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Results 1 through 20 out of 3499

in category genetics

 

1: Massive migration from the steppe is a source for Indo-European languages in Europe

Wolfgang Haak, Iosif Lazaridis et al.

41,777 downloads (posted 10 Feb 2015)

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6. By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe.

https://rxivist.org/papers/10661
https://doi.org/10.1101/013433

2: Eight thousand years of natural selection in Europe

Iain Mathieson, Iosif Lazaridis et al.

34,076 downloads (posted 14 Mar 2015)

The arrival of farming in Europe around 8,500 years ago necessitated adaptation to new environments, pathogens, diets, and social organizations. While indirect evidence of adaptation can be detected in patterns of genetic variation in present-day people, ancient DNA makes it possible to witness selection directly by analyzing samples from populations before, during and after adaptation events. Here we report the first genome-wide scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet a...

https://rxivist.org/papers/10561
https://doi.org/10.1101/016477

3: The genetic structure of the world's first farmers

Iosif Lazaridis, Dani Nadel et al.

21,264 downloads (posted 16 Jun 2016)

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongl...

https://rxivist.org/papers/10357
https://doi.org/10.1101/059311

4: Ancient human genomes suggest three ancestral populations for present-day Europeans

Iosif Lazaridis, Nick Patterson et al.

18,258 downloads (posted 23 Dec 2013)

We sequenced genomes from a ~7,000 year old early farmer from Stuttgart in Germany, an ~8,000 year old hunter-gatherer from Luxembourg, and seven ~8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient ...

https://rxivist.org/papers/10732
https://doi.org/10.1101/001552

5: The Genomic History Of Southeastern Europe

Iain Mathieson, Songül Alpaslan Roodenberg et al.

16,231 downloads (posted 09 May 2017)

Farming was first introduced to southeastern Europe in the mid-7th millennium BCE - brought by migrants from Anatolia who settled in the region before spreading throughout Europe. To clarify the dynamics of the interaction between the first farmers and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient DNA data from 223 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document previously uncharacterized genetic structure, showing a West-Eas...

https://rxivist.org/papers/9684
https://doi.org/10.1101/135616

6: Detection of human adaptation during the past 2,000 years

Yair Field, Evan A Boyle et al.

15,875 downloads (posted 07 May 2016)

Detection of recent natural selection is a challenging problem in population genetics, as standard methods generally integrate over long timescales. Here we introduce the Singleton Density Score (SDS), a powerful measure to infer very recent changes in allele frequencies from contemporary genome sequences. When applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past 2,000 years. We see strong signals of selection at lactase and HLA, and in favor of...

https://rxivist.org/papers/10394
https://doi.org/10.1101/052084

7: Genetic evidence for an origin of the Armenians from Bronze Age mixing of multiple populations

Marc Haber

14,484 downloads (posted 18 Feb 2015)

The Armenians are a culturally isolated population who historically inhabited a region in the Near East bounded by the Mediterranean and Black seas and the Caucasus, but remain underrepresented in genetic studies and have a complex history including a major geographic displacement during World War One. Here, we analyse genome-wide variation in 173 Armenians and compare them to 78 other worldwide populations. We find that Armenians form a distinctive cluster linking the Near East, Europe, and the Caucasus. We show that A...

https://rxivist.org/papers/10657
https://doi.org/10.1101/015396

8: The Genetic History of Northern Europe

Alissa Mittnik, Chuan-Chao Wang et al.

13,847 downloads (posted 03 Mar 2017)

Recent ancient DNA studies have revealed that the genetic history of modern Europeans was shaped by a series of migration and admixture events between deeply diverged groups. While these events are well described in Central and Southern Europe, genetic evidence from Northern Europe surrounding the Baltic Sea is still sparse. Here we report genome-wide DNA data from 24 ancient North Europeans ranging from ~7,500 to 200 calBCE spanning the transition from a hunter-gatherer to an agricultural lifestyle, as well as the adop...

https://rxivist.org/papers/10078
https://doi.org/10.1101/113241

9: Genome-wide genetic data on ~500,000 UK Biobank participants

Clare Bycroft, Colin Freeman et al.

13,772 downloads (posted 20 Jul 2017)

The UK Biobank project is a large prospective cohort study of ~500,000 individuals from across the United Kingdom, aged between 40-69 at recruitment. A rich variety of phenotypic and health-related information is available on each participant, making the resource unprecedented in its size and scope. Here we describe the genome-wide genotype data (~805,000 markers) collected on all individuals in the cohort and its quality control procedures. Genotype data on this scale offers novel opportunities for assessing quality is...

https://rxivist.org/papers/9821
https://doi.org/10.1101/166298

10: A tutorial on how (not) to over-interpret STRUCTURE/ADMIXTURE bar plots

Daniel J Lawson, Lucy van Dorp et al.

10,839 downloads (posted 28 Jul 2016)

Genetic clustering algorithms, implemented in popular programs such as STRUCTURE and ADMIXTURE, have been used extensively in the characterisation of individuals and populations based on genetic data. A successful example is reconstruction of the genetic history of African Americans who are a product of recent admixture between highly differentiated populations. Histories can also be reconstructed using the same procedure for groups which do not have admixture in their recent history, where recent genetic drift is stron...

https://rxivist.org/papers/9237
https://doi.org/10.1101/066431

11: Discovery Of The First Genome-Wide Significant Risk Loci For ADHD

Ditte Demontis, Raymond K Walters et al.

8,867 downloads (posted 03 Jun 2017)

Attention-Deficit/Hyperactivity Disorder (ADHD) is a highly heritable childhood behavioral disorder affecting 5% of school-age children and 2.5% of adults. Common genetic variants contribute substantially to ADHD susceptibility, but no individual variants have been robustly associated with ADHD. We report a genome-wide association meta-analysis of 20,183 ADHD cases and 35,191 controls that identifies variants surpassing genome-wide significance in 12 independent loci, revealing new and important information on the under...

https://rxivist.org/papers/9933
https://doi.org/10.1101/145581

12: The genetic ancestry of African, Latino, and European Americans across the United States.

Katarzyna Bryc, Eric Y Durand et al.

8,793 downloads (posted 18 Sep 2014)

Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans brought largely by the Trans-Atlantic slave trade, shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasiv...

https://rxivist.org/papers/10694
https://doi.org/10.1101/009340

13: Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression

Naomi R. Wray, Stephan Ripke et al.

8,726 downloads (posted 24 Jul 2017)

Major depressive disorder (MDD) is a notably complex illness with a lifetime prevalence of 14%. 1 It is often chronic or recurrent and is thus accompanied by considerable morbidity, excess mortality, substantial costs, and heightened risk of suicide. 2-7 MDD is a major cause of disability worldwide. 8 We conducted a genome-wide association (GWA) meta-analysis in 130,664 MDD cases and 330,470 controls, and identified 44 independent loci that met criteria for statistical significance. We present extensive analyses of thes...

https://rxivist.org/papers/9818
https://doi.org/10.1101/167577

14: Population genomics of the Viking world

Ashot Margaryan, Daniel Lawson et al.

8,528 downloads (posted 17 Jul 2019)

The Viking maritime expansion from Scandinavia (Denmark, Norway, and Sweden) marks one of the swiftest and most far-flung cultural transformations in global history. During this time (c. 750 to 1050 CE), the Vikings reached most of western Eurasia, Greenland, and North America, and left a cultural legacy that persists till today. To understand the genetic structure and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 B...

https://rxivist.org/papers/56007
https://doi.org/10.1101/703405

15: TP53 copy number expansion correlates with the evolution of increased body size and an enhanced DNA damage response in elephants

Michael Sulak, Lindsey Fong et al.

8,294 downloads (posted 06 Oct 2015)

A major constraint on the evolution of large body sizes in animals is an increased risk of developing cancer. There is no correlation, however, between body size and cancer risk. This lack of correlation is often referred to as "Peto′s Paradox". Here we show that the elephant genome encodes 20 copies of the tumor suppressor gene TP53 and that the increase in TP53 copy number occurred coincident with the evolution of large body sizes in the elephant (Proboscidean) lineage. Furthermore we show that several of the TP53 ret...

https://rxivist.org/papers/10282
https://doi.org/10.1101/028522

16: Exploring the genetic architecture of inflammatory bowel disease by whole genome sequencing identifies association at ADCY7

Yang Luo, Katrina M de Lange et al.

8,223 downloads (posted 11 Jun 2016)

In order to further resolve the genetic architecture of the inflammatory bowel diseases, ulcerative colitis and Crohn′s disease, we sequenced the whole genomes of 4,280 patients at low coverage, and compared them to 3,652 previously sequenced population controls across 73.5 million variants. To increase power we imputed from these sequences into new and existing GWAS cohorts, and tested for association at ~12 million variants in a total of 16,432 cases and 18,843 controls. We discovered a 0.6% frequency missense variant...

https://rxivist.org/papers/10360
https://doi.org/10.1101/058347

17: Genome-wide association analysis of lifetime cannabis use (N=184,765) identifies new risk loci, genetic overlap with mental health, and a causal influence of schizophrenia on cannabis use

Joelle A. Pasman, Karin J.H. Verweij et al.

8,143 downloads (posted 08 Jan 2018)

Cannabis use is a heritable trait [1] that has been associated with adverse mental health outcomes. To identify risk variants and improve our knowledge of the genetic etiology of cannabis use, we performed the largest genome-wide association study (GWAS) meta-analysis for lifetime cannabis use (N=184,765) to date. We identified 4 independent loci containing genome-wide significant SNP associations. Gene-based tests revealed 29 genome-wide significant genes located in these 4 loci and 8 additional regions. All SNPs combi...

https://rxivist.org/papers/9431
https://doi.org/10.1101/234294

18: Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe

Rosa Fregel, Fernando L. Méndez et al.

8,058 downloads (posted 21 Sep 2017)

The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities, or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present the first analysis of individuals' genome sequences from early and late Neolithic sites in Morocco, as well as Early Neolithic individuals from southern Iberia. ...

https://rxivist.org/papers/9322
https://doi.org/10.1101/191569

19: Recovery of trait heritability from whole genome sequence data

Pierrick Wainschtein, Deepti P Jain et al.

7,755 downloads (posted 25 Mar 2019)

Heritability, the proportion of phenotypic variance explained by genetic factors, can be estimated from pedigree data, but such estimates are uninformative with respect to the underlying genetic architecture. Analyses of data from genome-wide association studies (GWAS) on unrelated individuals have shown that for human traits and disease, approximately one-third to two-thirds of heritability is captured by common SNPs. It is not known whether the remaining heritability is due to the imperfect tagging of causal variants ...

https://rxivist.org/papers/46888
https://doi.org/10.1101/588020

20: Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry

Iosif Lazaridis, Anna Belfer-Cohen et al.

7,328 downloads (posted 21 Sep 2018)

The earliest ancient DNA data of modern humans from Europe dates to ~40 thousand years ago, but that from the Caucasus and the Near East to only ~14 thousand years ago, from populations who lived long after the Last Glacial Maximum (LGM) ~26.5-19 thousand years ago. To address this imbalance and to better understand the relationship of Europeans and Near Easterners, we report genome-wide data from two ~26 thousand year old individuals from Dzudzuana Cave in Georgia in the Caucasus from around the beginning of the LGM. S...

https://rxivist.org/papers/33080
https://doi.org/10.1101/423079