Tag: ADMIXTURE

Create simulated G25 coords from most Gedmatch calcs

There is added to Allelocator new script (author: Nganasankhan) which allows creation G25 simulated coords from most Gedmatch / Admixture Studio calculators. allelocator.ovh/simulatedg25.html Calculator results which could be used as input: Eurogenes K13 Eurogenes K15 Eurogenes K36 LM Genetics K47 MDLP K27 MDLP World 22 Michal World K25 Puntdnal K12…

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Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data

Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L et al. (2015) Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat Genet 47:217–225 CAS  PubMed  Article  Google Scholar  Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC…

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Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

Sampling the radiation To understand the phylogenetic relationships between Alpine whitefish, we carried out whole-genome resequencing on 96 previously collected whitefish (with associated phenotypic measurements including standard length and gill-raker counts; collected in accordance with permits issued by the cantons of Zurich (ZH128/15), Bern (BE68/15), and Lucerne (LU04/14); these fish…

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AURKA is a prognostic potential therapeutic target in skin cutaneous melanoma modulating the tumor microenvironment, apoptosis, and hypoxia

Aran D, Hu Z, Butte AJ (2017) xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biol 18(1):220. doi.org/10.1186/s13059-017-1349-1 CAS  Article  PubMed  PubMed Central  Google Scholar  Bajor DL, Mick R, Riese MJ, Huang AC, Sullivan B, Richman LP, Torigian DA, George SM, Stelekati E, Chen F, Melenhorst JJ, Lacey SF,…

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Genetic diversity of loquat (Eriobotrya japonica) revealed using RAD-Seq SNP markers & More Science News

Our research analyzed the genetic diversity of 95 cultivars and strains of loquat collected from everywhere in the world. On the premise of the evaluation of the inhabitants construction of 19 Chinese loquat cultivars and strains by RAD-Seq, Hubei Province in China has been recommended as the middle of origin…

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Seven Bridges, Brazilian Researchers Applying Graph Analysis to Build Diverse Reference Genome

CHICAGO – The latest of Seven Bridges Genomics’ efforts to diversify reference genomes is its largest and perhaps most complex to date, an attempt to address the Brazilian population. The Charlestown, Massachusetts-based bioinformatics company recently joined with the University of São Paulo (USP), the Associação Genomas Brasil (Brazil Genome Association),…

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Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)

Arlinghaus, R. et al. Governing the recreational dimension of global fisheries. Proc. Nat. Acad. Sci. USA 116, 5209–5213 (2019). CAS  PubMed  PubMed Central  Article  Google Scholar  Cowx, I. G. & Gerdeaux, D. The effects of fisheries management practises on freshwater ecosystems. Fish. Manag. Ecol. 11, 145–151 (2004). Article  Google Scholar …

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Frontiers | Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data

Introduction Incipient species are critical for evolutionary biologists to study speciation, but they also challenge taxonomy due to gene flow or ancestral polymorphism. The former and contrasting population size lead to larger intraspecific than interspecific variations, a phenomenon called the species-definition anomaly zone (Jiao and Yang, 2021). The latter results…

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Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure

Cattle are among the largest populations of domesticated animals and used as food resources for humans; therefore, their phenotypes and genetic structure have been shaped by artificial selection for human needs and natural adaptation to environmental changes. The phenotypic selection causes genomic changes in breeding traits within breeds, resulting in…

Continue Reading Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure

Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species

Sampling Six dioecious fig species (F. erecta, F. formosana, F. vaccinioides, F. abelii, F. pyriformis, and F. variolosa) and their pollinator wasp species were examined in this study. As mentioned in the Introduction, these fig species were considered to be well suited for this study because they are distributed in…

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Understanding signatures of positive natural selection in human zinc transporter genes

Datasets and populations We first compiled whole-genome sequencing data to analyze the patterns of variation in ZTGs on two geographical levels. Thus, we explored a worldwide dataset of 2,328 unrelated individuals representing 24 populations across Africa (AFR), Europe (EUR), East Asia (EAS), South Asia (SAS) and America (AMR), denoted as…

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Genomic variation from an extinct species is retained in the extant radiation following speciation reversal

Vamosi, J. C., Magallon, S., Mayrose, I., Otto, S. P. & Sauquet, H. Macroevolutionary patterns of flowering plant speciation and extinction. Annu. Rev. Plant Biol. 69, 685–706 (2018). CAS  PubMed  Google Scholar  Rhymer, J. M. & Simberloff, D. Extinction by hybridization and introgression. Annu. Rev. Ecol. Syst. 27, 83–109 (1996)….

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Genetic diversity and selection in Puerto Rican horses

Horses have been considered one of our most prized possessions, used for travel, work, food, and pleasure for at least five and a half millennia17,18,19,20. Nevertheless, the ancestry of various horse breeds and their characteristic traits remains unclear21. In this paper, we describe the patterns and the origins of genetic…

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Haplogroup M (mtDNA)

In human genetics, Haplogroup M is a human mitochondrial DNA (mtDNA) haplogroup. An enormous haplogroup spanning many continents, the macro-haplogroup M is a branch of the haplogroup L3. M is believed to have originated in Asia [Gonzalez et al., [www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1945034 Mitochondrial lineage M1 traces an early human backflow to Africa]…

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Systems biology analysis of human genomes points to key pathways conferring spina bifida risk

Significance Genetic investigations of most structural birth defects, including spina bifida (SB), congenital heart disease, and craniofacial anomalies, have been underpowered for genome-wide association studies because of their rarity, genetic heterogeneity, incomplete penetrance, and environmental influences. Our systems biology strategy to investigate SB predisposition controls for population stratification and avoids…

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upload ancestry dna to gedmatch

That fee is less expensive than retesting, but V4 customers should consider retesting to obtain fully compatible matching. By Brad Bergan. GEDmatch users may upload their autosomal DNA test data from commercial DNA companies to identify … Like 23and Me, it shows the proportion of your DNA from a particular…

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Diversity | Free Full-Text | MtDNA D-loop Diversity in Alpine Cattle during the Bronze Age

The Bronze Age in Europe is characterized by major socio-economic changes, including certain aspects of animal husbandry. In the Alpine region archaeozoological data, though not very abundant, reveal that cattle were the most important domestic animals in this time period. They were probably used differently in the lowlands than at…

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The faces of three ancient Egyptians appeared thanks to the remains of DNA more than 2,000 years ago

The faces of three ancient Egyptians are brought back to life thanks to DNA group of scientists Recreate The faces of three ancient Egyptian men using DNA that is more than 2,000 years old. According to the magazine NEWSWEEKIt is believed that this is the first time that modern techniques…

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Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas

Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664 CAS  PubMed  PubMed Central  Article  Google Scholar  Alexander DH, Shringarpure SS, Novembre J, Lange K (2015) Admixture 1.3 software manual. UCLA Hum Genet Softw Distrib, Los Angeles Google Scholar  Angert AL, Bontrager…

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Ancient DNA Analysis Highlights Three Ancestral Populations in Japan

NEW YORK – An ancient DNA analysis reaching back thousands of years has provided a more detailed view of the ancestral groups contributing to present-day populations in Japan, uncovering genetic signals from three historical populations spanning pre- and post-agricultural periods. “[O]ur study provides a detailed look into the changing genomic…

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Faces of Three Ancient Egyptians Brought to Life Using 2,000-Year-Old DNA

The faces of three ancient Egyptian men have been brought to life by scientists, using DNA that is more than 2,000 years old. This is thought to be the first time modern techniques have been used on human DNA of this age, with the trio of samples estimated to be…

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The sardine run in southeastern Africa is a mass migration into an ecological trap

INTRODUCTION Large-scale annual migrations occur in an extraordinary range of animals, from insects to the great whales. While the driving mechanisms of these migrations are varied and sometimes poorly understood, they often represent a way of optimizing conditions for breeding and adult fitness when these are in conflict. Often, populations…

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Parabon Recreates Egyptian Mummy Faces From Ancient DNA

New Snapshot methods for low-coverage sequencing bring hidden data to life Scientific Poster Image Scientific Poster Image Scientific Poster Image RESTON, Va., Sept. 15, 2021 (GLOBE NEWSWIRE) — At the 32nd International Symposium on Human Identification (ISHI), being held this week in Orlando, Florida, Parabon NanoLabs will unveil for the…

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What do biological anthropologists think of homemade ancestry tools like GEDmatch and Global25? : AskAnthropology

With consumer ancestry DNA tests available to many people today, we have the ability to extract our raw DNA data from those tests and input them into programs with admixture calculators like GEDmatch and Global25. They claim to be able to breakdown ancestry into different components and measure your distance…

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High frequency of an otherwise rare phenotype in a small and isolated tiger population

Significance Small and isolated populations have low genetic variation due to founding bottlenecks and genetic drift. Few empirical studies demonstrate visible phenotypic change associated with drift using genetic data in endangered species. We used genomic analyses of a captive tiger pedigree to identify the genetic basis for a rare trait,…

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Biomolecular insights into North African-related ancestry, mobility and diet in eleventh-century Al-Andalus

Uniparental genetic background of the Segorbe Giant We confirmed that the individual was genetically male (RY > 0.077; Supplementary Fig. S3), and both his uniparental markers point towards North African origins (Supplementary Table S2). He belongs to mtDNA haplogroup U6a1a1a (nomenclature according to Hernández et al.28). Although U6 in general, and U6a in…

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How do I perform a plot from admixture analysis with multiple runs

How do I perform a plot from admixture analysis with multiple runs 2 Hi all, I am wondering how I can perform a plot from admixture analysis with multiple runs. I have obtained 100 runs for each K value from 1 to 10. So my question is what to do…

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gmod prop hunt not working

I’ve let the server stay open so you can join it and test for yourself. Game Garry’s Mod. It’s just textures (and maps, if you need it) for use as an addon to Garry’s Mod. From hunting down everyday objects in Prop Hunt to strangling and trampling pigs in Open…

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Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands

Significance Some of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is…

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Use of GenotypeGVCFs in population genetic studies

Use of GenotypeGVCFs in population genetic studies 0 I have 16 whole genome sequenced samples from two populations (8 for each population). My goal is detection of signature of selection and introgression. I performed read cleaning, mapping to reference, mark duplication. SNP calling was performed using HaplotypeCaller in GATK for…

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Haplogroup H1e1a

Phylogenetic tree of complete haplogroup H1e1a sequences. Y-DNA Haplogroup R-M207 Summary Haplogroup R is defined by a DNA marker known as M207. Significant frequencies of sub-Saharan L haplogroups (6. Haplogroup H is a human mitochondrial DNA (mtDNA) haplogroup. The report also said 0. Just out of curiosity, I noticed that…

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Genome of a middle Holocene hunter-gatherer from Wallacea

1. McColl, H. et al. The prehistoric peopling of Southeast Asia. Science 361, 88–92 (2018). CAS  PubMed  Article  ADS  Google Scholar  2. Hasanuddin. Gua Panningnge di Mallawa, Maros: kajian tentang gua hunian berdasarkan artefak batu dan sisa fauna. Naditira Widya 11, 81–96 (2017). Article  Google Scholar  3. Bulbeck, D., Pasqua,…

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PNAS Papers on Turkish Populations, Pericentromeric Non-Coding RNA, Global Genome Repair

Editor’s Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted this week. An international team tallies genetic variation and population structure in present-day Turkey, using a combination of exome and whole-genome sequencing. Based on exome sequences for…

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