This webpage was completed as an assignment for an undergraduate course at Davidson College.
Thanks to the emerging field of paleogenomics, a team of researchers was able to reconstruct the genomes of 40 ancient individuals found throughout the vast geographic region of Northeast Asia. This technology has brought the past to life and allowed scientists to reconstruct the complex and dynamic history of ancient human populations (Kilnic et al. 2021).
The field of paleogenomics has revolutionized our understanding of ancient human populations and has revealed a rich and complex history of admixture and gene flow events that have substantially enhanced our understanding of how ancient human populations moved and changed overtime. The study of ancient DNA has important implications on our modern understanding of our genome. Through sequencing of ancient human genomes, researchers have gained new insights into the evolutionary forces that have shaped the structure and regulation of modern genomes (Pont et al. 2015). Ancient genomes provide researchers with novel perspectives that provide important tools for predicting future population changes and how factors such as disease, breeding with other populations, and global warming will affect the genetic diversity of future populations.
Sequencing of ancient genomes also has important implications in the field of anthropology, as it provides new insights on evolutionary relationships between distinct populations (Hodgson and Disotell 2010). This reveals a lens into the past that expands our understanding of human history and provides a timeline to examine changes in population dynamics.
In this study, researchers reconstructed the genomes of 40 individuals dating from 16,900 to 550 years old throughout different regions of northeast Asia using next generation sequencing of whole genomes. Northeast Asia is one of the most sparsely populated regions in the world, however it is home to multiple ethnic groups and is the source of the people of the Americas (Kilnic et al. 2021). In this comprehensive genomic study, the researchers focused on how mobility, admixture processes (presence of DNA in an individual from a distantly-related population; occurs as a result of interbreeding), and pandemics have affected northeast Asia throughout the Holocene, our current geological epoch. The purpose of this study was to uncover information regarding the genetic histories of human populations in northeast Asia.
The researchers gathered samples from five general geographic regions within Northeast Asia: Yakutia, Trans-Baikal, Cis-Baikal, Amur Oblast, and Krasnoyarsk Krai. There were 10 individuals from Yakutia, 8 from Trans-Baikal, 20 from Cis-Baikal, and 1 from Amur Oblast and Krasnoyarsk Krai.
Using the genomic data from the Northeast Asian studies in addition to genomic data from modern-day world populations, a principal component analysis (PCA) was conducted. PCAs are a dimensionality-reduction method that helps to simplify large data sets by quantifying correlations. The PCA initially revealed that ancient Northeast Asian individuals demonstrated genetic similarities to present-day populations of Central and South Asians. The researchers also conducted an admixture analysis to understand the ancestral composition of each individual based on shared ancestral genomic sequences. In order to better understand the dynamics of the ancient populations in Northeast Asia, the researchers started by analyzing the oldest individual in the data set and proceeded to investigate population transformations chronologically (Klinic et al. 2021).
All of the individuals in this study’s ages were estimated using radiocarbon dating. The oldest sample in the study was an individual referred to as Khaiyrgas-1, who was estimated to be 16,900 years old . On the PCR analysis, Khaiyrgas-1 represented a lineage that was distinct from the Ancient Northern Siberian (ANS) population that had settled in the region ~38,000 years ago. This lineage contributed directly to the later groups in the region, including the Ancient-Paleo Siberians, who settled in the region ~9,800 years ago and eventually moved into the Americas.
The Yakutia region underwent major genetic shifts in the transition from the paleolithic to the neolithic period between 13,000 and 2,500 years ago. Admixture analyses from this period revealed an increase in Northeast Asian-related genetic ancestry and a decrease in Native American-related genetic ancestry throughout this period, which provided evidence for a west to east gene flow.
While Yakutia saw major population transformations, the Trans-Baikal populations remained relatively stable and for the most part formed a distinct group from ~8,500-3,000 years ago. However, an 8,500 year old individual named Dzyhlinda-1 displayed more genetic drift to Yakutia compared to the other Trans-Baikal individuals, which suggests that the people who settled the Trans-Baikal area are ancestral to the Yakutia populations. In contrast to the stable gene pool of the Trans-Baikal populations, the Cis-Baikal region represented the most genetically diverse group in the PCA analysis.
Next, the researchers estimated the degree of genetic diversity and population sizes utilizing heterozygosity and runs of homozygosity (RoH) measurements respectively. Genetic diversity is generally assessed based on the amount of heterozygosity present in a sample. Higher levels of heterozygosity are indicative of greater genetic variation. Yakutia and Trans-Baikal exhibited the lowest rates of genetic diversity while Cis-Baikal possessed the highest level of genetic diversity. Larger populations have fewer, shorter RoH, while smaller populations have more, longer RoH due to the fact that higher rates of homozygosity decrease fitness (Ceballos et al. 2018). Individuals from the Cis-Baikal region consistently displayed low levels of short RoHs, signifying a larger population size compared to the more geographically isolated regions of Yakutia and Trans-Baikal. However, it is important to note that there is a significant dip in the population size of Cis-Baikal around 4,400 years ago. Interestingly, the researchers identified 9,395 Y. pestis (bubonic plague causing bacterium) sequence-specific reads in an individual of this age, which suggests that pandemics had an impact on the population size and genetic diversity of Northeast Asian populations.
This study exemplifies how paleogenomics can reshape our understanding of human history and gain insights into human population changes overtime. It would be intriguing to look further into the impacts of diseases such as Y. pestis on population dynamics in Northeast Asia. The identification of causative alleles in ancient DNA could provide fundamental information on how diseases have developed overtime and the effects they have had on genetic diversity in populations.
Kade McCulloch is a sophomore pre-med student at Davidson College who is planning on majoring in biology and minoring in health & human values.
References
Ceballos, F., Joshi, P., Clark, D. et al. Runs of homozygosity: windows into population history and trait architecture. Nat Rev Genet 19, 220–234 (2018). https://doi.org/10.1038/nrg.2017.109
Hodgson, J.A., Disotell, T.R. Anthropological Genetics: Inferring the History of Our Species Through the Analysis of DNA. Evo Edu Outreach 3, 387–398 (2010). https://doi.org/10.1007/s12052-010-0262-9
Kilinc, G.M., Kashuba, Natalija., Koptekin, Dilek., et al. Human population dymanics and Yersinia pestis in ancient northeast asia. Science Advances 7, 2 (2021). https://doi.org10.1126/sciadv.abc4587
Pont, C., Wagner, S., Kremer, A. et al. Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA. Genome Biol 20, 29 (2019). https://doi.org/10.1186/s13059-019-1627-1
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