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.

Genetics and Ecology of wolves in British Columbia    More

The central coast of British Columbia is the largest intact coastal temperate rainforest in the world. The rugged landscape, comprised of innumerable islands separated by open ocean lies on the western side of the Coastal Mountain Range. Deep fjords punctuate the coastline. Its remote nature has protected it from the large-scale, industrial, clearcut logging that has severely altered the environment in adjacent southeast Alaska and Washington state. Because the “Great Bear Rainforest” is largely undeveloped and sparsely populated, it is supposed that this archipelago landscape still harbors large carnivores and their natural prey base in historical abundances. However, due to the inaccessibility of this habitat, basic parameters such as the distribution and density of large mammals, including wolves and their prey are unknown. With the help of the local Heiltsuk First Nations people, we explore this area by boat and collect data permitting an estimation of these fundamental parameters.

   

The island ecosystem may impose unique constraints on the activities of predator and prey. Based on data from adjacent areas, we believe that many of the islands are too small to support a sufficient number of deer to maintain a persistent population of wolves. Moreover, wolves have been observed swimming among islands, likely searching for areas where vulnerable prey has not been exhausted. The time lag between population recovery by deer and the island’s subsequent re-colonization by wolves defines a unique predator-prey system that has fundamentally different dynamics than terrestrial ecosystems. Classic survey techniques cannot easily be used to study patterns of abundance and movements among islands. Consequently, we utilize new non-invasive approaches involving systematic collection of feces across the region multiple times each year. Fecal typing has been shown to be a feasible and accurate method for monitoring activity of canids.

The coastal habitat, previously protected by ruggedness, is now being targeted by logging companies as the resources in the other areas are being exhausted. By comparing the ecological data we collect in this pristine forest with similar data collected previously in coastal southeast Alaska (which has been heavily impacted by logging and hunting), we will be able to assess potential impacts of logging on predator-prey dynamics.

Impact of hybridization with domestic dogs on the conservation of wild canids    More

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Distribution and Diversity of Wolves in Iberia    More

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Changes in populations through time    More

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Genomics of Selection    More

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Domestication    More

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Major collaborators

Raincoast Conservation Society
Chris Darimont, University of Victoria
Bob Wayne, University of California, Los Angeles
Paul Paquet, University of Calgary
Frank Hailer, Biodiversity and Climate Research Centre (BiK-F)
Violeta Muñoz-Fuentes, Senckenberg Research Institute and Natural History Museum of Frankfurt

Some related peer-reviewed articles

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

In the media

Qué fue de los lobos de Beringia, Excelenciencia 2015/03/19 [In Spanish]