Geographical patterns of cattle, sheep and goat diversity Clines, clusters, introgression, and a conservation dilemma Towards a strategy for the conservation of Sheep and goat genetic the genetic diversity of European cattle resources in marginal rural EU project ResGen CT98-118 areas sirs.epfl.ch/projets/econogene/ Utrecht Giessen Piacenza Madrid Tjele J.A. Lenstra G. Erhardt P. Ajmone- S. Dunner L.E. Holm I.J. Nijman O. Jann Marsan J. Cañón Oslo Malle C. Weimann R. Negrini Zaragoza I. Olsaker G. Mommens E. Prinzenberg E. Milanesi P. Zaragoza Jokioinen Berne Hannover Viterbo C. Rodellar J. Kantanen G. Dolf B. Harlizius A. Valentini I. Martín- Reykjavik M.C. Savarese Burriel Roslin Kiel E. Eythorsdottir E. Kalm C. Marchitelli Barcelona J.L. Williams Uppsala C. Looft Milano A. Sanchez P. Wiener B. Danell Munich M. Zanotti J. Piedrafita D. Burton Vilnas I. Medugorac G. Ceriotti Porto Dublin I. Miceikiene Grenoble Campo- A. Beja- D. Bradley Jelgava D.E. MacHugh P. Taberlet basso Pereira Z. Grislis R.A. Freeman G. Luikart F. Pilla N. Ferrand Jouy-en- C. Maudet A. Bruzzone Tartu H. Viinalass Josas D. Iamartino K. Moazami- Goudarzi D. Laloë Geographical patterns of cattle, sheep and goat diversity Clines, clusters, introgression, and a conservation dilemma Reconstruct history of the genetic landscape migration, introgression, breed formation > partitioning of diversity, relationships of breeds, geographic effects Compare cattle, sheep and goat Indicate priorities for conservation 1 Geographical patterns of cattle, sheep and goat diversity Clines, clusters, introgression, and a conservation dilemma Reconstruct history of the genetic landscape migration, introgression, breed formation > partitioning of diversity, relationships of breeds, geographic effects Compare cattle, sheep and goat Indicate priorities for conservation Geographical patterns of cattle, sheep and goat diversity Clines, clusters, introgression, and a conservation dilemma Microsatellites - cattle, core data set : 77 breeds, 25-50 animals/breed, 30 markers - cattle, previous data : 104 breeds, 25-50 animals/breeds, 15-26 markers - sheep : 56 sheep, 50 animals/breed, 31 markers (Giessen) - goat : 46 breeds, 50 animals/breeds, 30 markers (Berne, Madrid) AFLP ( Utrecht, Piacenza ) SNPs in candidate genes mtDNA variation in sheep and goat Y-chromosomal SNPs (SNPs in 7.5 kb Utrecht, Hubrecht Laboratory ) 2 Geographical patterns of cattle, sheep and goat diversity Clines, clusters, introgression, and a conservation dilemma Microsatellites - cattle, core data set : 77 breeds, 25-50 animals/breed, 30 markers - cattle, previous data : 104 breeds, 25-50 animals/breeds, 15-26 markers - sheep : 56 sheep, 50 animals/breed, 31 markers (Giessen) - goat : 46 breeds, 50 animals/breeds, 30 markers (Berne, Madrid) AFLP ( Utrecht, Piacenza ) SNPs in candidate genes mtDNA variation in sheep and goat Y-chromosomal SNPs (7.5 kb, 800 animals, Utrecht, Hubrecht Laboratory ) Geographical patterns of cattle, sheep and goat diversity Clines, clusters, introgression, and a conservation dilemma Microsatellites - cattle, core data set : 77 breeds, 25-50 animals/breed, 30 markers - cattle, previous data : 104 breeds, 25-50 animals/breeds, 15-26 markers - sheep : 56 sheep, 50 animals/breed, 31 markers (Giessen) - goat : 46 breeds, 50 animals/breeds, 30 markers (Berne, Madrid) Analysis - Model based-clustering of multilocus genotypes - Network representation of genetic distances Y-chromosomal SNPs (7.5 kb, 800 animals, Utrecht, Hubrecht Laboratory ) 3 Model-based clustering Structure, J. Pritchard (2000) Originally designed for detection of stratification in genetic association studies Finding subdivision by optimization of Hardy-Weinberg and linkage equilibria via Monte-Carlo procedure Bayesian assignment of individuals to k clusters Application to human genotypes (Rosenberg et al. , 2002, Science 298, 2381-2385 ) praised by the Lancet as ‘ the most relevant biomedical publication in 2002 ’ and already in textbooks Model-based clustering of cattle Swedish Swiss HF Bretonne BP Betizu B Germ. Simmental Swiss Brown Sayaguesa Podolica Red Polled British HF Charolais Pirenaica Simmental Germ. Br. Württemberg Alistano Romagnola Bohemian Red Jutland 1950 Ayrshire Blonde d'Aquitaine Hinterwaelder Germ. Br. Bavaria Rubia Gallega Chianina Polish Red Dutch Belted Highland Limousin German Yellow Germ. Br. Orig Asturiana Valles N'Dama Red Danish German BP-W Hereford Bazadais Evolene Bruna Pirineds Asturiana Montana Somba Angeln Friesian-Holland Dexter Gasconne Eringer Menorquina Tudanca Lagunaire MRY Belgian Blue Aberdeen Angus Aubrac Piemontese Mallorquina Tora de Lidia Borgou Red HF dual Germ. Shorthorn Jersey Salers Grigio Alpina Retinta Casta Navarra Zebu Peul k Red HF dairy Maine-Anjou Guernsey Montbéliard Rendena Morucha Hungarian Grey Groningen WH Normande Betizu A Pezzata Rossa Ital. Cabannina Avilena Istrian 2 Europe Africa 3 North-West SRP SHI ABA AYR JUT DA DEX R ANG HFR H W HER FRH G Y BPW DUB R M RH2, RHD BWB GUE J ER GSH NOR POR GSI GYE BOR BPN MA BRW BRB N HIW MBE GBO HGY CHA SIM SWB LIM ERI RENGRA B EVO RGA AZ SA AS L V IST AS B AUB A MTU DA PIMCAB LI D BET ROM P G CNA IR AS SAY CHI M BP OR AVI I RET POD MEN MAL TDL 4 Model-based clustering of cattle Swedish Swiss HF Bretonne BP Betizu B Germ. Simmental Swiss Brown Sayaguesa Podolica Red Polled British HF Charolais Pirenaica Simmental Germ. Br. Württemberg Alistano Romagnola Bohemian Red Jutland 1950 Ayrshire Blonde d'Aquitaine Hinterwaelder Germ. Br. Bavaria Rubia Gallega Chianina Polish Red Dutch Belted Highland Limousin German Yellow Germ. Br. Orig Asturiana Valles N'Dama Red Danish German BP-W Hereford Bazadais Evolene Bruna Pirineds Asturiana Montana Somba Angeln Friesian-Holland Dexter Gasconne Eringer Menorquina Tudanca Lagunaire MRY Belgian Blue Aberdeen Angus Aubrac Piemontese Mallorquina Tora de Lidia Borgou Red HF dual Germ. Shorthorn Jersey Salers Grigio Alpina Retinta Casta Navarra Zebu Peul k Red HF dairy Maine-Anjou Guernsey Montbéliard Rendena Morucha Hungarian Grey Groningen WH Normande Betizu A Pezzata Rossa Ital. Cabannina Avilena Istrian 2 Europe Africa 3 4 North-West Central Mediterranean SRP SHI ABA AYR JUT DA DEX R ANG HFR H W HER FRH G Y BPW DUB R > 3 main groups of breeds M RH2, RHD BWB GUE JER N GSH - North-West OR BOR POR GSI GYE BPN MA BRW BRB N HIW MBE GBO - Central HGY CHA SIM SWB LIM ERI RENGRA B EVO RGA AZ SA AS L - Mediterranean V IST AS B AUB A MTU DA PIMCAB LI D BET ROM P G CNA IR AS SAY CHI M BP OR AVI I RET POD MEN MAL TDL Model-based clustering of cattle Swedish Swiss HF Bretonne BP Betizu B Germ. Simmental Swiss Brown Sayaguesa Podolica Red Polled British HF Charolais Pirenaica Simmental Germ. Br. Württemberg Alistano Romagnola Bohemian Red Jutland 1950 Ayrshire Blonde d'Aquitaine Hinterwaelder Germ. Br. Bavaria Rubia Gallega Chianina Polish Red Dutch Belted Highland Limousin German Yellow Germ. Br. Orig Asturiana Valles N'Dama Red Danish German BP-W Hereford Bazadais Evolene Bruna Pirineds Asturiana Montana Somba Angeln Friesian-Holland Dexter Gasconne Eringer Menorquina Tudanca Lagunaire MRY Belgian Blue Aberdeen Angus Aubrac Piemontese Mallorquina Tora de Lidia Borgou Red HF dual Germ. Shorthorn Jersey Salers Grigio Alpina Retinta Casta Navarra Zebu Peul k Red HF dairy Maine-Anjou Guernsey Montbéliard Rendena Morucha Hungarian Grey Groningen WH Normande Betizu A Pezzata Rossa Ital. Cabannina Avilena Istrian 2 Europe Africa 3 4 Germanic Central Mediterranean SRP 4 SHI ABA AYR British JUT DA DEX R 3 5 ANG HFR H W HER FRH G Y BPW Baltic Lowland NW French Alpine Alpine Iberian DUBPodolianR M RH2, RHD Red Pied Intermediates Brown West Brown BWB GUE J Alpine ER GSH NOR POR GSI GYE BOR Intermediates BPN MA BRW BRB N HIW MB GBO E Y 8 clusters of breeds CH S HG A IM SWB LIM ERI RENGRA B EVO RGA AZ SA AS L V PRI IST AS B AUB A MTU DA PIMCAB LI D BET ROM 2 intermediate zones C P GA NA IR S SAY CHI M BP OR AVI I RET POD New classification of breeds MEN MAL TDL 5 Model-based clustering of cattle Swedish Swiss HF Bretonne BP Betizu B Germ. Simmental Swiss Brown Sayaguesa Podolica Red Polled British HF Charolais Pirenaica Simmental Germ. Br. Württemberg Alistano Romagnola Bohemian Red Jutland 1950 Ayrshire Blonde d'Aquitaine Hinterwaelder Germ. Br. Bavaria Rubia Gallega Chianina Polish Red Dutch Belted Highland Limousin German Yellow Germ. Br. Orig Asturiana Valles N'Dama Red Danish German BP-W Hereford Bazadais Evolene Bruna Pirineds Asturiana Montana Somba Angeln Friesian-Holland Dexter Gasconne Eringer Menorquina Tudanca Lagunaire MRY Belgian Blue Aberdeen Angus Aubrac Piemontese Mallorquina Tora de Lidia Borgou Red HF dual Germ. Shorthorn Jersey Salers Grigio Alpina Retinta Casta Navarra Zebu Peul k Red HF dairy Maine-Anjou Guernsey Montbéliard Rendena Morucha Hungarian Grey Groningen WH Normande Betizu A Pezzata Rossa Ital. Cabannina Avilena Istrian 2 Europe Africa 3 4 Germanic Central Mediterranean SRP 4 SHI ABA AYR British JUT DA DEX R 3 5 ANG HFR H W HER FRH G Y BPW Baltic Lowland NW French Alpine Alpine Iberian DUBPodolianR M RH2, RHD Red Pied Intermediates Brown West Brown BWB GUE J Alpine ER GSH NOR POR GSI GYE BOR Intermediates BPN MA BRW BRB N HIW MBE GBO HGY CHA SIM SWB LIM ERI RENGRA B EVO RGA AZ SA AS L V PRI IST AS B AUB A MTU DA PIMCAB LI D BET ROM Genetic distances? P GA CNA IR S SAY CHI M BP OR AVI I RET POD MEN MAL TDL Visualization of distance analysis Trees (hierarchical clustering) confounded by reticulation (e.g., relationships of breeds from different clusters)