scholarly journals MITOMIX, an Algorithm to Reconstruct Population Admixture Histories Indicates Ancient European Ancestry of Modern Hungarians

2018 ◽  
Author(s):  
Zoltán Maróti ◽  
Tibor Török ◽  
Endre Neparáczki ◽  
István Raskó ◽  
István Nagy ◽  
...  
Keyword(s):  
Bronze Age ◽  
Population Level ◽  
European Ancestry ◽  
Human Populations ◽  
Population Admixture ◽  
Genetic Composition ◽  
Depth Analysis ◽  
A Minor ◽  
Past Population ◽  
Shed Light

AbstractBy making use of the increasing number of available mitogenomes we propose a novel population genetic distance metric, named Shared Haplogroup Distance (SHD). Unlike FST, SHD is a true mathematical distance that complies with all metric axioms, which enables our new algorithm (MITOMIX) to detect population-level admixture based on SHD minimum optimization. In order to demonstrate the effectiveness of our methodology we analyzed the relation of 62 modern and 25 ancient Eurasian human populations, and compared our results with the most widely used FST calculation. We also sequenced and performed an in-depth analysis of 272 modern Hungarian mtDNA genomes to shed light on the genetic composition of modern Hungarians. MITOMIX analysis showed that in general admixture occurred between neighboring populations, but in some cases it also indicated admixture with migrating populations. SHD and MITOMIX analysis comply with known genetic data and shows that in case of closely related and/or admixing populations, SHD gives more realistic results and provides better resolution than FST. Our results suggest that the majority of modern Hungarian maternal lineages have Late Neolith/Bronze Age European origins (partially shared also with modern Danish, Belgian/Dutch and Basque populations), and a smaller fraction originates from surrounding (Serbian, Croatian, Slovakian, Romanian) populations. However only a minor genetic contribution (<3%) was identified from the IXth Hungarian Conquerors whom are deemed to have brought Hungarians to the Carpathian Basin. Our analysis shows that SHD and MITOMIX can augment previous methods by providing novel insights into past population processes.

scholarly journals Population variation of miRNAs and isomiRs and their impact on human immunity to infection

2020 ◽  
Author(s):  
Maxime Rotival ◽  
Katherine J Siddle ◽  
Martin Silvert ◽  
Julien Pothlichet ◽  
Hélène Quach ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Influenza A ◽  
Population Level ◽  
Population Variation ◽  
European Ancestry ◽  
Population Differences ◽  
Rich Cluster ◽  
Protein Coding ◽  
Expression Variability ◽  
A Minor

ABSTRACTMicroRNAs (miRNAs) are key epigenetic regulators of the immune system, yet their variation and contribution to intra- and inter-population differences in immune responses is poorly characterized. Here, we generated 977 miRNA-sequencing profiles from primary monocytes, from individuals of African and European ancestry, following activation of three TLR pathways (TLR4, TLR1/2 and TLR7/8) or infection with Influenza A virus. We find that immune activation leads to important modifications in the miRNA and isomiR repertoire, particularly in response to viral challenges. These changes are, however, much weaker than those observed for protein-coding genes, suggesting stronger selective constraints on the miRNA response to stimulation. This is supported by the limited genetic control of miRNA expression variability (miR-QTLs) — and the lower occurrence of G×E interactions — in stark contrast with eQTLs that are largely context-dependent. We also detect marked differences in miRNA expression between populations, which are mostly driven by non-genetic factors. Yet, on average, miR-QTLs explain ~60% of population differences in expression of their cognate miRNAs, and, in some cases, evolve adaptively, as shown in Europeans for a miRNA-rich cluster on chromosome 14. Finally, integrating miRNA and mRNA data from the same individuals, we provide evidence that the canonical model of miRNA-driven transcript degradation has a minor impact on miRNA-mRNA correlations, which are, in our setting, mainly driven by co-transcription. Together, our results shed new light onto the factors driving miRNA and isomiR diversity at the population level, and constitute a useful resource for evaluating their role in host differences of immunity to infection.

scholarly journals Analysis of Polygenic Score Usage and Performance in Diverse Human Populations

2018 ◽  
Author(s):  
LE Duncan ◽  
H Shen ◽  
B Gelaye ◽  
KJ Ressler ◽  
MW Feldman ◽  
...  
Keyword(s):  
Large Scale ◽  
Association Studies ◽  
African Ancestry ◽  
Population Level ◽  
European Ancestry ◽  
Human Populations ◽  
Genome Wide Association Studies ◽  
Polygenic Score ◽  
Methodological Choices ◽  
Polygenic Scores

AbstractStudies examining relationships between genotypic and phenotypic variation have historically been carried out on people of European ancestry. Efforts are underway to address this limitation, but until they succeed, the legacy of a Euro-centric bias will continue to hinder research, including the use of polygenic scores, which are individual-level metrics of genetic risk. Ongoing debate surrounds the generalizability of polygenic scores based on genome-wide association studies (GWAS) conducted in European ancestry samples, to non-European ancestry samples. We analyzed the first decade of polygenic scoring studies (2008-2017, inclusive), and found that 67% of studies included exclusively European ancestry participants and another 19% included only East Asian ancestry participants. Only 3.8% of studies were carried out on samples of African, Hispanic, or Indigenous peoples. We find that effect sizes for European ancestry-derived polygenic scores are only 36% as large in African ancestry samples, as in European ancestry samples (t=−10.056, df=22, p=5.5×10−10). Analyzing global populations, we show that relationships between height polygenic scores and height are highly dependent on methodological choices in polygenic score construction, highlighting the need for caution in interpreting population level differences in distributions of polygenic scores, as currently calculated. These findings bolster the rationale for large-scale GWAS in diverse human populations and highlight the need for better handling of linkage disequilibrium and variant frequencies when applying scores to non-European samples.

scholarly journals A comprehensive survey of models for dissecting local ancestry deconvolution in human genome

2018 ◽  
Vol 20 (5) ◽  
pp. 1709-1724 ◽  
Author(s):  
Ephifania Geza ◽  
Jacquiline Mugo ◽  
Nicola J Mulder ◽  
Ambroise Wonkam ◽  
Emile R Chimusa ◽  
...  
Keyword(s):  
Modern Human ◽  
Human Populations ◽  
Population Admixture ◽  
Local Ancestry ◽  
The Past ◽  
Challenges And Opportunities ◽  
Adaptive Processes ◽  
Comprehensive Survey ◽  
Simulation Results ◽  
Shed Light

Abstract Over the past decade, studies of admixed populations have increasingly gained interest in both medical and population genetics. These studies have so far shed light on the patterns of genetic variation throughout modern human evolution and have improved our understanding of the demographics and adaptive processes of human populations. To date, there exist about 20 methods or tools to deconvolve local ancestry. These methods have merits and drawbacks in estimating local ancestry in multiway admixed populations. In this article, we survey existing ancestry deconvolution methods, with special emphasis on multiway admixture, and compare these methods based on simulation results reported by different studies, computational approaches used, including mathematical and statistical models, and biological challenges related to each method. This should orient users on the choice of an appropriate method or tool for given population admixture characteristics and update researchers on current advances, challenges and opportunities behind existing ancestry deconvolution methods.

THE CONTRIBUTION OF THE AMARNA LETTERS TOWARDS A STUDY OF SYRO-PALESTINIAN SOCIAL STRUCTURE (1). TERMINOLOGY FOR GOVERNMENT OFFICIALS

2017 ◽  
Vol 25 (2) ◽  
pp. 788-832
Author(s):  
Lukas M. Muntingh
Keyword(s):  
Social Structure ◽  
Bronze Age ◽  
Social Stratification ◽  
Social Life ◽  
Upper Class ◽  
Government Officials ◽  
The Social ◽  
Amarna Letters ◽  
Free People ◽  
Shed Light

Egyptian domination under the 18th and 19th Dynasties deeply influenced political and social life in Syria and Palestine. The correspondence between Egypt and her vassals in Syria and Palestine in the Amarna age, first half of the fourteenth century B.C., preserved for us in the Amarna letters, written in cuneiform on clay tablets discovered in 1887, offer several terms that can shed light on the social structure during the Late Bronze Age. In the social stratification of Syria and Palestine under Egyptian rule according to the Amarna letters, three classes are discernible:1) government officials and military personnel, 2) free people, and 3) half-free people and slaves. In this study, I shall limit myself to the first, the upper class. This article deals with terminology for government officials.

基层档案揭示的农业合化作运动：以江苏省宝应县为例 1953–1957

Rural China ◽  
2016 ◽  
Vol 13 (2) ◽  
pp. 288-305
Keyword(s):  
Rural China ◽  
Jiangsu Province ◽  
Archival Data ◽  
Ordinary Sense ◽  
Government Officials ◽  
Traditional Methods ◽  
Depth Analysis ◽  
Political Struggles ◽  
Resistance Forces ◽  
Shed Light

Agricultural collectivization was a movement in the early 1950s that profoundly changed the traditional methods of production and lifestyle in rural China. Drawing on original archives from Baoying county of Jiangsu province, this article delves into the actual implementation of, and resistance by different stratum of the peasantry to, this movement. The wealth of archival data and details included in this study shed light on the multifaceted realities of the movement that have been obscured in past studies, in particular, the complexity of the mentality of the peasants and their various forms of resistance, as well as the efforts by government officials to divide and put down the resistance forces and carry out the state’s policies. These data further enable an in-depth analysis of the basic issues about agricultural collectivization. It is shown that this movement was more than a transformation of economic institutions in the ordinary sense; it involved intense political struggles. 上世纪五十年代初开始的农业合作化运动深深改变了中国农民传统的生产生活方式。本文以江苏省宝应县的原始档案为依据，试图从底层的角度探究这一运动的具体实施过程，以及各阶层农民对这一运动的真实反应。本文以大量数据和细节揭示了农业合作化运动的多重面相，特别是以往研究中被忽视的部分，如农民对这一运动的复杂心态和种种抗争，以及当政者如何分化瓦解各种反对力量、步步推进其政策的过程。基于这些事实，本文就农业合作化运动中存在的基本问题进行了讨论，并提出这场运动已经超越了一般经济制度的改革，其实质是一场严峻的政治斗争。 (This article is in Chinese.)

The cretulae and the Linear A accounting system

1960 ◽  
Vol 55 ◽  
pp. 200-210
Author(s):  
Maurice Pope
Keyword(s):  
Bronze Age ◽  
Near East ◽  
Great Majority ◽  
Coherent System ◽  
Accounting System ◽  
Seal Impressions ◽  
Shed Light ◽  
Proper Analysis

Cretulae is the name given in this article to the small clay nodules, stamped with one or more seal impressions, that have been found in quantity at most Bronze Age sites in the Near East. The Minoan examples are generally smaller than those found at other sites, and the great majority of them have a hole through which string once passed. That is to say, they are lumps of clay squeezed round string and then sealed. At most of the sites in Crete where they are known, they have been found in conjunction with inscribed clay tablets and clay disks. At Hagia Triada they are unique in being for the most part countermarked with a sign of the Linear A script. The interrelationships of the countermarks and sealings have not previously been recorded, and it is the primary purpose of this article to publish them. The catalogue will be found in Appendix A. Proper analysis of it should shed light on Minoan methods of administration, and perhaps too on the purpose of the Linear A tablets. That the tablets, or some of them, belong to a coherent system of administration, and are not all mere inventory lists of what happened to be coming into or going out of store at a particular moment, seems guaranteed by the fact, to which I shall revert later, that totals in the same numerical proportion are found at widely distant sites.

scholarly journals Epidemiological trends in digestive cancers compared to trends in alcohol consumption. Facts from Romania: correlation or coincidence?

2018 ◽  
Vol 91 (4) ◽  
pp. 376-386
Author(s):  
Simona Valean ◽  
Romeo Chira ◽  
Dan Dumitrascu
Keyword(s):  
Alcohol Consumption ◽  
Population Level ◽  
Epidemiological Data ◽  
Epidemiological Studies ◽  
Incidence Rates ◽  
Human Populations ◽  
Causative Relationship ◽  
Consumption Data ◽  
Digestive Cancers ◽  
Epidemiological Trends

Cancer has emerged as the leading cause of death in human populations, according to recent estimations. Epidemiological studies emphasized the role of life style and of environmental factors in promoting the risk for digestive cancers. The contribution of alcohol was highly suspected. Even for digestive cancers with dominant infection etiology, like liver cancer and gastric cancer, the contribution of alcohol should be assessed. At population level there is therefore a need to compare trends in epidemiological data of gastrointestinal cancers and data on alcohol consumption, in order to extrapolate any causative relationship. The purpose of this review was to analyze the time trend of digestive cancers in Romania, in terms of mortality rates (between 1955-2012), and incidence rates (between 2008-2012), in males and females, and to analyze the alcohol consumption data, aiming to find out if there is any association.

scholarly journals Quantifying the prevalence of assortative mating in a human population

2019 ◽  
Author(s):  
Klaus Jaffe
Keyword(s):  
Assortative Mating ◽  
Genetic Relatedness ◽  
Random Mating ◽  
Human Populations ◽  
Genetic Composition ◽  
Genetic Studies ◽  
Maintenance Of Sex ◽  
Animal Populations ◽  
The Uk ◽  
First Time

AbstractFor the first time, empirical evidence allowed to construct the frequency distribution of a genetic relatedness index between the parents of about half a million individuals living in the UK. The results suggest that over 30% of the population is the product of parents mating assortatively. The rest is probably the offspring of parents matching the genetic composition of their partners randomly. High degrees of genetic relatedness between parents, i.e. extreme inbreeding, was rare. This result shows that assortative mating is likely to be highly prevalent in human populations. Thus, assuming only random mating among humans, as widely done in ecology and population genetic studies, is not an appropriate approximation to reality. The existence of assortative mating has to be accounted for. The results suggest the conclusion that both, assortative and random mating, are evolutionary stable strategies. This improved insight allows to better understand complex evolutionary phenomena, such as the emergence and maintenance of sex, the speed of adaptation, runaway adaptation, maintenance of cooperation, and many others in human and animal populations.

SOME COMMENTS ABOUT THE INFLUENCE OXUS CIVILIZATION IN THEARABIAN GULF

2021 ◽  
Vol 4 (10) ◽  
pp. 97-103
Author(s):  
Khayitmurod Khurramov ◽  
Keyword(s):  
Material Culture ◽  
Bronze Age ◽  
Arabian Gulf ◽  
Cultural Relations ◽  
Unique Material ◽  
History Of ◽  
The Bronze Age ◽  
Shed Light ◽  
Written Sources ◽  
Marine Shell

It is known that the Oxus civilization in the Bronze Age, with its unique material culture, interacted with a number of cultural countries: the Indian Valley, Iran, Mesopotamia, Elam and other regions. As a result of these relationships, interactions and interactions are formed. Archaeologists turn to archaeological and written sources to shed light on the historiography of this period. This research is devoted to the history of cultural relations between the Oxus civilization and the countries of the Arabian Gulf in the Bronze Age. The article highlights cultural ties based on an analysis of stamp seals and unique artifacts.Key words: Dilmun, Magan, marine shell, Arabian Gulf, Bahrain, Mesopotamia, Harappa, Gonur, Afghanistan

TRAVELLING WITH THE POTTER'S WHEEL IN THE EARLY BRONZE AGE AEGEAN

2020 ◽  
Vol 115 ◽  
pp. 59-104
Author(s):  
Maria Choleva
Keyword(s):  
Material Culture ◽  
Bronze Age ◽  
Social Identities ◽  
Early Bronze Age ◽  
Linear Diffusion ◽  
Craft Knowledge ◽  
Technological Tradition ◽  
Technological Study ◽  
Comparative Examination ◽  
Shed Light

By adopting the chaîne opératoire approach as a dynamic theoretical and methodological framework for studying ancient technologies, this paper investigates the modalities behind the appearance of the potter's wheel in the Aegean during the Early Bronze Age II (c. 2550–2200 bc). Based on the comparative examination of ceramic assemblages from different Aegean sites, an extended technological study has been carried out in order to track the earliest wheel-made pottery and reconstruct the craft behaviours perpetrated by the use of the potter's wheel across the Aegean. The paper presents the results of this multi-site study and aims to (a) trace out the wheel-based technological traditions, (b) explore the contexts of the learning and transmission of the new tool, (c) shed light on the connectivity among Aegean and western Anatolian communities that enabled the transfer of the new craft knowledge, and, finally, (d) bring into view the mechanisms behind its emergence and appropriation. By considering technologies as representing an entire social system of knowing, perceiving and acting on the material world, it will be argued that the spread of the potter's wheel in the Aegean does not reflect a moment of linear diffusion of a technological innovation, adopted thanks to certain techno-functional advantages. Instead, it discloses the resilience of social identities and values embedded through the practical engagement of individuals in the production of their material culture. The potter's wheel, in fact, emerges as a socially and culturally mediated practice, specific to small groups of potters trained within a technological tradition of Anatolian origin, performing their craft in the Aegean socio-cultural milieus. Furthermore, its transfer reveals a multidirectional and dynamic crossing of material cultures that designated a navigable world where traditions, objects and people travelled, mixed and merged in unpredictable ways.

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