Genetic relationships between the mtDNA CR sequences (582 bp). (a) ML-evaluated NJ tree for the dog (unlabeled) and wolf (filled square) haplotypes, rooted by coyote (Coy) sequences (branch length reduced by 55%). The six main phylogenetic clades (A–F) of dog haplotypes are indicated. The geographical origin of wolf samples are for the wolf haplotypes (filled squares) from top to bottom: Mongolia (1 individual); China (1); Mongolia (1); Afghanistan (5); Romania (1); China (1); Yugoslavia (4); Canada (1); China (1); China (1); Spain (1); Spain (1); Sweden (1); Saudi Arabia (1); China (4); China (1); China (1) and Mongolia (1); China (2); China (1); Mongolia (2); Yugoslavia (3); Russia (1); Saudi Arabia (1); Mongolia (2). (b) MS networks showing the relationships between the haplotypes in dog clades A, B, and C, and the representation of the haplotypes in different geographical regions. The haplotypes are symbolized by circles (colored or white) and are separated by one substitutional step (ignoring indels); black dots are hypothetical intermediates. The 14 “universally occurring” haplotypes (UTs) are indicated with bold lining. The representation of haplotypes in the geographical regions is shown by the color and size of the circles. A colored circle indicates the presence of the haplotype (blue for haplotypes shared with other regions and orange for haplotypes unique to the region); white denotes nonrepresented haplotypes. The size of the circle is proportional to the frequency of the haplotype in the region. To simplify the figure, the circle size is reduced for the most frequent haplotypes for East Asia (eight most frequent haplotypes reduced by 30%) and West (most frequent haplotype reduced by 50%, next seven most frequent haplotypes by 30%). For definition of geographical regions, see Note to . (The region denoted “Sib, Mon, Kor, Jap” represents Siberia, Mongolia, Korea, and Japan.) (c) The CR haplotypes chosen for analysis of the mtDNA genome, indicated by color. The different colors refer to the subclades (six for clade A, two each for B and C) subsequently identified (see ). Clade A: subclade a1 orange, a2 green, a3 red (upper part of network), a4 red (lower part of network), a5 blue, and a6 yellow. Clade B: subclades b1 orange, b2 green. Clade C: subclades c1 green, c2 orange.

Genetic relationships between the mtDNA genome sequences (16,195 bp). (a) ML tree for dog and wolf sequences, rooted by coyote sequences (branch length reduced by 87%). The sample identity for the dogs is given as the name of the CR haplotype (purple indicates that the CR haplotype is a UT [“universally occurring haplotype”]), and an individual number for samples with identical CR haplotype. The geographical origin of the dog samples is given in . “W” indicates wolf (geographical origin from top to bottom: China, Saudi Arabia, Saudi Arabia, Sweden, Canada, Spain, China, and Russia) and “Coy” coyote. Dog clades A, B, and C (marked by *) were supported by bootstrap values ≥92% and Bayesian values = 100%, and their subclades a1–a6, b1–b2, and c1–c2, by bootstrap values ≥87% and Bayesian values ≥99%. (b) MS networks showing the relationships between the haplotypes in dog clades A, B, and C. The haplotypes are represented by ellipses (UTs indicated with bold lining) and are separated by the number of substitutions indicated next to the connecting lines, no number indicating a single substitution. The sample identity is the same as in (identical samples are given within the same ellipse). Colors indicate geographical origin: Red, Eastern Asia (China, Southeast Asia, Japan, Korea, Mongolia, and Siberia); Blue, Europe; Green, SW Asia; Purple, Africa; and Yellow, India.

Genetic diversity for CR data, among regions across the Old World. (a) Genetic diversity across the Old World. Pie diagrams show the proportion of individuals having clades A (blue), B (red), and C (yellow). Boxes show 1) UT: the proportion of individuals having one of the 14 universally occurring haplotypes, 2) UTd: the proportion having a UT-derived haplotype, that is, a haplotype that is either a UT or differs by a single substitution from a UT, and 3) SC: the representation of the 6 nonuniversal (of the totally 10) subclades of clades A, B, and C. (Eur N/S cont—Europe North/South continent; N/C China—North/Central China [north of Yellow River/between Yellow and Yangtze River]; ASY—Asia South of Yangtze River). (b) Genetic diversity in southeastern Asia. Boxes show UT, UTd, and SC as defined in . Sampled regions are indicated by color. LHS—Liaoning, Hebei, and Shanxi; GG—Guanxi and Guangdong. SE Asia—Vietnam, Thailand, and Cambodia. Tibet includes samples from Qinghai and Nepal.