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.

Archive

Categories

Fitz and Funk publish a new book chapter on “Genomics for Genetic Rescue”!

Hypothetical scenario of a fragmented species that would likely benefit from gene flow augmentation (A) in which a species from a previously continuous distribution (outlined in grey) now exists in isolated populations (black circles) along an environmental gradient. Several small populations outlined by red dashes have already gone extinct. Extant populations range in inbreeding coefficient (F) and genome-wide heterozygosity (B). Neighbor-joining trees (C) using non-outlier versus outliner marker sets show different patterns of population similarity.

Sarah Fitzpatrick and Chris‘ book chapter on “Genomics for Genetic Rescue” has been published as part of the Population Genomics book series edited by Paul Hohenlohe. Genetic rescue, in which the infusion of new genetic variation increases population growth, has successfully reversed population declines in several iconic species. However, genetic rescue is rarely used in management due to concerns over outbreeding depression and genomic swamping. The goal of this chapter is to explain how genomics can improve implementation of genetic rescue, so that it can be used more effectively to reverse declines and extinctions of threatened and endangered populations.

Citation: Fitzpatrick SW, Funk WC (2019) Genomics for genetic rescue. In: Population Genomics (ed. Hohenlohe PA). Springer, Cham, in press.

Congratulations to Rebecca Cheek for passing her comprehensive exam!

Rebecca and her PhD committee (Lise Aubry, Cam Ghalambor, Chris Funk, and Scott Sillett (remotely) after her successful comprehensive exam.

Rebecca Cheek, PhD CANDIDATE!!

Amphibiomics, unveiled!

Genome sizes for different orders of amphibians. Y-axis is on a natural log scale and reports C-values in picograms (pg), where 1 pg = 978 megabases of DNA sequence.

Kelly Zamudio, Andrew Crawford, and Chris’ book chapter on the application of new genomic approaches for advancing understanding of the evolution, ecology, and behavior of amphibians and informing their conservation has been published! This chapter is part of Springer’s new Population Genomics book series.

Citation: Funk WC, Zamudio KR, Crawford AJ (2018) Advancing understanding of amphibian evolution, ecology, behavior, and conservation with massively-parallel sequencing. In: Population Genomics (ed. Hohenlohe PA), pp. XX-XX. Springer, Cham, in press.

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.