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 and colleagues publish new paper on the exciting potential and remaining uncertainties of genetic rescue

Genetic rescue has been used as a management strategy to increase population sizes of mountain pygmy possums (Photo: Andrew Weeks)

Theory and data show that genetic rescue–a decrease in extinction probability due to gene flow–is an effective management tool for small, isolated populations. Despite this, genetic rescue is rarely used to boost population sizes, which has spurred a call for a paradigm shift for widespread use of genetic rescue. In this opinion piece led by Donovan Bell and Zak Robinson from the Whiteley lab at the University of Montana, we argue that although genetic rescue is promising and should be applied more widely, several questions remain regarding the duration and magnitude of genetic rescue effects and when negative effects might occur. In addition, we conclude by highlighting how new genomic methods can improve implementation of genetic rescue.

Daryl’s paper on puma landscape genomics accepted in Molecular Ecology!

Camera trap photo of mountain lion in the Colorado Front Range (Photo: Jesse Lewis)

Large apex predators are sensitive to urbanization because of their dependence on extensive contiguous habitats to support their large home rages and an abundant prey base. In a paper recently published in Molecular Ecology, postdoc Daryl Trumbo and colleagues performed a landscape genomics study on pumas (Puma concolor; also known colloquially as mountain lions, cougars, panthers, catamounts) using over 12,000 single nucleotide polymorphisms (SNPs) from 130 pumas across an urban-rural divide in Colorado. This large SNP data set revealed differing patterns of dispersal and gene flow in rural versus urban settings, indicating ecological and behavioral differences in movement patterns between these contrasting landscapes. Although there was evidence that urbanization impacts gene flow and effective population sizes, no effect on genetic diversity was detected. This suggests that Colorado pumas are affected by increasing levels of urbanization in this rapidly growing state, but are not yet experiencing the extensive genomic impacts that pumas are in more fragmented landscapes like southern California and Florida.

Collaborative research on genetic rescue featured in Science magazine!

Trinidadian guppy pair. Photo credit: Paul Bentzen.

Our collaborative research on genetic rescue was featured in Science magazine. Former Funk Lab PhD student, Dr. Sarah Fitzpatrick (now an Assistant Professor at Michigan State University), was featured prominently in the article written by Elizabeth Pennisi. Sarah talked about our latest research using guppies as a model system for testing the effectiveness of genetic rescue. In addition, our new opinion piece on genetic rescue published last week in Trends in Ecology and Evolution was highlighted.

Congratulations to Brenna Forester for co-authoring a paper published in PNAS!!

Myotis escalerai in flight in Soria, Spain (photo credit: Daniel Fernandez Alonso)

Forecasts of species vulnerability and extinction risk under future climate change commonly ignore local adaptations despite their importance for determining the potential of populations to respond to future changes. In a paper recently published in PNAS, Dr. Orly Razgour, leading a team of international collaborators including Funk Lab postdoc Brenna Forester, present an approach to assess the impacts of global climate change on biodiversity that takes into account adaptive genetic variation and evolutionary potential. Focusing on two Mediterranean bat species, the team showed that considering local climatic adaptations reduced range loss projections but increased the potential for competition between species. These findings suggest that failure to account for within-species variability can result in overestimation of future biodiversity losses. Therefore, it is important to identify the climate-adaptive potential of populations and to increase landscape connectivity between populations to enable the spread of adaptive genetic variation. See HERE for popular article by Wired on this paper.

Congratulations to Amanda Cicchino for winning a Graduate Research Excellence Grant – RC Lewontin Early Award from the Society for the Study of Evolution!

Adult coastal tailed frog (Ascaphus truei)

Amanda Cicchino was awarded a Graduate Student Excellence Grant – RC Lewontin Early Award from the Society for the Study of Evolution to test whether thermal tolerance changes throughout development in tailed frogs (Ascaphus spp.). Most studies on thermal tolerance focus on a single life history stage, but if another life history stage has lower thermal thermal tolerance, then inferences about vulnerability to climate change may miss the mark. Stay tuned to see what Amanda finds out! This is part of our ongoing work on landscape phenomics in tailed frogs.

Coastal tailed frog (Ascaphus truei) tadpole

Congratulations to Sarah Hays for winning third place for her poster at the Front Range Student Ecology Symposium and Celebrate Undergraduate Research and Creativity Showcase!

Sarah Hays sharing her research results on nest construction in Santa Catalina Island Orange-crowned warblers.

Congratulations to Funkling Sarah Hays for getting third place for her poster at the Front Range Student Ecology Symposium and Celebrate Undergraduate Research and Creativity Showcase! Sarah’s research was funded by the Research Mentoring to Advance Inclusivity in STEM (RMAIS) Fellowship program awarded to her mentor, Rebecca Cheek. Their research has shown that Orange Crowned Warblers of Santa Catalina Island (Vermivora celata sordida) demonstrate remarkable flexibility in their nest construction behavior. Keep an eye out for their manuscript to find out more!

Orange-crowned warbler (Vermivora celata sordida) nest from Santa Catalina Island.

Amanda Cicchino gets a paper from her Master’s accepted to Behavioral Ecology!

Pseudacris crucifer, the Spring Peeper (Photo credit: Nick Cairn)

In this paper, Amanda and her coauthors show that arboreal calling behavior is subject to environmentally-mediated tradeoffs across the [vast] range of the spring peeper, Pseudacris crucifer. The authors show that these frogs experience a benefit when calling arboreally both in terms of call transmission (further) and call degradation (less); however, arboreal calling subjects individuals to a faster rate of desiccation. Temperature and humidity levels across the range of the spring peeper mediate this tradeoff and explain the variation in calling behavior among populations.

Congratulations to Amanda Cicchino for being awarded an NSERC Postgraduate Fellowship!

Amanda Cicchino and the world’s coolest frog, Ascaphus truei.

A huge congratulations to Amanda Cicchino for being awarded an NSERC (Natural Sciences and Engineering Research Council of Canada) Postgraduate Fellowship-Doctoral (PGS-D). This is a highly competitive and prestigious fellowship which is similar to an NSF Graduate Research Fellowship in the U.S. Amanda will use this to advance her dissertation research on the conservation genomics and physiology of tailed frogs (Ascaphus). To learn more about Amanda and her research, check out her newly launched website.

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!!