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Species. Lineage. Supplemental Figure 3. Domestic cat European wild cat Chinese desert cat African wild cat Sand cat Black-footed cat Jungle cat. 64/61/67 0.98/0.98. Felis catus. Felis silvestris. Domestic Cat. Felis bieti. 91/78/89 1.0/1.0. Felis libyca. Felis margarita.

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  1. Species Lineage Supplemental Figure 3 Domestic cat European wild cat Chinese desert cat African wild cat Sand cat Black-footed cat Jungle cat 64/61/67 0.98/0.98 Felis catus Felis silvestris Domestic Cat Felis bieti 91/78/89 1.0/1.0 Felis libyca Felis margarita 74/87/75 1.0/1.0 Felis nigripes Felis chaus 92/60/65 0.95/0.95 Fishing cat Flat-headed cat Asian leopard cat 93/96/98 0.95/0.95 Prionailurus viverrinus Asian Leopard Cat Prionailurus planiceps Prionailurus bengalensis Pallas cat Cheetah Puma Jaguarondi Otocolobus manul Puma Acinonyx jubatus Puma concolor Puma yagouaroundi Rusty-spotted cat** Iberian lynx Siberian lynx Canadian lynx Bobcat 68/80/75 1.0/1.0 94/97/97 1.0/1.0 Prionailurus rubiginosus** Lynx pardinus Lynx 80/89/89 1.0/1.0 Lynx lynx Lynx canadensis 0/60/53 0.50/0.51 55/ * / * 0.53/0.49 Lynx rufus Serval Caracal African golden cat 97/100/100 1.0/1.0 Caracal serval 100/100/100 1.0/1.0 Caracal Caracal caracal Caracal aurata Tigrina Guigna Geoffroy’s cat Pampas cat Ocelot Margay 89/88/86 1.0/1.0 69/62/63 0.96/0.96 Leopardus tigrinus Leopardus guigna 97/99/100 1.0/1.0 Leopardus geoffroyi Ocelot Leopardus colocolo Leopardus pardalis 75/65/70 0.95/0.94 Leopardus weidii 100/99/100 1.0/1.0 Marbled cat Asian golden cat Bay Cat Pardofelis marmorata Pardofelis temminckii Clouded leopard Tiger Leopard Lion Jaguar Snow leopard Neofelis nebulosa * / * / 53 0.91/0.91 Panthera tigris Panthera Panthera pardus Panthera leo 100/99/100 1.0/1.0 Panthera onca Panthera uncia 0.01

  2. Species Lineage 94/ 82 /96 1 / 1 Lynx lynx 99/ 92 /100 1 / 1 Lynx canadensis Lynx pardinus Lynx rufus 86/ 91 /89 1 / 1 Acinonyx jubatus Puma jagouaroundi Puma concolor 68/ 68 /73 0.98 / 0.98 Caracal serval Caracal caracal 91/ 96 / 87 1 / 1 Caracal aurata 96/ 99 /91 1 / 1 Leopardus tigrinus 89/ 100 /57 0.92 / 0.91 Leopardus guigna 90/ 95 /86 1 / 1 Leopardus geoffroyi Leopardus colocolo 99/ 92 / 100 1 / 1 Leopardus pardalis Leopardus weidii Supplemental Figure 4 66 / * / 59 0.99 /0.99 African wild cat European wild cat Domestic cat Chinese desert cat Sand cat Black-footed cat Jungle cat Felis libyca D 67/ 65 /70 0.96 /0.97 Felis silvestris D 67/ 70 /71 1 / 1 Felis catus Domestic Cat 59 / 84 / 59 0.96/ 0.96 Felis bieti Felis margarita 95/ 64 / 99 1 / 1 Felis nigripes Felis chaus Flat-headed cat Asian leopard cat Fishing cat Rusty-spotted cat Pallas cat 70/ 62 /65 0.99 / 0.99 Prionailurus planiceps 64/ 95 / 62 0.95 / 0.95 Asian Leopard Cat */*/* 0.78 / 0.79 Prionailurus bengalensis 64 / * / 71 1 / 1 Prionailurus viverrinus 100 / 68 /99 1 / 1 Prionailurus rubiginosus Otocolobus manul Cheetah Jaguarondi Puma Puma Siberian lynx Canadian lynx Iberian lynx Bobcat 54/ 60 /53 0.90 / 0.91 Lynx Tigrina Guigna Geoffroy’s cat Pampas cat Ocelot Margay Ocelot Serval Caracal African golden cat Caracal Marbled cat Asian golden cat 100/ 91 /100 1 / 1 Pardofelis marmorata Bay Cat Pardofelis temminckii Clouded leopard Leopard Lion Jaguar Snow leopard Tiger Neofelis nebulosa 54// * /* 0.75 / 0.76 100/100 /100 1 / 1 Panthera pardus Panthera leo Panthera Panthera onca 75/ 100 /75 0.91 / 0.92 Panthera uncia 98/ 98 /94 1 /1 0.005 substitutions/site Panthera tigris

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