Tag: ADMIXTURE

The Evolution from HG19 to HG38

Welcome to another blog post! ‍ Reference genomes are essential benchmarks of a species’ genome that facilitate the accurate comparison of individual genomes and are crucial tools for identifying genetic variants and diagnosing rare diseases. Here, we will explore the evolution of the human reference genome, focusing on the transition…

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Genomic insights into Plasmodium vivax population structure and diversity in central Africa | Malaria Journal

Hamblin MT, Di Rienzo A. Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am J Hum Genet. 2000;66:1669–79. Article  CAS  PubMed  PubMed Central  Google Scholar  Hamblin MT, Thompson EE, Di Rienzo A. Complex signatures of natural selection at the Duffy blood group…

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Characterization of the Spectrum of Mitochondrial DNA Nucleotide Substitutions in Human Populations in High Altitude Environments

Burtscher, J., Mallet, R.T., Pialoux, V., et al., Adaptive responses to hypoxia and/or hyperoxia in humans, Antioxid. Redox Signal., 2022, vol. 37, pp. 887—912. doi.org/10.1089/ars.2021.0280 Article  PubMed  Google Scholar  Chandel, N.S., McClintock, D.S., Feliciano, C.E., et al., Reactive oxygen species generated at mitochondrial complex III stabilize hypoxia-inducible factor-1alpha during hypoxia: a…

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Characterization of runs of Homozygosity revealed genomic inbreeding and patterns of selection in indigenous sahiwal cattle

Almeida OAC, Moreira GCM, Rezende FM et al (2019) Identification of selection signatures involved in performance traits in a paternal broiler line. BMC Genomics 20:1–20. doi.org/10.1186/s12864-019-5811-1 Article  Google Scholar  Alshawi A, Essa A, Al-Bayatti S, Hanotte O (2019) Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and…

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Assessment of genetic diversity, population structure and wolf-dog hybridisation in the Eastern Romanian Carpathian wolf population

Kershaw, F. et al. The Coalition for Conservation Genetics: Working across organizations to build capacity and achieve change in policy and practice. Conserv. Sci. Pract. 4, e12635 (2022). Article  Google Scholar  Waits, L. P. & Paetkau, D. Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations…

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Call for papers – Ancient DNA

Genome Biology is calling for submissions to our Collection on the extraction, sequencing, and analysis of genetic material from ancient biological remains, providing a unique window into the past.  The study of ancient DNA represents a pivotal frontier in genomics with profound implications for our understanding of history, evolution, ecology, and…

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Study uncovers unique genetic diversity in Australian Indigenous populations

Scientists at the Australian National University (ANU) have comprehensively analyzed the genomes of Australian Indigenous communities and found a rich genetic diversity. Their study is published in the journal Nature. Study: Indigenous Australian genomes show deep structure and rich novel variation. Image Credit: ChameleonsEye / Shutterstock Background Genetic structures of Australian Indigenous…

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Archaic Introgression Shaped Human Circadian Traits | Genome Biology and Evolution

Abstract When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultraviolet radiation and increased variation in…

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Indigenous Australian genomes show deep structure and rich novel variation

Inclusion and ethics The DNA samples analysed in this project form part of a collection of biospecimens, including historically collected samples, maintained under Indigenous governance by the NCIG11 at the John Curtin School of Medical Research at the Australian National University (ANU). NCIG, a statutory body within ANU, was founded…

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Benchmarking DNA isolation methods for marine metagenomics

Scheme of the study The overall pipeline of our study is presented in Fig. 1 and is described in detail in the methods section. We processed three types of samples: fresh water, sea sediment, and digestive system of a marine invertebrate M. gigas (“gut flora”). These samples were treated in triplicates…

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Infer ancestry for RNA-seq data

Infer ancestry for RNA-seq data 0 I generated VCF files with bcftools for 4 patient RNA-seq samples. I was also able to generate bed, bim, and fam files with PLINK for these files. I want some guidance on how to infer ancestry for these RNA-seq samples: How do I find…

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Whole genomes from Angola and Mozambique inform about the origins and dispersals of major African migrations

A novel collection of genomes from Cabinda, Angola and Maputo, Mozambique Genomic DNA was extracted using saliva samples collected with informed consent and sequenced using the Illumina HiSeq X™ platform to an average autosomal read depth of ~12X from 300 individuals sampled in Cabinda and 50 individuals sampled in Maputo…

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Population-specific distribution of TPMT deficiency variants

Introduction Thiopurine S-methyltransferase (TPMT) is a cytoplasmic enzyme that catalyzes the S-methylation of purine analogs, including azathioprine, 6-mercaptopurine (6-MP), and thioguanine.1 The metabolism of these drugs results in two types of metabolites: S-methylmercaptopurine and S-methylthioguanine, which are generally described as inactive metabolites, and S-methyl-thioinosine monophosphate, an inhibitor of de novo…

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Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing

Loftus, R. T., MacHugh, D. E., Bradley, D. G., Sharp, P. M. & Cunningham, P. Evidence for two independent domestications of cattle. Proc. Natl Acad. Sci. USA 91, 2757–2761 (1994). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Verdugo Marta, P. et al. Ancient cattle genomics, origins, and rapid turnover…

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It’s not ‘woke’ to portray prehistoric Europeans with dark skin. It’s evolution.

Picture this: Almost 6,000 years ago, a girl walks along Lolland’s south coast and spits a piece of birch tar into the reeds. It didn’t taste great, but it helped to soothe her tooth ache. Fast forward 6,000 years, Danish archaeologists working on the Fehmarnbelt project stumble across the piece…

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Pan-Cancer Analysis and Validation of Opioid-Related Receptors Reveals

Introduction The potential role of opioids used in oncology patients has been controversial. Epidemiological and retrospective studies have demonstrated that lower opioid doses and regional anesthesia (epidural, intrathecal, or paravertebral) for breast,1 colon,2 or melanoma3 are linked to lower rates of cancer recurrence, while general anesthesia with high opioid doses…

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Analysis of nucleoporin 107 overexpression

Introduction Lung cancer is one of the most common types of cancer worldwide and the leading cause of cancer death.1 The main category of lung cancer is non-small cell lung cancer, accounting for about 85%, and lung adenocarcinoma, as a kind of non-small cell lung cancer, is the most frequently…

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Unraveling the mitochondrial phylogenetic landscape of Thailand reveals complex admixture and demographic dynamics

Higham, C. Early Mainland Southeast Asia (Antiquity (River Books Press Dist A C, 2014). Google Scholar  O’Connell, J. F. et al. When did homo sapiens first reach Southeast Asia and Sahul?. Proc. Natl. Acad. Sci. U. S. A. 115, 8482–8490 (2018). Article  ADS  PubMed  PubMed Central  Google Scholar  Freidline, S….

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Genetics study shines light on health dispari

image:  Left: Chromosome painting for an African American control carrying four inferred causal Sazonovs et al. variants. Right: Chromosome painting for an African American IBD case carrying four inferred causal Sazonovs et al. variants. The blue and pink colors in the chromosome paintings represent African and European, respectively. view more …

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Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance

De novo genome assemblies and genome annotation We assembled a de novo genome of a seven-year-old male SED from Ubon Ratchathani Zoo using a combination of Illumina short-reads (92.94 × coverage) and PacBio long-reads (61.6 × coverage) (GenBank accession number: JACCHN000000000). Additionally, we used MGI short-reads (52.15 × coverage) to assemble a de novo genome of…

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Bioconductor – CountClust

DOI: 10.18129/B9.bioc.CountClust     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see CountClust. Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models Bioconductor version: 3.10 Fits grade of membership models (GoM, also known as admixture models) to cluster RNA-seq gene expression…

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Study unveils complex admixture in European ancestry populations

A recent study published in the journal Nature Communications provides evidence of subcontinental admixture in people with European ancestry, in contrast to previous genetic association studies that recognize European ancestry populations as stratified and not as admixed.   Study: Unappreciated subcontinental admixture in Europeans and European Americans and implications for genetic epidemiology…

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When Did Humans Arrive in the Americas? Lice Help Answer That Head-Scratcher | Science

Contact between Europeans and Native Americans is recorded in the DNA of head lice. Vincent Smith, Natural History Museum, London, CC-BY 4.0 The first humans to arrive in America left scattered evidence behind, from ancient stone tools to fossilized footprints. And among descendants on either side of the Bering Strait,…

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Insights into expression patterns and immunotherapy response prediction

[1] D. Schadendorf, D. E. Fisher, C. Garbe, J. E. Gershenwald, J. Grob, A. Halpern, et al., Melanoma, Nat. Rev. Dis. Primers, 1 (2015), 15003. doi.org/10.1038/nrdp.2015.3 doi: 10.1038/nrdp.2015.3 [2] A. M. M. Eggermont, A. Spatz, C….

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Genome sequences of 36,000- to 37,000-year-old modern humans at Buran-Kaya III in Crimea

Hajdinjak, M. et al. Initial upper palaeolithic humans in europe had recent neanderthal ancestry. Nature 592, 253–257 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  Slimak, L. et al. Modern human incursion into Neanderthal territories 54,000 years ago at Mandrin, France. Sci. Adv. 8, eabj9496 (2022). Article  CAS  PubMed  PubMed…

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IJMS | Free Full-Text | Whole-Genome Sequencing of 502 Individuals from Latvia: The First Step towards a Population-Specific Reference of Genetic Variation

1. Introduction Human population genetics benefitted from the completion of the human genome sequence [1], which was further advanced by creating the reference of global genome variation [2] and, finally, the establishment of regional references assessing fine details of local variation in whole-genome sequences. Although European populations are relatively well…

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Mexican Biobank advances population and medical genomics of diverse ancestries

Encuesta Nacional de Salud 2000 Since 1988, Mexico has established periodical National Health Surveys (Encuesta Nacional de Salud (ENSA), originally conceived as National Nutrition Surveys) for surveillance of Mexican population-based nutrition and health metrics. In this study, we use data and samples collected from the survey carried out in 2000,…

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Genotyping, sequencing and analysis of 140,000 adults from Mexico City

Recruitment of study participants The MCPS was established in the late 1990s following discussions between Mexican scientists at the National Autonomous University of Mexico (UNAM) and British scientists at the University of Oxford about how best to measure the changing health effects of tobacco in Mexico. These discussions evolved into…

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Habitat and climate influence hybridization among three genetically distinct Canada jay (Perisoreus canadensis) morphotypes in an avian hybrid zone complex

Adams RV, Burg TM (2015) Gene flow of a forest-dependent bird across a fragmented landscape. PLoS One 10:1–22 Article  Google Scholar  Aguillon S, Rohwer V (2022) Revisiting a classic hybrid zone: movement of the northern flicker hybrid zone in contemporary times. Evolution 76:1082–1090 Article  PubMed  Google Scholar  Aktas C (2020)…

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Does ploidy in variant calling affect admixture detection with TreeMix?

Does ploidy in variant calling affect admixture detection with TreeMix? 0 Admixture and hybridization are common in domesticated yeasts. I need to run TreeMix to detect or rule out (there isn’t much evidence for it in our strains at the moment, as very few alleles are shared with other groups)…

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Cuban genome, a particular witness to history

Our time is a specialist in creating absences. Ailton Krenak, Brazilian indigenous leader   Most of us have heard or treasure in our personal lineage the story of a great-grandmother or great-great-grandfather who came to Cuba to found, whether voluntarily or involuntarily, a new family history and, also, that of…

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Special Issue: Ancient DNA | Lab Manager

In this Special Issue of Science, three Reviews highlight how recent advances in the field of ancient DNA have greatly advanced our understanding of the evolutionary history of many plants and animals, including our own species. “This special issue examines the changing landscape of how ancient DNA (aDNA) is studied…

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Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits

Swingle, W. T. & Reece, P. C. In The Citrus Industry, History, World Distribution, Botany, and Varieties, Vol. 1 (eds Reuther, W. et al.) 190–143 (Univ. of California Press, 1967). Morton, C. M. & Telmer, C. New subfamily classification for the Rutaceae. Ann. Mo. Bot. Gard. 99, 620–641 (2014). Article …

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Molecular classification of hormone receptor-positive HER2-negative breast cancer

Siegel, R. L., Miller, K. D. & Jemal, A. Cancer statistics, 2020. CA Cancer J. Clin. 70, 7–30 (2020). Article  PubMed  Google Scholar  Huppert, L. A., Gumusay, O., Idossa, D. & Rugo, H. S. Systemic therapy for hormone receptor-positive/human epidermal growth factor receptor 2-negative early stage and metastatic breast cancer….

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Probing the deep genetic structure of Africa

image: Namib desert in the southwest of Angola. view more  Credit: © Sandra Oliveira Africa is the birthplace of modern humans and the continent with the highest level of genetic diversity. While ancient DNA studies are revealing some aspects of the genetic structure of Africa before the spread of food production,…

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Dingoes found to have more harmful mutations than most inbred dog breeds

(a) The scatter graph showing the results from the principal component analysis (PCA) using the whole genomes of dogs, dingoes, and wolves. (b) The proportion of genetic admixture in each canine genome is shown. This analysis was performed assuming four ancestries for canines (K = 4). Credit: Ecology and Evolution (2023). DOI:…

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More than a decade of genetic research on the Denisovans

Stoneking, M. An Introduction to Molecular Anthropology (Wiley, 2017). Fuhlrott, J. C. & Schaaffhausen, H. Über die Knochenfunde aus dem Neandertal bei Mettmann. Verhandlungen naturwissenschaftlicher-historischer Ver. preussisch Rheinl. Westfal. Correspondenz-Bl. 14, 50–52 (1857). Google Scholar  Meyer, M. et al. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos…

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Association analysis of agronomic traits and construction of genetic networks by resequencing of 306 sugar beet (Beta vulgaris L.) lines

Genome resequencing approach for genotyping 306 sugar beet germplasm resources In this study, we performed high-depth genome-wide resequencing of 306 sugar beet accessions using an Illumina HiSeq 2000 sequencer, obtaining 1977.12 Gb of sequencing data. This collection included 72 endemic accessions from Northeast China (Harbin), 114 endemic accessions from North China…

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The genomic footprint of whaling and isolation in fin whale populations

Samples and sequencing Tissue samples from 50 fin whales (Balaenoptera physalus) were collected using a standard protocol to obtain skin biopsies from free-ranging cetacean species, which use a small stainless-steel biopsy dart deployed from a crossbow or rifle73,74. These samples were collected throughout the Eastern North Pacific (ENP; N = 30, represented…

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Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes

Orr, H. A. The genetic theory of adaptation: A brief history. Nat. Rev. Genet. 6, 119–127 (2005). Article  CAS  PubMed  Google Scholar  Dillon, M. E. & Lozier, J. D. Adaptation to the abiotic environment in insects: the influence of variability on ecophysiology and evolutionary genomics. Curr. Opin. Insect Sci. 36,…

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West Asian Admixture on Gedmatch

Can anyone tell me what’s exactly the “West Asian admixture” stands for and what are the differences between that and Caucasian admixture or Gedrosian admixture? Or are all these admixtures same? Thanks. west asian = from Anatolia, the caucasus, north of the Zargos mountains, Iran/Paersia, Balochi, Gedrosian, Bactrians, Sogdians, turkmenisatn,…

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Ancient DNA reveals genetic admixture in China during tiger evolution

Johnson, W. E. et al. The late Miocene radiation of modern felidae: a genetic assessment. Science 311, 73–77 (2006). Article  CAS  PubMed  Google Scholar  Li, G., Davis, B. W., Eizirik, E. & Murphy, W. J. Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae). Genome Res. 26,…

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How heteroplasmic mutations influence aging

The interesting phenomenon known as heteroplasmic mutations, which occur in mitochondrial DNA, is key to understanding the riddles of age-related disorders.  The existence of various genetic differences inside a person’s mitochondrial DNA pool is referred to as these mutations.  Diverse cellular landscapes are produced by heteroplasmic mutations, which differ from…

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Analysis of endoplasmic reticulum stress-related gene signature for the prognosis and pattern in diffuse large B cell lymphoma

Swerdlow, S. H. et al. The 2016 revision of the World Health Organization classification of lymphoid neoplasms. Blood 127, 2375–2390 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Sehn, L. H. & Salles, G. Diffuse large B-cell lymphoma. N. Engl. J. Med. 384, 842–858 (2021). Article  CAS  PubMed  PubMed Central …

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dark skin, bald head, Anatolian ancestry

LEIPZIG.- tzi’s genome was decoded for the first time more than ten years ago. This was also the first time the genome of a mummy had been sequenced. The results provided important insights into the genetic makeup of prehistoric Europeans. Advances in sequencing technology have now enabled a research team…

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Dark skin, bald head, Anatolian ancestry — ScienceDaily

A research team has used advanced sequencing technology to analyze Ötzi’s genome to obtain a more accurate picture of the Iceman’s appearance and genetic origins. Ötzi’s genome was decoded for the first time more than ten years ago. This was also the first time the genome of a mummy had…

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Reanalysis of Iceman’s genome reveals dark skin, baldness and Anatolian ancestry

Since 2012, which is when Ötzi’s genome was sequenced for the first time, DNA sequencing technologies have advanced enormously. This new study reveals that compared to other contemporary Europeans, Ötzi’s genome had an unusually high proportion of genes in common with those of early farmers from Anatolia, that his skin…

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Infection of sheep by Echinococcus multilocularis in Gansu, China: evidence from mitochondrial and nuclear DNA analysis | Infectious Diseases of Poverty

Craig PS, Hegglin D, Lightowlers MW, Torgerson PR, Wang Q. Echinococcosis: control and prevention. Adv Parasitol. 2017;96:55–158. Article  CAS  PubMed  Google Scholar  Deplazes P, Dinkel A, Mathis A. Molecular tools for studies on the transmission biology of Echinococcus multilocularis. Parasitology. 2003;127(Suppl):S53–61. Article  CAS  PubMed  Google Scholar  Deplazes P, Rinaldi L,…

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Dissecting human population variation in single-cell responses to SARS-CoV-2

Sample collection The individuals of self-reported African (AFB) and European (EUB) descent studied are part of the EVOIMMUNOPOP cohort18. In brief, 390 healthy male donors (188 AFB and 202 EUB) were recruited between 2012 and 2013 in Ghent (Belgium), thus, before the COVID-19 pandemic. Blood was obtained from the healthy…

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Stone Age Population Patterns in Central, Eastern Europe Spelled Out in Ancient DNA Study

Uppsala University researchers reporting in Communications Biology outline population patterns identified in Central and Eastern Europe during the Stone Age, or Neolithic, transition, highlighting hunter-gatherer groups present in different parts of the region prior to the arrival of agricultural migrants from Anatolia. Using whole-genome sequencing, the team profiled 56 Mesolithic,…

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Multiple domestications of Asian rice

Doebley, J. F., Gaut, B. S. & Smith, B. D. The molecular genetics of crop domestication. Cell 127, 1309–1321 (2006). Article  CAS  PubMed  Google Scholar  Allaby, R. G., Fuller, D. Q. & Brown, T. A. The genetic expectations of a protracted model for the origins of domesticated crops. Proc. Natl…

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The meaning of wild: Genetic and adaptive consequences from large-scale releases of domestic mallards

Grabenstein, K. C. & Taylor, S. A. Breaking barriers: causes, consequences, and experimental utility of human-mediated hybridization. Trends Ecol. Evol. 33, 198–212 (2018). Article  PubMed  Google Scholar  Crispo, E., Moore, J. S., Lee‐Yaw, J. A., Gray, S. M. & Haller, B. C. Broken barriers: human‐induced changes to gene flow and…

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Genetic profiles of Schistosoma haematobium parasites from Malian transmission hotspot areas | Parasites & Vectors

Agniwo P, Sidibé B, Diakité AT, Niaré SD, Guindo H, Akplogan A, et al. Ultrasound aspects and risk factors associated with urogenital schistosomiasis among primary school children in mali. Infect Dis Poverty. 2022;3:80. Google Scholar  Angora EK, Vangraefschepe A, Allienne J-F, Menan H, Coulibaly JT, Meïté A, et al. Population…

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Einkorn genomics sheds light on history of the oldest domesticated wheat

Plant materials The plant material used in this study was selected from a collection of 733 accessions of wild and domesticated einkorn held at the Wheat Genetics Resource Center (WGRC) at Kansas State University42. To generate reference assemblies, we selected one domesticated einkorn accession (T. monococcum L. subsp. monococcum; TA10622)…

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Contrasting whole-genome and reduced representation sequencing for population demographic and adaptive inference: an alpine mammal case study

Aguirre-Liguori JA, Ramírez-Barahona S, Gaut BS (2021) The evolutionary genomics of species’ responses to climate change. Nat Ecol Evol 5:1350–1360. doi.org/10.1038/s41559-021-01526-9 Article  PubMed  Google Scholar  Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA (2016) Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet 17:81–92….

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Ancient DNA Analysis Uncovers Middle Bronze Age Population Shift in East-Central Europe

NEW YORK – New research suggests that people living in East-Central Europe between 3,200 and 4,400 years ago, during the Early and Middle Bronze Age, belonged to patrilocal populations with European hunter-gatherer ancestry that participated in collective burials resembling those found in earlier Neolithic populations. “The demographic history of East-Central…

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A diverse ancestrally-matched reference panel increases genotype imputation accuracy in a underrepresented population

In the present study, we enrolled 412 participants from the Southeast Asian Brugada syndrome cohort (ClinicalTrials.gov number, NCT04232787). The study was approved by the Institutional Review Board (IRB) of the Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand (IRB No. 431/58). All methods were performed in accordance with relevant guidelines/regulations. Informed…

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Whole genome sequencing reveals signals of adaptive admixture in Creole cattle

Rodero Serrano, E., Rodero Franganillo, A. & Delgado-Bermejo, J. V. Primitive andalusian livestock and their implications in the discovery of America. Arch. Zootec. 41(154), 383–400 (1992). Google Scholar  Primo, A. El hanado bovino ibérico en las Américas: 500 años después. Arch. Zootec. 41(154), 421–432 (1992). Google Scholar  Maillard, J.-C. &…

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Extensive pedigrees reveal the social organization of a Neolithic community

Fox, R. Kinship and Marriage: An Anthropological Perspective (Cambridge Univ. Press, 1983). Morgan, L. H. Ancient Society: Or, Researches in the Lines of Human progress from Savagery, Through Barbarism to Civilization (C. H. Kerr, 1877). Lévi-Strauss, C. The Elementary Structures of Kinship (Beacon Press, 1971). Schneider, D. M. A Critique…

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Sequencing Study Shines Light on Population Dynamics Spanning Copper Age in Western Eurasia

NEW YORK – New research on ancient DNA samples spanning the Neolithic, Copper, and Early Bronze Age has spelled out population events that accompanied the spread of farming and subsequent shifts to pastoralist lifestyles in western Eurasia. “Our study highlights the importance of integrating archaeological evidence on the socio-economic background…

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Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Ethics We confirm our research complies with all relevant ethical regulations and was approved by the animal ethics committee of the School of Biology at the University of St Andrews on 26 July 2018 www.st-andrews.ac.uk/research/environment/committees/awerb/. The three new contemporary dolphin samples analysed in this study were collected under the relevant…

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Ancient Bottlenose Dolphin Genome Gives Insight Into Coastal Adaptations

Common bottlenose dolphins (Tursiops truncatus) rapidly adapted to new coastal environments when they emerged thousands of years ago, a new study in Nature Communications reports. An international team of researchers analyzed the genomes of four ancient dolphins that lived in the eastern North Atlantic Ocean between about 5,600 years and…

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Extinct warbler was distinct species

New research has shown that the presumed extinct Bachman’s Warbler was a full species. Bachman’s Warbler was last seen in North America some 40 years ago, with the last widely accepted sightings in the 1960s. Although not yet officially recognised as Extinct by IUCN, the species is widely believed to…

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Identification of pyroptosis-related signature and development of a novel prognostic model in diffuse large B-cell lymphoma

Aglietti RA, Dueber EC (2017) Recent Insights into the Molecular Mechanisms Underlying Pyroptosis and Gasdermin Family Functions. Trends Immunol 38:261–271. doi.org/10.1016/j.it.2017.01.003 Article  CAS  PubMed  Google Scholar  Ahechu P et al (2018) NLRP3 inflammasome: a possible link between obesity-associated low-grade chronic inflammation and colorectal cancer development. Front Immunol 9:2918. doi.org/10.3389/fimmu.2018.02918 Article …

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interpretation of qpAdm results

interpretation of qpAdm results 0 Hello I am using the R version of Admixtools. My goal is to find if a wheat population (DEW) was created by an admixture event between 2 populations (JUD & WEWNE).The data I use is of 6 populations with 16-134 individuals genotyped with 8100 SNP….

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An extended mtDNA phylogeography for the alpine newt illuminates the provenance of introduced populations

Abstract Many herpetofauna species have been introduced outside of their native range. MtDNA barcoding is regularly used to determine the provenance of such populations. The alpine newt has been introduced across the Netherlands, the United Kingdom and Ireland. However, geographical mtDNA structure across the natural range of the alpine newt…

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bad alloc with admixture32

bad alloc with admixture32 0 Hello everyone, I’m having a problem calculating delta K with the admixture32 pipeline on my RADseq data generated by STACKS. Here is the command I use: #!/bin/bash #SBATCH -J mpi_job #SBATCH –nodes=1 #SBATCH –time=80:00:00 #SBATCH –cpus-per-task=10 #SBATCH –mem=20G for K in 4 5; \ do…

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Whole mitogenomes reveal that NW Africa has acted both as a source and a destination for multiple human movements

Callaway, E. Oldest Homo sapiens fossil claim rewrites our species’ history. Nature. doi.org/10.1038/NATURE.2017.22114 (2017). Article  PubMed  Google Scholar  Lucas-Sánchez, M., Serradell, J. M. & Comas, D. Population history of North Africa based on modern and ancient genomes. Hum. Mol. Genet. 30(R1), R17–R23. doi.org/10.1093/HMG/DDAA261 (2021). Article  PubMed  Google Scholar  Scerri, E….

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Incongruence in the phylogenomics era

Simpson, G. G. The Principles of Classification and a Classification of Mammals Vol. 85 (American Museum of Natural History, 1945). Jarvis, E. D. et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320–1331 (2014). Article  CAS  PubMed  PubMed Central  Google Scholar  Parks,…

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harappaworld gedmatch

17 89.3% utahn-white (hapmap) + 10.7% georgia-jew (behar) @ 1.21 12 italian + orcadian + orcadian + utahn-white @ 2.277 Any feedback anyone might give me would be very appreciated. ok so i have read through all the instructions and notes and cant figure out how to get standardize.r to…

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Construction & ID of an NLRs-associated Prognostic Signature

Introduction Skin cutaneous melanoma (SKCM) is the most severe dermatologic malignancy, and its incidence has increased worldwide in recent years.1 SKCM accounts for 1% of all skin cancer patients, yet it is responsible for roughly 80% of all skin cancer deaths.2 Early-stage SKCM (localized or regional) can be surgically removed,…

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Postdoctoral Scholar Department of Genetics, Genomics and Bioinformatics in Memphis, TN for Memphis

Conduct analysis of admixture patterns in the Biorepository and Integrative Genomics (BIG) Initiative cohort using sequence data and pangenomic techniques. – Create individual-level maps of genetic ancestry for all subjects in the cohort. – Develop pipelines and methodologies for admixture mapping of disease-related phenotypic traits. – Enhance the set of…

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Scoping review of Culex mosquito life history trait heterogeneity in response to temperature | Parasites & Vectors

Zell R. Global climate change and the emergence/re-emergence of infectious diseases. Int J Med Microbiol IJMM. 2004;293:16–26. PubMed  Google Scholar  Gage KL, Burkot TR, Eisen RJ, Hayes EB. Climate and vectorborne diseases. Am J Prev Med. 2008;35:436–50. Article  PubMed  Google Scholar  Elbers ARW, Koenraadt CJM, Meiswinkel R. Mosquitoes and Culicoides…

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SNP analysis with an assembly

Hi there, I am new in SNP analyses so before starting doing anything I would like to check if my pipeline is correct. What I have now is : RNA-seq samples (.fq.gz) + Trinity assembly (from those reads). My model organism has not an assembled genome, that’s the way I…

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ddRAD sequencing based genotyping of six indigenous dairy cattle breeds of India to infer existing genetic diversity and population structure

Quality control, alignment and SNP calling The ddRAD sequencing based genotyping of 58 individuals belonging to six native cattle breeds; Gir, Sahiwal, Tharparkar, Rathi, Red Sindhi and Kankrej cattle with their geographical and ecological distribution (Fig. 1) including the productive purpose, coat colour, representative agroclimatic zone, breeding tract, the geographical co-ordinate…

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A graph-based genome and pan-genome variation of the model plant Setaria

Variation and evolution in Setaria We collected genome-wide resequencing data for 630 wild (S. viridis), 829 landrace and 385 modern cultivated accessions from the Setaria genus with an average sequencing depth of ~15×, of which 1,004 were newly generated and 840 were from previous studies16,21 (Supplementary Table 1). After aligning…

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North African Agriculture Influenced by Incoming Neolithic Populations From Europe, the Levant

NEW YORK – By sequencing DNA from several ancient individuals in the Maghreb region, researchers have linked the transition from foraging to food production in northwestern Africa to the arrival of individuals from Iberia and the Levant, who appeared to introduce agricultural approaches that were quickly adopted by local populations….

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admixture plot ggplot2

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct. ggplot2 is a well-known data visualization package to use in R. As ggplot2 is well developed from the beginning, engineers can spend more…

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New genomic insights into the conformation of Lipizzan horses

The researchers noted that Lipizzan horses of a lighter type are associated with higher Arabian admixture proportions. They used a “horse shape space model” to gain genetic insights into the breed. Image by SparklingGirl Researchers have pinpointed the genetic origins of some body traits in Lipizzaners, in a step toward…

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Backcrossing to different parents produced two distinct hybrid species

Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinforma 12:246. doi.org/10.1186/1471-2105-12-246 Article  Google Scholar  Anderegg WRL, Flint A, Huang C-Y, Flint L, Berry JA, Davis FW et al. (2015) Tree mortality predicted from drought-induced vascular damage. Nat Geosci 8:367–371 Article  CAS  Google Scholar …

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Massive Reference Genome Project Characterizes Primate Variation

The need for a more complete understanding of primate genetic diversity is urgent, especially given the threats posed by factors such as climate change, habitat loss, and illegal trading and hunting. Characterizing primate variation not only allows us to better understand and conserve these species in the wild, but it…

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LSU Researchers Show Mobile Elements Monkeying Around the Genome

Mark Batzer is an elected fellow of the American Association for the Advancement of Science and a National Academy of Inventors senior member. His research at LSU has been supported by multiple federal and state agencies, including the National Institutes of Health, the National Science Foundation and the Louisiana Board…

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Pooled whole genome sequencing of the endangered Banff Springs Snail, Physella johnsoni, reveals genetic separation to P. gyrina and cryptic micro-geographical genetic structure

Allendorf FW, Hohenlohe PA, Luikart G (2010) Genomics and the future of conservation genetics. Nat Rev Genet 11:697–709. doi.org/10.1038/nrg2844 Article  CAS  PubMed  Google Scholar  Beheregaray LB, Caccone A (2007) Cryptic biodiversity in a changing world. J Biol. doi.org/10.1186/jbiol60 Article  PubMed  PubMed Central  Google Scholar  Bickford D, Lohman DJ, Sodhi NS…

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most rare haplogroups

The oldest haplogroup is haplogroup A00. B, (This followed the publication of: Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS. Haplogroup X is one of rarest matrilinear haplogroups in Europe, being found only is about 1% of the overall population. The cost of full Y-DNA and mtDNA sequence tests…

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Genomic variation in the genus Beta based on 656 sequenced beet genomes

Beta accessions analysed in this study We analysed a large number of beet genomes on the molecular level making use of the more than 600 sequenced wild and cultivated Beta accessions published recently3 comprising Beta vulgaris ssp. vulgaris (mainly sugar beet, plus a few accessions described as fodder beet or…

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Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds

Asalone KC, Ryan KM, Yamadi M, Cohen AL, Farmer WG, George DJ, Joppert C, Kim K, Mughal MF, Said R, Toksoz-Exley M, Bisk E, Bracht JR (2020) Regional sequence expansion or collapse in heterozygous genome assemblies. PLoS Comput Biol. doi.org/10.1371/journal.pcbi.1008104 Article  PubMed  PubMed Central  Google Scholar  Bankevich A, Nurk S,…

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New study sheds light on complex genetics of autism in East African families: Newsroom

(Photo Credit: Getty Images) DALLAS – May 22, 2023 – UT Southwestern Medical Center researchers have identified hundreds of genomic variants associated with autism spectrum disorder (ASD) in East African families who have a markedly higher prevalence of the neurodevelopmental condition than other populations worldwide. The study, published in Cell Genomics, is the…

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Screening/validation of pivotal pancreatic cancer gene DPYD

Introduction Pancreatic cancer (PC) is a malignant tumor with a very high mortality rate for which there is no effective treatment other than surgery.1,2 PC is prone to metastasis and invasion in the early stage, and there is no effective means for early detection. Most patients often have cancer metastasis…

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Identifying signatures of positive selection in human populations from North Africa

Henn, B. M. et al. Genomic ancestry of North Africans supports back-to-Africa migrations. PLOS Genet. 8, e1002397 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Arauna, L. R. et al. Recent historical migrations have shaped the gene pool of Arabs and Berbers in North Africa. Mol. Biol. Evol. 34, 318–329…

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Human Evolution Study Suggests Multiple Early Lineages in Africa

NEW YORK – Investigators at McGill University; the University of California, Davis; and other centers in the US and South Africa have used genetic data from present-day populations in southern, eastern, and western Africa to retrace human origins on the continent. Based on the results, they came up with a…

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Multi-ancestry meta-analysis and fine-mapping in Alzheimer’s disease

Tanzi RE, Bertram L. New frontiers in Alzheimer’s disease genetics. Neuron. 2001;32:181–4. Article  CAS  PubMed  Google Scholar  Holland D, Frei O, Desikan R, Fan C-C, Shadrin AA, Smeland OB, et al. The genetic architecture of human complex phenotypes is modulated by linkage disequilibrium and heterozygosity. Genetics. 2021;217:iyaa046. Article  PubMed  PubMed…

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Tracing the introduction of the invasive common myna using population genomics

Acclimatisation (6 January 1877) Southland Times. Page 2. paperspast.natlib.govt.nz/newspapers/ST18770105.2.7. Accessed 21 January 2022 Adamack AT, Gruber B (2014) PopGenReport: simplifying basic population genetic analyses in R. Methods Ecol Evol 5:384–387. doi.org/10.1111/2041-210x.12158 Article  Google Scholar  Andrews S (2010) FastQC. A quality control tool for high throughput sequence data. www.bioinformatics.babraham.ac.uk/projects/fastqc/ Andrews KR,…

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Integrated microbiome-metabolome-genome axis data of Laiwu and Lulai pigs

Animal rearing and samples collection Our experiment was designed to compare eight female Laiwu pigs (LW) with eight female Lulai pigs (LU) which crossbred between LW and Yorkshire breeds. All pigs were born and raised for approximately two years (715 ± 33 days, Table 1) under uniform housing and feeding conditions at Jing-Qi-Shen…

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Bantu people came from Congo, genetic data shows

This is a relatively well-known story. About 4,000 years ago, a band of Bantu speakers left West Africa and moved to colonise half of Africa. They pushed through the Congo rainforest spreading to southern and eastern Africa. Some eventually settled in what is modern-day Kenya. They migrated further from Kenya…

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How can I create more accurate admixture plot like this?

How can I create more accurate admixture plot like this? 0 I made simple vcf file processing as plink –vcf Asp_multicall2.vcf.gz –double-id –allow-extra-chr \ –set-missing-var-ids @:# \ –set-missing-var-ids @:# \ for K in 1 2 3 4 5 do admixture –cv plink.bed $K | tee log${K}.out done As you can…

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Electronic structure, chemical bonding features, and electron charge density of the double-cubane single crystal [Sb7S8Br2](AlCl4)3 | Applied Physics Letters

The present calculations were performed using all-electron full potential linearized augmented plane wave method based on the density functional theory. We have optimized the structure of the double-cubane single crystal [Sb7S8Br2](AlCl4)3⁠, starting with the x-ray diffraction data Zhang et al, [J. Am. Chem. Soc. 131, 9896 (2009)], by minimization of the…

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Detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole-genome sequencing

After trimming the sequence data obtained in this study based on strict criteria, more than 95% of all read pairs were mapped to the Gallus reference genome, although some variation in depth was observed. Thus, the assembled sequence data were considered high quality. In addition, the detection of junglefowl ERV-LTRs…

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Possible origins and implications of atypical morphologies and domestication-like traits in wild golden jackals (Canis aureus)

Camera surveillance and spatial analyses Camera surveillance took place between August and December 2020, at twelve ~ 30 km2 sites located in the central and northern Golan Heights (Supplementary Table 1). The sampling sites designated for this study belonged to four different land-use categories: “high culling risk”, “low culling risk”, nature reserves…

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Resurrecting the alternative splicing landscape of archaic hominins using machine learning

Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014). Article  PubMed  Google Scholar  Prüfer, K. et…

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Ancient Sequences Provide Window Into Pict Population History, Modern-Day Relationships

NEW YORK – New ancient DNA research has revealed genetic relationships for the Picts, a mysterious and culturally distinct group that ruled Scotland and other parts of northern Britain during the first millennium CE, during a period of Roman occupation at sites to the south. “Overall, our results are in…

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