Books

• Allendorf FW, Funk WC, Aitken SN, Byrne M, Luikart G (2022) Conservation and the Genomics of Populations, 3rd edition. Oxford University Press, Oxford.

Refereed Journal Articles and Book Chapters Published or In Press

Symbols indicate postdoctoral (‡), graduate (*), and undergraduate (†) co-authors

2024

• Leigh DM‡, Vandergast A, Hunter ME, Crandall E, Funk WC, Garroway CJ, Hoban S, Oyler-McCance SJ, Rellstab C, Segelbacher G, Schmidt C‡, Vázquez-Domínguez E, Paz-Vinas I‡ (2024) Don’t make genetic data disposable: Best practices for genetic and genomic data archiving. Nature Ecology and Evolution, in press.

• Hardy B*, Muths E, Funk WC, Bailey L (2024) Quantifying intraspecific variation in host resistance and tolerance to a lethal pathogen. Journal of Animal Ecology, in press.

• Páez-Vacas M*, Funk WC (2024) Thermal limits along tropical elevation gradients: poison frog tadpoles show plasticity but maintain divergence across elevation. Journal of Thermal Biology, in press.

2023

• Trumbo D‡, Hardy B*, Crockett H, Muths E, Forester BR, Check RG*, Zimmerman S, Corey-Rivas S, Bailey L, Funk WC (2023) Conservation genomics of an endangered montane amphibian reveals low population structure, low genomic diversity, and selection pressure from disease. Molecular Ecology 32, 6777-6795.

• Cicchino AS*, Shah AA, Forester BR, Dunham JB, Poff NL, Ghalambor CK, Funk WC (2023) Acclimation capacity of critical thermal maximum varies among populations: consequences for estimates of physiological vulnerability. Ecosphere 14, e4691.

• Cicchino AS*, Martinez CM†, Funk WC, Forester BR‡ (2023) Temperature and development drive variation in oral morphology among tailed frog (Ascaphus spp.) populations. Ichthyology and Herpetology 111, 448-455.

• Cicchino AS*, Shah AA, Forester BR, Dunham JB, Ghalambor CK, Funk WC (2023) Multi-scale relationships in thermal limits within and between two cold-water frog specialists uncover different trends in physiological vulnerability. Freshwater Biology 68, 1267-1278.

• Cicchino AS*, Ghalambor CK, Funk WC (2023) Linking critical thermal maximum to mortality from thermal stress in a cold-water frog. Biology Letters 19, 20230106.

• Turbek SP, Funk WC, Ruegg KC (2023) Where to draw the line? Expanding the delineation of conservation units to highly mobile taxa. Journal of Heredity, in press. 

• Hoban S, Bruford MW, da Silva JM, Funk WC, Frankham R, Gill MJ, Grueber CE, Heuertz M, Hunter ME, Kershaw F, Lacy RC, Lees C, Lopes-Fernandes M, MacDonald AJ, Mastretta-Yanes A, McGowan PJK, Meek MH, Mergeay J, Millette KL, Mittan-Moreau CS, Navarro LM, O’Brien D, Ogden R, Segelbacher G, Paz-Vinas I, Vernesi C, Laikre L (2023) Genetic diversity Goals and Targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework. Conservation Genetics 24, 181-191. 

• Hardy B*, Muths E, Lambert B, Schneider S, Funk WC, Bailey L (2023) Compensatory recruitment unlikely in high elevation amphibian populations challenged with disease. Journal of Animal Ecology 60, 121-131.

2022

• 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.

• Forester BR‡, Murphy MA, Mellison C, Petersen J, Pilliod D, Van Horne R, Harvey J, Funk WC (2022) Genomics-informed delineation of conservation units in a desert amphibian. Molecular Ecology 31, 5249-5269.

• Hoban S, Archer F, Bertola L, Bragg J, Breed M, Bruford M, Coleman M, Ekblom R, Funk WC, Grueber C, Hand B, Jaffé R, Jensen E, Johnson J, Kershaw F, Liggins L, MacDonald A, Mergeay J, Miller J, Muller-Karger F, O'Brien D, Paz-Vinas I, Potter K, Razgour O, Vernesi C, Hunter M (2022) Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition. Biological Reviews 97, 1511-1538.

• 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.

• 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.

2021

• 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.

• Hoban S, Campbell CD, da Silva J, Ekblom R, Funk WC, Garner BA, Godoy JA, Kershaw F, MacDonald AJ, Mergeay J, Minter M, O’Brien D, Paz-Vinas I, Pearson SK, Pérez-Espona S, Potter KM, Russo I-RM, Segelbacher G, Vernesi C, Hunter ME (2021) Genetic diversity is considered important but interpreted narrowly in country reports to the Convention on Biological Diversity: current actions and indicators are insufficient. Biological Conservation 261, 109233.

• Schweizer RM‡, Saarman N, Ramstad KM, Forester BR‡, Kelley JL, Hand BK, Malison RL, Ackiss AS‡, Watsa M, Nelson T, Beja-Pereira A, Waples RS, Funk WC, Luikart G (2021) Big data in conservation genomics: boosting skills, hedging bets, and staying current in the field. Journal of Heredity 112, 313-327.

• Hoban S, Bruford M, Lopes-Fernandes M, Funk WC, Galbusera P, Griffith P, Grueber C, Heuertz M, Hunter M, Hvilsom C, Kershaw F, Kalamujic Stroil B, Khoury C, Laikre L, MacDonald A, Mergeay J, Meek M, Mittan C*, Mukassabi T, O’Brien D, Ogden R, Palma da Silva C, Ramakrishnan U, Segelbacher G, Shaw R, Sjogren-Gulve P, Velickovic N, Vernesi C (2021) Global commitments to conserving genetic diversity are now necessary and feasible. BioScience 71, 964-976.

• Laikre L, Hohenlohe PA, Allendorf FW, Bertola LD, Breed MF, Bruford MW, Funk WC, Gajardo G, González-Rodríguez A, Grueber CE, Hedrick PW, Heuertz M, Hunter ME, Johannesson K, Liggins L, MacDonald AJ, Mergeay J, Moharrek F, O’Brien D, Ogden R, Orozco-terWengel P, Palma-Silva C, Pierson J, Paz-Vinas I, Russo I-RM, Ryman N, Segelbacher G, Sjögren-Gulve P, Waits LP, Vernesi C, Hoban S (2021) Continued improvement to genetic diversity indicator for CBD. Conservation Genetics  22, 533-536.

• Hohenlohe PA, Funk WC, Rajora OP (2021) Population genomics for wildlife conservation and management. Molecular Ecology 30, 62-82.

• Hoban S, Paz-Vinas I, Aitken S, Bertola LD, Breed M, Bruford M, Funk WC, Grueber CE, Heuertz M, Hohenlohe P, Hunter ME, Jaffé R, Lopes Fernandes M, Mergeay J, Moharrek F, O’Brien D, Segelbacher G, Vernesi C, Waits L, Laikre L (2021) Effective population size remains a suitable, pragmatic indicator of genetic diversity for all species, including forest trees. Biological Conservation 253, 108906.

2020

• 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.

• Barbosa S‡, Hendricks SA‡, Funk WC, Rajora OP, Hohenlohe PA (2020) Wildlife population genomics: applications and approaches. In: Population Genomics: Wildlife (eds. Hohenlohe PA, Rajora OP), pp. 3-59. Springer, Cham.

• Funk WC, Zamudio KR, Crawford AJ (2020) Advancing understanding of amphibian evolution, ecology, behavior, and conservation with massively-parallel sequencing. In: Population Genomics: Wildlife (eds. Hohenlohe PA, Rajora OP), pp. 211-254. Springer, Cham.

• Fitzpatrick SW, Funk WC (2020) Genomics for genetic rescue. In: Population Genomics: Wildlife (eds. Hohenlohe PA, Rajora OP), pp. 437-471. Springer, Cham.

2019

• Bell DA*, Robinson ZL*, Funk WC, Fitzpatrick SW, Allendorf FW, Tallmon DA, Whiteley AR (2019) The exciting potential and remaining uncertainties of genetic rescue. Trends in Ecology and Evolution 34, 1070-1079.

• 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.

• Fitak RR, Antonides JD, Baitchman EJ, Bonaccorso E, Braun J, Kubiski S, Chiu E, Fagre AC, Gagne RB, Lee JS, Malmberg JL, Stenglein MD, Dusek RJ, Forgacs D, Fountain-Jones NM, Gilbertson MLJ, Worsley-Tonks KEL, Funk WC, Trumbo DR, Ghersi BM, Grimaldi W, Heisel SE, Jardine CM, Kamath PL, Karmacharya D, Kozakiewicz CP, Kraberger S, Loisel DA, McDonald C, Miller S, O’Rourke D, Ott-Conn CN, Páez-Vacas M, Peel AJ, Turner WC, VanAcker MC, VandeWoude S, Pecon-Slattery J (2019) The expectations and challenges of wildlife disease research in the era of genomics: forecasting with a horizon scan-like exercise. Journal of Heredity 110, 261-274.

• Billerman SM‡, Jesmer BR‡, Watts AG, Schlichting P‡, Fortin M-J, Funk WC, Hapeman P, Muths E, Murphy MA (2019) Testing theoretical metapopulation conditions with genotypic data from boreal chorus frogs (Pseudacris maculata). Canadian Journal of Zoology 97, 1042-1053.

2018

• 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.

• 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.

2017

• Catchen J, Hohenlohe P, Bernatchez L, Funk WC, Andrews K, Allendorf FW (2017) Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations. Molecular Ecology Resources 17, 362-365.

• 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.

• Lanier WE*, Bestgen KR, Funk WC, Bailey LL (2017) Unpalatable, yet unprotected: trout reduce survival and development rate of rare toad tadpoles despite chemical defense. Canadian Journal of Fisheries and Aquatic Sciences 74, 494-502.

• 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.

2016

• Amburgey SA*, Murphy MA, Funk WC (2016) Phenotypic plasticity in developmental rate is insufficient to offset high tadpole mortality in rapidly drying ponds. Ecosphere 7, e01386.

• Havird JC‡, Fitzpatrick SW‡, Funk WC, Kronenberger J*, Angeloni LM, Sloan DB (2016) Sex, mitochondria, and genetic rescue. Trends in Ecology and Evolution 31, 96-99.

• 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.

2015

• 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.

• Watts AG*, Schlichting P*, Billerman S*, Jesmer B*, Micheletti S*, Fortin M-J, Funk WC, Hapeman P, Muths EL, Murphy MA (2015) How spatio-temporal habitat connectivity affects amphibian genetic structure. Frontiers in Genetics 6, 275.

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

2014

• Robertson JM‡, Langin KM*, Sillett TS, Morrison SA, Ghalambor CK, Funk WC (2014) Identifying Evolutionarily Significant Units and prioritizing populations for management on islands. Monographs of the Western North American Naturalist 7, 397-411.

• Amburgey SA*, Bailey LL, Murphy MA, Muths E, Funk WC (2014) The effects of hydropattern and predator communities on amphibian occupancy. Canadian Journal of Zoology 92, 927-937.

• 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.

2013

• Swanson JE†, Bailey LL, Muths E, Funk WC (2013) Factors influencing survival and mark retention in postmetamorphic boreal chorus frogs. Copeia 2013, 670-675.

• Fairman CM*, Bailey LL, Chambers RM, Russell TM, Funk WC (2013) Species-specific effects of acidity on pond occupancy in Ambystoma salamanders. Journal of Herpetology 47, 346-353.

• Matthews JH, Funk WC, Ghalambor CK (2013) Demographic approaches to assessing climate change impact: an application to pond-breeding frogs and shifting hydropatterns. In: Wildlife Conservation in a Changing Climate (eds. Brodie JF, Post E, Doak D), pp. 58-85. University of Chicago Press, Chicago.

• Trillo PA‡, Athanas KA*, Goldhill DH*, Hoke KL, Funk WC (2013) The influence of geographic heterogeneity in predation pressure on sexual signal divergence in an Amazonian frog species complex. Journal of Evolutionary Biology 26, 216-222.

2012

• Funk WC, McKay JK, Hohenlohe PA, Allendorf FW (2012) Harnessing genomics for delineating conservation units. Trends in Ecology and Evolution 27, 489-496.

• Amburgey SA†, Funk WC, Murphy MA, Muths E (2012) Effects of hydroperiod duration on survival, developmental rate, and size at metamorphosis in boreal chorus frog tadpoles (Pseudacris maculata). Herpetologica 68, 456-467.

• 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.

2011

• Phillipsen IC*, Funk WC, Hoffman E, Monsen K, Blouin M (2011) Comparative analyses of effective population size within and among species: ranid frogs as a case study. Evolution 65, 2927-2945.

• Funk WC, Garcia TS, Cortina GA†, Hill RH* (2011) Population genetics of introduced bullfrogs, Rana (Lithobates) catesbeianus, in the Willamette Valley, Oregon, USA. Biological Invasions 13, 651-658.

2010

• Funk WC, Murphy MA‡ (2010) Testing evolutionary hypotheses for phenotypic divergence using landscape genetics. Molecular Ecology 19, 427-430.

2009

• Funk WC, Cannatella DC, Ryan MJ (2009) Genetic divergence is more tightly related to call variation than landscape features in the Amazonian frogs Physalaemus petersi and P. freibergi. Journal of Evolutionary Biology 22, 1839-1853.

• Funk WC, Cannatella DC (2009) A new, large species of Chiasmocleis Mehely 1904 (Anura: Microhylidae) from the Iquitos region, Amazonian Peru. Zootaxa 2247, 37-50.

• Guayasamin JM, Funk WC (2009) The amphibian community at Yanayacu Biological Station, Ecuador, with a comparison of vertical microhabitat use among Pristimantis species and the description of a new species of the Pristimantis myersi group. Zootaxa 2220, 41-66.

• Greene AE†, Funk WC (2009) Sexual selection on morphology in an explosive breeding amphibian, the Columbia spotted frog (Rana luteiventris). Journal of Herpetology 43, 244-251.

2008

• Funk WC, Pearl CA, Draheim HM*, Adams MJ, Mullins TD, Haig SM (2008) Range-wide phylogeographic analysis of the spotted frog complex (Rana luteiventris and Rana pretiosa) in northwestern North America. Molecular Phylogenetics and Evolution 49, 198-210.

• Funk WC, Angulo A, Caldwell JP, Ryan MJ, Cannatella DC (2008) Comparison of morphology and calls of two cryptic species of Physalaemus (Anura: Leiuperidae). Herpetologica 64, 290-304.

• Greeney HF, Gelis RA, Funk WC (2008) Predation on caecilians (Caecilia orientalis) by Barred Hawks (Leucopternis princeps) depends on rainfall. Herpetological Review 39, 162-164.

2007 and earlier

• Boul KE, Funk WC (joint first author), Darst CR, Cannatella DC, Ryan MJ (2007) Sexual selection drives speciation in an Amazonian frog. Proceedings of the Royal Society B:  Biological Sciences 274, 399-406.

• Funk WC, Caldwell JP, Peden CE*, Padial JM, de la Riva I, Cannatella DC (2007) Tests of biogeographic hypotheses for diversification in the Amazonian forest frog, Physalaemus petersi. Molecular Phylogenetics and Evolution 44, 825-837.

• Guayasamin JM, Bustamante MR*, Almeida-Reinoso D*, Funk WC (2006) Glass frogs (Centrolenidae) of Yanayacu Biological Station, Ecuador, with the description of a new species and comments on centrolenid systematics. Zoological Journal of the Linnean Society 147, 489-513.

• Funk WC, Blouin MS, Corn PS, Maxell BA, Pilliod DS, Amish S*, Allendorf FW (2005) Population structure of Columbia spotted frogs (Rana luteiventris) is strongly affected by the landscape. Molecular Ecology 14, 483-496.

• Funk WC, Greene AE†, Corn PS, Allendorf FW (2005) High dispersal in a frog species suggests that it is vulnerable to habitat fragmentation. Biology Letters 1, 13-16.

• Funk WC, Fletcher-Lazo G, Nogales-Sornosa F*, Almeida-Reinoso D* (2004) First description of a clutch and nest site for the genus Caecilia (Gymnophiona: Caeciliidae). Herpetological Review 35, 128-130.

• Funk WC, Mills LS (2003) Potential causes of population declines in forest fragments in an Amazonian frog. Biological Conservation 111, 205-214.

• Funk WC, Almeida-Reinoso D*, Nogales-Sornosa F*, Bustamante MR* (2003) Monitoring population trends of Eleutherodactylus frogs. Journal of Herpetology 37, 245-256.

• Biek R, Funk WC, Maxell BA, Mills LS (2002) What is missing in amphibian decline research: Insights from ecological sensitivity analysis. Conservation Biology 16, 728-734.

• Tallmon DA, Funk WC, Dunlap WW, Allendorf FW (2000) Genetic differentiation among long-toed salamander (Ambystoma macrodactylum) populations. Copeia 2000, 27-35.

• Funk WC, Tallmon DA, Allendorf FW (1999) Small effective population size in the long-toed salamander. Molecular Ecology 8, 1633-1640.

• Funk WC, Dunlap WW (1999) Colonization of high-elevation lakes by long-toed salamanders (Ambystoma macrodactylum) after the extinction of introduced trout populations. Canadian Journal of Zoology 77, 1759-1767.

Non-refereed Journal Articles/Chapters

• Funk WC, Caminer M*, Ron SR (2012) In Amazonian frogs there is much more diversity than meets the eye. Froglog 100, 73.

• Lannoo M, Funk WC, Gadd M, Halliday T, Mitchell J (2007) Freshwater resources and associated terrestrial landscapes. In: Amphibian Conservation Action Plan (eds. Gascon C, Collins JP, Moore RD, et al.), pp. 16-18. IUCN/SSC Amphibian Specialist Group, Gland, Switzerland and Cambridge, UK.

• Angulo A, Funk WC (2006) Hyla calcarata (Rana de espolones) and Hyla fasciata (NCN). Defensive behavior. Herpetological Review 37, 203-204.

• Funk WC, Donnelly MA, Lips KR (2005) Alternative views of amphibian toe-clipping. Nature 433, 193-193.

Photo by Amanda Cicchino