The Near Eastern origin of cat domestication

Abstract

The world's domestic cats carry patterns of sequence variation in their genome that reflect a history of domestication and breed development. A genetic assessment of 979 domestic cats and their wild progenitors-Felis silvestris silvestris (European wildcat), F. s. lybica (Near Eastern wildcat), F. s. ornata (central Asian wildcat), F. s. cafra (southern African wildcat), and F. s. bieti (Chinese desert cat)-indicated that each wild group represents a distinctive subspecies of Felis silvestris. Further analysis revealed that cats were domesticated in the Near East, probably coincident with agricultural village development in the Fertile Crescent. Domestic cats derive from at least five founders from across this region, whose descendants were transported across the world by human assistance.

Fig. 1

(A) Current range of F. silvestris and areas of sample collection. Colored regions reflect the location of capture of individuals carrying different STR clade genotypes (defined at lower left). mtDNA haplotype frequencies are indicated in pie charts specifying the number of specimens carrying mtDNA haplotypes for each clade. Central Asian denotes Asian cats east of the Caspian Sea. Near Eastern denotes cats in Israel, Saudi Arabia, Bahrain, and the United Arab Emirates. European denotes specimens collected west of the Caspian Sea. Domestic cats (F. s. catus) are distributed worldwide and overwhelmingly carry clade IV mtDNA haplotypes (beige). Inset: Current and historical range of F. silvestris subspecies on the basis of traditional morphology-based taxonomy (2, 12, 13). The Chinese desert cat is referred to throughout as a wildcat subspecies, F. silvestris bieti (9, 12), as supported by data presented here. (B) Phenogram of 851 domestic and wild specimens created on the basis of STRs, Dps genetic distance, and minimum evolution (neighbor-joining) algorithm. Color groups correspond to geographic locales specified in (A). Symbols indicate cytonuclear-discordant individuals that contain a STR composite clade of the indicated cluster but carry mtDNA of an alternative locale (see text); in parentheses are the numbers of cats in each STR clade that carry various mtDNA clade haplotypes.

Fig. 2

(A) Phylogenetic tree of mitochondrial DNA sequence [minimum evolution (neighbor-joining) phylogram of 2604 bp of the ND5 and ND6 genes] of 176 haplotypes discerned from 742 cats sampled across the range of the domestic cat, European wildcat, Near Eastern wildcat, central Asian wildcat, southern African wildcat, Chinese desert cat, and sand cat. Trees created from Bayesian, maximum likelihood, and maximum parsimony methods result in identical topologies for principal clade groupings. Confidence/bootstrap values (from left to right: Bayes/maximum parsimony/maximum likelihood/minimum evolution) are based on 1000 iterations and are adjacent to nodes. The number of single-nucleotide differences is indicated in red below the corresponding branch. Clade designations and numbers of individuals are indicated in parentheses after the corresponding common name and taxonomic trinomial. A through E designate lineages within mtDNA clade IV. Confidence/bootstrap values for these nodes are as follows: A, 1.00/87/71/54; B, 1.00/82/80/80; C, 0.97/63/59/42; D, 1.00/98/99/88; E, 1.00/100/100/82. Purple and brown tree limbs within mtDNA clade IV reflect individuals from two locales that bear cytonuclear-discordant mtDNA versus STR genotypes (see text). Clade IV individuals bearing mtDNA haplotypes are found among domestic cats; in wild potentially admixed populations in Europe, Asia, or Africa (see Fig. 1A); and in Near Eastern wildcats (see text). (B) STRUCTURE-based populations resolved 851 cats into several wildcat groups, three domestic cat groups, and one group (brown) that included both domestic cats and Near Eastern wildcats. The y axis represents Q-value, the percent representation of resolved populations (colors) within each individual (listed on x axis). (C) Phylogenetic relationships among F. silvestris groups as defined by composite STR genotypes based on 36 STR loci. Tree is rooted at sand cat. Bootstrap values at corresponding nodes are based on 1000 iterations with the following measures (from left to right): Dps = 1 − (ps)/Dkf = 1 − (kf)/Dps = −ln(ps)/Dkf = −ln(kf). All methods resulted in identical topologies. Individuals were clustered into representative populations based on STRUCTURE Q-value of 0.80 or greater with the same loci (see text). All known domestic cats cluster into domestic-Asia, domestic-Europe, or Near Eastern wildcats, regardless of provenance, and these groups also cluster together.

Fig. 2

(A) Phylogenetic tree of mitochondrial DNA sequence [minimum evolution (neighbor-joining) phylogram of 2604 bp of the ND5 and ND6 genes] of 176 haplotypes discerned from 742 cats sampled across the range of the domestic cat, European wildcat, Near Eastern wildcat, central Asian wildcat, southern African wildcat, Chinese desert cat, and sand cat. Trees created from Bayesian, maximum likelihood, and maximum parsimony methods result in identical topologies for principal clade groupings. Confidence/bootstrap values (from left to right: Bayes/maximum parsimony/maximum likelihood/minimum evolution) are based on 1000 iterations and are adjacent to nodes. The number of single-nucleotide differences is indicated in red below the corresponding branch. Clade designations and numbers of individuals are indicated in parentheses after the corresponding common name and taxonomic trinomial. A through E designate lineages within mtDNA clade IV. Confidence/bootstrap values for these nodes are as follows: A, 1.00/87/71/54; B, 1.00/82/80/80; C, 0.97/63/59/42; D, 1.00/98/99/88; E, 1.00/100/100/82. Purple and brown tree limbs within mtDNA clade IV reflect individuals from two locales that bear cytonuclear-discordant mtDNA versus STR genotypes (see text). Clade IV individuals bearing mtDNA haplotypes are found among domestic cats; in wild potentially admixed populations in Europe, Asia, or Africa (see Fig. 1A); and in Near Eastern wildcats (see text). (B) STRUCTURE-based populations resolved 851 cats into several wildcat groups, three domestic cat groups, and one group (brown) that included both domestic cats and Near Eastern wildcats. The y axis represents Q-value, the percent representation of resolved populations (colors) within each individual (listed on x axis). (C) Phylogenetic relationships among F. silvestris groups as defined by composite STR genotypes based on 36 STR loci. Tree is rooted at sand cat. Bootstrap values at corresponding nodes are based on 1000 iterations with the following measures (from left to right): Dps = 1 − (ps)/Dkf = 1 − (kf)/Dps = −ln(ps)/Dkf = −ln(kf). All methods resulted in identical topologies. Individuals were clustered into representative populations based on STRUCTURE Q-value of 0.80 or greater with the same loci (see text). All known domestic cats cluster into domestic-Asia, domestic-Europe, or Near Eastern wildcats, regardless of provenance, and these groups also cluster together.