scholarly journals An ancient coronavirus-like epidemic drove adaptation in East Asians from 25,000 to 5,000 years ago

2020 ◽  
Author(s):  
Yassine Souilmi ◽  
M. Elise Lauterbur ◽  
Ray Tobler ◽  
Christian D. Huber ◽  
Angad S. Johar ◽  
...  
Keyword(s):  
Geographical Origin ◽  
East Asian ◽  
Modern Human ◽  
Evolutionary Information ◽  
Human Populations ◽  
Asian Populations ◽  
Human Genomes ◽  
Human Genes ◽  
Human Genomic ◽  
Information Tracing

SummaryThe current SARS-CoV-2 pandemic has emphasized the vulnerability of human populations to novel viral pressures, despite the vast array of epidemiological and biomedical tools now available. Notably, modern human genomes contain evolutionary information tracing back tens of thousands of years, which may help identify the viruses that have impacted our ancestors – pointing to which viruses have future pandemic potential. Here, we apply evolutionary analyses to human genomic datasets to recover selection events involving tens of human genes that interact with coronaviruses, including SARS-CoV-2, that started 25,000 years ago. These adaptive events were limited to ancestral East Asian populations, the geographical origin of several modern coronavirus epidemics. An arms race with an ancient corona-like virus may thus have taken place in ancestral East Asian populations. By learning more about our ancient viral foes, our study highlights the promise of evolutionary information to combat the pandemics of the future.

scholarly journals Genetic studies of human diversity in East Asia

2007 ◽  
Vol 362 (1482) ◽  
pp. 987-996 ◽  
Author(s):  
Feng Zhang ◽  
Bing Su ◽  
Ya-ping Zhang ◽  
Li Jin
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
East Asia ◽  
Pacific Islands ◽  
East Asian ◽  
Human Populations ◽  
Genetic Studies ◽  
The North ◽  
Asian Populations ◽  
Genetic Diversity And Structure

East Asia is one of the most important regions for studying evolution and genetic diversity of human populations. Recognizing the relevance of characterizing the genetic diversity and structure of East Asian populations for understanding their genetic history and designing and interpreting genetic studies of human diseases, in recent years researchers in China have made substantial efforts to collect samples and generate data especially for markers on Y chromosomes and mtDNA. The hallmark of these efforts is the discovery and confirmation of consistent distinction between northern and southern East Asian populations at genetic markers across the genome. With the confirmation of an African origin for East Asian populations and the observation of a dominating impact of the gene flow entering East Asia from the south in early human settlement, interpretation of the north–south division in this context poses the challenge to the field. Other areas of interest that have been studied include the gene flow between East Asia and its neighbouring regions (i.e. Central Asia, the Sub-continent, America and the Pacific Islands), the origin of Sino-Tibetan populations and expansion of the Chinese.

scholarly journals Complex haplotypes of metabolizing GSTM1 gene deletion harbors signatures of a selective sweep in East Asian populations

2018 ◽  
Author(s):  
M. Saitou ◽  
Y. Satta ◽  
O. Gokcumen
Keyword(s):  
Allele Frequency ◽  
Population Differentiation ◽  
East Asian ◽  
Rapid Change ◽  
Autoimmune Disorders ◽  
Human Populations ◽  
Single Nucleotide Variants ◽  
Evolutionary Forces ◽  
Asian Populations ◽  
Extended Homozygosity

ABSTRACTThe deletion of the metabolizing Glutathione S-transferase Mu 1 (GSTM1) gene was previously associated with multiple cancers, metabolic and autoimmune disorders, as well as drug response. It is unusually common, with allele frequency reaching up to 75% in some human populations. Such high allele frequency of a derived allele with apparent impact on an otherwise conserved gene is a rare phenomenon. To investigate the evolutionary history of this locus, we analyzed 310 genomes using population genetics tools. Our analysis revealed a surprising lack of linkage disequilibrium between the deletion and the flanking single nucleotide variants in this locus, indicating gene conversion events. Tests that measure extended homozygosity and rapid change in allele frequency identified signatures of an incomplete soft-sweep in the locus. Using empirical approaches, we identified the Tanuki haplogroup, which carries the GSTM1 deletion and is found in approximately 70% of East Asian chromosomes. This haplogroup has rapidly increased its frequency in East Asian populations, contributing to a high population differentiation among continental human populations. We showed that extended homozygosity and population differentiation for this haplogroup is incompatible with simulated neutral expectations in East Asian populations. In parallel, we revealed that the Tanuki haplogroup is significantly associated with the expression levels of other GSTM genes. Collectively, our results suggest that the Tanuki haplogroup has likely undergone a soft sweep in East Asia with multiple functional consequences. Our study provides the necessary framework for further studies to elucidate the evolutionary reasons that maintain disease-susceptibility variants in the GSTM1 locus.Lay summaryHere, we describe the evolutionary forces that shape the variation in a genomic region, which has been associated with bladder cancer, metabolic and autoimmune disorders and response to different drugs. Our results reveal a new genetic type common in Asian populations that may have important evolutionary and biomedical implications.

scholarly journals Neandertal signatures in modern human mitochondrial genome haplogroups?

2017 ◽  
Author(s):  
Renata C Ferreira ◽  
Camila R Rodrigues ◽  
James R Broach ◽  
Marcelo RS Briones
Keyword(s):  
Mitochondrial Genome ◽  
Homo Sapiens ◽  
Nuclear Genome ◽  
Principal Component ◽  
Modern Human ◽  
Current Data ◽  
Human Populations ◽  
Single Nucleotide Variants ◽  
Human Genomes ◽  
Human Mitochondrial Genome

Genetic contributions of Neandertals to the modern human genome have been evidenced by comparative analyses of present day human genomes and paleogenomes. The current data indicates that Neandertal introgression is higher in Asians and Europeans and lower in African lines of descent. Neandertal signatures in extant human genomes are attributed to intercrosses between Neandertals and ancient Homo sapiens lineages, or archaic Anatomically Modern Humans (AMH) that migrated from Africa into the Middle East and Europe in the last 50,000 years. It has been proposed however that there is no contribution of Neandertal mitochondrial DNA to contemporary human genomes. Here we show that the modern human mitochondrial genome might contain potential 66 Neandertal signatures, or Neandertal single nucleotide variants (N-SNVs) of which 7 are associated with traits such as cycling vomiting syndrome and Alzheimers' and Parkinsons' diseases and 2 N-SNVs associated with intelligence quotient. Principal component analysis and bootscan tests suggest rare recombination events. Also, contrary to what is observed in the nuclear genome, African mitochondrial haplogoups have more potential Neandertal signatures than Asian and European haplogroups. Based on our results we hypothesize that although most intercrosses occurred between Neandertal males and archaic AMH females, crosses between archaic AMH males and Neandertal females were extremely rare and with rare recombination events thus leaving few marks (66 out of 16,569bp) in present day mitochondrial genomes of human populations.

scholarly journals Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 358 ◽  
Author(s):  
Olga Dolgova ◽  
Oscar Lao
Keyword(s):  
Demographic History ◽  
Modern Human ◽  
Human Populations ◽  
Human Genomes ◽  
Fitness Consequences ◽  
Genome Wide ◽  
Anatomically Modern Humans ◽  
Genome Wide Data ◽  
History Of ◽  
Health And Disease

The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that AMH interbred with archaic hominins once they left the African continent. Current non-African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.

scholarly journals Introgression, hominin dispersal and megafaunal survival in Late Pleistocene Island Southeast Asia

2020 ◽  
Author(s):  
João C. Teixeira ◽  
Guy S. Jacobs ◽  
Chris Stringer ◽  
Jonathan Tuke ◽  
Georgi Hudjashov ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Fossil Record ◽  
Modern Human ◽  
Human Populations ◽  
Island Southeast Asia ◽  
Human Genomes ◽  
Anatomically Modern Humans ◽  
Archaic Admixture ◽  
Comprehensive Search ◽  
Archaic Introgression

AbstractThe hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic ‘super-archaic’ species – Homo luzonensis and H. floresiensis – were present around the time anatomically modern humans (AMH) arrived in the region >50,000 years ago. Contemporary human populations carry signals consistent with interbreeding events with Denisovans in ISEA – a species that is thought to be more closely related to AMH than the super-archaic endemic ISEA hominins. To query this disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes. Our results corroborate widespread Denisovan ancestry in ISEA populations but fail to detect any super-archaic admixture signals. By highlighting local megafaunal survival east of the Wallace Line as a potential signature of deep, pre-H. sapiens hominin-faunal interaction, we propose that this understudied region may hold the key to unlocking significant chapters in Denisovan prehistory.

scholarly journals Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

2018 ◽  
Author(s):  
Olga Dolgova ◽  
Oscar Lao
Keyword(s):  
Demographic History ◽  
Modern Human ◽  
Human Populations ◽  
Human Genomes ◽  
Fitness Consequences ◽  
Genome Wide ◽  
Anatomically Modern Humans ◽  
Genome Wide Data ◽  
History Of ◽  
Health And Disease

The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that AMH introgressed with archaic hominins once they left the African continent. Current out of African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.

1188-P: Glycemic Efficacy of Sitagliptin in East Asian Populations: A Pooled Analysis

Diabetes ◽  
2019 ◽  
Vol 68 (Supplement 1) ◽  
pp. 1188-P
Author(s):  
JOAO M. CONCEICAO ◽  
CLAUDIO D. GONZALEZ ◽  
SAMUEL S. ENGEL ◽  
JONGHO AHN ◽  
SHIGERU TOKITA ◽  
...  
Keyword(s):  
East Asian ◽  
Pooled Analysis ◽  
Asian Populations

Complications of Asian Double Eyelid Surgery: Prevention and Management

2020 ◽  
Vol 36 (05) ◽  
pp. 592-601
Author(s):  
Stephanie Ming Young ◽  
Yoon-Duck Kim
Keyword(s):  
East Asian ◽  
Eyelid Surgery ◽  
Patient Dissatisfaction ◽  
Optimal Outcomes ◽  
Asian Populations ◽  
Underlying Causes ◽  
Double Eyelid

AbstractDouble eyelid surgery remains one of the most popular aesthetic surgeries, especially among East Asian populations. Complications related to double eyelid surgery can be divided into various categories: (1) patient dissatisfaction, (2) problems with the eyelid crease, (3) problems with the eyelid height, (4) suture-related complications, and (5) complications related to eyelid surgery in general. As with all eyelid surgeries, it is important to understand and appreciate the normal and abnormal function and anatomy of the Asian eyelid to reduce the risk of complications. It is also important to recognize the various complications and their underlying causes so that the surgeon can confidently revise the surgery to achieve optimal outcomes.

scholarly journals A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome

2021 ◽  
Author(s):  
Seyoung Mun ◽  
Songmi Kim ◽  
Wooseok Lee ◽  
Keunsoo Kang ◽  
Thomas J. Meyer ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Genome Assembly ◽  
De Novo ◽  
Personal Genome ◽  
Human Populations ◽  
Whole Genome ◽  
Structural Variations ◽  
Insert Size ◽  
Human Genomes ◽  
Next Generation Sequencing Ngs

AbstractAdvances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have now been sequenced. Comparisons of these individual genomes have revealed substantial genomic differences between human populations as well as between individuals from closely related ethnic groups. Transposable elements (TEs) are known to be one of the major sources of these variations and act through various mechanisms, including de novo insertion, insertion-mediated deletion, and TE–TE recombination-mediated deletion. In this study, we carried out de novo whole-genome sequencing of one Korean individual (KPGP9) via multiple insert-size libraries. The de novo whole-genome assembly resulted in 31,305 scaffolds with a scaffold N50 size of 13.23 Mb. Furthermore, through computational data analysis and experimental verification, we revealed that 182 TE-associated structural variation (TASV) insertions and 89 TASV deletions contributed 64,232 bp in sequence gain and 82,772 bp in sequence loss, respectively, in the KPGP9 genome relative to the hg19 reference genome. We also verified structural differences associated with TASVs by comparative analysis with TASVs in recent genomes (AK1 and TCGA genomes) and reported their details. Here, we constructed a new Korean de novo whole-genome assembly and provide the first study, to our knowledge, focused on the identification of TASVs in an individual Korean genome. Our findings again highlight the role of TEs as a major driver of structural variations in human individual genomes.

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