Diversity and Conservation of Domestic and Wild Canids

We study the evolution of wild and domestic canids, and their interactions on each other. This system is particularly interesting from many points of view. Dogs are the oldest domesticated species, and have a special relationship with humans so learning about the domestication and evolution of dogs also illuminates our own history and culture. Also, because all of the canids are capable of hybridizing. Human action has dramatically changed the distribution and/ or abundance of many canids, and is continuing to impact all wild species to one degree or another. This impacts the selective forces acting upon, and in some cases the survival, of many populations. By changing the distribution and abundance of canid species human intervention changes interspecific relationships which in some cases leads to hybridization and introgression. This can happen between wild and domestic canids, or between different species of wild canids. In most cases this has detrimental effects on the canid populations, but in some cases introgressed genes are positively selected for in another.

We use a variety of tools including ancient DNA, fecal DNA and genomics, among others, to study the evolutionary history of canids, including domestication, ecology, hybridization, introgression, population structure, speciation, and adaptation to different habitats.

Some related peer-reviewed articles

Potential adaptive introgression from dogs into Iberian grey wolves (Canis lupus) Sarabia C, Salado I, Fernández-Gil A, vonHoldt BM, Hofreiter M, Vilà C, Leonard JA (2025) Molecular Ecology e17639		Link
Loss of mitochondrial genetic diversity despite population growth: the legacy of past wolf population declines Salado I, Preick M, Lupiáñez-Corpas N, Fernández-Gil A, Vilà C, Hofreiter M, Leonard JA (2023) Genes 14(1), 75		Link
High investment into reproduction is associated with reduced lifespan in dogs Bargas-Galarraga I, Vilà C, Gonzalez-Voyer A (2023) The American Naturalist 201(2)		Supp.Mat.
Planned cull endangers Swedish wolf population Laikre L, Allendorf FW, Aspi J, Carroll C, Dalén L, Fredrickson R, Hansen Wheat C, Hedrick P, Johannesson K, Kardos M, Peterson RO, Phillips M, Ryman N, Räikkönen J, Vilà C, Wheat CW, Vernesi C, Vucetich JA (2022) Science 377, 162-162
Grey wolf genomic history reveals a dual ancestry of dogs Bergström A, Stanton DWG, Taron UH et al. (2022) Nature, https://doi.org/10.1038/s41586-022-04824-9		Link
Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing Serres-Armero A, Povolotskaya IS, Quilez J, Ramirez O, Santpere G, Kuderna LFK, Hernandez-Rodriguez J, Fernandez-Callejo M, Gomez-Sanchez D, Freedman AH, Fan Z, Novembre J, Navarro A, Boyko A, Wayne R, Vilà C, Lorente-Galdos B, Marques-Bonet T (2017) BMC Genomics 18, 977		Link
Defense of an expanded historical range for the Mexican Wolf: A comment on Heffelfinger et al. Hendricks SA, Koblmüller S, Harrigan RJ, Leonard JA, Schweizer RM, VonHoldt BM, Kays R, Wayne RK (2017) The Journal of Wildlife Management 81(8):1331–1333
Wolf population genetics in Europe: a systematic review, meta-analysis and suggestions for conservation and management Hindrikson M, Remm J, Pilot M, Godinho R, Stronen AV, Baltrunaité L, Czarnomska SD, Leonard JA, Randi E, Nowak C, Åkesson M, López-Bao JV, Álvares F, Llaneza L, Echegaray J, Vilà C, Ozolins J, Rungis D, Aspi J, Paule L, Skrbinšek T, Saarma U (2016) Biological Reviews		Supp. Info.
Whole mitochondrial genomes illuminate ancient intercontinental dispersals of grey wolves (Canis lupus) Koblmüller S, Vilà C, Lorente-Galdos B, Dabad M, Ramirez O, Marques-Bonet O, Wayne RK, Leonard JA (2016) Journal of Biogeography 43, 1728–1738		Supp. Info. Press coverage: BBC

Fan Z, Silva P, Gronau I, Wang S, Serres Armero A, Schweizer RM, Ramirez O, Pollinger J, Galaverni M, Ortega Del-Vecchyo D, Du L, Zhang W, Zhang Z, Xing J, Vilà C, Marques-Bonet T, Godinho R, Yue B, Wayne RK (2016) Worldwide patterns of genomic variation and admixture in gray wolves. Genome Research 26 (2): 163-173. doi: 10.1101/gr.197517.115 Link

Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW, Gronau I, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Ramirez O, Hormozdiari F, Alkan C, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Marques-Bonet T, Ostrander EA, Wayne RK, Novembre J (2016) Demographically-based evaluation of genomic regions under selection in domestic dogs. PLoS Genetics 12(3): e1005851. doi:10.1371/journal.pgen.1005851 Link

de Groot GA, Nowak C, Skrbinšek T, Andersen LW, Aspi J, Fumagalli L, Godinho R, Harms V, Jansman HAH, Liberg O, Marucco F, Myslajek RW, Nowak S, Pilot M, Randi E, Reinhardt I, Smietana W, Szewczyk M, Taberlet P, Vilà C, Muñoz-Fuentes V (2016) Decades of population genetic research reveal the need for harmonization of molecular markers: the grey wolf Canis lupus as a case study. Mammal Review 46: 44-59. DOI: 10.1111/mam.12052

Koepfli K-P, Pollinge J, Godinho R, Robinson J, Lea A, Hendricks S, Schweizer RM, Thalmann O, Silva P, Fan Z, Yurchenko AA, Dobrynin P, Makunin A, Cahill JA, Shapiro B, Álvares F, Brito JC, Geffen E, Leonard JA, Helgen KM, Johnson WE, O’Brien SJ, Van Valkenburgh B, Wayne RK (2015) Genome-wide evidence reveals that African and Eurasian golden jackals are distinct species. Current Biology 25: 2158-2165. DOI: http://dx.doi.org/10.1016/j.cub.2015.06.060

Muñoz-Fuentes V, Marcet-Ortega M, Alkorta-Aranburu G, Linde Forsberg C, Morrell JM, Manzano-Piedras E, Söderberg A, Daniel K, Villalba A, Toth A, Di Rienzo A, Rogi I, Vilà C (2015) Strong artificial selection in domestic mammals did not result in an increased recombination rate. Molecular Biology and Evolution 32(2): 510-523.
Supporting information Journal Cover

Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, Hormozdiari F, Alkan C, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Ostrander EA, Marques-Bonet T, Wayne RK, Novembre J. (2014) Genome sequencing highlights the dynamic early history of dogs. PLoS Genetics 10(1): e1004016. Link

Baranowska Körberg I, Sundström E, Meadows JRS, Rosengren Pielberg G, Gustafson U, Hedhammar A, Karlsson EK, Seddon J, Söderberg A, Vilà C, Zhang X, Akesson M, Lindblad-Toh K, Andersson G, Andersson L (2014) A simple repeat polymorphism in the MITF-M promoter is a key regulator of white spotting in dogs. PLoS ONE 9: e104363. Link

Byrd BF, Cornellas A, Eerkens JW, Rosenthal JS, Carpenter TR, Leventhal A, Leonard JA (2013) The role of canids in ritual and domestic contexts: new ancient DNA insights from complex hunter-gatherer sites in prehistoric Central California. Journal of Archaeological Science 40: 2176-2189

Thalmann O, B Shapiro, P Cui, VJ Schuenemann, SK Sawyer, DL Greenfield, MB Germonpré, MV Sablin, F Lopez-Giraldez, X Domingo-Roura, H Napierala, H-P Uerpmann, DM Loponte, AA Acosta, L Giemsch, RW Schmitz, B Worthington, JE Buikstra, A Druzhkova, AS Graphodatsky, ND Ovodov, N Wahlberg, AH Freedman, RM Schweizer, K-P Koepfli, JA Leonard, M Meyer, J Krause, S Pääbo, RE Green, RK Wayne (2013) Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Science 342: 871-874 (Highlighted in Science) 

Druzhkova AS, Thalmann O, Trifonov VA, Leonard JA, Vorobieva NV, Ovodov ND, Graphodatsky AS, Wayne RK (2013) Ancient DNA analysis affirms the canid from Altai as a primitive dog. PLoS ONE 8 (3): e57754. Link

Losey RJ, Garvie-Lok S, Leonard JA, Katzenberg MA, Germonpré M, Nomokonova T, Sablin MV, Goriunova OI, Berdnikova EN, Savelev NA (2013) Burying dogs in ancient cis-Baikal, Siberia: Temporal trends and relationships with human diet and subsistence practices. PLoS ONE 8 (5): e63740 Link

Koblmüller S, Wayne RK, Leonard JA (2012) Impact of Quaternary climatic changes and interspecific competition on the demographic history of a highly mobile generalist carnivore, the coyote. Biology Letters 8 (4), 644-647

Larson G, Karlsson EK, Perri A, Webster MT, Ho SYW, Peters J, Stahl PW, Piper PJ, Lingaas F, Fredholm M, Comstock KE, Modiano JF, Schelling C, Agoulnik AI, Leegwater PA, Dobney K, Vigne J-D, Vilà C, Andersson L, Lindblad-Toh K (2012) Rethinking dog domestication by integrating genetics, archeology, and biogeography. Proc. Natl. Acad. Sci. USA 109 (23), 8878-8883

Castroviejo-Fisher S, Skoglund P, Valadez R, Vilà C, Leonard JA(2011) Vanishing native American dog lineages. BMC Evolutionary Biology 11, 73 Link

Losey RJ, Bazaliiskii VI, Garvie-Lok S, Germonpré M, Leonard JA, Allen AL, Katzenberg MA, Sablin MV (2011) Canids as persons: Early Neolithic dog and wolf burials, Cis-Baikal, Siberia. Journal of Anthropological Archaeology 30, 174-189

Muñoz-Fuentes V, Di Rienzo A, Vilà C (2011) Prdm9, a major determinant of meiotic recombination hotspots, is not functional in dogs and their wild relatives, wolves and coyotes. PLoS ONE 6, e25498.
Recomended by Faculty of 1000 (F1000) Link

Sastre N, Vilà C, Salinas M, Bologov VV, Urios V, Sánchez A, Francino O, Ramírez O (2011) Signatures of demographic bottlenecks in European wolf populations. Conservation Genetics 12, 701-712

Vaysse A, Ratnakumar A, Derrien T, Axelsson E, Rosengren Pielberg G, Sigurdsson S, Fall T, Seppälä EH, Hansen MST, Lawley CT, Karlsson EK, The LUPA Consortium, Bannasch D, Vilà C, Lohi H, Galibert F, Fredholm M, Häggström J, Hedhammar A, André C, Lindblad-Toh K, Hitte C, Webster MT (2011) Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PloS Genetics 7,10 Link

Muñoz-Fuentes V, Darimont CT,Paquet P, Leonard JA (2010) The genetic legacy of extirpation and re-colonization in Vancouver Island wolves. Conservation Genetics 11, 547-556

News coverage
Introgresion potencialmente adaptativa de perros en lobos de la Península Ibérica (Canis lupus) Nota de prensa CSIC, "Los lobos ibéricos tendrían una naturaleza única resultado de la hibridación con perros en el pasado" ABC, "Los lobos ibéricos son únicos porque hibridaron con perros en el pasado" 20minutos, "El lobo ibérico conserva genes de perro que podrían haberle ayudado a adaptarse a su entorno" La Razón, "La «naturaleza única» de los lobos ibéricos" Referred paper: Potential adaptive introgression from dogs into Iberian grey wolves (Canis lupus) Sarabia C et al. (2025) Molecular Ecology, e17639 Link	Iberian wolf Image credit: Isabel Salado
Iberian wolves are losing genetic diversity despite an increasing population Several Spanish newspapers spreaded the main findings that Isabel Salado and colleagues about the poor genetic diversity of the Iberian wolf population despite its population increase. For example: CSIC Press release. January 2023 ABC, La Vanguardia, El Diario, Europa Press. January 2023 Referred paper: Loss of mitochondrial genetic diversity despite population growth: the legacy of past wolf population declines Salado I et al. (2023) Genes 14(1), 75 Link	From Salado I et al. (2023) Genes 14(1), 75
Non-invasive genetic monitoring of a wolf population Isabel Salado tells us about the non-invasive genetic monitoring of a wolf population that she and her colleages performed during autumn of 2020. This field work was funded by an Heredity Fieldwork Grant from the Genetics Society. The role of habitat selection and local adaptation in the population structure of an apex predator. Salado I (2021) Genetics Society News 85, 55-56.
Wolf conservation El Pais [Spanish newspaper] February 2021 Carles Vilà talks about the causes that lead to the extinction of the Wolf in the South of the Iberian Peninsula
Wolf conservation El Periódico [Spanish newspaper] February 2021 Carles Vilà is asked about the recent steps to ban wolf hunting throughout Spain
Wolf conservation National Geographic Italia 2017 Carles Vilà's opinion about the controversial Italian Wolf action plan, which implies a much discussed culling of some individuals to a maximum of 5% of the actual population.	Photo by Silvano Paiola
Origin of North America's wolves BBC 2016 Referred paper: Whole mitochondrial genomes illuminate ancient intercontinental dispersals of grey wolves (Canis lupus) Koblmüller et al. (2016) Journal of Biogeography 43, 1728–1738.	Photo by Mark Miller/Alamy
Early history of dogs NBC News 2014 Referred paper: Genome sequencing highlights the dynamic early history of dogs Freedman et al. (2013) PLoS Genetics 10, e1004016. Link
European origin of domestic dogs Science 2013, Nature 2013, International Bussiness Times 2013, Richard Dawkins Foundation (Facebook) 2013, El Mundo (Spanish newspaper) 2013 Referred paper: Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs Thalmann et al. (2013) Science 342, 871-874.	Photo by Del Baston/Center for American Archaeology
Dogs, not wolves, eating sheep The Economist 2009, La Buvette des Alpages (French newspaper) 2009, RTVE (Spanish National Radio) 2010, RTVE (Spanish National Radio) - potcast 2010, Ecología verde (Spanish blog) 2010, El Correo (Spanish newspaper) - Interview 2009, El Correo (Spanish newspaper) 2010, El Correo (Spanish newspaper) (2nd article) 2010, El Correo (Spanish newspaper) blog 2010, rtvcyl (Spanish newspaper) 2010, 20 minutos (Spanish newspaper) 2010, Agrodigital (Spanish web) 2010, Basqueresearch (Spanish web) 2010 Referred paper: Noninvasive monitoring of wolves at the edge of their distribution and the cost of their conservation Echegaray & Vilà (2009) Animal Conservation 13, 157-161.
Black Gene in Wolves Science 2009 Los Angeles Times 2009, New York Times 2009, NBC News 2009, El Mundo (Spanish newspaper) 2009, UCLA's news blog 2009, Science Daily 2009, Phys Org 2009, Science 2.0 (blog) 2009, Popular Science (blog) 2009, Evolutionary Novelties (blog) 2009 Referred paper: Molecular and evolutionary history of melanism in North American gray wolves Anderson et al. (2009) Science 323, 1339-1343.	Monty Sloan
Qué fue de los lobos de Beringia, Excelenciencia 2015/03/19 [In Spanish]