Weekly Literature 202 1-09-28

Hello, everyone. What I shared with you this week was an article published in Nature on September 22nd, 20021year, about the genetic history behind Polynesian settlement time and navigation path.

Periodical: Nature

Impact factor: 2020 _ IF = 49.962 University of Science and Technology of China: Comprehensive Journal 1 Zone; Chinese sub-category: comprehensive journal 1 area; JCR partition: Q 1

Publishers: Stanford University in the United States, Research and Advanced Research Center (UGA) of National Institute of Technology in Mexico, University of Oslo in Norway, etc. 19 unit.

Background: Polynesia is one of the three largest islands in the Pacific Ocean, located in Oceania, which means "multi-island islands". Located in the middle of the Pacific Ocean. It is distributed in a huge triangle in the central and eastern Pacific Ocean. The top corner of the triangle is Hawaii, and the two bottom corners are New Zealand and Easter Island. The population is about 6.5438+0.42 million, mostly Polynesians, and the indigenous Maori in New Zealand are also Polynesians. Polynesia has a total land area of 27,000 square kilometers and a population of about 1, 420, 1. Recently, some common health problems on these islands have aroused the interest of medical scientists and geneticists.

Abstract: Polynesia was established in a series of unusual voyages across one third of the earth's oceans, but the time and order of human settlement in Polynesia islands has always been controversial. At present, the dates obtained by different archaeological investigations are separated by centuries. In this paper, the author reveals the detailed genetic history behind these vast and scattered Pacific islands based on the genome data of 430 contemporary humans in 2 1 Pacific islands and a new method for calculating and analyzing specific ancestors. The author's genome analysis of Polynesian immigrant branches reveals a series of migration processes, which are characterized by the loss of directionality of variation. The whole migration process originated in Samoa, first passed through Rarotonga, then spread to society islands (t not T not Tō taiete mā) in 1 1 century, and reached austral islands (Tuha 'a Pae) and Tuamotu Islands in12nd century. Finally, they arrived at Te Henua'Enana Islands in the north, Raivave Island in the south and Rapa Nui Island in the easternmost Polynesia Islands, and settled in Areba around AD 1200. At the same time, it is found that these islands scattered with prehistoric megalithic remains are genetically related, although they are separated from Wan Li.

In the mainland (and offshore islands) population, the large-scale historical migration, conquest and diffusion of human beings on land formed a genetic substructure, resulting in a two-dimensional genetic variation map reflecting geographical characteristics. The author finds that the population structure of Polynesians is high-dimensional and can't reflect the geographical features at all (Figure 1a). In fact, even in the ancestor-specific PCA of Polynesian individuals, the first two dimensions of the main genome variation (Figure 1A) are just opposite, and each continuous principal component captures the genetic drift of a specific island or island group (Figure 1b, c), indicating that the genetic variation between these islands is mainly determined by their founder effect, rather than diffusion gradient or migration gradient. In order to overcome the obstacle of visualizing the relationship between islands, the author applied t- SNE to dimensionality reduction, and only applied it to the genome fragments of Polynesian ancestors in sample individuals (Figure 1d). It is found that the western Pacific islands with ancestors, such as Taiwan Province Island, Southeast Asia Island (Sumatra Island), Fiji Island, Tonga Island and Samoa Island, are located on the left, and the recently settled eastern islands are located on the right.

Figure 1. Dimension reduction analysis of genetic variation in Pacific islanders. A–C, Islanders' pedigree-specific PCA (non-Asian pedigree, such as European pedigree in post-colonial period) shows that islands (a) are differentiated along different dimensions (b, c) due to the founder effect that genetic drift is independent of each island. Geographical location and settlement order cannot be distinguished. Points represent individuals and colors represent islands. D, t-SNE map of the specific ancestors of all sample islanders, providing advantages to separate each island group. The ancient western Pacific island is on the left, and the easternmost Polynesian island (Rapanui Island) is on the right. An important pattern is now clear; For example, Rarotonga and Palize Group appear in the center of East Polynesia, while other eastern islands take this as the radiation point, which is consistent with the settlement model inferred by the author below. T-SNE only keeps local relations.

Because individuals on each island form coherent and independent clusters in all nonlinear mutation-based predictions (t-SNE, UMAP and SOM), the author defines a meaningful mutation frequency vector on each island by averaging the single nucleotide polymorphism (SNP) dose vectors of all individuals on the island. The directivity index. psi. (fig. 2a) measures the overall increase in the frequency of rare mutations that remain in the whole genome along the direction of range expansion (fig. 2b) due to founder events. Statistics uses a directional arrow to describe the relationship between parents and children. This more robust algorithm based on directionality is used to reconstruct the settlement route of Polynesia (Figure 2a). In order to estimate the date of the inferred settlement event, the author examined DNA fragments inherited from the same ancestor (the same lineage (IBD)) of all paired individuals on different islands. Here, the author only considers the genome fragments of Polynesian ancestors. For each pair of islands A and B, the author collected all Polynesian IBD fragments shared by individuals on island A and island B, and fitted the exponential curve to the obtained fragment length distribution (Figure 2c). Fig. 2a shows the estimated differentiation dates of all island pairs connected by the settlement route.

Figure 2. The sequence and time of settlement in Polynesia. A genetic map of the Polynesian origin of the sample islands (not to scale). The direction, line width and date of each arrow are based on the keys and inter-island statistics described in the text. The location of prehistoric remains of stone buildings is also displayed (red asterisk). B, the range expansion statistics (ψ) show that the frequency of rare mutations retained along the settlement route increases steadily due to each successive founder effect (genetic surfing). It is worth noting that each matrix element is calculated on a different SNP set (rare changes are found in some samples of two islands at the same time), so the matrix does not have to have a similar order in all rows or columns. Rapa Nui Island (Easter Island) is the easternmost island in our data set, and its founder effect is the most complicated. C is an example of the length distribution of all individual pairs, one in Rapa Nui and the other in Mangareva (green), Paliser (blue), Rarotonga (red) and Samoa (black), which is used to fit their respective exponential decay constants (λ).

In a word, this paper reveals the kinship between Polynesians and their settlement time and route through the reconstruction of Polynesians. It is very important to study the genetic reasons behind these events, which will help people understand the common diseases in these islands.

All the pictures in this paper are from the path and time of Polynesian population in the genome network.

There are some improper expressions in the article, which is my problem. Please contact me backstage to modify it, or you can read the original text yourself. Thank you for your understanding and support. If any group or individual thinks that this article infringes your rights, please contact me to delete it.

The link address of the article is/articles/s 41586-021-03902-8.

References:

1. Baidu encyclopedia

2. Inferring the path and time of population growth in Polynesia from genome network. Nature 597,522–526 (2021). https://doi . org/ 10. 1038/s 4 1586-02 1-03902-8