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 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.

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

scholarly journals Mitochondrial phylogeography and population history of finless porpoises in Sino-Japanese waters

2008 ◽  
Vol 95 (1) ◽  
pp. 193-204 ◽  
Author(s):  
GUANG YANG ◽  
LI GUO ◽  
MICHAEL W. BRUFORD ◽  
FUWEN WEI ◽  
KAIYA ZHOU
Keyword(s):  
Population History ◽  
History Of ◽  
Japanese Waters

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

Phylogeography and population history of Leopardus guigna, the smallest American felid

2014 ◽  
Vol 15 (3) ◽  
pp. 631-653 ◽  
Author(s):  
Constanza Napolitano ◽  
Warren E. Johnson ◽  
Jim Sanderson ◽  
Stephen J. O’Brien ◽  
A. Rus Hoelzel ◽  
...  
Keyword(s):  
Population History ◽  
History Of ◽  
Leopardus Guigna

The Population History of Extant and Extinct Hyenas

2005 ◽  
Vol 22 (12) ◽  
pp. 2435-2443 ◽  
Author(s):  
Nadin Rohland ◽  
Joshua L. Pollack ◽  
Doris Nagel ◽  
Cédric Beauval ◽  
Jean Airvaux ◽  
...  
Keyword(s):  
Population History ◽  
History Of

A Genomic View of the Pleistocene Population History of Asia

2017 ◽  
Vol 58 (S17) ◽  
pp. S397-S405 ◽  
Author(s):  
Martin Sikora
Keyword(s):  
Population History ◽  
History Of
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