scholarly journals The paternal and maternal genetic history of Vietnamese populations

2019 ◽  
Vol 28 (5) ◽  
pp. 636-645 ◽  
Author(s):  
Enrico Macholdt ◽  
Leonardo Arias ◽  
Nguyen Thuy Duong ◽  
Nguyen Dang Ton ◽  
Nguyen Van Phong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linguistic Diversity ◽  
Genetic History ◽  
Majority Group ◽  
History Of ◽  
Low Levels ◽  
Potential Impact ◽  
The Many ◽  
Male Specific ◽  
Complete Mtdna

AbstractVietnam exhibits great cultural and linguistic diversity, yet the genetic history of Vietnamese populations remains poorly understood. Previous studies focused mostly on the majority Kinh group, and thus the genetic diversity of the many other groups has not yet been investigated. Here we analyze complete mtDNA genome sequences and ~2.3 Mb sequences of the male-specific portion of the Y chromosome from the Kinh and 16 minority populations, encompassing all five language families present in Vietnam. We find highly variable levels of diversity within and between groups that do not correlate with either geography or language family. In particular, the Mang and Sila have undergone recent, independent bottlenecks, while the majority group, Kinh, exhibits low levels of differentiation with other groups. The two Austronesian-speaking groups, Giarai and Ede, show a potential impact of matrilocality on their patterns of variation. Overall, we find that isolation, coupled with limited contact involving some groups, has been the major factor influencing the genetic structure of Vietnamese populations, and that there is substantial genetic diversity that is not represented by the Kinh.

scholarly journals The paternal and maternal genetic history of Vietnamese populations

2019 ◽  
Author(s):  
Enrico Macholdt ◽  
Leonardo Arias ◽  
Nguyen Thuy Duong ◽  
Nguyen Dang Ton ◽  
Nguyen Van Phong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linguistic Diversity ◽  
Genetic History ◽  
Majority Group ◽  
History Of ◽  
Low Levels ◽  
Potential Impact ◽  
The Many ◽  
Male Specific ◽  
Complete Mtdna

AbstractVietnam exhibits great cultural and linguistic diversity, yet the genetic history of Vietnamese populations remains poorly understood. Previous studies focused mostly on the majority Kinh group, and thus the genetic diversity of the many other groups has not yet been investigated. Here we analyze complete mtDNA genome sequences and 2.34 mB sequences of the male-specific portion of the Y chromosome from the Kinh and 16 minority populations, encompassing all five language families present in Vietnam. We find highly variable levels of diversity within and between groups that do not correlate with either geography or language family. In particular, the Mang and Sila have undergone recent, independent bottlenecks, while the majority group, Kinh, exhibits low levels of differentiation with other groups. The two Austronesian-speaking groups, Giarai and Ede, show a potential impact of matrilocality on their patterns of variation. Overall, we find that isolation, coupled with some limited contact involving some groups, has been the major factor influencing the genetic structure of Vietnamese populations, and that there is substantial genetic diversity that is not represented by the Kinh.

scholarly journals Clonal propagation history shapes the intra-cultivar genetic diversity in ‘Malbec’ grapevines

2020 ◽  
Author(s):  
Luciano Calderón ◽  
Nuria Mauri ◽  
Claudio Muñoz ◽  
Pablo Carbonell-Bejerano ◽  
Laura Bree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Clonal Propagation ◽  
Variant Calling ◽  
Red Wines ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Diversity Pattern ◽  
History Of ◽  
Potential Impact ◽  
Whole Genome Resequencing

AbstractGrapevine (Vitis vinifera L.) cultivars are clonally propagated to preserve their varietal attributes. However, novel genetic variation still accumulates due to somatic mutations. Aiming to study the potential impact of clonal propagation history on grapevines intra-cultivar genetic diversity, we have focused on ‘Malbec’. This cultivar is appreciated for red wines elaboration, it was originated in Southwestern France and introduced into Argentina during the 1850s. Here, we generated whole-genome resequencing data for four ‘Malbec’ clones with different historical backgrounds. A stringent variant calling procedure was established to identify reliable clonal polymorphisms, additionally corroborated by Sanger sequencing. This analysis retrieved 941 single nucleotide variants (SNVs), occurring among the analyzed clones. Based on a set of validated SNVs, a genotyping experiment was custom-designed to survey ‘Malbec’ genetic diversity. We successfully genotyped 214 samples and identified 14 different clonal genotypes, that clustered into two genetically divergent groups. Group-Ar was driven by clones with a long history of clonal propagation in Argentina, while Group-Fr was driven by clones that have longer remained in Europe. Findings show the ability of such approaches for clonal genotypes identification in grapevines. In particular, we provide evidence on how human actions may have shaped ‘Malbec’ extant genetic diversity pattern.

scholarly journals Extensive Ethnolinguistic Diversity in Vietnam Reflects Multiple Sources of Genetic Diversity

2020 ◽  
Vol 37 (9) ◽  
pp. 2503-2519 ◽  
Author(s):  
Dang Liu ◽  
Nguyen Thuy Duong ◽  
Nguyen Dang Ton ◽  
Nguyen Van Phong ◽  
Brigitte Pakendorf ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Southeast Asia ◽  
Linguistic Diversity ◽  
Published Data ◽  
Multiple Sources ◽  
Austronesian Languages ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
Mainland Southeast Asia

Abstract Vietnam features extensive ethnolinguistic diversity and occupies a key position in Mainland Southeast Asia. Yet, the genetic diversity of Vietnam remains relatively unexplored, especially with genome-wide data, because previous studies have focused mainly on the majority Kinh group. Here, we analyze newly generated genome-wide single-nucleotide polymorphism data for the Kinh and 21 additional ethnic groups in Vietnam, encompassing all five major language families in Mainland Southeast Asia. In addition to analyzing the allele and haplotype sharing within the Vietnamese groups, we incorporate published data from both nearby modern populations and ancient samples for comparison. In contrast to previous studies that suggested a largely indigenous origin for Vietnamese genetic diversity, we find that Vietnamese ethnolinguistic groups harbor multiple sources of genetic diversity that likely reflect different sources for the ancestry associated with each language family. However, linguistic diversity does not completely match genetic diversity: There have been extensive interactions between the Hmong-Mien and Tai-Kadai groups; different Austro-Asiatic groups show different affinities with other ethnolinguistic groups; and we identified a likely case of cultural diffusion in which some Austro-Asiatic groups shifted to Austronesian languages during the past 2,500 years. Overall, our results highlight the importance of genome-wide data from dense sampling of ethnolinguistic groups in providing new insights into the genetic diversity and history of an ethnolinguistically diverse region, such as Vietnam.

scholarly journals The genetic history of the Indian subcontinent

2017 ◽  
Author(s):  
David G. Mahal
Keyword(s):  
Y Chromosome ◽  
Indian Subcontinent ◽  
Population Group ◽  
Ethnic Communities ◽  
Dna Test ◽  
Genetic History ◽  
Human Male ◽  
History Of ◽  
Male Specific ◽  
Random Change

The human male specific Y-chromosome passes from father to son essentially unchanged, but occasionally a random change, known as a mutation, occurs. These mutations, also called markers, serve as beacons and can be mapped. When geneticists identify a mutation in a DNA test, they try to determine when it first occurred and in which part of the world. Thus, the Y-chromosome haplogroup, which is a population group descended from a common ancestor, can be used to trace the paternal lines of men. The poster describes a research project that aims to identify the ancient geographical origins of key ethnic communities of the Indian subcontinent, based on their Y-DNA haplogroups.

scholarly journals The genetic history of the Indian subcontinent

2017 ◽  
Author(s):  
David G. Mahal
Keyword(s):  
Y Chromosome ◽  
Indian Subcontinent ◽  
Population Group ◽  
Ethnic Communities ◽  
Dna Test ◽  
Genetic History ◽  
Human Male ◽  
History Of ◽  
Male Specific ◽  
Random Change

The human male specific Y-chromosome passes from father to son essentially unchanged, but occasionally a random change, known as a mutation, occurs. These mutations, also called markers, serve as beacons and can be mapped. When geneticists identify a mutation in a DNA test, they try to determine when it first occurred and in which part of the world. Thus, the Y-chromosome haplogroup, which is a population group descended from a common ancestor, can be used to trace the paternal lines of men. The poster describes a research project that aims to identify the ancient geographical origins of key ethnic communities of the Indian subcontinent, based on their Y-DNA haplogroups.

Niklas Luhmann on Contingency and Law. The Theory Behind Systems Theory

2016 ◽  
Vol 20 (2) ◽  
Author(s):  
Klaus A. Ziegert
Keyword(s):  
Systems Theory ◽  
Legal Theory ◽  
Sociological Theory ◽  
Original Text ◽  
Niklas Luhmann ◽  
Genetic History ◽  
History Of ◽  
International Audience ◽  
Eye Opening ◽  
The Many

AbstractThe text which is at the centre of the discussion in this paper was one of the many manuscripts on which Niklas Luhmann worked concurrently until 1972, and which he left incomplete. This fragment has now (2013) been published posthumously in Germany (in German) as a book in an edited version. While the reasons as to why Luhmann never completed the text remain unclear, studying it now with hindsight reveals Luhmann’s work on contingency theory as a direct conduit from legal theory to systems theory while circumnavigating sociological theory. With an international audience in mind, this author has tried to introduce this eye-opening historical document in a particularly careful way which pays tribute to Niklas Luhmann’s original, perhaps peculiar, language and terminology. At the same time, this paper attempts to preserve the meaning of the original text by suggestions as to how that text could be understood in an English translation. There is some urgency for making the message of this particular piece of Luhmann’s work widely known because it appears to have an important, perhaps even crucial, place in the genetic history of Luhmann’s ideas and in his generative grammar of systems theory.

scholarly journals Extensive ethnolinguistic diversity in Vietnam reflects multiple sources of genetic diversity

2019 ◽  
Author(s):  
Dang Liu ◽  
Nguyen Thuy Duong ◽  
Nguyen Dang Ton ◽  
Nguyen Van Phong ◽  
Brigitte Pakendorf ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linguistic Diversity ◽  
Published Data ◽  
Multiple Sources ◽  
Austronesian Languages ◽  
Snp Data ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
Dense Sampling

AbstractVietnam features extensive ethnolinguistic diversity and occupies a key position in Mainland Southeast Asia (MSEA). Yet, the genetic diversity of Vietnam remains relatively unexplored, especially with genome-wide data, because previous studies have focused mainly on the majority Kinh group. Here we analyze newly-generated genome-wide SNP data for the Kinh and 21 additional ethnic groups in Vietnam, encompassing all five major language families in MSEA. In addition to analyzing the allele and haplotype sharing within the Vietnamese groups, we incorporate published data from both nearby modern populations and ancient samples for comparison. We find that the Vietnamese ethnolinguistic groups harbor multiple sources of genetic diversity that are associated with heterogeneous ancestry sharing profiles in each language family. However, linguistic diversity does not completely match genetic diversity; there have been extensive interactions between the Hmong-Mien and Tai-Kadai groups, and a likely case of cultural diffusion in which some Austro-Asiatic groups shifted to Austronesian languages. Overall, our results highlight the importance of genome-wide data from dense sampling of ethnolinguistic groups in providing new insights into the genetic diversity and history of an ethnolinguistically-diverse region, such as Vietnam.

scholarly journals Insights from genomic comparisons of genetically monomorphic bacterial pathogens

2012 ◽  
Vol 367 (1590) ◽  
pp. 860-867 ◽  
Author(s):  
Mark Achtman
Keyword(s):  
Genetic Diversity ◽  
Staphylococcus Aureus ◽  
Population Genetics ◽  
Comparative Genomics ◽  
High Throughput ◽  
Antibiotic Resistant ◽  
Bacterial Diseases ◽  
History Of ◽  
Low Levels ◽  
Historical Accounts

Some of the most deadly bacterial diseases, including leprosy, anthrax and plague, are caused by bacterial lineages with extremely low levels of genetic diversity, the so-called ‘genetically monomorphic bacteria’. It has only become possible to analyse the population genetics of such bacteria since the recent advent of high-throughput comparative genomics. The genomes of genetically monomorphic lineages contain very few polymorphic sites, which often reflect unambiguous clonal genealogies. Some genetically monomorphic lineages have evolved in the last decades, e.g. antibiotic-resistant Staphylococcus aureus , whereas others have evolved over several millennia, e.g. the cause of plague, Yersinia pestis . Based on recent results, it is now possible to reconstruct the sources and the history of pandemic waves of plague by a combined analysis of phylogeographic signals in Y. pestis plus polymorphisms found in ancient DNA. Different from historical accounts based exclusively on human disease, Y. pestis evolved in China, or the vicinity, and has spread globally on multiple occasions. These routes of transmission can be reconstructed from the genealogy, most precisely for the most recent pandemic that was spread from Hong Kong in multiple independent waves in 1894.

scholarly journals Occurrence of Male-Specific Bacteriophage in Feral and Domestic Animal Wastes, Human Feces, and Human-Associated Wastewaters

1998 ◽  
Vol 64 (12) ◽  
pp. 5027-5029 ◽  
Author(s):  
Kevin R. Calci ◽  
William Burkhardt ◽  
William D. Watkins ◽  
Scott R. Rippey
Keyword(s):  
Animal Species ◽  
Wastewater Treatment Plants ◽  
Great Majority ◽  
Domestic Animal ◽  
Aquatic Environments ◽  
Animal Wastes ◽  
Low Levels ◽  
Potential Impact ◽  
Male Specific ◽  
Specific Bacteriophage

ABSTRACT Male-specific bacteriophage (MSB) densities were determined in animal and human fecal wastes to assess their potential impact on aquatic environments. Fecal samples (1,031) from cattle, chickens, dairy cows, dogs, ducks, geese, goats, hogs, horses, seagulls, sheep, and humans as well as 64 sewerage samples were examined for MSB. All animal species were found to harbor MSB, although the great majority excreted these viruses at very low levels. The results from this study demonstrate that in areas affected by both human and animal wastes, wastewater treatment plants are the principal contributors of MSB to fresh, estuarine, and marine waters.

scholarly journals Clustering patterns mirror the geographical distribution and genetic history of Lemnos and Lesvos sheep populations

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247787
Author(s):  
Antonios Kominakis ◽  
Eirini Tarsani ◽  
Ariadne L. Hager-Theodorides ◽  
Ioannis Mastranestasis ◽  
Ioannis Hadjigeorgiou
Keyword(s):  
Genetic Diversity ◽  
Snp Array ◽  
Genetic Distances ◽  
Admixture Analysis ◽  
Ecosystem Integrity ◽  
Genetic History ◽  
Aegean Islands ◽  
History Of ◽  
North Aegean ◽  
Historic Data

Elucidating the genetic variation and structure of Lemnos and Lesvos sheep is critical for maintaining local genetic diversity, ecosystem integrity and resilience of local food production of the two North Aegean islands. In the present study, we explored genetic diversity and differentiation as well as population structure of the Lemnos and Lesvos sheep. Furthermore, we sought to identify a small panel of markers with the highest discriminatory power to assign animals across islands. A total number of n = 424 (n = 307, Lemnos and n = 117, Lesvos) ewes, sampled from n = 24 herds dispersed at different geographic regions on the two islands, were genotyped with the 50K SNP array. Mean observed heterozygosity was higher (but not statistically significantly different) in Lesvos than in Lemnos population (0.384 vs. 0.377) while inbreeding levels were higher in Lemnos than Lesvos herds (0.065 vs. 0.031). Results of principal components along with that of admixture analysis and estimated genetic distances revealed genetic clusters corresponding to Lesvos and Lemnos origin and the existence of infrastructure within islands that were associated with geographical isolation and genetic history of the studied populations. In particular, genetic analyses highlighted three geographically isolated herds in Lemnos that are located at mountainous areas of the island and are characterized as representatives of the local sheep by historic data and reports. Admixture analysis also showed a shared genetic background between Lemnos and Lesvos sheep attributable to past gene flow. Little overall genetic differentiation was detected between the two island sheep populations, while 150 discriminatory SNPs could accurately assign animals to their origin. Present results are comparable with those reported in the worldwide sheep breeds, suggesting geography related genetic patterns across and within islands and the existence of the local Lemnos sheep.

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