Original link: http://vis.pku.edu.cn/blog/y-tree/
As a special one of the 46 human chromosomes, the Y chromosome is only passed down from father to son, so that people can understand the development and migration of human patrilineal groups by studying the genetic evolution process of the Y chromosome. The human Y-chromosome lineage tree is the Y-chromosome evolutionary tree sorted out by Y-chromosome haplotype groups. In this tree, the root node is the genetically identified common ancestor of human paternal lineage, Adam, and each branch node represents the common ancestor of each evolutionary branch under the node.
A study of Chinese surname families based on the Y-chromosome genealogy tree, inferring the genetic markers of the family by analyzing the chromosomes of the tombs as well as the descendants of the family. The genetic markers of the family, the Y-chromosome genealogy tree and other historical information related to the family can confirm each other, and understand the development of the Chinese surname family from multiple perspectives.
Visualization and Interaction Design
Our system combines Y-chromosome genealogy trees and research findings on Chinese surname families to explore the relationships between surname families in China. Taking the surname as the entry, first explore the distribution of the selected surname on the evolutionary tree. Although inheritance of Y staining occurs only between father and son, there are a number of external factors that can cause surname changes. Therefore, even the same surnames do not necessarily have a closer common ancestor. This phenomenon is manifested in the evolutionary tree that a single surname may involve multiple different genetic branches, and there will also be different surname families on a unified genetic branch.
Through the Y-chromosome genealogy tree, significant genetic branches associated with selected surnames can then be discovered. Through interactive means and multi-view linkage, more detailed family relationship information can be displayed.
Considering that the Y chromosome lineage tree has many branches and the overall tree structure is wider, our system uses a circular layout to visualize this evolutionary tree. A surname ring is added on the left side to facilitate the selection of surnames that users are interested in and want to explore. Around the surname ring, we designed a schematic element of population distribution, and mapped the population proportion of surnames to the ring according to the geographical location of each province. By directly observing the primitives, you can roughly understand the population distribution of the current surname. On the evolutionary tree, the branches related to the selected surname are highlighted; at the same time, in the middle of the evolutionary tree, we have embedded a modern map showing the population distribution of the currently selected surname in the country.
Y Chromosome Lineage Tree – The branch of the Yang family on the Y Chromosome phylogenetic tree
In addition, we screened out the nodes related to Chinese surname families in the entire Y chromosome pedigree tree, reconstructed the family tree, and encoded the approximate time when the corresponding family or gene genetic markers were formed in the visualization. Nodes on the family tree support interactive exploration, and subtrees can be expanded or collapsed; the timeline on the left also supports swiping and dragging. The specific information of the selected family node will also be displayed above the family tree synchronously. The family tree and the entire pedigree tree can be linked together, and the user can change the currently displayed root node of the family tree by making selections on the pedigree tree.
Family tree – Zhu Yuanzhang family and related families
Case Study: Zhu Yuanzhang Family
Scholars found that in the population with the gene marker O-MF12415, Zhu surname accounted for as high as 41%, which is the first surname under this genetic branch, indicating that the relationship between this branch and Zhu surname is very significant. As a result, scholars speculate that this genetic marker should have a common ancestor of the surname Zhu. After further research, scholars speculate that the genetic marker was formed about 710 years ago, which corresponds to the era of Zhu Yuanzhang, the emperor of the Ming Dynasty. Therefore, it can be speculated that this gene marker belongs to the Zhu Yuanzhang family. As a Ming Dynasty royal family, the family is one of the families that benefited the most from the rapid population growth of the Ming Dynasty. In addition, after statistics, it is found that the population with genetic marker branches accounts for a large proportion in Shanxi and Henan, which is also in line with the distribution of Zhu Yuanzhang’s descendants in history.
In our system, choose the surname Zhu, you can see that there are multiple branches of the surname Zhu. Following the differentiation path of O-MF12415, a branch belonging to the Zhu Yuanzhang family can be found on the Y chromosome lineage tree. The highlighted part of the pedigree tree is the genetic branch related to the surname Zhu. Among them, the genetic marker O-MF12415 corresponding to the Zhu Yuanzhang family is under the O-N7 genetic marker.
Branches of the Zhu family on the Y chromosome evolutionary tree
By clicking on the O-N7 node on the pedigree tree, you can see the family relationship under this node on the family tree on the left. It can be seen that the Zhu Yuanzhang family is located in the lower right corner. The upstream part of the genetic branch where it is located was slowly differentiated for thousands of years, until a strong population explosion occurred in O-MF12415, the family of Zhu Yuanzhang. This is consistent with the prosperity and development of the imperial family in the Ming Dynasty, and it is also an argument in support of the Zhu Yuanzhang family inferring genetic markers.
The family tree filters out nodes that do not correspond to a clear family on the original family tree, providing users with a more concise and clear view. On this view, the vertical axis represents the time of family formation, and the tree structure is consistent with the evolutionary relationship expressed in the evolutionary tree. By clicking on the Zhu Yuanzhang family, you can read the information related to the family and the genetic markers corresponding to the family that have been analyzed and researched.
Family information related to the Zhu Yuanzhang family on the family tree
At present, the data used by our system mainly comes from the network. We collected relevant data on the Y-chromosome tree structure online and some family information of surnames. In real family history research, other aspects of information and data support need to be added, including historical events, family genealogy, family history, and so on. Multi-faceted information confirms and complements each other, in order to restore the migration routes and interrelationships of surname families in history. Only relying on the genetic relationship data of genes can only get the most ambiguous relationship between the major families. This is a very interesting analysis direction, and we look forward to improving the analysis system in the future based on more comprehensive data.
Course Design “Y Chromosome Haplogroups and Chinese Surname Families”
Panelists: Guo Hang from Beijing Forestry University, Guo Yuhan from Peking University, Li Jiaying from Peking University, Liu Guanqiu from Beijing Normal University, Mei Xiiyao from University of Electronic Science and Technology of China, Shao Hanning from Peking University, and Zhu Yiran from University of the Arts London
Instructors: Yuan Xiaoru of Peking University, Xu Ruige of Syracuse University
The excellent course design of the summer school will be successively included in the “Visualizing China” webpage
Summer School webpage
This article is reprinted from: http://vis.pku.edu.cn/blog/y-tree/
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