better learning outcomes. Jarrod L. Brown Jr. Mindy Findlater, Jessica Malisch: Conservation and climate research, which often have strong field science components, are not currently inclusive of the demographics of the United States. Innovative solutions to current problems should be derived from a diverse workforce and research cohorts who have a direct connection with impacted communities. ¿field curious?, is a weekend-long field research immersion experience being implemented at a Minority-Serving Institution (MSI), aimed at increasing students' sense of belonging in field research. During this no-cost program, students learn inclusivity-informed field safety, are gifted basic field research tools (e.g., backpack, outerwear, field notebook), engage in hands-on research experiences inside National Parks and state reserves, and receive mentorship from established scientists and graduate students who share similar life experiences to the participants. The short duration of the intervention is intentional to avoid impacts on employment and family obligations. Follow-up surveys and interviews with participants indicate that students complete the program with an enhanced sense of belonging in the field sciences as indicated by an enhanced desire to pursue a career with an outdoor component; reduced anxiety regarding pursuing a career based in the outdoors; an increased sense of belonging both in field science as well as our home institution, including for non-STEM majors; and an increased and affirmed dedication to climate and conservation issues. Students have also reported pride in being alumni of the program and demonstrate continued engagement with the program through becoming near-peer program leaders as well as executive officers in the student-generated ¿field curious? Club. This program runs six times a year and has an extensive waitlist, an additional indicator of the need and success of the program. Suzanne Ou, Erika Zavaleta, Abraham Borker, Roxanne Beltran: Conservation grows increasingly urgent as humanity feels the consequences of climate change and environmental injustices. Effective and equitable conservation must represent and include the diverse experiences and values of many groups historically excluded from conservation. Current conservation workforce demographics fail to reflect the racial, ethnic, and socioeconomic diversity of the United States (US), limiting the reach and potential for success in conservation actions. To address this issue, the Doris Duke Conservation Scholars Program at UCSC ran from 2016 to 2023 to support diverse cohorts of undergraduate Scholars and seed the conservation field with skilled leaders from marginalized backgrounds. Using this program as a case study, we examine a relationship-centered theory of change beginning with 1) attracting emerging conservation leaders from across the United States and territories and 2) preparing them for a career in conservation with professional development opportunities and support for intersectional identities. The program sought out first- and second-year undergraduates with a passion for, but not necessarily deep experience in, conservation. The program was centered on two paid, immersive eight-week summers between academic years: one an inquiry-led course in conservation leadership, and the second an immersive full-time internship in conservation. We provided Scholars with experiential training and mentorship, created strong peer and mentor communities, and maintained and grew long-term support and professional networks. As a measure of whether Scholars felt a sense of belonging in the field, we tracked post-undergrad career growth. Of the first 120 Scholars to finish the program, 43% have attained or are currently enrolled in graduate degrees related to the environment. Of the 45 Scholars in permanent positions, 73% are in work related to sustainability including research, journalism, policy, education, and in a range of settings (academia, non-governmental organizations, and government). Scholars have made critical contributions to conservation leadership in myriad ways by founding organizations, shifting conservation priorities toward equity, and changing the face of the professoriate. Scholars continue investing in the networks built through the program via alumni gatherings and peer support. The program serves as a case study for how the field can train and diversify practitioners that address historical impacts of conservation on marginalized groups and face future challenges in conservation with a stronger sense of belonging. Kari O'Connell, Stephanie Shaulskiy, Alison Jolley, Holly Cho, Holly White: Studies that have addressed a sense of belonging have primarily focused on belonging in traditional classroom settings. However, more work is needed to understand how belonging develops in field settings. To investigate this gap, the authors conducted 71 interviews with instructors and students, as well as 133 pre/post surveys on the sense of belonging in eight residential ecology and geoscience field courses. We divided the belonging-supportive teaching practices that emerged from the interviews into six categories: orientation, knowing your students, informal interactions, TAs and co-instructors, peer interactions, and teaching moves and messages. These data were used to develop a survey to further explore the extent to which faculty utilize these practices that are promising for fostering belonging (n = 84). Some example findings from the extensive faculty survey data include that 69% of faculty reported that they created a course agreement, yet only a quarter reported that any element of their course agreement was co-created with students. Additionally, almost all (95% of faculty) reported providing students with a packing list before the course; however, only 56% of faculty reported sharing guidance on physical preparation for field work. Almost all faculty (99%) reported checking in with students during their course at least a little for how they are handling challenges of the field setting, their mental health/emotional needs, peer interactions/relationships with classmates, and disability accommodations. Findings also highlighted the importance of instructor awareness of students' pronouns, accommodations, and mental health needs. Based on survey results, practices that faculty could consider using more include co-creating a course agreement, more comprehensive pre-course orientation (e.g., guidance on preparing physically for field work, guidance on managing menstruation in the outdoors, tips on where to get plus-size clothing, offer structured opportunity for students to meet each other before the field course) and getting to know their students before the course, particularly in areas of religious, cultural, and family needs. These findings can help instructors understand what new practices can be easily added to their field courses as well as improve their existing teaching practices. Holly White, Kayla McLagan, Katharine Ruskin, Alison Jolley: Undergraduate research experiences provide numerous benefits for undergraduate students in ecology, including increased confidence (Russell et al. 2007) and learning gains (Linn et al. 2015). However, traditional field research experiences often come with barriers such as high costs and selective application processes. To address this issue, the Ecology and Environmental Sciences program at the University of Maine implemented an accessible course-based research experience that offers students the opportunity to engage in ecological fieldwork. Field Research in Ecology and Environmental Sciences is offered to second- and third-year students, in which they design and execute a weekend-long, intensive field research project at Acadia National Park. The short duration of the field course does not require students to take extended periods of time away from work or family obligations. Beyond this, the course reduces barriers to participation by providing necessary gear, dormitory-style housing, and accessible field sites. From 2021 to 2023, we administered pre-post surveys (n = 148) to measure changes in belonging and research self-efficacy. Preliminary results indicate gains in belonging to the course and major, research identity, and confidence in research skills. These findings suggest that even short course-based field opportunities support positive student outcomes. We suggest that along with extended field opportunities, shorter field courses should also be available to students. These findings offer promise for promoting equity and inclusion in ecology. This organized oral session focused on several ongoing efforts to support a sense of belonging in undergraduate ecology education. The speakers demonstrated how field courses, research experiences, and undergraduate networks can be used to foster affective outcomes and make progress toward inclusivity and equity in ecology. The approaches varied in scale, institution type, and student characteristics, illustrating successful efforts in a wide range of contexts. Here, we highlight several important takeaways from the presentations: Several talks throughout this session focused on field courses or field experiences within ecology, calling attention to the promise of field settings for developing students' sense of belonging. Field-based education, often viewed as a “rite of passage” (Morales et al. 2020), at times fails to support belonging and inclusion (Whipple et al. 2021, Kamran and Jennings 2023, Lundin and Bombaci 2023, Morales and Reano 2023) and threatens retention in ecology. However, when intentionally designed, field-based opportunities can be transformative and positive experiences for undergraduate students (Zavaleta et al. 2020). This organized session put forth several approaches to reducing barriers for participation in field experiences including (but not limited to) inclusivity-informed field safety, accessible field sites, providing field gear to students, and mental health check-ins. O'Connell and colleagues highlighted the importance of knowing your student population in order to reduce barriers. For example, instructor awareness of students' pronouns, accommodation needs, and mental health needs (e.g., does the student need to have time blocked out on their schedule to continue attending therapy?) can support the development of student belonging in field courses. Two presentations illustrated positive student outcomes from weekend-long field courses, which can serve as alternatives to multi-week residential field courses (Brown et al.; White et al.). Mentorship is a critical element in developing an identity as a scientist (Atkins et al. 2020). Several speakers emphasized the importance of diverse role models for students, particularly for those from marginalized backgrounds. For example, Brown and colleagues found that students who participated in ¿field curious? gained a sense of belonging in the discipline by working with scientists and graduate students who shared lived experiences. Similarly, Woods and Miriti described a large-scale support network of diverse peers and mentors for undergraduate students provided by UNIDE. In addition, highlighting diverse role models emerged as a practice that supports the development of belonging in research by O'Connell and colleagues. Community is important at all scales from individual courses (Tinto 1997) to the discipline as a whole (e.g., O'Brien et al. 2020). The speakers in this session discussed how community building was fostered in field courses to produce positive affective outcomes. Vonesh and colleagues intentionally incorporated teamwork activities including team field projects. They also provided students with language and tools to evaluate their team dynamics. The Doris Duke Conservation Scholars Program highlighted by Ou and colleagues created a long-lasting community in their cohort by bringing students together for two consecutive summers and providing continued support through professional networks and other resources. One speaker focused on a large-scale community network, UNIDE (Woods and Miriti), which serves as a student support network for marginalized students in ecology. To further create a sense of community and belonging, instructors should consider co-developing community agreements with their students (O'Connell et al.). We hope that the organized oral session fosters future discussion and work on the topic of belonging in ecology. At least 50 people participated in the session; through this meeting review, we hope to share the findings with an even broader audience. For anyone who works with undergraduate students in ecology or related fields, these case studies and themes serve as starting points for refining the design and implementation of field education activities. Moreover, this session demonstrates how a sense of belonging can be measured to provide actionable insights for further refinement. There is an array of promising ongoing research in this area, but more work is needed to support the development of belonging to ecology, particularly for short, accessible field courses and first- and second-year students. Many courses and programs are oriented toward students who have already opted to join ecology majors or who have committed to immersive, longer-duration residential field courses. Field Research in Ecology and Environmental Sciences et and ¿field curious? (Brown et are both of how student outcomes can be in short, weekend-long field courses. However, ¿field curious? (Brown et at is one of the programs that provides these experiences to in both STEM and non-STEM disciplines. courses to a range of students, including both majors and is critical to in ecological work as 1) it help students ecology as a promising career and 2) it is important for all students to be as future leaders in any

  PublisherOA PDFDOI

• A centurial signature of anthropogenic nitrogen and carbon in California serpentine ecosystems

  Ecosphere · 2025-02-01

  articleOpen accessSenior author

  Abstract Increasing anthropogenic emissions of nitrogen (N) and carbon (C) are major threats to ecosystems globally. Although atmospheric N deposition is likely affecting N cycling and community composition in California's serpentine ecosystems, a historical record of N inputs to vegetation has yet to be reconstructed for these nutrient‐limited biodiversity hotspots. For leather oak ( Quercus durata var. durata), a foundational, serpentine‐endemic species, we investigated leaf N and C isotopic composition (δ 15 N and δ 13 C) and leaf %N of herbarium and modern leaf samples collected from 1899 to 2009 from serpentine ecosystems in two study areas in California: Santa Clara County, and Lake and Napa Counties combined. We also evaluated tree ring growth over a similar time period in long‐lived leather oak individuals. Leaf δ 15 N and δ 13 C values decreased over time in both study areas, likely reflecting changes in the regional and local atmospheric N and C pools caused by human perturbation. However, leaf %N values and stem growth did not change over time with increasing N deposition, indicating that increasing atmospheric N deposition and CO 2 concentration may not translate to increased N uptake or productivity in plants with conservative growth strategies, even in ecosystems thought to be N‐limited. In serpentine systems, this could competitively advantage nitrophilic invasive annual grasses and accelerate trends toward native species loss. While the rates of decline in leaf δ 15 N values were similar between study areas, rates of decline in leaf δ 13 C values were steeper in Santa Clara County, possibly reflecting its more urban environment. Herbarium samples combined with tree ring data can provide a valuable opportunity to explore the historical record of human‐induced changes in N and C cycling and their biotic impacts.

  PublisherDOI

• Identifying genomic adaptation to local climate using a mechanistic evolutionary model

  Methods in Ecology and Evolution · 2025-08-26 · 2 citations

  articleOpen access

  Abstract Identifying genomic adaptation is key to understanding species' evolutionary responses to environmental changes. However, current methods to identify adaptive variation have two major limitations. First, when estimating genetic variation, most methods do not account for observational uncertainty in genetic data because of finite sampling and missing genotypes. Second, many current methods use phenomenological models to partition genetic variation into adaptive and non‐adaptive components. We address these limitations by developing a hierarchical Bayesian model that explicitly accounts for observational uncertainty and underlying evolutionary processes. The first layer of the hierarchy is the data model that captures observational uncertainty by probabilistically linking RAD sequence data to genetic variation. The second layer is a process model that represents how evolutionary forces, such as local adaptation, mutation, migration and drift, maintain genetic variation. The third layer is the parameter model, which incorporates our knowledge about biological processes. For example, because most loci in the genome are expected to be neutral, the environmental sensitivity coefficients are assigned a regularized prior centred at zero. Together, the three models provide a rigorous probabilistic framework to identify local adaptation in wild organisms. Analysis of simulated RAD‐seq data shows that our statistical model can reliably infer adaptive genetic variation. To show the real‐world applicability of our method, we re‐analysed RAD‐Seq data (~105 k SNPs) from Willow Flycatchers ( Empidonax traillii ) in the United States. We found 30 genes close to 47 loci that showed a statistically significant association with temperature seasonality. Gene ontology suggests that several of these genes play a crucial role in egg mineralization, feather development and the ability to withstand extreme temperatures. Moreover, the data and process models can be modified to accommodate a wide range of genetic datasets (e.g. pool and low coverage genome sequencing) and demographic histories (e.g. range shifts) to study climatic adaptation in a wide range of natural systems.

  PublisherOA PDFDOI

• Sustaining Species of the Future: Climatic Nuclei for Climate Change Adaptation

  Global Change Biology · 2025-06-01 · 1 citations

  reviewOpen access

  Conservation of climatic refugia, or locations that will buffer vulnerable species from the effects of climate change, has recently emerged as a prominent climate adaptation strategy. Here, we introduce an important and complementary concept, 'climatic nuclei'-locations that harbor populations of species that are expected to expand under future conditions-which has so far received little attention. While the climatic refugia concept focuses on threatened species, the climatic nuclei concept focuses on species that are projected to expand with climate change to help create the functional, diverse, and locally unique ecosystems of the future. We evaluate where climatic nuclei are expected to occur; draw on lessons from the paleoecological and modern ecological literature to better understand how climatic nuclei could function; explore the concept's application to land stewardship and conservation; and provide suggestions for future research.

  PublisherOA PDFDOI

• Author response for "Identifying genomic adaptation to local climate using a mechanistic evolutionary model"

  2025-07-04

  peer-review
  PublisherDOI

Recent grants

• Biodiversity and ecosystem multifunctionality: Do species loss order and richness matter in a native-dominated serpentine ecosystem?

  NSF · $489k · 2009–2013

Frequent coauthors

• Jae R. Pasari

  Portland State University

  28 shared

• Daniel L. Hernández

  Hartnell College

  24 shared

• Paul C. Selmants

  Western Geographic Science Center

  23 shared

• Dena M. Vallano

  23 shared

• Zdravka Tzankova

  19 shared

• S. B. Weiss

  17 shared

• F. Stuart Chapin

  University of Alaska Fairbanks

  17 shared

• Corinne N. Morozumi

  Berkeley City College

  16 shared

Awards & honors

• Ecological Society of America’s Sustainability Science Award…
• California Book Award