Major Population Expansion of East Asians Began before Neolithic Time: Evidence of mtDNA Genomes

Zheng, Hou-Feng; Yan, Shi; Qin, Zhaoyu; Wang, Yi; Tan, Jingze; Li, Hui; Li, Jin

doi:10.1371/journal.pone.0025835

Cited by 69 publications

(56 citation statements)

References 48 publications

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“…As expected, from the BSP plot including all European samples in Macrohaplogroup N (Figure 5B), we found that the expansion began ~ 13 kya and showed a continuous trend to nowadays, which is very similar to the result of BSP analysis of East Asian14. The population expansion began ~ 13 kya might correlate to lineages H1, H3, J1c, J1c3, K1, T1, U5a1, V and W.…”

Section: Resultssupporting

confidence: 86%

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MtDNA analysis of global populations support that major population expansions began before Neolithic Time

Zheng

Yan

Qin

et al. 2012

Sci Rep

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Agriculture resulted in extensive population growths and human activities. However, whether major human expansions started after Neolithic Time still remained controversial. With the benefit of 1000 Genome Project, we were able to analyze a total of 910 samples from 11 populations in Africa, Europe and Americas. From these random samples, we identified the expansion lineages and reconstructed the historical demographic variations. In all the three continents, we found that most major lineage expansions (11 out of 15 star lineages in Africa, all autochthonous lineages in Europe and America) coalesced before the first appearance of agriculture. Furthermore, major population expansions were estimated after Last Glacial Maximum but before Neolithic Time, also corresponding to the result of major lineage expansions. Considering results in current and previous study, global mtDNA evidence showed that rising temperature after Last Glacial Maximum offered amiable environments and might be the most important factor for prehistorical human expansions.

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Section: Resultssupporting

confidence: 86%

“…Φ ST distances between populations in current study or previous analysis14213355565758596061 were calculated in Arlequin 3.11 also via coding regions, and plotted in PAST 1.8562 with a non-metric multidimensional scaling method (see Figure S1), showing that populations in each continent were clustered together.…”

Section: Methodsmentioning

confidence: 99%

MtDNA analysis of global populations support that major population expansions began before Neolithic Time

Zheng

Yan

Qin

et al. 2012

Sci Rep

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“…Furthermore, we detected an earlier expansion before NDT (9-11 kya). This scenario of MTBC lineage 2 is consistent with the latest anthropological findings that suggested the population expansion in East Asia started before the agriculture transition (45). Taken together, our data support a southern origin and a parallel evolution between MTBC lineage 2 and modern humans in East Asia.…”

Section: The Southern East Asia Origin and Parallel Evolution Of Mtbcsupporting

confidence: 90%

Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese

Luò

Comas

Luo

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

146

144

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The Beijing family is the most successful genotype of Mycobacterium tuberculosis and responsible for more than a quarter of the global tuberculosis epidemic. As the predominant genotype in East Asia, the Beijing family has been emerging in various areas of the world and is often associated with disease outbreaks and antibiotic resistance. Revealing the origin and historical dissemination of this strain family is important for understanding its current global success. Here we characterized the global diversity of this family based on whole-genome sequences of 358 Beijing strains. We show that the Beijing strains endemic in East Asia are genetically diverse, whereas the globally emerging strains mostly belong to a more homogenous subtype known as “modern” Beijing. Phylogeographic and coalescent analyses indicate that the Beijing family most likely emerged around 30,000 y ago in southern East Asia, and accompanied the early colonization by modern humans in this area. By combining the genomic data and genotyping result of 1,793 strains from across China, we found the “modern” Beijing sublineage experienced massive expansions in northern China during the Neolithic era and subsequently spread to other regions following the migration of Han Chinese. Our results support a parallel evolution of the Beijing family and modern humans in East Asia. The dominance of the “modern” Beijing sublineage in East Asia and its recent global emergence are most likely driven by its hypervirulence, which might reflect adaption to increased human population densities linked to the agricultural transition in northern China.

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“…Population genetic comparison showed that the T allele frequency of rs35356161 in our study cohorts was lower than that in CHB or CHS cohort in the 1,000 Genomes Project. As described, the CHB population was collected in Beijing surrounding areas and the CHS population was recruited in Hunan and Fujian Provinces (37). However, participants of the present study were collected in Yangtze River Delta.…”

Section: Discussionmentioning

confidence: 99%

The Rare Variant rs35356162 in UHRF1BP1 Increases Bladder Cancer Risk in Han Chinese Population

Wang

Chen

et al. 2020

Front. Oncol.

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Background: Seventeen loci have been found to be associated with bladder cancer risk by genome-wide association studies (GWAS) in European population. However, little is known about contribution of low-frequency and rare variants to bladder cancer susceptibility, especially in Eastern population. Methods:We performed a three-stage case-control study including 3,399 bladder cancer patients and 4,647 controls to identify low-frequency and rare variants associated with bladder cancer risk in Han Chinese. We examined exome-array data in 1,019 bladder cancer patients and 1,008 controls in discovery stage. Two replication stages were included to validate variants identified. Bonferroni adjustment was performed to define statistical significance. Logistic regression was conducted to evaluate single marker association with bladder cancer risk. We used SKAT-O method to perform gene level-based analysis. We also conduct additional experiments to explore the underlying mechanism of filtered gene(s). Results:We identified a novel rare coding variant (rs35356162 in UHRF1BP1: G > T, OR = 4.332, P = 3.62E-07 < 7.93E-07, Bonferroni cutoff) that increased bladder cancer risk in Han Chinese. Gene-level analysis showed a significant association of UHRF1BP1 (P = 4.47E-03) with bladder cancer risk. Experiments indicated down-regulation of UHRF1BP1 promoted migration and invasion through epithelial-mesenchymal transition in bladder cancer cell lines. Conclusion:The rare variant of UHRF1BP1, rs35356162, increases bladder cancer risk in Han Chinese and UHRF1BP1 might act as a tumor suppressor in bladder cancer development and progression.

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Major Population Expansion of East Asians Began before Neolithic Time: Evidence of mtDNA Genomes

Cited by 69 publications

References 48 publications

MtDNA analysis of global populations support that major population expansions began before Neolithic Time

MtDNA analysis of global populations support that major population expansions began before Neolithic Time

Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese

The Rare Variant rs35356162 in UHRF1BP1 Increases Bladder Cancer Risk in Han Chinese Population

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