Genetic diversity patterns of human ethnic groups as inferred from the 1000 genomes

Mapping Intimacies ◽

10.1101/2021.12.14.472684 ◽

2021 ◽

Author(s):

Zhiyi Xia ◽

Shi Huang

Keyword(s):

Genetic Diversity ◽

Native Americans ◽

Stop Codon ◽

Genetic Diseases ◽

Neutral Theory ◽

East Asians ◽

Entire Genome ◽

Diversity Patterns ◽

1000 Genomes ◽

Gain Loss

Human genetic diversity remains to be better understood. We here analyzed data from the 1000 Genomes Project and defined group specific fixed alleles (GSFAs) as those that are likely fixed in one ethnic group but non-fixed in at least one other group. The fraction of derived alleles in GSFAs indicates relative distance to apes because such alleles are absent in apes. Our results show that different groups differed in GSFA numbers consistent with known genetic diversity patterns, but also differed in the fraction of derived alleles in GSFAs throughout the entire genome, with East Asians having the largest fraction, followed by South Asians, Europeans, Native Americans, and Africans. Fast evolving sites such as intergenic regions were enriched with derived alleles and showed greater differences in GSFA numbers between East Asians and Africans. Furthermore, GSFAs in East Asians are mostly not fixed in other groups especially Africans, which was particularly more pronounced for fast evolving noncoding variants, while GSFAs in Africans are mostly also fixed in East Asians. Finally, variants that are likely non-neutral such as those leading to stop codon gain/loss and splice donor/acceptor gain/loss showed patterns similar to those of fast-evolving noncoding variants. These results can be accounted for by the maximum genetic diversity theory but not by the neutral theory or its inference that Eurasians suffered bottlenecks, and have implications for better management of group specific genetic diseases.

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The Negative Impact of the Hominin’s DPP4 Gene Inherited from Neanderthals to Pandemic of COVID-19

Open Access Journal of Mycology & Mycological Sciences ◽

10.23880/oajmms-16000135 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Sorush Niknamian

Keyword(s):

Native Americans ◽

Negative Impact ◽

Middle Eastern ◽

Genetic Material ◽

Modern Human ◽

Modern Humans ◽

East Asians ◽

Dipeptidyl Peptidase 4 ◽

The Difference ◽

South Americans

Background: According to preliminary sequences from 2010, 99.7% of the nucleotide sequences of the modern human and Neanderthal genomes are identical, compared to humans sharing around 98.8% of sequences with the chimpanzee. In contrast, the difference between chimpanzees and modern humans is approximately 1,462 mtDNA base pairs. Materials and Methods: Neanderthal-inherited genetic material is found in all non-African populations and was initially reported to comprise 1 to 4 percent of the genome. This fraction was later refined to 1.5 to 2.1 percent. We had gone through many researches of Neanderthals affected gene flow in humans. Results: It is estimated that 20 percent of Neanderthal DNA currently survives in modern humans. Modern human genes involved in making keratin, a protein constituent of skin, hair, and nails, have especially high levels of introgression. For example, approximately 66% of East Asians contain a POUF23L variant introgressed from Neanderthals, while 70% of Europeans possess an introgressed allele of BNC2. Our finding shines a light on an enzyme called dipeptidyl peptidase-4 (DPP4). Scientists already know the protein allows another coronavirus, which causes Middle Eastern respiratory syndrome (MERS), to bind to and enter human cells. The new analysis, of DPP4 gene variants among COVID-19 patients, suggests the enzyme also provides SARS-CoV-2 with a second door into our cells, along with its usual infection route via the angiotensinconverting enzyme 2 (ACE2) receptor on cell surfaces. Conclusion: Most Europeans, Asians, and Native Americans harbor a handful of genes from Neanderthals, up 1.8% to 2.6% of their DNA. Studies of ancient DNA in Neanderthal fossils have shown the hominin’s DPP4 gene subtly differs from the typical human one. Conclusion: The hominin’s DPP4 gene inherited from Neanderthals plays a major role in Immune System Disorders and Lower Immune response in many diseases. This gene plays a major role in affecting humans with COVID-19 and spreading it through the world. All humans contain this gene from 1 to 4 percent. East Asians, Europeans, Middle and South Americans conveys more, hence; native Africans contain less amounts of hominin’s DPP4 gene. Therefore; East Asians, Europeans, Middle and South Americans are prone to severe COVID-19.

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Genetic diversity patterns in Curcuma reflect differences in genome size

Botanical Journal of the Linnean Society ◽

10.1111/j.1095-8339.2011.01122.x ◽

2011 ◽

Vol 165 (4) ◽

pp. 388-401 ◽

Cited By ~ 14

Author(s):

ELIŠKA ZÁVESKÁ ◽

TOMÁŠ FÉR ◽

OTAKAR ŠÍDA ◽

JANA LEONG-ŠKORNIČKOVÁ ◽

MAMYIL SABU ◽

...

Keyword(s):

Genetic Diversity ◽

Genome Size ◽

Diversity Patterns

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Genetic diversity patterns in an endangered desert shrub from north-western China: implications for conservation

Australian Journal of Botany ◽

10.1071/bt18192 ◽

2019 ◽

Vol 67 (7) ◽

pp. 571

Author(s):

Zhihao Su ◽

Liuqiang Wang ◽

Li Zhuo ◽

Xiaolong Jiang ◽

Wenjun Li

Keyword(s):

Genetic Diversity ◽

Tarim Basin ◽

Dna Sequences ◽

Gene Diversity ◽

Isolation By Distance ◽

In Situ Conservation ◽

Western China ◽

Niche Modelling ◽

Diversity Patterns ◽

North Western

Tamarix taklamakanensis is an endangered shrub endemic to the Tarim Basin and adjacent Kumtag Desert in north-western China. Here, we used two chloroplast DNA sequences, namely, psbA-trnH and trnS-trnG, to examine the genetic diversity patterns of this species across its entire covered range. A total of nineteen haplotypes were detected. The total gene diversity within the species is high. Genetic variation mainly occurred among populations, SAMOVA groups, and geographic regions. The test for isolation-by-distance showed a significant correlation between genetic and geographical distances, and the genetic landscape shape analysis showed a significant genetic divergence between the Tarim Basin and Kumtag Desert. T. taklamakanensis likely had a potential geographic range during the Last Glacial Maximum period that was much smaller than the present range predicted by ecological niche modelling. The cold and dry climate during the glacial periods of the Quaternary might be a driver of the genetic isolation and divergence detected within T. taklamakanensis, and climatic oscillations might account for the habitat fragmentation of the species. Within the inner of the basin, populations have a higher level of genetic diversity and harbor most of this genetic diversity, thus a nature reserves should be set up in this area for the in situ conservation. In addition, five genetically distinct groups within T. taklamakanensis should be treated as different management units (MUs) when implementing conservation activities.

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Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors

Molecular Biology and Evolution ◽

10.1093/molbev/msaa210 ◽

2020 ◽

Vol 38 (1) ◽

pp. 244-262

Author(s):

Alexander T Ho ◽

Laurence D Hurst

Keyword(s):

Population Size ◽

Effective Population Size ◽

Stop Codon ◽

Neutral Theory ◽

Error Rates ◽

Species Variation ◽

Effective Population ◽

Weak Selection ◽

Error Mitigation ◽

Good Proxy

Abstract In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also explain variation in phenotypic error rates and in abundance of error mitigation mechanisms? Translational read-through provides a model to investigate both issues as it is common, mostly nonadaptive, and has good proxy for rate (TAA being the least leaky stop codon) and potential error mitigation via “fail-safe” 3′ additional stop codons (ASCs). Prior theory of translational read-through has suggested that when population sizes are high, weak selection for local mitigation can be effective thus predicting a positive correlation between ASC enrichment and Ne. Contra to prediction, we find that ASC enrichment is not correlated with Ne. ASC enrichment, although highly phylogenetically patchy, is, however, more common both in unicellular species and in genes expressed in unicellular modes in multicellular species. By contrast, Ne does positively correlate with TAA enrichment. These results imply that local phenotypic error rates, not local mitigation rates, are consistent with a drift barrier/nearly neutral model.

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