Research

Overview

Our research is at the interface of conservation, genomics, ecology, and evolution. We strive to understand the ecological and evolutionary mechanisms that generate and maintain biodiversity, and how rapid global environmental change affects these processes. We address questions by integrating population genomics, quantitative field methods, controlled experiments, and computational analysis in a variety of taxonomic groups (amphibians, fish, stream insects, birds, mammals, reptiles, and terrestrial insects). Much of our research focuses on freshwater habitats, such as streams, rivers, ponds, wetlands, and lakes. Research in the Funk Lab has been funded by a diversity of agencies and organizations, including the US National Science Foundation, the US Fish and Wildlife Service, the US Geological Survey, the US Forest Service, the US Bureau of Land Management, the Department of Defense, Colorado Parks and Wildlife, The Nature Conservancy, The Moore Foundation, and the National Geographic Society. We are an inclusive and supportive lab that firmly believes that diverse people and perspectives strengthen our science, and enrich our lives.

Conservation Genomics

An important dimension of our research program is conservation genomics, which harnesses population genetics theory and cutting-edge sequencing technology to address a variety of conservation questions. Our lab uses genomic approaches to inform conservation of many species of conservation concern by delineating conservation units, estimating effective population sizes, quantifying adaptive potential, etc., particularly in amphibians as part of AmphibiaGen. Chris is deeply involved in improving the integration of genomics into national and international conservation policy. At the national level, he works extensively with the US Fish and Wildlife Service to advise them how best to incorporate genetic considerations into US Endangered Species Act listing decisions. At the international level, he serves as a member of the IUCN Conservation Genetics Specialist Group, GEO BON Genetic Composition Working Group, and Coalition for Conservation Genetics to advance genetic targets in international conservation policy, most recently focusing on the Convention on Biological Diversity (CBD).

Example publications in this subject area:

Allendorf FW, Funk WC, Aitken SN, Byrne M, Luikart G (2022) Conservation and the Genomics of Populations, 3rd edition. Oxford University Press, Oxford.
Kardos M, Armstrong EE*, Fitzpatrick SW, Hauser S‡, Hedrick PW, Miller J‡, Tallmon DA, Funk WC (2021) The crucial role of genome-wide genetic variation in conservation. Proceedings of the National Academy of Sciences of the United States of America 118, e2104642118.
Hohenlohe PA, Funk WC, Rajora OP (2021) Population genomics for wildlife conservation and management. Molecular Ecology 30, 62-82.
Hoban S, Bruford M, D’Urban Jackson J, Fernandes-Lopes M, Heuertz M, Hohenlohe PA, Sjögren-Gulve P, Segelbacher G, Vernesi C, Aitken S, Bertola LD, Bloomer P, Breed M, Rodríguez-Correa H, Funk WC, Grueber CE, Hunter ME, Jaffe R, Liggins L, Mergeay J, Moharrek F, O’Brien D, Ogden R, Palma-Silva C, Paz-Vinas I, Pierson J, Ramakrishnan U, Simo-Droissart M, Tani N, Waits L, Laikre L (2020) Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved. Biological Conservation 248, 108654.
Funk WC, Forester BR‡, Converse SJ, Darst C, Morey S (2019) 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 20, 115-134.
Funk WC, McKay JK, Hohenlohe PA, Allendorf FW (2012) Harnessing genomics for delineating conservation units. Trends in Ecology and Evolution 27, 489-496.

Photo credit: Xerces Society / Stephanie McKnight

Vulnerability and Resilience to Climate Change

Climate change is the defining issue of our times. Increasing temperatures and extreme weather events are already impacting people, places, and nature, and these impacts will worsen for decades to come, even under the most optimistic greenhouse gas emission scenarios. A primary research focus of the Funk Lab is to understand taxonomic and spatial variation in vulnerability and resilience to climate change. By identifying which species and populations are most sensitive, we can target conservation efforts appropriately.

Example publications in this subject area:

Forester BR‡, Beever E, Darst C, Szymanski J, Funk WC (2022) Linking evolutionary potential to extinction risk: applications and future directions. Frontiers in Ecology and the Environment 20, 507-515.
Cayuela H, Dorant Y, Forester BR‡, Jeffries DL, McCaffery RM, Eby L, Hossack B, Gippet JMW, Pilliod DS, Funk WC (2022) Genomic signatures of thermal adaptation are associated with clinal shifts of life history in a broadly distributed frog. Journal of Animal Ecology 91, 1222-1238.
Poff NL, Larson EI*, Salerno PE‡, Morton SG*, Kondratieff BC, Flecker AS, Zamudio KR, Funk WC (2018) Extreme streams: Species persistence mechanisms and evolutionary change in montane stream insect populations across a flood disturbance gradient. Ecology Letters 21, 425-525.
Shah A*, Gill B*, Encalada A, Flecker A, Funk WC, Guayasamin JM, Kondratieff B, Poff N, Thomas S, Zamudio KR, Ghalambor CK (2017) Climate variability predicts thermal limits of aquatic insects across elevation and latitude. Functional Ecology 31, 2118-2127.
Pilliod DS, Arkle RS, Robertson JM, Murphy MA, Funk WC (2015) Effects of changing climate on aquatic habitat and connectivity for remnant populations of a wide-ranging frog species in an arid landscape. Ecology and Evolution 5, 3979-3994.

Photo credit: Brenna Forester

Tropical ecology and conservation

Another important component of our research program focuses on discovering, understanding, and conserving tropical biodiversity. The Funk Lab has discovered and described many cryptic frog species in tropical South America, which has made us passionate about trying to understand the mechanisms that cause speciation in “megadiverse” tropical countries such as Colombia, Ecuador, Peru, and Brazil. We are particularly fascinated with an extremely speciose group of frogs in the family Strabomantidae.

Example publications in this subject area:

Páez-Vacas M*, Trumbo DR‡, Funk WC (2022) Contrasting environmental drivers of genetic and phenotypic divergence in an Andean poison frog (Epipedobates anthonyi). Heredity 128, 33-44.
Lessmann J, Troya MJ, Flecker AS, Funk WC, Guayasamin JM, Ochoa-Herrera V, Poff NL, Suarez E, Encalada AC (2019) Validating anthropogenic threat maps as a tool for assessing river ecological integrity in Andean-Amazon basins. PeerJ 7, e8060.
Polato NR‡, Gill BA*, Shah AA*, Gray MM, Casner KL, Barthelet A, Messer PW, Simmons MP, Guayasamin JM, Encalada AC, Kondratieff BC, Flecker AS, Thomas SA, Ghalambor CK, Poff NL, Funk WC, Zamudio KR (2018) Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains. Proceedings of the National Academy of Sciences of the United States of America 49, 12471-12476.
Guayasamin JM, Hutter C, Tapia E, Coloma LA, Culebras J, Peñafiel N, Morochz C, Funk WC, Arteaga A (2017) Diversification of the rainfrog Pristimantis ornatissimus in the lowlands and Andean foothills of Ecuador. PLoS ONE 12, e0172615.
Cole EM*, Bustamante MR, Almeida-Reinoso D, Funk WC (2014) Spatial and temporal variation in population dynamics of Andean frogs: Effects of forest disturbance and evidence for declines. Global Ecology and Conservation 1, 60-70.
Funk WC, Caminer M†, Ron SR (2012) High levels of cryptic species diversity uncovered in Amazonian frogs. Proceedings of the Royal Society B: Biological Sciences 279, 1806–1814.

Photo credit: W. Chris Funk

Ecology of infectious disease

Infectious diseases pose an increasing risk to biodiversity. Humans, agricultural species on which we depend, and wildlife have always lived with disease, but this risk is becoming greater due to exponentially increasing global trade, climate change, and other anthropogenic modifications to the environment. Emerging infectious diseases have already devastated amphibian, bat, and many other populations of wildlife in the last few decades. A major research prong of the Funk Lab is to understand disease transmission dynamics, disease resistance, and interactions among the environment, hosts, and their pathogens to inform conservation management of wildlife species impacted by disease.

Example publications in this subject area:

Fountain-Jones NM‡, Kraberger S, Gagne R, Gilbertson MLJ*, Trumbo DR‡, Charleston M, Salerno P, Funk WC, Crooks K, Logan K, Alldredge M, Dellicour S, Baele G, Didelot X, VandeWoude S, Carver S, Craft ME (2022) Hunting alters viral transmission and evolution. Nature Ecology and Evolution 6, 174-182.
Gagne RB‡, Crooks K, Craft ME, Chiu ES*, Fountain-Jones NM‡, Malmberg JL, Carver S, Funk WC, VandeWoude S (2022) Parasites as conservation tools. Conservation Biology 36, e13719.
Fountain-Jones NM‡, Kraberger S‡, Gagne RB‡, Trumbo DR‡, Salerno PE‡, Funk WC, Crooks KR, Biek R, Alldredge M, Logan K, Baele G, Dellicour S, Ernest HB, VandeWoude S, Carver S, Craft ME (2021) Host relatedness and landscape connectivity shape pathogen spread in the puma, a large secretive carnivore. Communications Biology 4, 12.
Kozakiewicz CP*, Burridge CP, Funk WC, Craft ME, Crooks KR, Fisher RN, Fountain-Jones NM‡, Jennings MK, Kraberger SJ‡, Lee JS, Lyren LM, Riley SPD, Serieys LEK, VandeWoude S, Carver S (2020) Does the virus cross the road? Viral phylogeographic patterns among bobcat populations reflect a history of urban development. Evolutionary Applications 13, 1806-1817.
Kozakiewicz C*, Burridge C, Funk WC, VandeWoude S, Craft M, Crooks K, Ernest H, Fount-Jones N‡, Carver S (2018) Pathogens in space: advancing understanding of pathogen dynamics and disease ecology through landscape genetics. Evolutionary Applications 11, 1763-1778.
Converse SJ, Bailey LL, Mosher BA*, Funk WC, Gerber BD‡, Muths E (2017) A model to inform management actions as a response to chytridiomycosis-associated decline. EcoHealth 14, S144-S155.

Photo credit: Jesse Lewis

Adaptive divergence

Evolutionary biologists have long been interested in understanding the environmental and microevolutionary drivers of adaptive divergence among populations. An important avenue of investigation in the Funk Lab focuses on determining the relative roles of divergent selection, gene flow, and genetic drift in causing adaptive differentiation, as well as the ultimate environmental factors underlying local adaptation. As adaptive differences among populations are an importance source of genetic variation for adapting to rapid environmental change, this area of research naturally segues into the lab's research on vulnerability to climate change.

Example publications in this subject area:

Páez-Vacas M*, Trumbo DR‡, Funk WC (2022) Contrasting environmental drivers of genetic and phenotypic divergence in an Andean poison frog (Epipedobates anthonyi). Heredity 128, 33-44.
Gamboa MP, Ghalambor CK, Sillett TS, Morrison SA, Funk WC (2022) Adaptative divergence in bill morphology and other thermoregulatory traits is facilitated by restricted gene flow in song sparrows on the California Channel Islands. Molecular Ecology 31, 603-619.
Funk WC, Lovich RE, Hohenlohe PA, Hofman CA*, Morrison SA, Sillett TS, Ghalambor CK, Maldonado JE, Rick TC, Day MD, Polato NR‡, Fitzpatrick SW‡, Coonan TJ, Crooks KR, Dillon A, Garcelon DK, King JL, Boser CL, Gould N*, Andelt WF (2016) Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis). Molecular Ecology 25, 2176-2194.
Funk WC, Murphy MA, Hoke KL, Muths E, Amburgey SA*, Lemmon EM, Lemmon AR (2016) Elevational speciation in action? Restricted gene flow associated with adaptive divergence across an altitudinal gradient. Journal of Evolutionary Biology 29, 241-252.
Langin KM*, Sillett TS, Funk WC, Morrison SA, Desrosiers MA*, Ghalambor CK (2015) Islands within an island: Repeated adaptive divergence in a single population. Evolution 69, 653-665.
Fitzpatrick SW*, Gerberich JC†, Kronenberger J*, Angeloni LM, Funk WC (2015) Locally adapted traits maintained in the face of high gene flow. Ecology Letters 18, 37-47.

Photo credit: Katie Langin

Photo credit: W. Chris Funk

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