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 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.

scholarly journals Unsupervised genome-wide cluster analysis: nucleotide sequences of the omicron variant of SARS-CoV-2 are similar to sequences from early 2020

2021 ◽  
Author(s):  
Georg Hahn ◽  
Sanghun Lee ◽  
Dmitry Prokopenko ◽  
Tanya Novak ◽  
Julian Hecker ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Cluster Analysis ◽  
Entire Range ◽  
Principal Component ◽  
Jaccard Index ◽  
Genome Wide ◽  
A Genome ◽  
The World ◽  
Unsupervised Cluster Analysis

The GISAID database contains more than 100,000 SARS-CoV-2 genomes, including sequences of the recently discovered SARS-CoV-2 omicron variant and of prior SARS-CoV-2 strains that have been collected from patients around the world since the beginning of the pandemic. We applied unsupervised cluster analysis to the SARS-CoV-2 genomes, assessing their similarity at a genome-wide level based on the Jaccard index and principal component analysis. Our analysis results show that the omicron variant sequences are most similar to sequences that have been submitted early in the pandemic around January 2020. Furthermore, the omicron variants in GISAID are spread across the entire range of the first principal component, suggesting that the strain has been in circulation for some time. This observation supports a long-term infection hypothesis as the omicron strain origin.

scholarly journals A Genome-Wide Scan for Evidence of Selection in a Maize Population Under Long-Term Artificial Selection for Ear Number

Genetics ◽  
2013 ◽  
Vol 196 (3) ◽  
pp. 829-840 ◽  
Author(s):  
Timothy M. Beissinger ◽  
Candice N. Hirsch ◽  
Brieanne Vaillancourt ◽  
Shweta Deshpande ◽  
Kerrie Barry ◽  
...  
Keyword(s):  
Artificial Selection ◽  
Maize Population ◽  
Genome Wide ◽  
A Genome ◽  
Selection For ◽  
Ear Number ◽  
Genome Wide Scan

scholarly journals Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching

2019 ◽  
Author(s):  
Zachary L. Fuller ◽  
Veronique J.L. Mocellin ◽  
Luke Morris ◽  
Neal Cantin ◽  
Jihanne Shepherd ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Genome Wide Association ◽  
Conservation Strategies ◽  
Genome Sequences ◽  
Acropora Millepora ◽  
Genome Wide ◽  
A Genome ◽  
In The Wild

AbstractAlthough reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly heritable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We then obtained whole genome sequences for 237 phenotyped samples collected at 12 reefs distributed along the Great Barrier Reef, among which we inferred very little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We further used 213 of the samples to conduct a genome-wide association study of visual bleaching score, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for the use of genomics-based approaches in conservation strategies.

scholarly journals From conservation genetics to conservation genomics: a genome-wide assessment of blue whales ( Balaenoptera musculus ) in Australian feeding aggregations

2018 ◽  
Vol 5 (1) ◽  
pp. 170925 ◽  
Author(s):  
Catherine R. M. Attard ◽  
Luciano B. Beheregaray ◽  
Jonathan Sandoval-Castillo ◽  
K. Curt S. Jenner ◽  
Peter C. Gill ◽  
...  
Keyword(s):  
Population Structure ◽  
Adaptive Divergence ◽  
Balaenoptera Musculus ◽  
Blue Whale ◽  
Conservation Genomics ◽  
Next Generation Sequencing Technology ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range ◽  
Blue Whales

Genetic datasets of tens of markers have been superseded through next-generation sequencing technology with genome-wide datasets of thousands of markers. Genomic datasets improve our power to detect low population structure and identify adaptive divergence. The increased population-level knowledge can inform the conservation management of endangered species, such as the blue whale ( Balaenoptera musculus ). In Australia, there are two known feeding aggregations of the pygmy blue whale ( B. m. brevicauda ) which have shown no evidence of genetic structure based on a small dataset of 10 microsatellites and mtDNA. Here, we develop and implement a high-resolution dataset of 8294 genome-wide filtered single nucleotide polymorphisms, the first of its kind for blue whales. We use these data to assess whether the Australian feeding aggregations constitute one population and to test for the first time whether there is adaptive divergence between the feeding aggregations. We found no evidence of neutral population structure and negligible evidence of adaptive divergence. We propose that individuals likely travel widely between feeding areas and to breeding areas, which would require them to be adapted to a wide range of environmental conditions. This has important implications for their conservation as this blue whale population is likely vulnerable to a range of anthropogenic threats both off Australia and elsewhere.

scholarly journals What do we learn from a Genome Wide Association Study performed on HIV-1 infected Long Term Non Progressors individuals?

Retrovirology ◽  
2009 ◽  
Vol 6 (S2) ◽  
Author(s):  
Julien Guergnon ◽  
◽  
Cyril Dalmasso ◽  
Ioannis Theodorou ◽  
Agostino Riva
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Hiv 1

scholarly journals Ancestral contributions to contemporary European complex traits

2021 ◽  
Author(s):  
Davide Marnetto ◽  
Vasili Pankratov ◽  
Mayukh Mondal ◽  
Francesco Montinaro ◽  
Katri Pärna ◽  
...  
Keyword(s):  
Bronze Age ◽  
Complex Traits ◽  
Phenotypic Variability ◽  
Complex Trait ◽  
Blood Cholesterol ◽  
Hunter Gatherers ◽  
Genetic Components ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

The contemporary European genetic makeup formed in the last 8000 years as the combination of three main genetic components: the local Western Hunter-Gatherers, the incoming Neolithic Farmers from Anatolia and the Bronze Age component from the Pontic Steppes. When meeting into the post-Neolithic European environment, the genetic variants accumulated during their three distinct evolutionary histories mixed and came into contact with new environmental challenges. Here we investigate how this genetic legacy reflects on the complex trait landscape of contemporary European populations, using the Estonian Biobank as a case study. For the first time we directly connect the phenotypic information available from biobank samples with the genetic similarity to these ancestral groups, both at a genome-wide level and focusing on genomic regions associated with each of the 27 complex traits we investigated. We also found SNPs connected to pigmentation, cholesterol, sleep, diastolic blood pressure, and body mass index (BMI) to show signals of selection following the post Neolithic admixture events. We recapitulate existing knowledge about pigmentation traits, corroborate the connection between Steppe ancestry and height and highlight novel associations. Among others, we report the contribution of Hunter Gatherer ancestry towards high BMI and low blood cholesterol levels. Our results show that the ancient components that form the contemporary European genome were differentiated enough to contribute ancestry-specific signatures to the phenotypic variability displayed by contemporary individuals in at least 11 out of 27 of the complex traits investigated here.

scholarly journals Review: Population Structure in Genetic Studies: Confounding Factors and Mixed Models

2016 ◽  
Author(s):  
Lana S. Martin ◽  
Eleazar Eskin
Keyword(s):  
Population Structure ◽  
Mixed Models ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Laboratory Mouse ◽  
Mouse Strains ◽  
Genetic Studies ◽  
The Past ◽  
Genome Wide ◽  
A Genome

AbstractA genome-wide association study (GWAS) seeks to identify genetic variants that contribute to the development and progression of a specific disease. Over the past 10 years, new approaches using mixed models have emerged to mitigate the deleterious effects of population structure and relatedness in association studies. However, developing GWAS techniques to effectively test for association while correcting for population structure is a computational and statistical challenge. Using laboratory mouse strains as an example, our review characterizes the problem of population structure in association studies and describes how it can cause false positive associations. We then motivate mixed models in the context of unmodeled factors.

scholarly journals Inference of Population Genetic Structure and High Linkage Disequilibrium Among Alternaria spp. Collected from Tomato and Potato Using Genotyping by Sequencing

2019 ◽  
Author(s):  
Tika B. Adhikari ◽  
Brian J. Knaus ◽  
Niklaus J. Grünwald ◽  
Dennis Halterman ◽  
Frank J. Louws
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Plant Pathogens ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Allelic Association ◽  
Nucleotide Polymorphisms ◽  
Entire Genome ◽  
Genome Wide ◽  
A Genome

ABSTRACTGenotyping by sequencing (GBS) is considered a powerful tool to discover single nucleotide polymorphisms (SNPs), which are useful to characterize closely related genomes of plant species and plant pathogens. We applied GBS to determine genome-wide variations in a panel of 187 isolates of three closely related Alternaria spp. that cause diseases on tomato and potato in North Carolina (NC) and Wisconsin (WI). To compare genetic variations, reads were mapped to both A. alternata and A. solani draft reference genomes and detected dramatic differences in SNPs among them. Comparison of A. linariae and A. solani populations by principal component analysis revealed the first (83.8% of variation) and second (8.0% of variation) components contained A. linariae from tomato in NC and A. solani from potato in WI, respectively, providing evidence of population structure. Genetic differentiation (Hedrick’s G’ST) in A. linariae populations from Haywood, Macon, and Madison counties in NC were little or no differentiated (G’ST 0.0 - 0.2). However, A. linariae population from Swain county appeared to be highly differentiated (G’ST > 0.8). To measure the strength of the linkage disequilibrium (LD), we also calculated the allelic association between pairs of loci. Lewontin’s D (measures the fraction of allelic variations) and physical distances provided evidence of linkage throughout the entire genome, consistent with the hypothesis of non-random association of alleles among loci. Our findings provide new insights into the understanding of clonal populations on a genome-wide scale and microevolutionary factors that might play an important role in population structure. Although we found limited genetic diversity, the three Alternaria spp. studied here are genetically distinct and each species is preferentially associated with one host.

scholarly journals A dynamic 6,000-year genetic history of Eurasia’s Eastern Steppe

2020 ◽  
Author(s):  
Choongwon Jeong ◽  
Ke Wang ◽  
Shevan Wilkin ◽  
William Timothy Treal Taylor ◽  
Bryan K. Miller ◽  
...  
Keyword(s):  
Bronze Age ◽  
Population History ◽  
Complex Interplay ◽  
Cultural Changes ◽  
Genetic History ◽  
Nomadic Pastoralists ◽  
Eurasian Steppe ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of

SummaryThe Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the region’s population history. Here we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher Eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe.

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