Dataset Information

Full Chromosomal Relationships Between Populations and the Origin of Humans.

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.

SUBMITTER: Dong R

PROVIDER: S-EPMC8847220 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Publications

Full Chromosomal Relationships Between Populations and the Origin of Humans.

Dong Rui R Pei Shaojun S Guan Mengcen M Yau Shek-Chung SC Yin Changchuan C He Rong L RL Yau Stephen S-T SS

Frontiers in genetics 20220202

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 genom ...[more]

PMID: 35186019

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Project description:Background/objectivesThe thermogenic function of brown adipose tissue (BAT) is generally activated in winter and tightly regulated through various metabolic processes. However, the mechanisms mediating these changes have not been elucidated in humans. Here, we investigated the relationships between BAT density (BAT-d) and lipid metabolites in plasma from men and women in the winter and summer.Subjects/methodsIn total, 92 plasma samples were obtained from 23 men and 23 women, aged 21-55 years, on two different occasions (summer and winter). Lipid metabolites were comprehensively quantified using liquid chromatography-time-of-flight-mass spectrometry. BAT-d was evaluated by measuring total hemoglobin concentrations in the supraclavicular region using near-infrared time-resolved spectroscopy. Anthropometric parameters, such as the percentage of whole body fat and visceral fat area (VFA), were evaluated. Factors influencing BAT-d were investigated by univariate and multivariate regression analyses.ResultsA variety of metabolite peaks, such as glycerophospholipids (168 peaks), steroids and derivatives (78 peaks), fatty acyls (62 peaks), and glycerolipids (31 peaks), were detected. Univariate regression analysis, corrected by false discovery rate to yield Q values, revealed significant correlations in BAT-d and phosphatidylethanolamine (PE(46:2), r = 0.62, Q = 4.9 × 10-2) in the summer, androgens (r = 0.75, Q = 7.0 × 10-3) in the winter, and diacylglycerol (DG(36:1), r = -0.68, Q = 4.9 × 10-2) in the summer in men, but not in women. Multivariate regression analysis in the winter revealed a significant correlation between BAT-d and plasma androgens (P = 5.3 × 10-5) in men and between BAT-d and VFA (P = 2.2 × 10-3) in women.ConclusionsCertain lipids in plasma showed unique correlations with BAT-d depending on sex and season. BAT-d showed a specific correlation with plasma androgens in men in the winter.

Project description:Rabies spreads in both Arctic (Vulpes lagopus) and red foxes (Vulpes vulpes) throughout the Canadian Arctic but limited wildlife disease surveillance, due to the extensive landmass of the Canadian north and its small widely scattered human population, undermines our knowledge of disease transmission patterns. This study has explored genetic population structure in both the rabies virus and its fox hosts to better understand factors that impact rabies spread. Phylogenetic analysis of 278 samples of the Arctic lineage of rabies virus recovered over 40 years identified four sub-lineages, A1 to A4. The A1 lineage has been restricted to southern regions of the Canadian province of Ontario. The A2 lineage, which predominates in Siberia, has also spread to northern Alaska while the A4 lineage was recovered from southern Alaska only. The A3 sub-lineage, which was also found in northern Alaska, has been responsible for virtually all cases across northern Canada and Greenland, where it further differentiated into 18 groups which have systematically evolved from a common predecessor since 1975. In areas of Arctic and red fox sympatry, viral groups appear to circulate in both hosts, but both mitochondrial DNA control region sequences and 9-locus microsatellite genotypes revealed contrasting phylogeographic patterns for the two fox species. Among 157 Arctic foxes, 33 mitochondrial control region haplotypes were identified but little genetic structure differentiating localities was detected. Among 162 red foxes, 18 control region haplotypes delineated three groups which discriminated among the Churchill region of Manitoba, northern Quebec and Labrador populations, and the coastal Labrador locality of Cartwright. Microsatellite analyses demonstrated some genetic heterogeneity among sampling localities of Arctic foxes but no obvious pattern, while two or three clusters of red foxes suggested some admixture between the Churchill and Quebec-Labrador regions but uniqueness of the Cartwright group. The limited population structure of Arctic foxes is consistent with the rapid spread of rabies virus subtypes throughout the north, while red fox population substructure suggests that disease spread in this host moves most readily down certain independent corridors such as the northeastern coast of Canada and the central interior. Interestingly the evidence suggests that these red fox populations have limited capacity to maintain the virus over the long term, but they may contribute to viral persistence in areas of red and Arctic fox sympatry.

Dataset Information

Full Chromosomal Relationships Between Populations and the Origin of Humans.

Publications

Full Chromosomal Relationships Between Populations and the Origin of Humans.

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