Supplemental Information for: Local adaptations of Mediterranean sheep and goats through an integrative approach Bruno Serranito 1,2# , Marco Cavalazzi 3# , Pablo Vidal 4, Dominique Taurisson-Mouret 5, Elena Ciani 6, Marie Bal 3, Eric Rouvellac 3, Bertrand Servin 7, Carole Moreno-Romieux 7, Gwenola Tosser-Klopp 7, Stephen J. G. Hall 8, Johannes A. Lenstra 9, François Pompanon 10 , Badr Benjelloun 10,11 , Anne Da Silva 1* #: Serranito B. and Cavalazzi M. should be considered joint first author * Correspondence: [email protected] Table of Contents: Supplementary Table 1. Initial list breeds for the constitution of the datasets. Page 1 Supplementary Figure 1. Synthetic schema of the main steps for the Page 2 proposed approach. Supplementary Figure 2. Goat and sheep cradles description as a function of Pages 3-4 environmental variables: Synthetic descriptions of cradles and some characteristic breed phenotypic traits. Supplementary Table 2. Description of the breeds included in the sheep and Pages 5 -16 goat datasets. Number of individuals considered, country of origin, information on the breed history, geographical definition of the cradle, description of the breed, use and status. Supplementary Figure 3. LD analyses for sheep and goats. Page 17 Supplementary Text 1. Genetic structure assessment: admixture analyses, Pages 18 -20 sNMF cross-entropies and Mantel tests. Supplementary Figure 4 . Mapping display for sheep and goats, of the Pages 21 -22 geographical cradles and the GPS coordinates of the sampled points; statistical comparisons for the variables Annual Mean Temperature, Annual Mean Precipitation and Altitude between the distributions obtained by the cradle method and the GPS area method, display of the results via boxplots. Supplementary Figure 5. Display of the selection signatures obtained with Pages 23-25 the goat dataset for the different methods tested, i.e. cradle method, GPS area method and individual GPS method, using the LFMM approach and considering individually the variables: Annual Mean Temperature, Annual Mean Precipitation and Altitude Supplementary Figure 6 . Display of the selection signatures obtained on the Page 26 goat dataset for the cradle method and the GPS area method, using the LFMM approach; cradles and GPS areas were characterized by all the environmental variables available; a PCA followed by an HCPC allowed to group areas according to their similarity in terms of environment. Supplementary Figure 7. Goat “GPS areas” analyzed as a function of Page 27 environmental variables. 1) Mapping display of the “GPS areas” coloured according to the result of the clustering. 2) Hierarchical Clustering on Principal Component (HCPC) analysis. a) Scree plot. b) PCA correlation circle. c) PCA score plot of goat cradles. Colours represent the main clusters obtained by HCPC for K=5. PC 1 and PC 2 represent respectively principal components 1 and 2; numbers in brackets show the variance explained by each PC. 3) Boxplot representation for the variables Annual Mean Temperature, Annual Mean Precipitation and Altitude for the different groups and associated numerical values. Alt.: Altitude in m (meters), T°: Temperature in °C×10, prec.: Precipitation in mm (millimeters), min.: minimal, max.: maximal, s.d.: standard deviation. Supplementary Figure 8. PCAdapt scree plots, a) considering the goat Page 28 dataset, b) considering the sheep dataset. Supplementary Table 3. Selection signatures identified in goats according to Pages 29-41 the LFMM and PCAdapt approach and using the cradle method: detailed literature review. Supplementary Table 4. Selection signatures identified in sheep according Pages 42-53 to the LFMM and PCAdapt approach and using the cradle method: detailed literature review. Supplementary Table 5 . Details concerning the selection signatures Page 54-69 identified in goats and sheep: name and position of the SNPs. Supplementary Table 6 . Display of the selection signatures identified in the Page 70-86 goat dataset. The figures have been modified from outputs obtained via NCBI Genome Data Viewer (https://www.ncbi.nlm.nih.gov/genome/gdv/): ARS1. SNPs under selection (see their name and position in Supplementary Table 5) are symbolized by stars; red stars = SNPs identified by PCAdapt (and plots associated), green stars = SNPs identified by LFMM. Supplementary Table 7 . Display of the selection signatures identified in the Page 87-99 sheep dataset. The figures have been modified from outputs obtained via NCBI Genome Data Viewer (https://www.ncbi.nlm.nih.gov/genome/gdv/): Oar_v3.1. SNPs under selection (see their name and position in Supplementary Table 5) are symbolized by stars; red stars = SNPs identified by PCAdapt (and plots associated), green stars = SNPs identified by LFMM. Supplementary Figure 9. Gorilla enrichment analysis for goats. The colored Page 100 areas correspond to the identified processes. Supplementary Figure 10 . Gorilla enrichment analysis for sheep. The Page 101 colored areas correspond to the identified processes. Supplementary Text 2 . Discussion and classification of identified genes Page 102-115 according to the literature. Goat breed country Sheep breed country Alpine France Mourerous Alpes du Sud France Angora France Mérino s d'Arles France Corse France Lacaune (lait) France Fosses France Blanche du Massif Central France Poitevine France Berrichon du Cher France Provencale France Romane France Pyrenean France Rouge de l'Ouest France Saanen France Mérino s de Rambouillet France Alpine Italy Tarasconnaise France Argentata Italy Rava France Aspromontana Italy Noire du Velay France Bionda dell'Adamello Italy Limousine France Ciociara Grigia Italy Lacaune (viande) France Di Teramo Italy Préalpes du Sud France Garganica Italy Manech tête rousse France Girgentana Italy Corse France Jonica Italy Romanov France Maltese sarda Italy Suffolk France Maltese Italy Vendéen France Nicastrese Italy Charollais France Orobica Italy Causses du Lot France Rossa Mediterranea Italy Ouessant (Bretagne) France Saanen Italy Charmoise France Sarda Italy Roussin de la Hague France Valdostana Italy Île -de -France France Valpassiria Italy Texel France Bermeya Spain Altamurana Italy Mallorquina Spain Comisana Italy Malaguena Spain Leccese Italy Murciano -Granadina Spain Sarda Italy Palmera (Canaria island breed) Spain Appenninica Italy Blanca de Rasquera Spain Sopravissana Italy Gentile Di Puglia Italy Delle Langhe Italy Pinzirita Italy Bergamasca Italy Bagnolese Italy Laticauda Italy Alpagota Italy Altamurana Italy Massese Italy Fabrianese Italy Ripollesa Spain Xisqueta Spain Roja Mallorquina Spain Canaria de pelo Spain Gallega Spain Segureña Spain Castellana Spain Churra Spain Ojalada Spain 1 2 3 4 Goat Breeds (code country Origin/History Cradle of the Description/adaptation Production/ Status (according to and number of breed/transhumant area if use FAO 2007 if not individuals) practiced in the past and/or mentioned) today Bionda dell Adamello The breed seems to be ancient. A The Val Camonica in the province Medium to large size Milk also Not at risk (BIO, n=24) painting from around 1760 by the of Brescia, in Lombardy in long hair ranging from light meat Milanese painter Francesco northern Italy. It takes its name brown to blonde Extensive Londonio shows a goat of the from the massif of the Adamello, two white streaks on the management Bionda dell'Adamello type (Bigi & part of the Adamello-Presanella muzzle Zanon, 2008). subsection of the Rhaetian Alps. Transhumance in Alpine pasture Adaptation to pasture in the (Caballero et al., 2009). mountains Valdostana Publications dating back to 1917 Aosta Valley in northwestern Medium-large-sized animals Milk/meat Critical (also called mention its existence, and suggest Italy, particularly in the lower Short dark blond hair Extensive Chamoisée an older origin. It would have been Ayas and Lys valleys. large horns (selection for the management Valdôtaine) the result of hybridation between traditional "Batailles de (VAL, n=24) wild and domesticated animals Transhumance in Alpine pasture, Chèvres", Talenti et al., 2017) Italy (http://www.agraria.com). (Caballero et al., 2009). Adaptation to pasture in the mountains Orobica Ancient breed: The Milanese The Val Gerola in the province of Medium size Milk Endangered (ORO, n=24) painter (17th century) Lonati Verri Sondrio, in the Bergamo Alps of long horns with flat section in Extensive represents goats of the Orobica northern Italy. males and erect ears management type. A Milanese lithograph from fine long hair, with a colour the early 19th century depicts a Transhumance in Alpine pasture varying from uniform ash-grey goatherd with some of his animals (Caballero et al., 2009). to violet-beige near the Eastern Porta (now Porta Venezia). Official documents Adaptation to pasture in the mention the existence of the breed mountains as early as 1829 (Corti et al., 1997; Corti, 2006). 5 Val Passiria Breed that seems to have Adapted to the valleys bordering Medium size Meat Unkown (also called Passiria/ originated from Switzerland Austria (Val Passiria, Upper Medium to long hair Extensive Camosciata delle (Porter, 2002). Isarco, Sarntal and Val Senales) dark coat (from black to grey) management Alpi/Passeirer Gebirgsziege/Chèvre Transhumance in Alpine pasture Adaptation to pasture in the Chamoisée) (Caballero et al., 2009). mountains/ good adaptation (VSS, n=24) to the most extreme areas Di Teramo Indigenous breed of the province of Province of Teramo, Abruzzi Medium size Milk Critical (DIT, n=24) Teramo, unkown origin