Abstract
A comprehensive description of human genomes is essential for understanding human evolution and relationships between modern populations. However, most published literature focuses on local alignment comparison of several genes rather than the complete evolutionary record of individual genomes. Combining with data from the 1,000 Genomes Project, we successfully reconstructed 2,504 individual genomes and propose Divided Natural Vector method to analyze the distribution of nucleotides in the genomes. Comparisons based on autosomes, sex chromosomes and mitochondrial genomes reveal the genetic relationships between populations, and different inheritance pattern leads to different phylogenetic results. Results based on mitochondrial genomes confirm the “out-of-Africa” hypothesis and assert that humans, at least females, most likely originated in eastern Africa. The reconstructed genomes are stored on our server and can be further used for any genome-scale analysis of humans (http://yaulab.math.tsinghua.edu.cn/2022_1000genomesprojectdata/). This project provides the complete genomes of thousands of individuals and lays the groundwork for genome-level analyses of the genetic relationships between populations and the origin of humans.
Highlights
Genetic analysis of hominins has yielded insights about modern populations, superpopulations and their histories
We propose an improved version of NV method named Divided Natural Vector (DNV), which integrates local nucleotide information together with global distribution data
We constructed phylogenetic trees using Unweighted Pair Group Method with Arithmetic mean (UPGMA)/NeighborJoining and DNV/NV with results shown in Supplementary Figures S4, S5
Summary
Genetic analysis of hominins has yielded insights about modern populations, superpopulations and their histories. The relationship between modern and ancient humans remains controversial and of great importance for understanding our phylogenetic position in the tree of life. Besides the regular study about the relationships between genotype and phenotypes such as diseases, this provides an ideal material for phylogenetic analysis about relationships among populations on genome level. The neutral theory, which largely sounds as a null model and framework of pre-saturation evolutionary processes, has met with great difficulty as an explanatory framework for most molecular evolutionary phenomena and as such should not have been so freely used to account for genetic diversity patterns (Yuan et al, 2019). A comprehensive description of human evolutionary patterns is essential for studying the relationships between modern populations and, if combined with the information on ancient hominins, can be used to study the origin of modern humans
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