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.

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Brian Gill Awarded NSF Doctoral Dissertation Improvement Grant for the project “Temporal Sampling and DNA Metabarcoding to Test the Climate Variability Hypothesis”

Volcan Antisana, Napo Province, Ecuador (Photo credit: Brian Gill)

Volcan Antisana, Napo Province, Ecuador (Photo credit: Brian Gill)

Brian Gill and his PhD co-advisors Chris Funk and Boris Kondratieff will use this grant to build on their work estimating elevation range sizes of mountain stream insect taxa in Colorado and Ecuador to test the Climate Variability Hypothesis. In both the Rockies and Andes, they will sample aquatic insect communities at many different elevations over time to look at how the position of stream insect taxa changes over the course of these species’ life cycles. They will use a DNA metabarcoding approach to determine the composition of whole stream insect communities. This work will provide new insights useful for understanding latitudinal differences in species vulnerability to rapid climate change. This project builds off of our existing collaborative EvoTRAC project.

Chris awarded a Fulbright Scholar Award for the project “Massively parallel sequencing meets megadiversity: Harnessing genomics to uncover the mechanisms generating Colombia’s exceptional biodiversity”

Fig. 1. (A) Proposed sampling sites superimposed on elevation layer (elevation ranges from 0–5452 m in Colombia). Black circles = Palm Rocket Frog sampling sites; white circles = Gray-breasted Wood-wren sampling sites; half black and half white circles = both species sampled. Inset shows study area. (B) Variation in annual mean temperature (which ranges from -4.6–29.2 °C in Colombia). (C) Variation in annual mean precipitation (which ranges from 0.26–11.31 m in Colombia). All GIS layers are from WorldClim.

Fig. 1. (A) Elevation layer (elevation ranges from 0–5452 m in Colombia). Inset shows study area. (B) Variation in annual mean temperature (which ranges from -4.6–29.2 °C in Colombia). (C) Variation in annual mean precipitation (which ranges from 0.26–11.31 m in Colombia). All GIS layers are from WorldClim.

Chris was awarded a Fulbright-Colciencias Innovation and Technology Award for the project entitled “Massively parallel sequencing meets megadiversity:  Harnessing genomics to uncover the mechanisms generating Colombia’s exceptional biodiversity”. Colombia is the second most biodiverse country in the World, yet the mechanisms generating its incredible biodiversity are poorly understood. Colombia’s three Andean cordilleras provide multiple independent elevational gradients for testing the effects of landscape factors–including striking variation in temperature and precipitation–on population divergence and speciation (Fig. 1). Chris will develop a new collaboration with Colombian biologists to uncover the mechanisms that generate Colombia’s “megadiversity” (exceptionally high levels of biodiversity) using new genomic biotechnology. He will also host two workshops on genomic biotechnology at the Universidad de Los Andes and La Universidad Industrial de Santander.

Courtney Hofman’s paper on rapid evolution of dwarf island foxes accepted!

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Photo by Julie King

Courtney Hofman (Smithsonian Institution) and colleagues used whole mitochondrial genomes to investigate the evolutionary history of island foxes, which occupy 6 of the 8 California Channel Islands. Our results are consistent with initial fox colonization of the Channel Islands probably by rafting or human introduction ~9200-7100 years ago, followed quickly by human translocation to all of the remaining unoccupied islands. Our data document rapid morphological evolution of dwarf island foxes from larger mainland gray foxes in ~2000 years or less.

Citation: Hofman CA*, Rick TC, Hawkins MTR, Funk WC, Ralls K, Boser C, Collins PW, Coonan T, King J, Morrison SA, Newsome SD, Sillett TS, Fleischer R, Maldonado JE (In Press) Mitochondrial genomes reveal rapid evolution of dwarf California Channel Islands foxes (Urocyon littoralis). PLoS One.

 

Chris selected as a 2015 Leopold Leadership Fellow

Leopold_logo Chris was selected as a 2015 Leopold Leadership Fellow by the Stanford Woods Institute for the Environment. Twenty researchers were chosen from across the country to participate in the program, which has the goal of providing “outstanding academic researchers with the skills, approaches, and theoretical frameworks for translating their knowledge to action and for catalyzing change to address the world’s most pressing sustainability challenges.” Leopold Fellows attend a week-long intensive leadership and communications training, practice their skills over the next year, and then meet again at the end of the practice year.

Additional press about Chris’ Leopold Leadership Fellowship:

CSU Source

Genetic rescue review featured on cover of Trends in Ecology and Evolution

Whiteley et al_2015_TREE_genetic rescue review_cover Our new review on genetic rescue was featured on the cover of Trends in Ecology and Evolution. See earlier post for more info on the major conclusions of our review.

Citation: Whiteley AR, Fitzpatrick SW, Funk WC, Tallmon DA (2015) Genetic rescue to the rescue. Trends in Ecology and Evolution 30, 42-49.

New paper by Dr. Katie Langin and colleagues on adaptive divergence in a single population of Island Scrub-Jays

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Island Scrub-Jay (Aphelocoma insularis) (Photo credit: Katie Langin)

Adaptive divergence within populations is thought to be rare due to the constraining effects of gene flow. Surprisingly, Dr. Katie Langin and colleagues found repeated adaptive divergence in bill size and shape in Island Scrub-Jays (Aphelocoma insularis) in three separate stands of pine surrounded by a sea of oak on Santa Cruz Island, California, USA. Importantly, this variation in bill morphology was heritable, suggesting it is not solely the result of phenotypic plasticity. Moreover, jays mated non-randomly with respect to bill morphology, resulting in a pattern of assortative mating (pairs of jays tended to have similar sized bills). Lastly, analysis of neutral molecular markers demonstrated isolation by distance across the east-west axis of the island, as well as a subtle genetic discontinuity across the boundary between the largest pine stand and adjacent oak habitat. These results challenge the prevailing view that adaptive divergence is unlikely in the face of high gene flow over small spatial scales. This paper has been accepted pending minor revision in Evolution.

Citation: Langin KM, Sillett TS, Funk WC, Morrison SA, Desrosiers MA, Ghalambor CK (Accepted pending minor revisions) Islands within an island: Repeated adaptive divergence in a single population. Evolution.

Review on genetic rescue accepted in Trends in Ecology and Evolution (TREE)

Authors of TREE paper. Andrew Whiteley, University of Massachusetts Amherst (top left); Dave Tallmon, University of Alaska Southeast (top right); Sarah Fitzpatrick, Colorado State University (bottom left), W. Chris Funk, Colorado State University (bottom right).

Authors of TREE paper. Andrew Whiteley, University of Massachusetts Amherst (top left); Dave Tallmon, University of Alaska Southeast (top right); Sarah Fitzpatrick, Colorado State University (bottom left), W. Chris Funk, Colorado State University (bottom right).

Genetic rescue is an increase in population fitness caused by the immigration of new alleles into a small or declining population. In this recently accepted paper, Andrew Whiteley (Assistant Professor at the University of Massachusetts Amherst), Sarah Fitzpatrick (PhD Candidate at Colorado State University), W. Chris Funk (Associate Professor at Colorado State University), and Dave Tallmon (Associate Professor at the University of Alaska Southeast) reviewed genetic rescue studies to assess its effectiveness and provide recommendations for future research and implementation of genetic rescue. Despite the reluctance of managers to use genetic rescue out of fears of diluting local gene pools, the majority of studies reviewed found a net positive benefit on population fitness. Genetic rescue is a tool that can provide population resilience and will become increasingly useful if integrated with advances in genomics.

Citation: Whiteley AR, Fitzpatrick SW, Funk WC, Tallmon DA (In Press) Genetic rescue to the rescue. Trends in Ecology and Evolution.

Historic guppy transplant experiments in Trinidad provide a replicated test of the balance between selection and gene flow in nature, revealing that adaptive traits are maintained in the face of high gene flow

IMG_1213 Sarah Fitzpatrick (PhD candidate), Lisa Angeloni (Associate Professor), Jill Gerberich (REU student), John Kronenberger (PhD student), and Chris Funk (Associate Professor) set out to the streams of Trinidad to investigate the impacts of previous transplant experiments where Trinidadian guppies were moved from stream localities with many predators into upstream tributaries with few predators. Guppies from these introduced populations have provided one of the best examples of rapid adaptation in the wild. But until now, the impact of the non-native guppies, as they get washed downstream and interact with native populations, was unknown.

Using genetic markers, our team found that the genetic signature of introduced guppies swept to long downstream distances, indicating high levels of gene flow downstream from all introduction sites on a rapid timescale. However, despite genetic uniformity caused by introductions, guppies maintained phenotypic traits that best allowed them to survive and reproduce, given their local predator community. In other words, genetic homogenization did not cause the loss of locally adapted phenotypes.

Citation: Fitzpatrick SW, Gerberich JC, Kronenberger J, Angeloni LM, Funk WC (In Press) Locally adapted traits maintained in the face of high gene flow. Ecology Letters.

Chris’ first Ecuador study abroad class a huge success!

20140616_Black_howler_1_croppedMantled howler monkey (Alouatta palliata) on Ecuadorian coast. Chris’ first Ecuador study abroad course in June and July 2014 was a huge success. CSU undergraduate students visited many of Ecuador’s diverse habitats (lowland Amazonian rainforest, cloud forest, páramo, coast); learned how to conduct field research; and got academic credit for it! The course will be taught next in January 2015. Click here to learn more and register.
20140618_group_photo_4Group photo near Volcán Antisana. 20140622_Clouds draping C GuacamayoView of clouds draping the Cordillera Guacamayo from the world’s best cloud forest research station, Yanayacu Biological Station.

NSF EEID proposal on the effects of landscape structure and management interventions on mountain lion disease dynamics funded!!!

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Puma (Photo by Jesse Lewis)

We’re thrilled to announce that our collaborative NSF EEID (Ecology and Evolution of Infectious Diseases) proposal to investigate the effects of landscape structure and management interventions on mountain lion disease dynamics was funded! Our research team includes Sue VandeWoude (CSU Microbiology, Immunology, and Pathology), Kevin Crooks (CSU Fish, Wildlife, and Conservation Biology), Meggan Craft (University of Minnesota), Scott Carver (University of Tasmania), and Chris Funk (CSU Biology). The research will trace the spread of two apathogenic, contact-dependent retroviral agents in geographically distinct puma populations under three different management regimes: (1) supplementation and recovery of the highly endangered Florida panther, (2) large-scale manipulative harvest experiments of a rural Colorado puma population, and (3) steady-state management of puma populations in the Colorado Front Range and Southern California. In addition, the research will inform the disease dynamics of pathogenic diseases from models developed using apathogenic diseases.