scholarly journals Assessing the performance of qpAdm: a statistical tool for studying population admixture

Genetics ◽  
2021 ◽  
Author(s):  
Éadaoin Harney ◽  
Nick Patterson ◽  
David Reich ◽  
John Wakeley
Keyword(s):  
Best Practices ◽  
Relative Proportion ◽  
Population History ◽  
Source Population ◽  
Population Admixture ◽  
Single Model ◽  
Statistical Tool ◽  
History Of ◽  
Data Coverage ◽  
Source Populations

Abstract qpAdm is a statistical tool for studying the ancestry of populations with histories that involve admixture between two or more source populations. Using qpAdm, it is possible to identify plausible models of admixture that fit the population history of a group of interest and to calculate the relative proportion of ancestry that can be ascribed to each source population in the model. Although qpAdm is widely used in studies of population history of human (and nonhuman) groups, relatively little has been done to assess its performance. We performed a simulation study to assess the behavior of qpAdm under various scenarios in order to identify areas of potential weakness and establish recommended best practices for use. We find that qpAdm is a robust tool that yields accurate results in many cases, including when data coverage is low, there are high rates of missing data or ancient DNA damage, or when diploid calls cannot be made. However, we caution against co-analyzing ancient and present-day data, the inclusion of an extremely large number of reference populations in a single model, and analyzing population histories involving extended periods of gene flow. We provide a user guide suggesting best practices for the use of qpAdm.

scholarly journals Assessing the Performance of qpAdm: A Statistical Tool for Studying Population Admixture

2020 ◽  
Author(s):  
Éadaoin Harney ◽  
Nick Patterson ◽  
David Reich ◽  
John Wakeley
Keyword(s):  
Best Practices ◽  
Relative Proportion ◽  
Population History ◽  
Source Population ◽  
Population Admixture ◽  
Single Model ◽  
Statistical Tool ◽  
History Of ◽  
Data Coverage ◽  
Source Populations

ABSTRACTqpAdm is a statistical tool for studying the ancestry of populations with histories that involve admixture between two or more source populations. Using qpAdm, it is possible to identify plausible models of admixture that fit the population history of a group of interest and to calculate the relative proportion of ancestry that can be ascribed to each source population in the model. Although qpAdm is widely used in studies of population history of human (and non-human) groups, relatively little has been done to assess its performance. We performed a simulation study to assess the behavior of qpAdm under various scenarios in order to identify areas of potential weakness and establish recommended best practices for use. We find that qpAdm is a robust tool that yields accurate results in many cases, including when data coverage is low, there are high rates of missing data or ancient DNA damage, or when diploid calls cannot be made. However, we caution against co-analyzing ancient and present-day data, the inclusion of an extremely large number of reference populations in a single model, and analyzing population histories involving extended periods of gene flow. We provide a user guide suggesting best practices for the use of qpAdm.

scholarly journals Insights into human genetic variation and population history from 929 diverse genomes

2019 ◽  
Author(s):  
Anders Bergström ◽  
Shane A. McCarthy ◽  
Ruoyun Hui ◽  
Mohamed A. Almarri ◽  
Qasim Ayub ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Central Africa ◽  
Population History ◽  
Human Populations ◽  
Genome Sequences ◽  
High Coverage ◽  
Geographical Regions ◽  
History Of ◽  
Different Populations ◽  
Source Populations

AbstractGenome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented private genetic variation in southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the last 10,000 years, a potentially major population growth episode after the peopling of the Americas, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations. We also demonstrate benefits to the study of population relationships of genome sequences over ascertained array genotypes. These genome sequences are freely available as a resource with no access or analysis restrictions.

scholarly journals Insights into human genetic variation and population history from 929 diverse genomes

Science ◽  
2020 ◽  
Vol 367 (6484) ◽  
pp. eaay5012 ◽  
Author(s):  
Anders Bergström ◽  
Shane A. McCarthy ◽  
Ruoyun Hui ◽  
Mohamed A. Almarri ◽  
Qasim Ayub ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Central Africa ◽  
Population History ◽  
Human Populations ◽  
Genome Sequences ◽  
High Coverage ◽  
Geographical Regions ◽  
History Of ◽  
Different Populations ◽  
Source Populations

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.

Inferences on population history of a seed chalcid wasp: invasion success despite a severe founder effect from an unexpected source population

2012 ◽  
Vol 21 (24) ◽  
pp. 6086-6103 ◽  
Author(s):  
M.-A. Auger-Rozenberg ◽  
T. Boivin ◽  
E. Magnoux ◽  
C. Courtin ◽  
A. Roques ◽  
...  
Keyword(s):  
Founder Effect ◽  
Population History ◽  
Invasion Success ◽  
Source Population ◽  
History Of ◽  
Chalcid Wasp

scholarly journals Autosomal admixture levels are informative about sex bias in admixed populations

2014 ◽  
Author(s):  
Amy Goldberg ◽  
Paul Verdu ◽  
Noah A Rosenberg
Keyword(s):  
Sex Chromosomes ◽  
Sex Bias ◽  
Source Population ◽  
Effective Population ◽  
History Of ◽  
Specific Source ◽  
Unequal Number ◽  
Admixed Population ◽  
Source Populations

AbstractSex-biased admixture has been observed in a wide variety of admixed populations. Genetic variation in sex chromosomes and ratios of quantities computed from sex chromosomes and autosomes have often been examined in order to infer patterns of sex-biased admixture, typically using statistical approaches that do not mechanistically model the complexity of a sex-specific history of admixture. Here, expanding on a model of Verdu & Rosenberg (2011) that did not include sex specificity, we develop a model that mechanistically examines sex-specific admixture histories. Under the model, multiple source populations contribute to an admixed population, potentially with their male and female contributions varying over time. In an admixed population descended from two source groups, we derive the moments of the distribution of the autosomal admixture fraction from a specific source population as a function of sex-specific introgression parameters and time. Considering admixture processes that are constant in time, we demonstrate that surprisingly, although the mean autosomal admixture fraction from a specific source population does not reveal a sex bias in the admixture history, the variance of autosomal admixture is informative about sex bias. Specifically, the long-term variance decreases as the sex bias from a contributing source population increases. This result can be viewed as analogous to the reduction in effective population size for populations with an unequal number of breeding males and females. Our approach can contribute to methods for inference of the history of complex sex-biased admixture processes by enabling consideration of the effect of sex-biased admixture on autosomal DNA.

The Population History of Britain and Ireland 1500-1750

1996 ◽  
Vol 50 (2) ◽  
pp. 284-285
Author(s):  
Eilidh Garrett
Keyword(s):  
Population History ◽  
History Of

Trying to Professionalize Expert Knowledge (Part I): The Short Life of the Municipal Administration Service, 1926-1933

Public Voices ◽  
2017 ◽  
Vol 15 (1) ◽  
pp. 9 ◽  
Author(s):  
Mordecai Lee
Keyword(s):  
Best Practices ◽  
Public Administration ◽  
Expert Knowledge ◽  
Building Blocks ◽  
Early History ◽  
Short Life ◽  
Organizational History ◽  
Municipal Administration ◽  
History Of ◽  
Wide Dissemination

One of the building blocks of the professionalization of American public administration was the recognition of the need for expert knowledge and the wide dissemination of that information to practitioners. Municipal civil servants could adopt and adapt these best practices in their localities. Such was the purpose of the Municipal Administration Service (1926-1933), initially founded by the National Municipal League and funded by the Rockefeller philanthropies. This article is an organizational history of the Service. It presents the life cycle of the agency, including its operations, funding, problems, and the behind-the-scenes public administration politics which led to its demise. In all, the Municipal Administration Service captures the early history of American public administration, its attempt to demonstrate that it was a full-fledged profession with recognized experts and managerial advice that ultimately proved unable to perpetuate itself.

Searching for Justice After the Holocaust

2019 ◽  
Author(s):  
Michael J. Bazyler ◽  
Kathryn Lee Boyd ◽  
Kristen L. Nelson ◽  
Rajika L. Shah
Keyword(s):  
Best Practices ◽  
Legal History ◽  
Holocaust Survivors ◽  
European Parliament ◽  
Slave Labor ◽  
Insurance Policies ◽  
The Holocaust ◽  
History Of ◽  
Nazi Era ◽  
Property Restitution

The Nazis and their cohorts stole mercilessly from the Jews of Europe. In the aftermath of the Holocaust, returning survivors had to navigate unclear and hostile legal paths to recover their stolen property from governments and neighbors who often had been complicit in their persecution and theft. While the return of Nazi-looted art and recent legal settlements involving dormant Swiss bank accounts, unpaid insurance policies and use of slave labor by German companies have been well-publicized, efforts by Holocaust survivors and heirs over the last 70 years to recover stolen land and buildings were forgotten. In 2009, 47 countries convened in Prague to deal with the lingering problem of restitution of prewar private, communal, and heirless property stolen during the Holocaust. The outcome was the Terezin Declaration on Holocaust Era Assets and Related Issues, aiming to “rectify the consequences” of the wrongful Nazi-era immovable property seizures. This book sets forth the legal history of Holocaust immovable property restitution in each of the Terezin Declaration signatory states. It also analyzes how each of the 47 countries has fulfilled the standards of the Guidelines and Best Practices of the Terezin Declaration. These standards were issued in 2010 in conjunction with the establishment of the European Shoah Legacy Institute (ESLI), a state-sponsored NGO created to monitor compliance. The book is based on the Holocaust (Shoah) Immovable Property Restitution Study commissioned by ESLI, written by the authors and issued in Brussels in 2017 before the European Parliament.

Network Visualization

2020 ◽  
pp. 351-367
Author(s):  
James Moody ◽  
Ryan Light
Keyword(s):  
Best Practices ◽  
Social Relationships ◽  
Visual Display ◽  
Network Visualization ◽  
Making Sense ◽  
Complex Information ◽  
Underlying Network ◽  
History Of ◽  
Effective Network ◽  
Data Visualizations

This chapter provides an overview of social network visualization. Network analysis encourages the visual display of complex information, but effective network diagrams, like other data visualizations, result from several best practices. After a brief history of network visualization, the chapter outlines several of those practices. It highlights the role that network visualizations play as heuristics for making sense of networked data and translating complicated social relationships, such as those that are dynamic, into more comprehensible structures. The goal in this chapter is to help identify the methods underlying network visualization with an eye toward helping users produce more effective figures.

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