Spectrum of Neandertal introgression across modern-day humans indicates multiple episodes of human-Neandertal interbreeding

Mapping Intimacies ◽

10.1101/343087 ◽

2018 ◽

Author(s):

Fernando A. Villanea ◽

Joshua G. Schraiber

Keyword(s):

East Asian ◽

Human Migration ◽

Demographic Models ◽

Asian Populations ◽

Asymmetric Pattern ◽

Anatomically Modern Humans ◽

Out Of Africa ◽

Multiple Episodes ◽

Admixture Event

1AbstractNeandertals and anatomically modern humans overlapped geographically for a period of over 30,000 years following human migration out of Africa. During this period, Neandertals and humans interbred, as evidenced by Neandertal portions of the genome carried by non-African individuals today. A key observation is that the proportion of Neandertal ancestry is ∼12-20% higher in East Asian individuals relative to European individuals. Here, we explore various demographic models that could explain this observation. These include distinguishing between a single admixture event and multiple Neandertal contributions to either population, and the hypothesis that reduced Neandertal ancestry in modern Europeans resulted from more recent admixture with a ghost population that lacked a Neandertal ancestry component (the “dilution” hypothesis). In order to summarize the asymmetric pattern of Neandertal allele frequencies, we compile the joint fragment frequency spectrum (FFS) of European and East Asian Neandertal fragments and compare it to both analytical theory and data simulated under various models of admixture. Using maximum likelihood and machine learning, we found that a simple model of a single admixture does not fit the empirical data, and instead favor a model of multiple episodes of gene flow into both European and East Asian populations. These findings indicate more long-term, complex interaction between humans and Neandertals than previously appreciated.

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Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations

Communications Biology ◽

10.1038/s42003-020-01162-2 ◽

2020 ◽

Vol 3 (1) ◽

Cited By ~ 1

Author(s):

Takashi Gakuhari ◽

Shigeki Nakagome ◽

Simon Rasmussen ◽

Morten E. Allentoft ◽

Takehiro Sato ◽

...

Keyword(s):

East Asia ◽

Genome Sequence ◽

Phylogenetic Analyses ◽

Human Migration ◽

Whole Genome Sequence ◽

Migration Patterns ◽

Asian Populations ◽

Anatomically Modern Humans ◽

History Of ◽

Northeast Asian

AbstractAnatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia.

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Polymorphism of genes associated with infectious lung diseases in Northern Asian populations and in patients with community-acquired pneumonia

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj21.51-o ◽

2021 ◽

Vol 1 (1) ◽

Author(s):

S. V. Mikhailova ◽

L. V. Shcherbakova ◽

N. I. Logvinenko ◽

I. I. Logvinenko ◽

M. I. Voevoda

Keyword(s):

Odds Ratio ◽

Lung Diseases ◽

East Asian ◽

Community Acquired Pneumonia ◽

Climatic Conditions ◽

Human Migration ◽

Gene Pools ◽

Northern Asia ◽

Asian Populations ◽

Significant Difference

The innate immune system is the first to respond to invading pathogens. It is responsible for invader recognition, immune-cell recruitment, adaptive-immunity activation, and regulation of inflammation intensity. Previously, two single-nucleotide polymorphisms of innate-immunity genes – rs5743708 (Arg753Gln) of the TLR2 gene and rs8177374 (Ser180Leu) of the TIRAP gene – have been shown to be associated with both pneumonia and tuberculosis in humans, but the data are contradictory among different ethnic groups. It has also been reported that rs10902158 at the PKP3-SIGGIR-TMEM16J genetic locus belongs to a haplotype race-specifically associated with tuberculosis. Meanwhile, a gradient of its frequency is observed in Asia. The aim of this work was to assess the effect of selection for the genotypes of the above-mentioned SNPs on the gene pools of populations living in harsh climatic conditions that contribute to the development of infectious lung diseases. We estimated the prevalence of these variants in white and Asian (Chukchis and Yakuts) population samples from Northern Asia and among patients with community-acquired pneumonia (CAP). Carriage of the rs5743708 A allele was found to predispose to severe CAP (odds ratio 2.77, p = 0.021), whereas the GG/CT genotype of rs5743708/rs8177374 proved to be protective against it (odds ratio 0.478, p = 0.022) in white patients. No association of rs10902158 with CAP (total or severe) was found among whites. Stratification of CAP by causative pathogen may help eliminate the current discrepancies between different studies. No significant difference in rs5743708 or rs8177374 was found between adolescent and long-lived white samples. Carriage of the alleles studied is probably not associated with predisposition to longevity among whites in Siberia. Both white and Asian populations studied were different from Western European and East Asian populations in the variants’ prevalence. The frequency of the rs8177374 T (Ser180Leu) variant was significantly higher in the Chukchi sample (p = 0, χ2 = 63.22) relative to the East Asian populations. This result may confirm the hypothesis about the selection of this allele in the course of human migration into areas with unfavorable climatic conditions.

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Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations

10.1101/2021.06.05.447065 ◽

2021 ◽

Author(s):

Harry Thorpe ◽

Elise Tourrette ◽

Koji Yahara ◽

Filipa Vale ◽

Siqi Liu ◽

...

Keyword(s):

Helicobacter Pylori ◽

African Ancestry ◽

Deleterious Mutations ◽

Bacterial Populations ◽

Synonymous Mutations ◽

Anatomically Modern Humans ◽

Population Sizes ◽

Out Of Africa ◽

H Pylori

All genomes mutate but the consequences of the resulting deleterious mutational load are poorly understood. Helicobacter pylori lives in the human stomach, has a higher mutation rate than most bacteria and has accompanied anatomically modern humans in migrations including the out-of-Africa expansion more than 50,000 years ago. H. pylori from East Asia have accumulated at least 500 more non-synonymous mutations than African strains, which we propose is due to reduced efficacy of selection during the out-of-Africa bottleneck. H. pylori from Europe and the Middle East trace a substantially higher fraction of ancestry from modern African populations than the humans that carry them, which we find is due to at least three separate admixture events. African ancestry is elevated at positions in the genome where non-synonymous mutations are at high frequency in Asia. We propose that this is due to replacement of deleterious mutations that accumulated during the bottleneck, with the high overall African ancestry proportion due to clonal expansion of strains of African origin. We use simulations to show that a Muller's ratchet like effect can lead to long-term segregation of deleterious mutations within bacterial populations after a bottleneck, despite high rates of homologous recombination, but that population fitness can be restored by migration of small numbers of bacteria from non-bottlenecked populations. Our results demonstrate that population bottlenecks can have long-term genomic and demographic consequences, even in species with enormous population sizes.

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

Diabetes ◽

10.2337/db19-1188-p ◽

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

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Are Family Firms More Levered? An Analysis of Family and Non-Family Firms

SAGE Open ◽

10.1177/21582440211022322 ◽

2021 ◽

Vol 11 (2) ◽

pp. 215824402110223

Author(s):

Jahanzaib Haider ◽

Abdul Qayyum ◽

Zalina Zainudin

Keyword(s):

Family Firms ◽

East Asian ◽

Ordinary Least Squares ◽

Maturity Structure ◽

The Family ◽

Asian Economies ◽

The Board Of Directors ◽

East Asian Economies ◽

Combined Data

This study analyzes the leverage policies of the family and non-family firms of eight East Asian Economies (Hong Kong, Indonesia, Japan, Korea, Malaysia, Philippines, Singapore, and Taiwan) by using combined data of 690 family and non-family firms with 3,224 firm–years over the period 2006–2010. This study has used an ordinary least squares (OLS) regression for analyzing the data for the first question, while for the second question, logit regression has been used as the dependent variable (a binary variable). Prior research on family and non-family firms has revealed that family firms issue less (high) debt than non-family firms. Our analysis on a sample of East Asian Economies discloses that family firms have significantly different leverage levels than non-family firms, but their signs are not consistent. On the contrary, when the owner works as CEO/Chairman or member of the Board of Directors, then the family firms issue less debt than the non-family firms. Besides that, this study adds a new question that has not been addressed in the prior studies. The new question has focused on the speed of leverage adjustment. It is found that family firms and non-family firms regarding their debt maturity structure (short-term debt and long-term debt), the speed of leverage adjustments, and their decision to issue securities (i.e., debt vs. equity) are not significantly different. This study concluded that though family firms have a strong influence on each economy, but in South-East Asian countries, leverage policies of the family firms are not much different than that of non-family firms.

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Long-Term Experimental Evolution in Escherichia coli. VI. Environmental Constraints on Adaptation and Divergence

Genetics ◽

10.1093/genetics/146.2.471 ◽

1997 ◽

Vol 146 (2) ◽

pp. 471-479 ◽

Cited By ~ 2

Author(s):

Michael Travisano

Keyword(s):

Escherichia Coli ◽

Genetic Variation ◽

Experimental Evolution ◽

Population Genetic ◽

Environmental Constraints ◽

Asymmetric Pattern ◽

Nutrient Environment ◽

Mean Fitness ◽

Population Genetic Variation

The effect of environment on adaptation and divergence was examined in two sets of populations of Escherichia coli selected for 1000 generations in either maltose- or glucose-limited media. Twelve replicate populations selected in maltose-limited medium improved in fitness in the selected environment, by an average of 22.5%. Statistically significant among-population genetic variation for fitness was observed during the course of the propagation, but this variation was small relative to the fitness improvement. Mean fitness in a novel nutrient environment, glucose-limited medium, improved to the same extent as in the selected environment, with no statistically significant among-population genetic variation. In contrast, 12 replicate populations previously selected for 1000 generations in glucose-limited medium showed no improvement, as a group, in fitness in maltose-limited medium and substantial genetic variation. This asymmetric pattern of correlated responses suggests that small changes in the environment can have profound effects on adaptation and divergence.

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Selective sweep for an enhancer involucrin allele identifies skin barrier adaptation out of Africa

Nature Communications ◽

10.1038/s41467-021-22821-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Mary Elizabeth Mathyer ◽

Erin A. Brettmann ◽

Alina D. Schmidt ◽

Zane A. Goodwin ◽

Inez Y. Oh ◽

...

Keyword(s):

Selective Sweep ◽

Skin Barrier ◽

Human Migration ◽

Epidermal Differentiation ◽

Human Populations ◽

Epidermal Differentiation Complex ◽

Regulatory Module ◽

Reporter Assays ◽

Out Of Africa

AbstractThe genetic modules that contribute to human evolution are poorly understood. Here we investigate positive selection in the Epidermal Differentiation Complex locus for skin barrier adaptation in diverse HapMap human populations (CEU, JPT/CHB, and YRI). Using Composite of Multiple Signals and iSAFE, we identify selective sweeps for LCE1A-SMCP and involucrin (IVL) haplotypes associated with human migration out-of-Africa, reaching near fixation in European populations. CEU-IVL is associated with increased IVL expression and a known epidermis-specific enhancer. CRISPR/Cas9 deletion of the orthologous mouse enhancer in vivo reveals a functional requirement for the enhancer to regulate Ivl expression in cis. Reporter assays confirm increased regulatory and additive enhancer effects of CEU-specific polymorphisms identified at predicted IRF1 and NFIC binding sites in the IVL enhancer (rs4845327) and its promoter (rs1854779). Together, our results identify a selective sweep for a cis regulatory module for CEU-IVL, highlighting human skin barrier evolution for increased IVL expression out-of-Africa.

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Complications of Asian Double Eyelid Surgery: Prevention and Management

Facial Plastic Surgery ◽

10.1055/s-0040-1717147 ◽

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.

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