scholarly journals The impact of recent events on human genetic diversity

2012 ◽  
Vol 367 (1590) ◽  
pp. 793-799 ◽  
Author(s):  
Mark A. Jobling
Keyword(s):  
Genetic Diversity ◽  
Historical Record ◽  
Social Selection ◽  
New Methods ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Male Specific ◽  
Demographic Impact ◽  
The Impact ◽  
And Linguistics

The historical record tells us stories of migrations, population expansions and colonization events in the last few thousand years, but what was their demographic impact? Genetics can throw light on this issue, and has mostly done so through the maternally inherited mitochondrial DNA (mtDNA) and the male-specific Y chromosome. However, there are a number of problems, including marker ascertainment bias, possible influences of natural selection, and the obscuring layers of the palimpsest of historical and prehistorical events. Y-chromosomal lineages are particularly affected by genetic drift, which can be accentuated by recent social selection. A diversity of approaches to expansions in Europe is yielding insights into the histories of Phoenicians, Roma, Anglo-Saxons and Vikings, and new methods for producing and analysing genome-wide data hold much promise. The field would benefit from more consensus on appropriate methods, and better communication between geneticists and experts in other disciplines, such as history, archaeology and linguistics.

scholarly journals Revealing the impact of the Caucasus region on the genetic legacy of Romani people from genome-wide data

PLoS ONE ◽  
2018 ◽  
Vol 13 (9) ◽  
pp. e0202890 ◽  
Author(s):  
Zsolt Bánfai ◽  
Valerián Ádám ◽  
Etelka Pöstyéni ◽  
Gergely Büki ◽  
Márta Czakó ◽  
...  
Keyword(s):  
The Caucasus ◽  
Caucasus Region ◽  
Genome Wide ◽  
Genome Wide Data ◽  
The Impact

scholarly journals A COMPRESSED SENSING BASED APPROACH FOR SUBTYPING OF LEUKEMIA FROM GENE EXPRESSION DATA

2011 ◽  
Vol 09 (05) ◽  
pp. 631-645 ◽  
Author(s):  
WENLONG TANG ◽  
HONGBAO CAO ◽  
JUNBO DUAN ◽  
YU-PING WANG
Keyword(s):  
Gene Expression ◽  
Compressed Sensing ◽  
Gene Expression Analysis ◽  
Expression Data ◽  
Data Set ◽  
New Methods ◽  
Genome Wide ◽  
Different Types ◽  
Genome Wide Data ◽  
Improved Accuracy

With the development of genomic techniques, the demand for new methods that can handle high-throughput genome-wide data effectively is becoming stronger than ever before. Compressed sensing (CS) is an emerging approach in statistics and signal processing. With the CS theory, a signal can be uniquely reconstructed or approximated from its sparse representations, which can therefore better distinguish different types of signals. However, the application of CS approach to genome-wide data analysis has been rarely investigated. We propose a novel CS-based approach for genomic data classification and test its performance in the subtyping of leukemia through gene expression analysis. The detection of subtypes of cancers such as leukemia according to different genetic markups is significant, which holds promise for the individualization of therapies and improvement of treatments. In our work, four statistical features were employed to select significant genes for the classification. With our selected genes out of 7,129 ones, the proposed CS method achieved a classification accuracy of 97.4% when evaluated with the cross validation and 94.3% when evaluated with another independent data set. The robustness of the method to noise was also tested, giving good performance. Therefore, this work demonstrates that the CS method can effectively detect subtypes of leukemia, implying improved accuracy of diagnosis of leukemia.

scholarly journals Genome-wide data inferring the evolution and population demography of the novel pneumonia coronavirus (SARS-CoV-2)

2020 ◽  
Author(s):  
Bin Fang ◽  
Linlin Liu ◽  
Xiao Yu ◽  
Xiang Li ◽  
Guojun Ye ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Sliding Window ◽  
The Novel ◽  
Population Demography ◽  
Short Term ◽  
Genome Wide ◽  
The World ◽  
Genome Wide Data ◽  
Neutrality Tests

AbstractAs the highly risk and infectious diseases, the outbreak of coronavirus disease 2019 (COVID-19) poses unprecedent challenges to global health. Up to March 3, 2020, SARS-CoV-2 has infected more than 89,000 people in China and other 66 countries across six continents. In this study, we used 10 new sequenced genomes of SARS-CoV-2 and combined 136 genomes from GISAID database to investigate the genetic variation and population demography through different analysis approaches (e.g. Network, EBSP, Mismatch, and neutrality tests). The results showed that 80 haplotypes had 183 substitution sites, including 27 parsimony-informative and 156 singletons. Sliding window analyses of genetic diversity suggested a certain mutations abundance in the genomes of SARS-CoV-2, which may be explaining the existing widespread. Phylogenetic analysis showed that, compared with the coronavirus carried by pangolins (Pangolin-CoV), the virus carried by bats (bat-RaTG13-CoV) has a closer relationship with SARS-CoV-2. The network results showed that SARS-CoV-2 had diverse haplotypes around the world by February 11. Additionally, 16 genomes, collected from Huanan seafood market assigned to 10 haplotypes, indicated a circulating infection within the market in a short term. The EBSP results showed that the first estimated expansion date of SARS-CoV-2 began from 7 December 2019.

scholarly journals Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina

2017 ◽  
Author(s):  
Benjamin Laenen ◽  
Andrew Tedder ◽  
Michael D. Nowak ◽  
Per Toräng ◽  
Jörg Wunder ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mating System ◽  
Purifying Selection ◽  
Mixed Mating ◽  
Genome Wide ◽  
Outcrossing Rates ◽  
Arabis Alpina ◽  
Whole Genome Resequencing ◽  
Evolutionary Consequences ◽  
The Impact

Plant mating systems have profound effects on levels and structuring of genetic variation, and can affect the impact of natural selection. While theory predicts that intermediate outcrossing rates may allow plants to prevent accumulation of deleterious alleles, few studies have empirically tested this prediction using genomic data. Here, we study the effect of mating system on purifying selection by conducting population genomic analyses on whole-genome resequencing data from 38 European individuals of the arctic-alpine crucifer Arabis alpina. We find that outcrossing and mixed-mating populations maintain genetic diversity at similar levels, whereas highly self-fertilizing Scandinavian A. alpina show a strong reduction in genetic diversity, most likely as a result of a postglacial colonization bottleneck. We further find evidence for accumulation of genetic load in highly self-fertilizing populations, whereas the genome-wide impact of purifying selection does not differ greatly between mixed-mating and outcrossing populations. Our results demonstrate that intermediate levels of outcrossing may allow efficient selection against harmful alleles whereas demographic effects can be important for relaxed purifying selection in highly selfing populations. Thus, both mating system and demography shape the impact of purifying selection on genomic variation in A. alpina. These results are important for an improved understanding of the evolutionary consequences of mating system variation and the maintenance of mixed-mating strategies.SignificanceIntermediate outcrossing rates are theoretically predicted to maintain effective selection against harmful alleles, but few studies have empirically tested this prediction using genomic data. We used whole-genome resequencing data from alpine rock-cress to study how genetic variation and purifying selection vary with mating system. We find that populations with intermediate outcrossing rates have similar levels of genetic diversity as outcrossing populations, and that purifying selection against harmful alleles is efficient in mixed-mating populations. In contrast, self-fertilizing populations from Scandinavia have strongly reduced genetic diversity, and accumulate harmful mutations, likely as a result of demographic effects of postglacial colonization. Our results suggest that mixed-mating populations can avoid the negative evolutionary consequences of high self-fertilization rates.

scholarly journals Heterogeneity in effective size across the genome: effects on the Inverse Instantaneous Coalescence Rate (IICR) and implications for demographic inference under linked selection.

2021 ◽  
Author(s):  
Simon Boitard ◽  
Armando Arredondo ◽  
Camille Noûs ◽  
Lounes Chikhi ◽  
Olivier Mazet
Keyword(s):  
Genetic Diversity ◽  
Balancing Selection ◽  
Effective Population ◽  
Recombination Rates ◽  
Genome Wide ◽  
Coalescence Rate ◽  
Demographic Inference ◽  
The Impact ◽  
Linked Selection ◽  
Coalescence Times

The relative contribution of selection and neutrality in shaping species genetic diversity is one of the most central and controversial questions in evolutionary theory. Genomic data provide growing evidence that linked selection, i.e. the modification of genetic diversity at neutral sites through linkage with selected sites, might be pervasive over the genome. Several studies proposed that linked selection could be modelled as first approximation by a local reduction (e.g. purifying selection, selective sweeps) or increase (e.g. balancing selection) of effective population size (Ne). At the genome-wide scale, this leads to a large variance of Ne from one region to another, reflecting the heterogeneity of selective constraints and recombination rates between regions. We investigate here the consequences of this variation of Ne on the genome-wide distribution of coalescence times. The underlying motivation concerns the impact of linked selection on demographic inference, because the distribution of coalescence times is at the heart of several important demographic inference approaches. Using the concept of Inverse Instantaneous Coalescence Rate, we demonstrate that in a panmictic population, linked selection always results in a spurious apparent decrease of Ne along time. Balancing selection has a particularly large effect, even when it concerns a very small part of the genome. We quantify the expected magnitude of the spurious decrease of Ne in humans and Drosophila melanogaster, based on Ne distributions inferred from real data in these species. We also find that the effect of linked selection can be significantly reduced by that of population structure.

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.

Impact of plant breeding on genetic diversity of agricultural crops: searching for molecular evidence

2006 ◽  
Vol 4 (1) ◽  
pp. 71-78 ◽  
Author(s):  
Yong-Bi Fu
Keyword(s):  
Genetic Diversity ◽  
Plant Breeding ◽  
Genetic Background ◽  
Genetic Improvement ◽  
Agricultural Practices ◽  
Molecular Evidence ◽  
Agricultural Crops ◽  
Crop Genetic Diversity ◽  
Genome Wide ◽  
The Impact

There is a long-standing concern that modern plant breeding reduces crop genetic diversity, which may have consequences for the vulnerability of crops to changes in pests, diseases, climate and agricultural practices. Recent molecular assessments of genetic diversity changes in existing genepools of major agricultural crops may shed some light on the impact of plant breeding on crop genetic diversity. Reviewing published assessments revealed different impacts of plant breeding on improved genepools, not only narrowing or widening their genetic base, but also shifting their genetic background. In general, the genome-wide reduction of crop genetic diversity accompanying genetic improvement over time is minor, but allelic reduction at individual chromosomal segments is substantial. More efforts are needed to assess what proportion of lost alleles is associated with undesirable traits.

scholarly journals Genome-wide mapping of genomic DNA damage: methods and implications

2021 ◽  
Author(s):  
Stefano Amente ◽  
Giovanni Scala ◽  
Barbara Majello ◽  
Somaiyeh Azmoun ◽  
Helen G. Tempest ◽  
...  
Keyword(s):  
Dna Damage ◽  
Genomic Dna ◽  
Positional Information ◽  
Cellular Function ◽  
Molecular Approaches ◽  
Genome Wide ◽  
Genomic Location ◽  
Mutational Hotspots ◽  
Genome Wide Data ◽  
The Impact

AbstractExposures from the external and internal environments lead to the modification of genomic DNA, which is implicated in the cause of numerous diseases, including cancer, cardiovascular, pulmonary and neurodegenerative diseases, together with ageing. However, the precise mechanism(s) linking the presence of damage, to impact upon cellular function and pathogenesis, is far from clear. Genomic location of specific forms of damage is likely to be highly informative in understanding this process, as the impact of downstream events (e.g. mutation, microsatellite instability, altered methylation and gene expression) on cellular function will be positional—events at key locations will have the greatest impact. However, until recently, methods for assessing DNA damage determined the totality of damage in the genomic location, with no positional information. The technique of “mapping DNA adductomics” describes the molecular approaches that map a variety of forms of DNA damage, to specific locations across the nuclear and mitochondrial genomes. We propose that integrated comparison of this information with other genome-wide data, such as mutational hotspots for specific genotoxins, tumour-specific mutation patterns and chromatin organisation and transcriptional activity in non-cancerous lesions (such as nevi), pre-cancerous conditions (such as polyps) and tumours, will improve our understanding of how environmental toxins lead to cancer. Adopting an analogous approach for non-cancer diseases, including the development of genome-wide assays for other cellular outcomes of DNA damage, will improve our understanding of the role of DNA damage in pathogenesis more generally.

scholarly journals Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina

2018 ◽  
Vol 115 (4) ◽  
pp. 816-821 ◽  
Author(s):  
Benjamin Laenen ◽  
Andrew Tedder ◽  
Michael D. Nowak ◽  
Per Toräng ◽  
Jörg Wunder ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mating System ◽  
Purifying Selection ◽  
Mating Strategies ◽  
Genomic Variation ◽  
The Arctic ◽  
Mixed Mating ◽  
Genome Wide ◽  
Arabis Alpina ◽  
The Impact

Plant mating systems have profound effects on levels and structuring of genetic variation and can affect the impact of natural selection. Although theory predicts that intermediate outcrossing rates may allow plants to prevent accumulation of deleterious alleles, few studies have empirically tested this prediction using genomic data. Here, we study the effect of mating system on purifying selection by conducting population-genomic analyses on whole-genome resequencing data from 38 European individuals of the arctic-alpine crucifer Arabis alpina. We find that outcrossing and mixed-mating populations maintain genetic diversity at similar levels, whereas highly self-fertilizing Scandinavian A. alpina show a strong reduction in genetic diversity, most likely as a result of a postglacial colonization bottleneck. We further find evidence for accumulation of genetic load in highly self-fertilizing populations, whereas the genome-wide impact of purifying selection does not differ greatly between mixed-mating and outcrossing populations. Our results demonstrate that intermediate levels of outcrossing may allow efficient selection against harmful alleles, whereas demographic effects can be important for relaxed purifying selection in highly selfing populations. Thus, mating system and demography shape the impact of purifying selection on genomic variation in A. alpina. These results are important for an improved understanding of the evolutionary consequences of mating system variation and the maintenance of mixed-mating strategies.

scholarly journals Paleo-Eskimo genetic legacy across North America

2017 ◽  
Author(s):  
Pavel Flegontov ◽  
N. Ezgi Altinişik ◽  
Piya Changmai ◽  
Nadin Rohland ◽  
Swapan Mallick ◽  
...  
Keyword(s):  
Native American ◽  
North America ◽  
Allele Frequency ◽  
Genetic Relationship ◽  
Rare Allele ◽  
Comprehensive Model ◽  
Haplotype Sharing ◽  
New Methods ◽  
Genome Wide ◽  
Genome Wide Data

AbstractPaleo-Eskimos were the first people to settle vast regions of the American Arctic around 5,000 years ago, and were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yupik. The genetic relationship between Paleo-Eskimos and Native American populations remains uncertain. We analyze ancient and present-day genome-wide data from the Americas and Siberia, including new data from Alaskan Iñupiat and West Siberian populations, and the first genome-wide DNA from ancient Aleutian Islanders, ancient northern Athabaskans, and a 4,250-year-old individual of the Chukotkan Ust'-Belaya culture. Employing new methods based on rare allele and haplotype sharing as well as established methods based on allele frequency correlations, we show that Paleo-Eskimo ancestry is widespread among populations who speak Na-Dene and Eskimo-Aleut languages. Using phylogenetic modelling with allele frequency correlations and rare variation, we present a comprehensive model for the complex peopling of North America.

Sign in / Sign up

Export Citation Format

Share Document