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Mitochondrial DNA (mDNA) passes along the maternal line and can date back thousands of years. Therefore, phylogenetic analysis of mDNA sequences within a species provides a history of maternal lineages that can be represented as a phylogenetic tree.

In 2013, a study analysed the complete and partial mitochondrial genome sequences of 18 fossil canids dated from 1,000 to 36,000 YBP from the Old and New Worlds, and compared these with the complete mitochondrial genome sequences from modern wolves and dogs. Phylogenetic analysis showed that modern dog mDNA haplotypes resolve into four monophyletic clades with strong statistical support, and these have been designated by researchers as clades A-D. Based on the specimens used in this study, clade A included 64% of the dogs sampled and these were sister to a 14,500 YBP wolf sequence from the Kessleroch cave near Thayngen in the canton of Schaffhausen, Switzerland, with a most recent common ancestor estimated to 32,100 YBP. This group of dogs matched three fossil pre-Columbian New World dogs dated between 1,000 and 8,500 YBP, which supported the hypothesis that pre-Columbian dogs in the New World share ancestry with modern dogs and that they likely arrived with the first humans to the New World. Clade B included 22% of the dog sequences and was related to modern wolves from Sweden and the Ukraine, with a common recent ancestor estimated to 9,200 YBP. However, this relationship might represent mitochondrial genome introgression from wolves because dogs were domesticated by this time.
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Wolf distribution
Wolf populations throughout Northern and Central Asia are largely unknown, but are estimated in the hundreds of thousands based on annual harvests. Since the fall of the Soviet Union, continent-wide culling of wolves has ceased, and wolf populations have increased to about 25,000–30,000 animals throughout the former Soviet Union. In China and Mongolia, wolves are only protected in reserves. Mongolian populations have been estimated at 10,000–30,000, while the status of wolves in China is more fragmentary. The north has a declining population of an estimated 400 wolves, while Xinjiang and Tibet hold about 10,000 and 2,000 respectively. In 2008, an authoritative reference stated that the gray wolf could be found across mainland China.

In 2017, a comprehensive study found that the gray wolf was present across all of mainland China, both in the past and today. It exists in southern China, which refutes claims made by some researchers in the Western world that the wolf had never existed in southern China. In 2019, a genomic study on the wolves of China included museum specimens of wolves from southern China that were collected between 1963-1988. The wolves in the study formed 3 clades: north Asian wolves that included those from northern China and eastern Russia, Himalayan wolves from the Tibetan Plateau, and a unique population from southern China. One specimen from Zhejiang province in eastern China shared gene flow with the wolves from southern China, however its genome was 12-14 percent admixed with a canid that may be the dhole or an unknown canid that predates the genetic divergence of the dhole. The wolf population from southern China is believed to be still existing in that region.

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