scholarly journals Population relationships based on 170 ancestry SNPs from the combined Kidd and Seldin panels

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Andrew J. Pakstis ◽  
William C. Speed ◽  
Usha Soundararajan ◽  
Haseena Rajeevan ◽  
Judith R. Kidd ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Native American ◽  
Principal Component ◽  
Population Data ◽  
Reference Population ◽  
Human Populations ◽  
Genotype Data ◽  
The World ◽  
The Individual ◽  
Strong Cluster

AbstractThe benefits of ancestry informative SNP (AISNP) panels can best accrue and be properly evaluated only as sufficient reference population data become readily accessible. Ideally the set of reference populations should approximate the genetic diversity of human populations worldwide. The Kidd and Seldin AISNP sets are two panels that have separately accumulated thus far the largest and most diverse collections of data on human reference populations from the major continental regions. A recent tally in the ALFRED allele frequency database finds 164 reference populations available for all the 55 Kidd AISNPs and 132 reference populations for all the 128 Seldin AISNPs. Although much more of the genetic diversity in human populations around the world still needs to be documented, 81 populations have genotype data available for all 170 AISNPs in the union of the Kidd and Seldin panels. In this report we examine admixture and principal component analyses on these 81 worldwide populations and some regional subsets of these reference populations to determine how well the combined panel illuminates population relationships. Analyses of this dataset that focused on Native American populations revealed very strong cluster patterns associated with many of the individual populations studied.

scholarly journals Genotypes of informative loci from 1000 Genomes data allude evolution and mixing of human populations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sridevi Padakanti ◽  
Khong-Loon Tiong ◽  
Yan-Bin Chen ◽  
Chen-Hsiang Yeang
Keyword(s):  
Population Distribution ◽  
Principal Component ◽  
Functional Enrichment ◽  
Weighted Sums ◽  
Small Subset ◽  
Human Populations ◽  
Demographic Model ◽  
Genotype Data ◽  
Founder Population ◽  
1000 Genomes

AbstractPrincipal Component Analysis (PCA) projects high-dimensional genotype data into a few components that discern populations. Ancestry Informative Markers (AIMs) are a small subset of SNPs capable of distinguishing populations. We integrate these two approaches by proposing an algorithm to identify necessary informative loci whose removal from the data deteriorates the PCA structure. Unlike classical AIMs, necessary informative loci densely cover the genome, hence can illuminate the evolution and mixing history of populations. We conduct a comprehensive analysis to the genotype data of the 1000 Genomes Project using necessary informative loci. Projections along the top seven principal components demarcate populations at distinct geographic levels. Millions of necessary informative loci along each PC are identified. Population identities along each PC are approximately determined by weighted sums of minor (or major) alleles over the informative loci. Variations of allele frequencies are aligned with the history and direction of population evolution. The population distribution of projections along the top three PCs is recapitulated by a simple demographic model based on several waves of founder population separation and mixing. Informative loci possess locational concentration in the genome and functional enrichment. Genes at two hot spots encompassing dense PC 7 informative loci exhibit differential expressions among European populations. The mosaic of local ancestry in the genome of a mixed descendant from multiple populations can be inferred from partial PCA projections of informative loci. Finally, informative loci derived from the 1000 Genomes data well predict the projections of an independent genotype data of South Asians. These results demonstrate the utility and relevance of informative loci to investigate human evolution.

scholarly journals Genetic Diversity and Distribution ofBlastocystisSubtype 3 in Human Populations, with Special Reference to a Rural Population in Central Mexico

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Liliana Rojas-Velázquez ◽  
Patricia Morán ◽  
Angélica Serrano-Vázquez ◽  
Leonardo D. Fernández ◽  
Horacio Pérez-Juárez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Human Population ◽  
Haplotype Diversity ◽  
Haplotype Network ◽  
Human Populations ◽  
High Haplotype Diversity ◽  
Genetic Diversity And Structure ◽  
High Prevalence ◽  
The World ◽  
Parasitic Protist

Blastocystissubtype 3 (ST3) is a parasitic protist found in the digestive tract of symptomatic and asymptomatic humans around the world. While this parasite exhibits a high prevalence in the human population, its true geographic distribution and global genetic diversity are still unknown. This gap in knowledge limits the understanding of the spread mechanisms, epidemiology, and impact that this parasite has on human populations. Herein, we provided new data on the geographical distribution and genetic diversity ofBlastocystisST3 from a rural human population in Mexico. To do so, we collected and targeted the SSU-rDNA region in fecal samples from this population and further compared its genetic diversity and structure with that previously observed in populations ofBlastocystisST3 from other regions of the planet. Our analyses reveled that diversity ofBlastocystisST3 showed a high haplotype diversity and genetic structure to the world level; however, they were low in the Morelos population. The haplotype network revealed a common widespread haplotype from which the others were generated recently. Finally, our results suggested a recent expansion of the diversity ofBlastocystisST3 worldwide.

scholarly journals Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia

2018 ◽  
Author(s):  
Leonardo Arias ◽  
Roland Schröder ◽  
Alexander Hübner ◽  
Guillermo Barreto ◽  
Mark Stoneking ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Native American ◽  
Cultural Practices ◽  
Demographic History ◽  
Population History ◽  
Human Populations ◽  
Effective Population ◽  
Trade Networks ◽  
Males And Females ◽  
The Impact

ABSTRACTHuman populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the non-recombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native-American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic-exogamy, a marital practice in which men are required to marry women speaking a different language.We identified 2,969 SNPs in the NRY sequences; only 925 SNPs were previously described. The NRY and mtDNA data showed that males and females experienced different demographic histories: the female effective population size has been larger than that of males through time, and both markers show an increase in lineage diversification beginning ~5,000 years ago, with a male-specific expansion occurring ~3,500 years ago. These dates are too recent to be associated with agriculture, therefore we propose that they reflect technological innovations and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, our study provides evidence of the impact of postmarital residence rules and linguistic exogamy on genetic diversity patterns. Finally, we highlight the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between males and females.

scholarly journals Evaluation of genetic diversity and management of disease in Border Collie dogs

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pamela Xing Yi Soh ◽  
Wei Tse Hsu ◽  
Mehar Singh Khatkar ◽  
Peter Williamson
Keyword(s):  
Genetic Diversity ◽  
Common Ancestor ◽  
Neuronal Ceroid Lipofuscinosis ◽  
Reference Population ◽  
Pedigree Information ◽  
Genotype Data ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
Maximum Loss ◽  
High Level

AbstractMaintaining genetic diversity in dog breeds is an important consideration for the management of inherited diseases. We evaluated genetic diversity in Border Collies using molecular and genealogical methods, and examined changes to genetic diversity when carriers for Trapped Neutrophil Syndrome (TNS) and Neuronal Ceroid Lipofuscinosis (NCL) are removed from the genotyped population. Genotype data for 255 Border Collies and a pedigree database of 83,996 Border Collies were used for analysis. Molecular estimates revealed a mean multi-locus heterozygosity (MLH) of 0.311 (SD 0.027), 20.79% of the genome consisted of runs of homozygosity (ROH ) > 1 Mb, effective population size (Ne) was 84.7, and mean inbreeding (F) was 0.052 (SD 0.083). For 227 genotyped Border Collies that had available pedigree information (GenoPed), molecular and pedigree estimates of diversity were compared. A reference population (dogs born between 2005 and 2015, inclusive; N = 13,523; RefPop) and their ancestors (N = 12,478) were used to evaluate the diversity of the population that are contributing to the current generation. The reference population had a Ne of 123.5, a mean F of 0.095 (SD 0.082), 2276 founders (f), 205.5 effective founders (fe), 28 effective ancestors (fa) and 10.65 (SD 2.82) founder genomes (Ng). Removing TNS and NCL carriers from the genotyped population had a small impact on diversity measures (ROH > 1 Mb, MLH, heterozygosity), however, there was a loss of > 10% minor allele frequency for 89 SNPs around the TNS mutation (maximum loss of 12.7%), and a loss of > 5% for 5 SNPs around the NCL mutation (maximum 5.18%). A common ancestor was identified for 38 TNS-affected dogs and 64 TNS carriers, and a different common ancestor was identified for 33 NCL-affected dogs and 28 carriers, with some overlap of prominent individuals between both pedigrees. Overall, Border Collies have a high level of genetic diversity compared to other breeds.

scholarly journals Detecting Heterogeneity in Population Structure Across the Genome in Admixed Populations

2015 ◽  
Author(s):  
Caitlin McHugh ◽  
Timothy A Thornton ◽  
Lisa Brown
Keyword(s):  
Population Structure ◽  
Native American ◽  
Native Americans ◽  
Random Mating ◽  
Phase Iii ◽  
European Ancestry ◽  
Human Populations ◽  
Genotype Data ◽  
Local Ancestry ◽  
Genomic Regions

The genetic structure of human populations is often characterized by aggregating measures of ancestry across the autosomal chromosomes. While it may be reasonable to assume that population structure patterns are similar genome-wide in relatively homogeneous populations, this assumption may not be appropriate for admixed populations, such as Hispanics and African Americans, with recent ancestry from two or more continents. Recent studies have suggested that systematic ancestry differences can arise at genomic locations in admixed populations as a result of selection and non-random mating. Here, we propose a method, which we refer to as the chromosomal ancestry differences (CAnD) test, for detecting heterogeneity in population structure across the genome. CAnD uses local ancestry inferred from SNP genotype data to identify chromosomes harboring genomic regions with ancestry contributions that are significantly different than expected. In simulation studies with real genotype data from Phase III of the HapMap Project, we demonstrate the validity and power of CAnD. We apply CAnD to the HapMap Mexican American (MXL) and African American (ASW) population samples; in this analysis the software RFMix is used to infer local ancestry at genomic regions assuming admixing from Europeans, West Africans, and Native Americans. The CAnD test provides strong evidence of heterogeneity in population structure across the genome in the MXL sample ($p=4e-05$), which is largely driven by elevated Native American ancestry and deficit of European ancestry on the X chromosomes. Among the ASW, all chromosomes are largely African derived and no heterogeneity in population structure is detected in this sample.

scholarly journals Genetic diversity of maize inbred lines as inferred from SSR markers

Genetika ◽  
2015 ◽  
Vol 47 (2) ◽  
pp. 489-498
Author(s):  
Ana Nikolic ◽  
Dragana Ignjatovic-Micic ◽  
Dragan Kovacevic ◽  
Zoran Camdzija ◽  
Milomir Filipovic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Principal Component ◽  
Inbred Lines ◽  
Yield Potential ◽  
Pedigree Data ◽  
Maize Breeding ◽  
Breeding Programs ◽  
Maize Inbred Lines ◽  
The World

Creating new maize hybrids with greater yield potential is a permanent goal of breeding programs all over the world. Long-time existing and new problems related to different biotic and abiotic stresses and the growing needs of the world market require constant work on finding new ways for advancing maize production. Molecular marker technology is one of the fastest developing fields and its implementation has already given results in solving different problems related to maize breeding improvement. The aim of the study presented herein was characterization and genetic similarity assessment of twenty-nine maize inbred lines from Maize Research Institute collection using Simple Sequence Repeats (SSR) markers. The analysis was done using 20 pairs of SSR primers with clearly visible and reproducible results. A total of 119 alleles were detected with a mean of 5.8 per locus. PIC (Polymorphism Information Content) values were in the range from 0.45 to 0.92 (average 0.74). Genetic similarities calculated using Jaccard?s coefficient ranged from 0.27 to 0.99. Cluster and Principal Component Analysis (PCA) analysis were done using matrices of similarity in the NTSYSpc software, version 2.1. Results of both classifications were moderately in agreement with the pedigree data of analysed genotypes. The information about genetic diversity of maize inbred lines revealed by SSR markers could be useful in planning strategies for future maize breeding programs.

scholarly journals The Metabolization Profile of the CYP2D6 Gene in Amerindian Populations: A Review

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 262 ◽  
Author(s):  
Luciana P. C. Leitão ◽  
Tatiane P. Souza ◽  
Juliana C. G. Rodrigues ◽  
Marianne R. Fernandes ◽  
Sidney Santos ◽  
...  
Keyword(s):  
Native Americans ◽  
Scientific Publication ◽  
The United States ◽  
Progressive Increase ◽  
Human Populations ◽  
Cyp2d6 Gene ◽  
Publication Rates ◽  
Group Methods ◽  
The World ◽  
The Individual

Background: the CYP2D6 gene is clinically important and is known to have a number of variants. This gene has four distinct metabolization profiles that are determined by the different allelic forms present in the individual. The relative frequency of these profiles varies considerably among human populations around the world. Populations from more isolated regions, such as Native Americans, are still relatively poorly studied, however. Even so, recent advances in genotyping techniques and increasing interest in the study of these populations has led to a progressive increase in publication rates. Given this, the review presented here compiled the principal papers published on the CYP2D6 gene in Amerindian populations to determine the metabolic profile of this group. Methods: a systematic literature review was conducted in three scientific publication platforms (Google Scholar, Science Direct, and Pubmed). The search was run using the keywords “CYP2D6 Amerindians” and “CYP2D6 native Americans”. Results: a total of 13 original papers met the inclusion criteria established for this study. All the papers presented frequencies of the different CYP2D6 alleles in Amerindian populations. Seven of the papers focused specifically on Amerindian populations from Mexico, while the others included populations from Argentina, Chile, Costa Rica, Mexico, Paraguay, Peru, and the United States. The results of the papers reviewed here showed that the extensive metabolization profile was the most prevalent in all Amerindian populations studied to date, followed by the intermediate, slow, and ultra-rapid, in that order. Conclusion: the metabolization profiles of the Amerindian populations reviewed in the present study do not diverge in any major way from those of other populations from around the world. Given the paucity of the data available on Amerindian populations, further research is required to better characterize the metabolization profile of these populations to ensure the development of adequate therapeutic strategies.

scholarly journals A Systematic Review on Various Therapeutic Options for Coronavirus Outbreak

2021 ◽  
Vol 11 (2-S) ◽  
pp. 185-194
Author(s):  
Sharib Raza Khan ◽  
Babita Sharma ◽  
Sankha Bhattacharya
Keyword(s):  
Public Health Emergency ◽  
Human Populations ◽  
Global Public Health ◽  
Virus Spread ◽  
Fish Market ◽  
Global Pandemic ◽  
The World ◽  
Waterborne Transmission ◽  
Human Coronaviruses ◽  
The Individual

SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) or coronavirus disease that emerged in Wuhan, China's Hubei province. According to a Wuhan citizen, the virus spread from the Wuhan fish market to humans via a form of waterborne transmission. The WHO proclaimed the SARS-CoV-2 Pandemic a global public health emergency in March of the following year. Rather than influencing the individual animals mostly, the movement of humans and a few days later, the infection spread to other parts of the world by the distribution of specimens to animals and by the movement of humans, causing considerable illness in human populations. An estimated one and a total of nearly sixty-eight million two hundred and fifty-six million people have been impacted, including one and a million thousand five hundred and sixty thousand fatalities in more than two hundred countries around the world. As of the present, there are no medicines or vaccinations against the world's first SARS-CoV-2 virus are in clinical trials molecular and cellular studies of CoVs, as well as their care, were reviewed in this latest assessment. Keywords:  SARS-CoV-2, WHO, Global pandemic, Human coronaviruses, Pathogenesis, Treatments

New walls to keep the bad out: populism and the totalitarian psyche

2019 ◽  
Vol 1 (2) ◽  
pp. 120-130
Author(s):  
Coline Covington
Keyword(s):  
Cold War ◽  
Balance Of Power ◽  
Berlin Wall ◽  
Group Solidarity ◽  
Freedom Of Movement ◽  
Psychological Understanding ◽  
Psychic Development ◽  
The World ◽  
The Individual ◽  
The Cold War

The Berlin Wall came down on 9 November 1989 and marked the end of the Cold War. As old antagonisms thawed a new landscape emerged of unification and tolerance. Censorship was no longer the principal means of ensuring group solidarity. The crumbling bricks brought not only freedom of movement but freedom of thought. Now, nearly thirty years later, globalisation has created a new balance of power, disrupting borders and economies across the world. The groups that thought they were in power no longer have much of a say and are anxious about their future. As protest grows, we are beginning to see that the old antagonisms have not disappeared but are, in fact, resurfacing. This article will start by looking at the dissembling of a marriage in which the wall that had peacefully maintained coexistence disintegrates and leads to a psychic development that uncannily mirrors that of populism today. The individual vignette leads to a broader psychological understanding of the totalitarian dynamic that underlies populism and threatens once again to imprison us within its walls.

Virginia Woolf and Being-in-the-world

2017 ◽  
Author(s):  
Emma Simone
Keyword(s):  
Virginia Woolf ◽  
Historical Context ◽  
The Political ◽  
Cartesian Dualism ◽  
Self And Other ◽  
The World ◽  
Binary Oppositions ◽  
The Individual ◽  
The Relationship ◽  
Existential Perspective

Virginia Woolf and Being-in-the-world: A Heideggerian Study explores Woolf’s treatment of the relationship between self and world from a phenomenological-existential perspective. This study presents a timely and compelling interpretation of Virginia Woolf’s textual treatment of the relationship between self and world from the perspective of the philosophy of Martin Heidegger. Drawing on Woolf’s novels, essays, reviews, letters, diary entries, short stories, and memoirs, the book explores the political and the ontological, as the individual’s connection to the world comes to be defined by an involvement and engagement that is always already situated within a particular physical, societal, and historical context. Emma Simone argues that at the heart of what it means to be an individual making his or her way in the world, the perspectives of Woolf and Heidegger are founded upon certain shared concerns, including the sustained critique of Cartesian dualism, particularly the resultant binary oppositions of subject and object, and self and Other; the understanding that the individual is a temporal being; an emphasis upon intersubjective relations insofar as Being-in-the-world is defined by Being-with-Others; and a consistent emphasis upon average everydayness as both determinative and representative of the individual’s relationship to and with the world.

Sign in / Sign up

Export Citation Format

Share Document