scholarly journals The genetic legacy of Zoroastrianism in Iran and India: Insights into population structure, gene flow and selection

2017 ◽  
Author(s):  
Saioa López ◽  
Mark G. Thomas ◽  
Lucy van Dorp ◽  
Naser Ansari-Pour ◽  
Sarah Stewart ◽  
...  
Keyword(s):  
Population Structure ◽  
Historical Records ◽  
Genome Wide ◽  
Mitochondrial Data ◽  
The World ◽  
Rich Information ◽  
Second Millennium Bce ◽  
The Rich ◽  
Genomic Regions ◽  
Iranian Populations

AbstractZoroastrianism is one of the oldest extant religions in the world, originating in Persia (present-day Iran) during the second millennium BCE. Historical records indicate that migrants from Persia brought Zoroastrianism to India, but there is debate over the timing of these migrations. Here we present novel genome-wide autosomal, Y-chromosome and mitochondrial data from Iranian and Indian Zoroastrians and neighbouring modern-day Indian and Iranian populations to conduct the first genome-wide genetic analysis in these groups. Using powerful haplotype-based techniques, we show that Zoroastrians in Iran and India show increased genetic homogeneity relative to other sampled groups in their respective countries, consistent with their current practices of endogamy. Despite this, we show that Indian Zoroastrians (Parsis) intermixed with local groups sometime after their arrival in India, dating this mixture to 690-1390 CE and providing strong evidence that the migrating group was largely comprised of Zoroastrian males. By exploiting the rich information in DNA from ancient human remains, we also highlight admixture in the ancestors of Iranian Zoroastrians dated to 570 BCE-746 CE, older than admixture seen in any other sampled Iranian group, consistent with a long-standing isolation of Zoroastrians from outside groups. Finally, we report genomic regions showing signatures of positive selection in present-day Zoroastrians that might correlate to the prevalence of particular diseases amongst these communities.

scholarly journals Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

2019 ◽  
Vol 5 (9) ◽  
pp. eaaw3492 ◽  
Author(s):  
A. Raveane ◽  
S. Aneli ◽  
F. Montinaro ◽  
G. Athanasiadis ◽  
S. Barlera ◽  
...  
Keyword(s):  
Population Structure ◽  
Bronze Age ◽  
The Caucasus ◽  
Italian Peninsula ◽  
Nomadic Pastoralists ◽  
Genome Wide ◽  
A Genome ◽  
The World ◽  
European Populations

European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non–steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.

scholarly journals Genome-wide DNA Variants Identify Genetic Diversity and Population Structure of Leptosphaeria maculans in Western Canada

2020 ◽  
Author(s):  
Qilin Chen ◽  
Gary Peng ◽  
Randy Kutcher ◽  
Fengqun Yu
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genome Wide Association Study ◽  
Leptosphaeria Maculans ◽  
Western Canada ◽  
Effective Management ◽  
Genome Wide ◽  
Population Structure Analysis ◽  
Dna Variants ◽  
Genomic Regions

Abstract Background: Leptosphaeria maculans is a serious concern for canola production in Canada. For effective management, knowledge of the pathogen’s genetic variability and population structure is a prerequisite. Despite some information on race dynamics of the western Canadian L. maculans population in recent years, genetic diversity based on a large number of genome-wide DNA variants has not been investigated.Results: From 1,590 L. maculans isolates collected from 23 field sites in three provinces: Manitoba, Saskatchewan and Alberta, Canada, in the years 2007-2008 and 2012-2014, 150 representative isolates were selected and whole-genome sequenced, and 31,870 polymorphic DNA variants (SNPs and InDels) were used to study L. maculans genetic diversity and population structure. Cluster analysis showed that the genetic diversity levels and isolate groupings varied with the number and genomic regions of the variants involved; isolates collected in 2012-2014 were more genetically diverse than those collected in 2007-2008 when genome-wide variants were considered. The genome wide association study (GWAS) detected variants in egn4_Lema_T86290 (AvrLm4-7), egn4_Lema_T86300 and egn4_Lema_T86310 associated with the year of collection, but no variants was found to be associated with the province or specific location from which the isolates were collected. Population structure analysis indicated the presence of three distinct sub-populations in western Canada. While isolates from Saskatchewan were mainly of one sub-population (sub-pop1), the Alberta isolates comprised two sub-populations (sub-pop1 and sub-pop2), and all the 3 subpopulations were found in Manitoba.Conclusion: The genetic diversity of the western Canadian L. maculans population varied among provinces. It was highly admixed in Manitoba, followed by that in Alberta. The Saskatchewan population had the lowest genetic diversity. Significant genome variation between 2007-2008 and 2012-2014 occurred in the genes egn4_Lema_T86290 (AvrLm4-7), egn4_Lema_T86300 and egn4_Lema_T86310), with AvrLm4-7 becoming much more common in the L. maculans population in the later period.

scholarly journals Evaluating the use of ABBA-BABA statistics to locate introgressed loci

2013 ◽  
Author(s):  
Simon H. Martin ◽  
John W. Davey ◽  
Chris D. Jiggins
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Ancestral Population ◽  
Whole Genome ◽  
Effective Population ◽  
Genome Data ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson?s D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic f̂d, a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. f̂d is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and f̂d outliers tend to cluster in regions of low absolute divergence (dXY), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.

scholarly journals Deciphering the genic basis of environmental adaptations by simultaneous forward and reverse genetics in Saccharomyces cerevisiae

2016 ◽  
Author(s):  
Calum J. Maclean ◽  
Brian P.H. Metzger ◽  
Jian-Rong Yang ◽  
Wei-Chin Ho ◽  
Bryan Moyers ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Population Structure ◽  
Association Mapping ◽  
Cell Biology ◽  
Reverse Genetics ◽  
Dna Barcode ◽  
Genome Wide ◽  
Environmental Adaptations ◽  
Yeast Genes ◽  
Genomic Regions

ABSTRACTThe budding yeast Saccharomyces cerevisiae is the best studied eukaryote in molecular and cell biology, but its utility for understanding the genetic basis of natural phenotypic variation is limited by the inefficiency of association mapping owing to strong and complex population structure. To facilitate association mapping, we analyzed 190 high-quality genomes of diverse strains, including 85 newly sequenced ones, to uncover yeast’s population structure that varies substantially among genomic regions. We identified 181 yeast genes that are absent from the reference genome and demonstrated their expression and role in important functions such as drug resistance. We then simultaneously measured the growth rates of over 4500 lab strains each deficient of a nonessential gene and 81 natural strains across multiple environments using unique DNA barcode present in each strain. We combined the genome-wide reverse genetic information with genome-wide association analysis to determine potential genomic regions of importance to environmental adaptations, and for a subset experimentally validated their role by reciprocal hemizygosity tests. The resources provided permit efficient and reliable association mapping in yeast and significantly enhances its value as a model for understanding the genetic mechanisms of phenotypic polymorphism and evolution.

scholarly journals Zoroastranisme en die ontstaan van apokaliptiese denke

2003 ◽  
Vol 59 (4) ◽  
Author(s):  
Marius Nel
Keyword(s):  
The Other ◽  
Greek Version ◽  
Indus Valley ◽  
The World ◽  
Second Millennium Bce ◽  
The Rich ◽  
First Time ◽  
Good And Evil

Zoroastrianism and the origin of apocalyptic thinkingWhere and how did apocalyptic thought originate? Ancient cultures looked at the world as a changeless essence. A battle between good and evil, order and chaos is distinctive of the world. But the victory of good and order is guaranteed. At the turn of the second millennium BCE the proto-Indo-Iranians trekked from what today are the Steppes of Russia, through Caucasia to different destinations. The Vedic Indians established themselves in the rich Indus valley, while the other group settled in the east of what is the Iran of today. The Vedic Indians preserved the ancient doctrine of a changeless universe, while an Iranian prophet by the name of Zarathustra, often better known by the Greek version thereof, Zoroaster, started teaching that this world would come to an end. Zoroaster subscribed to the doctrine of a battle between good and evil but, for the first time in history formulated the belief that a final victory of good over evil would lead to a new earth and a new heaven.

scholarly journals Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

2018 ◽  
Author(s):  
Alessandro Raveane ◽  
Serena Aneli ◽  
Francesco Montinaro ◽  
Georgios Athanasiadis ◽  
Simona Barlera ◽  
...  
Keyword(s):  
Population Structure ◽  
Bronze Age ◽  
The Caucasus ◽  
Italian Peninsula ◽  
Low Genetic Diversity ◽  
Nomadic Pastoralists ◽  
Genome Wide ◽  
A Genome ◽  
The World

European populations display low genetic diversity as the result of long term blending of the small number of ancient founding ancestries. However it is still unclear how the combination of ancient ancestries related to early European foragers, Neolithic farmers and Bronze Age nomadic pastoralists can fully explain genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the overall continental diversity, but to date have been systematically understudied. Here we characterised the ancestry profiles of modern-day Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe and the rest of the world. Italian genomes captured several ancient signatures, including a non-steppe related substantial ancestry contribution ultimately from the Caucasus. Differences in ancestry composition as the result of migration and admixture generated in Italy the largest degree of population structure detected so far in the continent and shaped the amount of Neanderthal DNA present in modern-day populations.

ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America

2019 ◽  
Vol 28 (10) ◽  
pp. 2594-2609 ◽  
Author(s):  
Philip Lavretsky ◽  
Jeffrey M. DaCosta ◽  
Michael D. Sorenson ◽  
Kevin G. McCracken ◽  
Jeffrey L. Peters
Keyword(s):  
Population Structure ◽  
North America ◽  
Genome Wide ◽  
Close Relatives ◽  
Genomic Regions ◽  
Wide Population

scholarly journals Population demographic history and population structure for Pakistani Nili-Ravi breeding bulls based on SNP genotyping to identify genomic regions associated with male effects for milk yield and body weight

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242500
Author(s):  
Saher Islam ◽  
Umesh K. Reddy ◽  
Purushothaman Natarajan ◽  
Venkata Lakshmi Abburi ◽  
Amna Arshad Bajwa ◽  
...  
Keyword(s):  
Body Weight ◽  
Population Structure ◽  
Association Study ◽  
Milk Yield ◽  
Genome Wide Association Study ◽  
Water Buffalo ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Genomic Regions

The domestic Nili-Ravi water buffalo (Bubalus bubalis) is the best dairy animal contributing 68% to total milk production in Pakistan. In this study, we identified genome-wide single nucleotide polymorphisms (SNPs) to estimate various population genetic parameters such as diversity, pairwise population differentiation, linkage disequilibrium (LD) distribution and for genome-wide association study for milk yield and body weight traits in the Nili-Ravi dairy bulls that they may pass on to their daughters who are retained for milking purposes. The genotyping by sequencing approach revealed 13,039 reference genome-anchored SNPs with minor allele frequency of 0.05 among 167 buffalos. Population structure analysis revealed that the bulls were grouped into two clusters (K = 2), which indicates the presence of two different lineages in the Pakistani Nili-Ravi water buffalo population, and we showed the extent of admixture of these two lineages in our bull collection. LD analysis revealed 4169 significant SNP associations, with an average LD decay of 90 kb for these buffalo genome. Genome-wide association study involved a multi-locus mixed linear model for milk yield and body weight to identify genome-wide male effects. Our study further illustrates the utility of the genotyping by sequencing approach for identifying genomic regions to uncover additional demographic complexity and to improve the complex dairy traits of the Pakistani Nili-Ravi water buffalo population that would provide the lot of economic benefits to dairy industry.

Sandra Ramos Revisited

2020 ◽  
Vol 2 (4) ◽  
pp. 32-54
Author(s):  
Silvia Spitta
Keyword(s):  
United States ◽  
The United States ◽  
Ancient Greek ◽  
Graphic Arts ◽  
Left Behind ◽  
The World ◽  
The Usa ◽  
Political Choices ◽  
The Rich

Sandra Ramos (b. 1969) is one of the few artists to reflect critically on both sides of the Cuban di-lemma, fully embodying the etymological origins of the word in ancient Greek: di-, meaning twice, and lemma, denoting a form of argument involving a choice between equally unfavorable alternatives. Throughout her works she shines a light on the dilemmas faced by Cubans whether in Cuba or the United States, underlining the bad personal and political choices people face in both countries. During the hard 1990s, while still in Havana, the artist focused on the traumatic one-way journey into exile by thousands, as well as the experience of profound abandonment experienced by those who were left behind on the island. Today she lives in Miami and operates a studio there as well as one in Havana. Her initial disorientation in the USA has morphed into an acerbic representation and critique of the current administration and a deep concern with the environmental collapse we face. A buffoonlike Trumpito has joined el Bobo de Abela and Liborio in her gallery of comic characters derived from the rich Cuban graphic arts tradition where she was formed. While Cuba is now represented as a rotten cake with menacing flies hovering over it ready to pounce, a bombastic Trumpito marches across the world stage, trampling everything underfoot, a dollar sign for a face.

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