Conservation and Evolutionary Genetics Group
  We use molecular tools to study the evolution of diversity, and assist in its conservation

photo of Jennifer Jennifer Leonard

Conservation and Evolutionary Genetics Group
Estación Biológica de Dońana - CSIC
Avda. Américo Vespucio, 26
41092 Sevilla, Spain
Phone: +34-954 232340 ex. 1418

Research interests

My research interests lie in the effect of changes in the environment on the genetic diversity of natural populations, with emphasis on the temporal perspective using ancient DNA. This type of research can be applied to fundamental questions in evolution, conservation and domestication. Many major environmental and population/species level changes have occurred in rapid succession since the late Pleistocene. The last 60,000 years in North America include a full glacial cycle; the opening and closing of the Bering land bridge; large changes in precipitation, temperature and vegetation; the arrival of humans and some other large mammal species; and a mass extinction event. The more recent end of this time frame includes the period in which animals were domesticated and humans expanded into the New World and across the Pacific. During the last millennia, a lot of human mediated changes have occurred, from the “discovery” of the New World by European explorers to historic predator control programs and changes in land use. Recent advances in molecular genetics enable DNA to be obtained from many bone remains spanning this age range. Although most of the work done with DNA from such old remains has involved just one or a few samples and aimed to determine the relationship between extinct and extant taxa such as the wooly rhino and extant rhinos, these techniques have opened the possibility of being able to look at genetic changes in these populations directly as the environment changed. It is now possible to apply powerful population genetics techniques to these past populations to complement demographic and ecological studies.

Current Collaborators

Evolution of Biodiversity on the Sunda Shelf
Jesus Maldonado, Smithsonian Institution
Richard Thorington, Smithsonian Institution
Kris Helgen, Smithsonian Institution

Diversity and conservation of domestic and wild canids
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 Muńoz-Fuentes, Senckenberg Research Institute and Natural History Museum of Frankfurt


Peer-reviewed Articles



The generic status of Rattus annandalei (Bonhote, 1903) (Rodentia, Murinae) and its evolutionary implications
Camacho-Sanchez M, Leonard JA , Fitriana Y, Tilak M-K, Fabre P-H (2017)
Journal of Mammalogy, in press



A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog
Montero-Mendieta S, Grabherr M, Lantz H, De la Riva I, Leonard JA, Webster MT, Vilŕ C (2017)
PeerJ 5:e3702

Quick Guide to Build De-novo Assemblies |


Bone loss from carcasses in Mediterranean ecosystems
Bernáldez-Sánchez E, García-Vińas E, Sanchez-Donoso I, Leonard JA (2017)
Palaios 32, 288–294




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, Ĺkesson M, López-Bao JV, Álvares F, Llaneza L, Echegaray J, Vilŕ C, Ozolins J, Rungis D, Aspi J, Paule L, Skrbinšek T, Saarma U (2017)
Biological Reviews 92, 1601-1629


Supp. Info.|



A novel MC1R allele for black coat colour reveals the Polynesian ancestry and hybridisation patterns of Hawaiian feral pigs
Linderholm A, Spencer D, Battista V, Frantz L, Barnett R, Fleischer R, James HF, Duffy D, Sparks JP, Clements DR, Andersson L, Dobney K, Leonard JA, Larson G (2016)
Royal Society Open Science 3, 160304



Whole mitochondrial genomes illuminate ancient intercontinental dispersals of grey wolves (Canis lupus)
Koblmüller S, Vilŕ 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


Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens
Hawkins MTR, Leonard JA, Helgen KM, McDonough MM, Rockwood LL, Maldonado JE (2016)
BMC Evolutionary Biology 16, 80



Phylogeny, biogeography and systematic revision of plain long-nosed squirrels (genus Dremomys, Nannosciurinae)
Hawkins MTR, Helgen KM, Maldonado JE, Rockwood LL, Tsuchiya MTN, Leonard JA (2016)
Molecular Phylogenetics and Evolution 94, 752-764



59. 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.

58. Brandariz-Fontes C*, Camacho-Sanchez M*, Vilŕ C, Vega-Pla JL, Rico C, Leonard JA (2015) Effect of the enzyme and PCR conditions on the quality of high-throughput DNA sequencing results. Scientific Reports 5: Article 8056. (*Equal contribution) Link |

57. Leonard JA, den Tex R-J, Hawkins MTR, Muńoz-Fuentes V, Thorington R, Maldonado JE (2015) Phylogeography of vertebrates on the Sunda Shelf: a multi-species comparison. Journal of Biogeography 42: 871-879. |


56. Leonard JA (2014) Ecology drives evolution in grey wolves. Evolutionary Ecology Research 16: 461-473. Link |

55. Leonard JA (2014) Adapting to global change. Evolutionary Ecology Research 16: 441-444. Link |

54. den Tex R-J & Leonard JA (2014) The phylogeography of red and yellow coppersmith barbets (Aves: Megalaima haemacephala). Frontiers in Ecology and Evolution, 2: 00016. doi: 10.3389/fevo.2014.00016  Link


53. 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) 

52. Brandariz-Fontes C, Leonard JA, Vega-Pla JL, Backström N, Lindgren G, Lippold S, Rico C (2013) Y-chromosome analysis in Retuertas horses. PLoS ONE 8 (5): e64985 Link

51. 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

50. Camacho-Sanchez M, Burraco P, Gomez-Mestre I, Leonard JA (2013) Preservation of RNA and DNA from mammal samples under field conditions. Molecular Ecology Resources 13 (4): 663-673.

49. Hailer F, Kutschera VE, Hallström BM, Fain SR, Leonard JA, Arnanson U, Janke A (2013) Response to comment on: Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage. Science 339: 1522

48. Den Tex R, Leonard JA (2013) A molecular phylogeny of Asian barbets: Speciation and extinction in the tropics. Molecular Phylogenetics and Evolution 68: 1-13

47. 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

46. 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

45. Gonzalez-Voyer A, den Tex R, Castello A, Leonard JA (2013) Evolution of acoustic and visual signals in Asian barbets. Journal of Evolutionary Biology 26: 647-659


44. Fox-Dobbs K, Nelson AA, Koch PL, Leonard JA (2012) Faunal isotope records reveal trophic and nutrient dynamics in 20th century Yellowstone grasslands. Biology Letters 8 (5): 838-841

43. 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

42. Hailer F, Kutschera VE, Hallström BM, Klassert D, Fain SR, Leonard JA, Arnanson U, Janke A (2012) Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage. Science 336 (6079), 344-347


41. Lorenzen ED, Nogués-Bravo D, Orlando L, Weinstock J, Binladen J, Marske KA, Ugan A, Borregaard MK, Gilbert MTP, Nielsen R, Ho SYW, Goebel T, Graf KE, Byers D, Stenderup JT, Rasmussen M, Campos PF, Leonard JA, Koepfli K-P, Froese D, Zazula G, Stafford TW, Aaris-Sřrensen K, Batra P, Haywood AM, Singarayer JS, Valdes PJ, Boeskorov G, Burns JA, Davydov SP, Haile J, Jenkins DL, Kosintsev P, Kuznetsova T, Lai X, Martin LD, McDonald HG, Mol D, Meldgaard M, Munch K, Stephan E, Sablin M, Sommer RS, Sipko T, Scott E, Suchard MA, Tikhonov A, Willerslev R, Wayne RK, Cooper A, Hofreiter M, Sher A, Shapiro B, Rahbek C, Willerslev E (2011) Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 479, 359-364

40. Lippold S, Knapp M, Kuznetsova T, Leonard JA, Benecke N, Ludwig A, Rasmussen M, Weinstock J, Willerslev E, Shapiro B, Hofreiter M (2011) Discovery of lost diversity of paternal horse lineages using ancient DNA. Nature Communications 2, 450

39. 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

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


37. Den Tex R, Maldonado JE, Thorington R and Leonard JA (2010) Nuclear copies of mitochondrial genes: another problem for ancient DNA. Genetica 138, 979-984

36. Den Tex R, Thorington R, Maldonado JE, Leonard JA (2010) Speciation dynamics in the SE Asian tropics: putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus. Molecular Phylogenetics and Evolution 55, 711-720

35. Muńoz-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


34. Koblmüller S, Nord M, Wayne RK, Leonard JA (2009) More is Better - Reply. Molecular Ecology 18, 4994-4996

33. Slater GJ, Thalmann O, Leonard JA, Schweizer RM, Koepfli K-P, Pollinger JP, Rawlence NJ, Austin JJ, Cooper A, Wayne RK (2009) Evolutionary history of the Falklands wolf. Current Biology 19, R937-938

32. Koblmüller S, Nord M, Wayne RK, Leonard JA (2009) Origin and status of the Great Lakes wolf. Molecular Ecology 18, 2313-2316

31. Barsh GS, Anderson TM, Vonholdt BM, Candille SI, Musiani M, Stahler DR, Leonard JA, Padhukasahasram B, Randi E, Bustamante CD, Ostrander EA, Tang H, Wayne RK (2009) How the Gray Wolf Got Its Color - Response. Science 325, 33-34

30. Muńoz-Fuentes V, Darimont CT, Wayne RK, Paquet P, Leonard JA (2009) Ecological factors drive differentiation in wolves from British Columbia. Journal of Biogeography 36, 1516-1531
  Article selected for the cover. Journal of Biogeography Editor's Choice highlighted articles

29. Anderson TM, VonHoldt BM, Candille SI, Musiani M, Greco C, Stahler DR, Smith DW, Padhukasahasram B, Randi E, Leonard JA, Bustamante CD, Ostrander EA, Tang H, Wayne RK, Barsh GS (2009) Molecular and evolutionary history of melanism in North American gray wolves. Science 323, 1339-1343

28. Leonard JA, Wayne RK (2009) Wishful thinking: Imagining that the current Great Lakes wolf is the same entity that existed historically. Biology Letters 5, 67-68


27. Hailer F, Leonard JA (2008) Hybridization among three native North American Canis species in a region of natural sympatry. PLoS ONE 3, e3333. Link

26. Leonard JA (2008) Ancient DNA applications for wildlife conservation. Molecular Ecology 17, 4186-4196

25. Reinius B, Saetra P, Leonard JA, Blekhman R, Gilad Y, Jazin E (2008) An evolutionarily conserved sexual signature in the primate brain. PloS Genetics 4, e1000100. Link

24. Fox-Dobbs K, Leonard JA, Koch PL (2008) Pleistocene megafauna from eastern Beringia: paleoecological and paleoenvironmental interpretations of stable carbon and nitrogen isotope and radiocarbon records. Palaeogeography, Palaeoclimatology, Palaeoecology 261, 30-46

23. Leonard JA, Wayne RK (2008) Native Great Lakes wolves were not restored. Biology Letters 4, 95-98


22. Musiani* M, Leonard* JA, Cluff HD, Gates CC, Mariani S, Paquet PC, Vilŕ C, Wayne RK (2007) Differentiation of tundra/taiga boreal coniferous forest wolves: genetics, coat color and association with migratory caribou. Molecular Ecology 16, 4149-4170 (*equal contribution)

21. Leonard JA, Vilŕ C, Fox-Dobbs K, Koch PL, Wayne RK, Van Valkenburgh B (2007) Megafaunal extinctions and the disappearance of a specialized wolf ecomorph. Current Biology 17, 1146-1150

20. Leonard JA, Shanks O, Hofreiter M, Kreuz E, Hodges L, Ream W, Wayne RK, Fleischer RC (2007) Animal DNA in PCR reagents plagues ancient DNA research. Journal of Archaeological Science 34, 1361-1366


19. Sundqvist A-K, Björnerfeldt S, Leonard JA, Hailer F, Hedhammar Ĺ, Ellegren H, Vilŕ C (2006) Unequal contribution of sexes in the origin of dog breeds. Genetics 172, 1121-1128

18. Maldonado JE, Leonard JA, Miranda GA, Ortega J, Wayne RK, Aguilera RJ (2006) Ten polymorphic microsatellite loci for the endangered Buena Vista Lake shrew (Sorex ornatus relictus). Molecular Ecology Notes 6, 349-352

17. Barnett R, Barnes I, Phillips MJ, Martin LD, Harington CR, Leonard JA, Cooper A (2005) Evolution of the extinct sabretooths (Smilodon and Homotherium) and American cheetahlike cat (Miracinonyx). Current Biology 15, 589-590

16. Leonard JA, Rohland N, Glaberman S, Fleischer RC, Caccone A, Hofreiter M (2005) A rapid loss of stripes: the evolutionary history of the extinct quagga. Biology Letters 1, 291-295

15. Leonard JA, Vilŕ C, Wayne RK (2005) Legacy lost: genetic variability and population size of extirpated US gray wolves (Canis lupus). Molecular Ecology 14, 9-17

14. Saetre P, Lindberg J, Leonard JA, Olsson K, Pettersson U, Ellegren H, Bergström TF, Vilŕ C, Jazin E (2004) From wild wolf to domestic dog: gene expression changes in the brain. Molecular Brain Research 126, 198-206

13. Vilŕ C, Leonard JA, Iriarte A, O'Brien SE, Johnson WE, Wayne RK (2004) Detecting the vanishing populations of the highly endangered Darwin's fox, Pseudalopex fulvipes. Animal Conservation 7, 147-153

12. Orlando L, Leonard JA, Laudet V, Guerin C, Hänni C (2003) Ancient DNA analysis reveals wooly rhino evolutionary relationships. Molecular Phylogenetics and Evolution 28, 76-90

11. Adams JR, Leonard JA, Waits LP (2003) Widespread occurrence of a domestic dog mitochondrial DNA haplotype in southeastern USA coyotes. Molecular Ecology 12, 541-546

10. Leonard JA, Wayne RK, Wheeler J, Valadez R, Guillén S, Vilŕ C (2002) Ancient DNA evidence for Old World origin of New World dogs. Science 298, 1613-1616

9. Paxinos EE, James HF, Olson SL, Ballou JD, Leonard JA, Fleischer RC (2002) Prehistoric decline of genetic diversity in the nene. Science 296, 1827

8. Vilŕ C, Ellegren H, Götherström A, Leonard JA, Wayne RK (2001) Tales from the DNA of domestic horses-Reply. Science 292, 218-219

7. Torres E, Lees DC, Vane-Wright RI, Kremen C, Leonard JA, Wayne RK (2001) Examining Monophyly in a Large Radiation of Madagascan Butterflies (Lepidoptera: Satyrinae: Myscalesina) Based on Mitochondrial DNA Data. Molecular Phylogenetics and Evolution 20, 460-473

6. Vilŕ C, Leonard JA, Götherström A, Marklund S, Sandberg K, Lindén K, Wayne RK, Ellegren H (2001) Widespread origins of domestic horse lineages. Science 291, 474-477

5. Leonard JA, Wayne RK, Cooper A (2000) Population genetics of Ice Age brown bears. Proceedings of the National Academy of Sciences, USA 97, 1651-1654

4. Wayne RK, Leonard JA, Cooper A (1999) Full of sound and fury: the recent history of ancient DNA. Annual Review of Ecology and Systematics 30, 457-477

3. Vilŕ C, Amorim IR, Leonard JA, Posada D, Castroviejo J, Petrucci-Fonseca F, Crandall KA, Ellegren H, Wayne RK (1999) Mitochondrial DNA phylogeography and population history of the grey wolf Canis lupus. Molecular Ecology 8, 2089-2103

2. Hadly EA, Kohn MH, Leonard JA, Wayne RK (1998) A genetic record of population isolation in pocket gophers during holocene climatic change. Proceedings of the National Academy of Science, USA 95, 6893-6896

1. Gonzalez S, Maldonado JE, Leonard JA, Vilŕ C, Barbanti Duarte JM, Merino M, Brum-Zorrilla N, Wayne RK (1998) Conservation genetics of the endangered Pampas deer (Ozotoceros bezoarticus). Molecular Ecology 7, 47-56

Book Chapters

10. Leonard JA, Echegaray J, Randi E, Vilŕ C (2014) Impact of hybridization with domestic dogs on the conservation of wild canids. In: M Gompper (ed.) Free-Ranging Dogs and Wildlife Conservation. Oxford University Press.

9. Leonard JA, Vilŕ C (2012) The domestic horse (Equus caballus L. 1758). In: T. Denham, G. Larson, V. Paz, P. Rowley (eds.) Agriculture and Domesticación. Encyclopedia of Global Archaeology. Springer.

8. Vilŕ C, Leonard JA (2012) Canid phylogeny and origin of the domestic dog. In: Ostrander EA, Ruvinsky A (eds.) The genetics of the dog. 2nd edition. CAB International.

7. Snyder LM, Leonard JA (2011) The Diversity and Origin of American Dogs. In: Smith BD (ed.) The Subsistence Economies of Indigenous North American Societies. Washington, D.C. : Smithsonian Institution Scholarly Press; Lanham, Md.: Published in cooperation with Rowman & Littlefield Publishers.

6. Leonard JA, Hofreiter M (2010) Ancient DNA: From Individuals to Populations. In: Dorado G (ed.) Molecular Markers, PCR, Bioinformatics and Ancient DNA - Technology and Applications. Science Publishers, New York. In press

5. Vilŕ C, Leonard JA (2007) Origin of dog breed diversity. In: Jensen P (ed.) The Behavioural Biology of Dogs. CAB International.

4. Snyder LM, Leonard JA (2006) Dog. In: Sturtevant WC (editor general), Stanford D, Smith BD, Ubelaker DH, Szathmáry EJE (eds.) Handbook of North American Indians, vol.3 Environment, Origins, and Population. Smithsonian Institution.

3. Wayne RK, Leonard JA, Vilŕ C (2006) Genetic Analysis of Dog Domestication. In: Zeder MA, Decker-Walters D, Bradley D, Smith BD (eds.) Documenting Domestication: New Genetic and Archaeological Paradigms. California University Press.

2. Vilŕ C, Leonard JA, Beja-Pereira A (2006) Genetic documentation of horse and donkey domestication. In: Zeder MA, Decker-Walters D, Bradley D, Smith BD (eds.) Documenting Domestication: New Genetic and Archaeological Paradigms. California University Press.

1. Leonard JA, Vilŕ C, Wayne RK (2006) From wild wolf to domestic dog. In: Ostrander EA, Giger U, Lindblad-Toh K (eds.) The Dog and Its Genome. Cold Spring Harbor Laboratory Press.