Tianming Lan:
|
Ancient DNA can make up for the inadequacy of modern DNA in explaining long-standing questions in phylogeny, evolution, taxonomy, and adaptations, because the ancient DNA records the genetic information in the past. Thereby it can provide the most direct evidence to help people know what happened in the past. Ancient DNA related technologies, including experimental protocols and bioinformatics, greatly improved ancient DNA research. Although these technologies have become more and more mature, difficulties in ancient DNA research still remain.
Here I present three improved bioinformatics pipelines for ancient DNA analysis, including an improved genome mapping strategy, separation of endogenous ancient DNA from homologous contaminations, and species identification of ancient mammals. These improved strategies could be valuable in research in palaeontology, archaeology, evolution and even forensic science. Combining these improved bioinformatics methods and previously published well-defined methods, I also conducted several ancient DNA studies. 1) Designed a primer pair of L15123/ H15240 to specifically amplify a 116 bp Cyt b fragment from the three extant elephants and the woolly mammoth with high sensitivity, reproducibility and resolution. This becomes the first validated method that can precisely distinguish the extant elephants from the woolly mammoth, and it will further provide new insights into the investigation of ivory laundering cases. 2) We identified 16 amino acids that were under positive selection with strong evidence in the mitochondrial DNA sequences of the woolly mammoth. Of these 16 amino acids, 11 amino acids were located at the complex I, and other five amino acids were located at another complex. The positively selected amino acid sites and substitutions of these amino acid sites suggested adaptations in the mitochondrial genome of woolly mammoths to the extreme dry and cold environment. 3) By using the historical samples, we evaluated the split time of the Qinling and Sichuan giant panda subspecies; the separation was inferred to between 10 to 12 kya, which is far more than that in a previous report. Further, comparative genomic analysis revealed possible genetic mechanisms of reduced inner organ size with evidence of fast evolving genes, divergently evolved UCNE, and giant panda-specific mutations in genes involved in the Hippo pathway. We also find the loss of regulatory element and specific mutations in the giant panda, which may contribute to the low reproductive capacity of the giant panda. 4) 27 ancient Chinese goat samples from the Late Neolithic period to the Iron Age were collected and sequenced, together with 177 modern goat samples from all over the world and 54 previously published ancient goat genome sequence, we revealed the north-south genetic structure of Chinese goats, and the possibly origin of the Chinese from the eastern Fertile Crescent. FGF5 and EDA2R, two genes that are related to hair follicle development, were detected to be highly divergent between the northern Chinese population and the southern Chinese population. Further analysis identified a deletion with high frequency in the FGF5 gene and standing variation dating to the Neolithic in the EDA2R gene, which may contribute to the local adaptation of these two populations, thereby adding to our understanding of the genetic makeup and local evolution of Chinese goats.