scholarly journals Insight into the genomic history of the Near East from whole-genome sequences and genotypes of Yemenis

2019 ◽  
Author(s):  
Marc Haber ◽  
Riyadh Saif-Ali ◽  
Molham Al-Habori ◽  
Yuan Chen ◽  
Daniel E. Platt ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Bronze Age ◽  
Near East ◽  
African Ancestry ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
High Coverage ◽  
The North ◽  
The Bronze Age

AbstractWe report high-coverage whole-genome sequencing data from 46 Yemeni individuals as well as genome-wide genotyping data from 169 Yemenis from diverse locations. We use this dataset to define the genetic diversity in Yemen and how it relates to people elsewhere in the Near East. Yemen is a vast region with substantial cultural and geographic diversity, but we found little genetic structure correlating with geography among the Yemenis – probably reflecting continuous movement of people between the regions. African ancestry from admixture in the past 800 years is widespread in Yemen and is the main contributor to the country’s limited genetic structure, with some individuals in Hudayda and Hadramout having up to 20% of their genetic ancestry from Africa. In contrast, individuals from Maarib appear to have been genetically isolated from the African gene flow and thus have genomes likely to reflect Yemen’s ancestry before the admixture. This ancestry was comparable to the ancestry present during the Bronze Age in the distant Northern regions of the Near East. After the Bronze Age, the South and North of the Near East therefore followed different genetic trajectories: in the North the Levantines admixed with a Eurasian population carrying steppe ancestry whose impact never reached as far south as the Yemen, where people instead admixed with Africans leading to the genetic structure observed in the Near East today.

scholarly journals Some Balkan and Danubian Connexions of Troy

1919 ◽  
Vol 39 ◽  
pp. 185-201
Author(s):  
Ida Carleton Thallon
Keyword(s):  
Bronze Age ◽  
West Coast ◽  
Near East ◽  
Single Site ◽  
Neolithic Period ◽  
Northern Limit ◽  
The West ◽  
Aegean Area ◽  
The North ◽  
The Bronze Age

Prehistoric research shows us that in the troubled section of Europe known as the Near East there existed as early as the neolithic period several culture groups which may be classified under four heads as follows:—(1) The Aegean, Minoan-Mycenaean group.(2) The Thessalian.(3) The Upper Balkan and Danubian.(4) The South Russian and allied groups.The first of these is so familiar that we need only emphasize its continuity from the neolithic period through the Bronze Age, and the fact that, although eventually it was widely diffused through the Mediterranean from Spain to Cyprus and the coast of Palestine, in the Aegean area itself the northern limit on the west coast was Thessaly, which it reached in the L. M. period, and on the opposite shore the single site toward the north is Troy, where L. M. is contemporary with the VIth city. The sporadic examples on the coast from Thessaly to Troy are very late and apparently had little influence.The excavations by Messrs. Wace and Thompson in prehistoric Thessaly, which included considerably more than one hundred sites, have led them to differentiate a large number of styles of pottery, including red monochrome, red or black incised, or else painted either light on dark or dark on light in many varieties. The designs are predominantly rectilinear and more closely akin to the northern groups than to the Minoan.

scholarly journals Rapid Genotype Refinement for Whole-Genome Sequencing Data using Multi-Variate Normal Distributions

2015 ◽  
Author(s):  
Rudy Arthur ◽  
Jared O'Connell ◽  
Ole Schulz-Trieglaff ◽  
Anthony J Cox
Keyword(s):  
Markov Models ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
High Coverage ◽  
Multivariate Gaussian Distribution ◽  
Data Set ◽  
Normal Distributions ◽  
Computationally Expensive ◽  
Low Coverage

Whole-genome low-coverage sequencing has been combined with linkage-disequilibrium (LD) based genotype refinement to accurately and cost-effectively infer genotypes in large cohorts of individuals. Most genotype refinement methods are based on hidden Markov models, which are accurate but computationally expensive. We introduce an algorithm that models LD using a simple multivariate Gaussian distribution. The key feature of our algorithm is its speed, it is hundreds of times faster than other methods on the same data set and its scaling behaviour is linear in the number of samples. We demonstrate the performance of the method on both low-coverage and high-coverage samples.

scholarly journals A population-specific reference panel for improved genotype imputation in African Americans

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Jared O’Connell ◽  
Taedong Yun ◽  
Meghan Moreno ◽  
Helen Li ◽  
Nadia Litterman ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
African Ancestry ◽  
Genotype Imputation ◽  
Whole Genome Sequencing Data ◽  
Specific Reference ◽  
Whole Genome ◽  
Sequencing Data ◽  
High Quality ◽  
Sub Saharan

AbstractThere is currently a dearth of accessible whole genome sequencing (WGS) data for individuals residing in the Americas with Sub-Saharan African ancestry. We generated whole genome sequencing data at intermediate (15×) coverage for 2,294 individuals with large amounts of Sub-Saharan African ancestry, predominantly Atlantic African admixed with varying amounts of European and American ancestry. We performed extensive comparisons of variant callers, phasing algorithms, and variant filtration on these data to construct a high quality imputation panel containing data from 2,269 unrelated individuals. With the exception of the TOPMed imputation server (which notably cannot be downloaded), our panel substantially outperformed other available panels when imputing African American individuals. The raw sequencing data, variant calls and imputation panel for this cohort are all freely available via dbGaP and should prove an invaluable resource for further study of admixed African genetics.

scholarly journals Development and evaluation of an outbreak surveillance system integrating whole genome sequencing data for non-typhoidal Salmonella in London and South East of England, 2016-17

2021 ◽  
pp. 1-26
Author(s):  
Karthik Paranthaman ◽  
Piers Mook ◽  
Daniele Curtis ◽  
Edward-Wynne Evans ◽  
Emma Crawley-Boevey ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Surveillance System ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data

scholarly journals Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

Heredity ◽  
2021 ◽  
Author(s):  
Axel Jensen ◽  
Mette Lillie ◽  
Kristofer Bergström ◽  
Per Larsson ◽  
Jacob Höglund
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Peripheral Populations ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Native Populations

AbstractThe use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

scholarly journals Comprehensive identification of transposable element insertions using multiple sequencing technologies

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chong Chu ◽  
Rebeca Borges-Monroy ◽  
Vinayak V. Viswanadham ◽  
Soohyun Lee ◽  
Heng Li ◽  
...  
Keyword(s):  
Transposable Element ◽  
Structure And Function ◽  
Endogenous Retroviruses ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Short Read ◽  
Sequencing Technologies ◽  
Long Read ◽  
And Function

AbstractTransposable elements (TEs) help shape the structure and function of the human genome. When inserted into some locations, TEs may disrupt gene regulation and cause diseases. Here, we present xTea (x-Transposable element analyzer), a tool for identifying TE insertions in whole-genome sequencing data. Whereas existing methods are mostly designed for short-read data, xTea can be applied to both short-read and long-read data. Our analysis shows that xTea outperforms other short read-based methods for both germline and somatic TE insertion discovery. With long-read data, we created a catalogue of polymorphic insertions with full assembly and annotation of insertional sequences for various types of retroelements, including pseudogenes and endogenous retroviruses. Notably, we find that individual genomes have an average of nine groups of full-length L1s in centromeres, suggesting that centromeres and other highly repetitive regions such as telomeres are a significant yet unexplored source of active L1s. xTea is available at https://github.com/parklab/xTea.

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