Acta Anthropologica Sinica ›› 2022, Vol. 41 ›› Issue (06): 1083-1096.doi: 10.16359/j.1000-3193/AAS.2022.0051

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An application prospect of paleoproteomic analysis in the evolution of East Asian populations

RAO Huiyun1,2()   

  1. 1. Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044
    2. CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044
  • Received:2021-12-01 Revised:2022-03-14 Online:2022-12-15 Published:2022-12-19


The evolutionary history of East Asian populations has involved several multidisciplinary approaches, but this review will bring in a different type of analysis, that of paleoproteomic analysis. Compared with ancient DNA, ancient proteins can preserve in (sub)tropical areas, thus offering significant potential in tracking human evolutionary history. Abundant human fossils have been discovered in East Asia, including Homo erectus, archaic Homo sapiens, early modern humans and late Homo sapiens, which generally form a continuous sequence. However, molecular evidences from the Pleistocene or earlier samples are scarce. In order to promote the application of paleoproteomic analysis in East Asia, this paper reviews its history, potential, challenges and future prospects. Key highlights are listed below. 1) Although ancient protein analysis goes back to 1954, its development was quite slow until the advent of soft-ionization mass spectrometry in 2000. Advances in high-resolution and high-throughput instrumentation now allow researchers to study ancient proteomes; a study that has been well employed in archaeological and evolutionary research. 2) Enamel, dentine and bone are three main substrates for protein preservation in human fossils, with enamel possessing the highest potential for deep-time survival. The earliest enamel proteome sequences were retrieved from a 1.9 MaBP Gigantopithecus molar from South China, with a thermal age of 11.8 MaBP at 10°C. 3) Different taxonomic groups and protein types have diverse amino acid substitution rates. Based on current researches, there are certain mutation positions along the main proteins of bones and teeth from human fossils that could help construct human evolutionary history in broader space and deeper time. 4) Paleoproteomic analysis faces the challenges of low endogenous protein content in fossil samples and a lack of full reference database. 5) Further methodological exploration should focus on three aspects, i.e., optimization of extraction methods, automatic species identification of ZooMS spectra and in-depth interpretation of mass spectrometry data. With an accumulation of more molecular evidence, especially from earlier human fossils which are out of reach for ancient DNA, paleoproteomic analysis could provide more clues in helping to draw a more accurate and clear phylogenetic tree on human evolutionary history in East Asia.

Key words: biological anthropology, phylogeny, palaeoproteomics, mass spectrometry, East Asia

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