| Domestic animal as an important component of global biodiversities played an important role in the origin and spread of human civilization, which resulted lifestyle of human changed from scattering and hunting to gathering and farming. Sheep and goats as important livestock were the earliest animals to be domesticated, providing people with many resources, such as meat, milk, skin and fiber, which have played very important roles on agricultural, economic, cultural, and even religious in China. Study on the origin and evolution of ancient domestic sheep and goats would not only help to better understand the origin and development of agriculture and animal husbandry, but also help to understand the lifestyle and migratory history of ancient people. Consequently, the origin and evolution of domestic sheep and goat have long been an area of interest in genetics and archaeology.Animal archaeology and molecular biology are two main methods for studying the origin and evolution of domestic sheep and goats. Animal archaeology is based on morphological characters of animal remains to identify and classify species, the number of species and the minimum number of individuals would reflect the lifestyle and economic type of the ancient population in the archaeological site. However, it is difficult to identify the animal species accurately by morphological characters when the animal remains were damaged in many archaeological sites, especially, two closely related species, such as sheep and goats.Molecular biology would provide an accurate and effective method for identifying the ancient remains. In this study, 35 animal remains from Xinzhouyaozi cemetery and the cemetery of Xiaoshuang city-site of south central Inner Mongolia were exampled by molecular identification of sheep and goat remains. The result showed that both mitochondrial DNA (mtDNA) control region sequences and cytochrome b gene fragments were good DNA markers to identify the animal remains of sheep and goats, cytochrome b gene is more suitable as DNA barcoding to distinguish the animal remains whether sheep or goats. 33 authentic ancient DNA sequences were successfully obtained from 35 samples. Among of the 33 samples, molecular identification of the major ancient samples were consistent with that of morphological identification, except 3 samples identified as goats by morphological method, but identified as sheep by molecular identification. Combined with the morphological analysis, the molecular identification of sheep and goat remains would provide more detailed genetic information, which is a powerful tool to identify the animal remains whether sheep or goats. The other 2 samples were not obtained ancient DNA sequences, so the identification species depended on morphological characters. Finally, among of the 35 samples, 24 samples were identified as sheep, and 11 samples were identified as goats. Both morphological and molecular biological methods have their own unique advantages, so it is the best choose to identify the animal remains by two methods, which would not only reduce difficult of species identification, but also increase accurate and reliable of the species identification result.To explore the origin and evolution of domestic sheep and goats, many studies have focused on genetic diversity of modern samples, but so far, a few studies have focused on genetic structure of ancient samples. While the ancient DNA of animal remains can cast off"time trap", and provide the genetic information of ancient domestic animals. The genetic structure of ancient sheep and goats would reveal the phylogenetic relationships of sheep and goats, which would help us to trace the origin and evolution of sheep and goats on molecular level.We analyzed mtDNA D-loop control region, cytochrome b (Cyt b) gene, and CO I gene of 24 ancient sheep, which were excavated from Inner Mongolia of northern China and dated about 2,500 years before present. Three maternal lineages with different frequencies (74% for lineage A, 17% for lineage B, and 9% for lineage C) were present in the ancient sheep population. Our results showed a close genetic relationship between ancient and modern sheep, which suggested that the genetic structure of Chinese sheep has been stabilized since 2,500 years before present. The divergence time of lineage A, B and C indicated that at least three independent sheep domestication events have occurred. Significantly, lineage A was predominant in the ancient sheep, which may contribute to further understanding about the origin and development of Chinese domestic sheep. We analyzed the 289bp fragments of mtDNA control region of 11 ancient goats, which were excavated from two archaeological sites in Inner Mongolia of northern China and dated about 2,500 years before present. 10 haplotypes were successfully obtained from 11 ancient goats. Phylogenetic analysis revealed the multiple maternal origins of Chinese domestic goats, three mtDNA lineages A, B and D were identified in the Chinese ancient individuals, in which lineage A was predominant (70%), lineages B was moderate (20%), and lineage D was present at low frequency (10%).The network analysis showed that lineage B was subdivided into two subgroups B1 and B2. One of the Chinese ancient goats shared the founder haplotype in the center of subgroup B1, and the shared sequences of the founder haplotypes of subgroups B1 and B2 distributed mainly in China. These results implied that lineage B including subgroups B1 and B2 probably originated from China, and further supported the hypothesis that China may be one of the goat domestication centers.In this study, molecular technology was used to analyze the ancient sheep and goat remains from Inner Mongolia during Eastern Zhou period. We developed a molecular identification of sheep and goat remains by mtDNA analysis, the molecular analysis of Chinese ancient sheep and goats would contribute to the phylogenetics of domestic sheep and goats in the global and shed light on tracing the evolution of Chinese ancient domestic animals. This study also reflects the prospect of ancient DNA technology in the area of origin and development of domestic animals, agriculture, and history of human activities.
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