scholarly journals Detection of human adaptation during the past 2,000 years

2016 ◽  
Author(s):  
Yair Field ◽  
Evan A Boyle ◽  
Natalie Telis ◽  
Ziyue Gao ◽  
Kyle J. Gaulton ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Complex Traits ◽  
Frequency Shifts ◽  
The Past ◽  
Polygenic Adaptation ◽  
Selection For ◽  
Frequency Changes ◽  
Long Timescales ◽  
Blue Eyes ◽  
New Evidence

AbstractDetection 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 blond hair and blue eyes. Turning to signals of polygenic adaptation we find, remarkably, that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we report suggestive new evidence for polygenic shifts affecting many other complex traits. Our results suggest that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans.

scholarly journals Distinct patterns of selective sweep and polygenic adaptation

2019 ◽  
Author(s):  
Neda Barghi ◽  
Christian Schlötterer
Keyword(s):  
Allele Frequency ◽  
Computer Simulations ◽  
Selective Sweep ◽  
Empirical Work ◽  
Selective Sweeps ◽  
Adaptive Architectures ◽  
Polygenic Adaptation ◽  
Frequency Changes ◽  
Independent Effects ◽  
Distinct Features

AbstractThe central paradigm of molecular population genetics is selective sweeps, where targets of selection have independent effects on the phenotype and quickly rise to fixation. In quantitative genetics, many loci contribute epistatically to adaptation and subtle frequency changes occur at many loci. Since both paradigms could result in a sweep-like genomic signature, additional criteria are needed to distinguish them. Using the framework of experimental evolution, we performed computer simulations to study the pattern of selected alleles under both paradigms. We identify several distinct patterns of selective sweeps and polygenic adaptation in populations of different sizes. These features could provide the foundation for development of quantitative approaches to differentiate the two paradigms.Author’s summaryThe selective sweep model assumes an independent frequency increase of favorable alleles and has been the basis of many tests for selection. While, polygenic adaptation is typically modelled by small frequency shifts in many loci. Recently, some theoretical and empirical work demonstrated that polygenic adaptation, similar to sweep, could also results in pronounced allele frequency changes. These results suggest that other distinct features need to be identified. Using computer simulations, we identified distinctive features for each paradigm that can be used to differentiate the sweep model from polygenic adaptation. Features such as allele frequency trajectories, time-series fitness, distribution of selected alleles on haplotypes, and parallelism among replicates can be used for development of suitable tests to distinguish between different adaptive architectures. These features provide the basis for theoretical modeling, design of selection experiments and data analysis.

scholarly journals Distance to trait optimum is a crucial factor determining the genomic signature of polygenic adaptation

2019 ◽  
Author(s):  
Eirini Christodoulaki ◽  
Neda Barghi ◽  
Christian Schlötterer
Keyword(s):  
Allele Frequency ◽  
Ad Hoc ◽  
Time Series Data ◽  
Series Data ◽  
Data Sets ◽  
Multiple Time ◽  
Adaptive Architecture ◽  
Polygenic Adaptation ◽  
Frequency Changes ◽  
Multiple Time Points

AbstractPolygenic adaptation is frequently associated with small allele frequency changes of many loci. Recent works suggest, that large allele frequency changes can be also expected. Laboratory natural selection (LNS) experiments provide an excellent experimental framework to study the adaptive architecture under controlled laboratory conditions: time series data in replicate populations evolving independently to the same trait optimum can be used to identify selected loci. Nevertheless, the choice of the new trait optimum in the laboratory is typically an ad hoc decision without consideration of the distance of the starting population to the new optimum. Here, we used forward-simulations to study the selection signatures of polygenic adaptation in populations evolving to different trait optima. Mimicking LNS experiments we analyzed allele frequencies of the selected alleles and population fitness at multiple time points. We demonstrate that the inferred adaptive architecture strongly depends on the choice of the new trait optimum in the laboratory and the significance cut-off used for identification of selected loci. Our results not only have a major impact on the design of future Evolve and Resequence (E&R) studies, but also on the interpretation of current E&R data sets.

scholarly journals Temporal allele frequency change and estimation of effective size in populations with overlapping generations.

Genetics ◽  
1995 ◽  
Vol 139 (2) ◽  
pp. 1077-1090 ◽  
Author(s):  
P E Jorde ◽  
N Ryman
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
Overlapping Generations ◽  
Temporal Frequency ◽  
Effective Size ◽  
Frequency Change ◽  
Effective Population ◽  
Frequency Shifts ◽  
Frequency Changes

Abstract In this paper we study the process of allele frequency change in finite populations with overlapping generations with the purpose of evaluating the possibility of estimating the effective size from observations of temporal frequency shifts of selectively neutral alleles. Focusing on allele frequency changes between successive cohorts (individuals born in particular years), we show that such changes are not determined by the effective population size alone, as they are when generations are discrete. Rather, in populations with overlapping generations, the amount of temporal allele frequency change is dependent on the age-specific survival and birth rates. Taking this phenomenon into account, we present an estimator for effective size that can be applied to populations with overlapping generations.

scholarly journals Emergency management of the paediatric patient with convulsive status epilepticus

2021 ◽  
Vol 26 (1) ◽  
pp. 50-57
Author(s):  
Kyle C McKenzie ◽  
Cecil D Hahn ◽  
Jeremy N Friedman
Keyword(s):  
Clinical Practice ◽  
Status Epilepticus ◽  
Emergency Management ◽  
Treatment Algorithm ◽  
Position Statement ◽  
Convulsive Status Epilepticus ◽  
Pharmacological Management ◽  
The Past ◽  
New Treatment ◽  
New Evidence

Abstract This guideline addresses the emergency management of convulsive status epilepticus (CSE) in children and infants older than 1 month of age. It replaces a previous position statement from 2011, and includes a new treatment algorithm and table of recommended medications based on new evidence and reflecting the evolution of clinical practice over the past several years. This statement emphasizes the importance of timely pharmacological management of CSE, and includes some guidance for diagnostic approach and supportive care.

Mathematical Issues Arising From the Directed Mutation Controversy

Genetics ◽  
2003 ◽  
Vol 164 (1) ◽  
pp. 373-379
Author(s):  
Qi Zheng
Keyword(s):  
Mathematical Reasoning ◽  
Large Body ◽  
Directed Mutation ◽  
The Past ◽  
New Evidence

Abstract During the past 14 years or so a large body of new evidence that supposedly supports the directed mutation hypothesis has accumulated. Interpretation of some of the evidence depends on mathematical reasoning, which can be subtler than it appears at first sight. This article attempts to clarify some of the mathematical issues arising from the directed mutation controversy, thereby offering alternative interpretations of some of the evidence.

scholarly journals EWAS Data Hub: a resource of DNA methylation array data and metadata

2019 ◽  
Vol 48 (D1) ◽  
pp. D890-D895 ◽  
Author(s):  
Zhuang Xiong ◽  
Mengwei Li ◽  
Fei Yang ◽  
Yingke Ma ◽  
Jian Sang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Complex Traits ◽  
Cell Types ◽  
Great Promise ◽  
Methylation Array ◽  
Array Data ◽  
The Past ◽  
Comprehensive Collection ◽  
Dna Methylation Array ◽  
Brain Parts

Abstract Epigenome-Wide Association Study (EWAS) has become an effective strategy to explore epigenetic basis of complex traits. Over the past decade, a large amount of epigenetic data, especially those sourced from DNA methylation array, has been accumulated as the result of numerous EWAS projects. We present EWAS Data Hub (https://bigd.big.ac.cn/ewas/datahub), a resource for collecting and normalizing DNA methylation array data as well as archiving associated metadata. The current release of EWAS Data Hub integrates a comprehensive collection of DNA methylation array data from 75 344 samples and employs an effective normalization method to remove batch effects among different datasets. Accordingly, taking advantages of both massive high-quality DNA methylation data and standardized metadata, EWAS Data Hub provides reference DNA methylation profiles under different contexts, involving 81 tissues/cell types (that contain 25 brain parts and 25 blood cell types), six ancestry categories, and 67 diseases (including 39 cancers). In summary, EWAS Data Hub bears great promise to aid the retrieval and discovery of methylation-based biomarkers for phenotype characterization, clinical treatment and health care.

Top resources and tools for physician management of chronic pain in the Canadian Armed Forces

2021 ◽  
pp. e20210039
Author(s):  
Paul Dhillon ◽  
Nickie Mathew ◽  
Richard Lee ◽  
Eric Juneau ◽  
Robert Dale ◽  
...  
Keyword(s):  
Chronic Pain ◽  
Armed Forces ◽  
Continuous Medical Education ◽  
Prescription Practices ◽  
The Past ◽  
Canadian Armed Forces ◽  
Busy Clinician ◽  
Primary Care Clinicians ◽  
Canadian Military ◽  
New Evidence

LAY SUMMARY Diagnosis and management of chronic pain in Canada by primary care clinicians is a challenging and changing field with new approaches, evidence, and tools emerging in the past few years. For a busy clinician, it is vital to integrate and become aware of new tools that can improve the care delivered to patients. This article summarizes new evidence-based tools, key guidelines and research, algorithms, and simplified prescription practices, in addition to continuous medical education resources that will allow busy clinicians to rapidly be brought up to speed on the latest in chronic pain management in the Canadian military context.

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