Welcome to the Funk Lab

We strive to understand the evolutionary and ecological mechanisms that generate and maintain biological diversity using population genomics, experimental manipulations, and field studies. Our goal is to not only test basic evolutionary and ecological theory, but also directly inform policy and management decisions that will ultimately determine the fate of biodiversity.



Funk Lab publishes PNAS paper on the causes of megadiversity in tropical mountains!

EvoTRAC field crew during stream “bioblitz” of the remote Oyacachi basin, Ecuador, way back in 2012.

Tropical mountains are the most biodiverse terrestrial ecosystems of the world, but the causes of this exceptional species richness have eluded biologists for centuries. In 1967, Dan Janzen postulated that reduced temperature seasonality in the tropics compared to the temperate zone should cause tropical species to evolve narrower thermal tolerances and lower dispersal abilities than temperate species. If true, the implication is that tropical species should have lower gene flow, greater population structure, and higher speciation rates than temperate species. In our recently published Proceedings of the National Academy of Sciences of the United States of America (PNAS) paper, we integrate physiological, genomic, and phylogenetic analyses to test Janzen’s “Mountain Passes are Higher in the Tropics” Hypothesis in stream insects in Colorado and Ecuador, and find strong support for it. This paper represents 7 years and countless hours of hard work in the field, lab, and in front of the computer by 17 coauthors and several field and lab assistants, as part of our NSF EvoTRAC project on vulnerability of stream insects to climate change. Funk Lab members on the paper included Nick Polato, Brian Gill, Alisha Shah, and W. Chris Funk. A non-technical summary of our findings written by Anne Manning from the CSU College of Natural Sciences can be found here.

Funk Lab and colleagues receive NSF grant to fund tailed frog (Ascaphus) research!!! Yes!

Rocky Mountain tailed frog (Ascaphus montanus). Photo credit: Brenna Forester

We are elated to announce that NSF funded our “Rules of Life” EAGER grant entitled “Landscape Phenomics: Predicting vulnerability to climate change by linking environmental heterogeneity to genetic and phenotypic variation.” The overarching goal of our project is to predict which populations are most vulnerable to environmental change by first understanding how environmental variation molds genetic and phenotypic variation in resilience traits. We chose tailed frogs (Ascaphus spp.) as our focal study system because they’re sensitive to high temperatures, play an important role as grazers in streams, and they’re amenable to the type of genomic and physiological work we plan on doing. AND…as the sister family to all other frogs, they’re just super unique and cool. Our impressive team on this grant include Amanda Cicchino, Brenna Forester, Cameron Ghalambor, Jason Dunham, and Erin Landguth.  You can find out more about this grant in the NSF award abstract here.

Congratulations to Team Ascaphus for another successful field season!

2018 Team Ascaphus: (from left to right) Brenna Forester, Amanda Cicchino, and Kat Pain.

Congratulations to 2018 Team Ascaphus (Brenna Forester [postdoc], Amanda Cicchino [PhD student], and Kat Pain [undergrad field assistant]) for completing another successful coastal tailed frog (Ascaphus truei) field season. They collected tissues, specimens, and thermal tolerance data in streams of the Oregon Cascades as part of our integrative project on adaptive divergence in resilience traits across multiple axes of environmental variation. One of many highlights was Kat Pain’s discovery of an albino A. truei tadpole (see photo below). See here for a description of this project.

Albino Ascaphus truei tadpole. Photo credit: Amanda Cicchino

Paper on the comparative landscape genetics of spotted frogs published in Molecular Ecology!

Columbia spotted frogs (Rana luteiventris) in amplexus (mating embrace) with egg clutch visible. Photo credit: W. Chris Funk

Our paper on the comparative landscape genetics of Oregon spotted frogs and Columbia spotted frogs in Oregon and Idaho has been published in Molecular Ecology! Our main finding was that species traits matter for predicting connectivity. In particular, connectivity was more closely tied to water for Oregon spotted frogs, which are more aquatic than Columbia spotted frogs. In addition, temperature consistently matters for predicting connectivity, although in some landscapes, connectivity is positively related to temperature, whereas in others, it’s negatively related to temperature. Thus, climate change may have different effects on connectivity in different regions. A huge thanks to Jeanne Robertson and Melanie Murphy for leading this collaborative effort. Both are former Funk Lab postdocs who have recently received tenure at California State University Northridge and the University of Wyoming, respectively.

Citation: Robertson JM, Murphy MA, Pearl CA, Adams MJ, Páez-Vacas MI, Haig SM, Pilliod DS, Storfer A, Funk WC (2018) Regional variation in drivers of connectivity for two frog species (Rana pretiosa and R. luteiventris) from the U.S. Pacific Northwest. Molecular Ecology 27:3242-3256.

Another productive retreat at CSU Mountain Campus to work on our NSF EEID puma disease project

We had another productive retreat at the CSU Mountain Campus to work on our NSF EEID puma disease project (aka, the “Felidae” project). Current Funk Lab members working on this project include Daryl Trumbo and Chris Funk. Read more about the project here.

Chris, Brenna, and colleagues publish new paper on integrating adaptive potential into the U.S. Endangered Species Act

Chris, Brenna Forester, and colleagues published a new paper on integrating adaptive potential into U.S. Endangered Species Act listing and recovery decisions. Rapid environmental change means that populations will often have to adapt, or go extinct. Characterizing adaptive potential using traditional approaches such as reciprocal transplant experiments, however, is often impossible for endangered species. Genomics has huge potential to improve our ability to characterize adaptive potential, but its application to real-world conservation decision making has been fairly limited to date. In this paper, we attempt to ameliorate this situation by providing specific guidelines on how genomics and other approaches can be used to characterize adaptive potential, and how this information can be incorporated into U.S. Endangered Species Act listing and recovery decisions. We hope that both conservation practitioners and conservation geneticists will find this to be a useful paper.

Citation: Funk WC, Forester BR, Converse SJ, Darst C, Morey S (2018) Improving conservation policy with genomics: A guide to integrating adaptive potential into U.S. Endangered Species Act decisions for conservation practitioners and geneticists. Conservation Genetics, in press.

Cameron Ghalambor, Scott Sillett, Brandt Ryder, Paul Hohenlohe, and Chris receive NSF grant to test mechanisms of microgeographic adaptation

Island scrub-jay (Aphelocoma insularis). Photo credit: Katie Langin

NSF has funded our collaborative research project aimed at understanding the mechanisms causing fine-scale adaptation in the face of ongoing gene flow in island scrub-jays. Growing evidence suggests that adaptive evolution can occur over small spatial distances. How this fine-scale adaptation arises and is maintained remains unresolved. On Santa Cruz Island, the Island scrub-jay has two morphologies. Birds in pine habitat have long and thin beaks where as those in oak habitats have short and deep beaks. These differences are known to facilitate feeding on pine cones versus acorns, but how such adaptive genetic differences are maintained over very small geographic distances is unknown. Our team will integrate modeling, genomics, telemetry, and behavioral experiments to uncover the mechanisms allowing this microgeographic adaptation. Funk Lab PhD student Rebecca Cheek will lead the dispersal and gene flow components of the project. Click here to read the NSF award abstract.

Harry Crockett, Larissa Bailey, and Chris receive grant to investigate boreal toad conservation genomics

Boreal toad (Anaxyrus boreas). Photo credit: Wendy Lanier and Brittany Mosher

Harry Crockett (Colorado Parks and Wildlife [CPW]), Larissa Bailey (CSU Dept. of Fish, Wildlife, and Conservation Biology), and Chris received a grant from CPW to study the conservation genomics of the Southern Rocky Mountain (SRM) boreal toad (Anaxyrus boreas) group, which has experienced severe declines in recent years due to infection by chytrid fungus (Batrachochytrium dendrobatidis [Bd]). Now, most remaining populations in the SRM are small and isolated, leaving them vulnerable to extinction. The two complementary aims of their grant are to use a genomic approach to: (1) delineate management units and characterize spatial patterns of adaptive differentiation; and (2) test for Bd resistance at candidate genes (e.g., MHC) and thousands of other genes throughout the boreal toad genome. Funk lab postdoc Daryl Trumbo will lead genomic analyses, and new PhD student Bennett Hardy (co-advised by Larissa and Chris) will develop a dissertation related to boreal toad population ecology and conservation.

Please meet DR. Shah!

DR. Shah!

Congratulations to Alisha Shah for successfully defending her dissertation! Dr. Shah completed an impressive dissertation focusing on variation in thermal tolerance across latitude and elevation in stream insects. She moves to Missoula in January to join the lab of Dr. Art Woods as an NSF postdoc (see previous post for more details).

Congrats to John Kronenberger for getting a job!!!

Thumbs up to getting a job.

Congratulations to John Kronenberger (former MS student co-advised with Lisa Angeloni), who has just landed a job as a Fisheries Genetics Lab Technician at US Forest Service’s National Genomics Center for Wildlife and Fish Conservation in Missoula, Montana! Another Funkling finding gainful employment doing something they love.