scholarly journals Brief Population Bottlenecks Are Beyond The Genetic Streetlight

2021 ◽  
Author(s):  
Jack Elliot-Higgins ◽  
S. Joshua Swamidass
Keyword(s):  
Population Genetics ◽  
Demographic History ◽  
Genetic Data ◽  
Population Bottleneck ◽  
Population Bottlenecks ◽  
Human Lineage ◽  
Important Goal ◽  
New Approach ◽  
Human Demographic History ◽  
Population Inference

Abstract Inferring human demographic history from extant genomes is an important goal of population genetics. To date, the sensitivity of coalescence-based methods in detecting population bottlenecks has not been well characterized. In this study, we find that brief bottlenecks, of just a few generations, are undetectable by current methods. A new approach to population inference, Lineage Time Inference (LiTI), uses data-derived windows to demarcate the limits of the genetic data. We find that a sharp population bottleneck at the time of the Youngest Toba Eruption, and also at more ancient timepoints in the human lineage, would be outside the genetic streetlight.

scholarly journals Ancient DNA helps trace the peopling of the world

2020 ◽  
Vol 42 (1) ◽  
pp. 18-22
Author(s):  
Bastien Llamas ◽  
Xavier Roca Rada ◽  
Evelyn Collen
Keyword(s):  
Common Ancestor ◽  
Demographic History ◽  
Genetic Data ◽  
Origin And Evolution ◽  
Human Demographic History ◽  
Human Morphology ◽  
Human Movements ◽  
The World ◽  
Powerful Means ◽  
And Linguistics

Many of us are fascinated by narratives regarding the origin and evolution of our species. Who are we? How did we people the world? Answers to these simple questions remain elusive even though researchers have been quite successful in describing past human morphology and culture using evidence from anthropology, archaeology, history, sociology and linguistics. However, when they address human migrations, archaeologists are somewhat restricted to surviving artifactual evidence and limited to descriptions of culture expansions, which may have occurred by the movement of either ideas or people. The advent of genomics, by which one can sequence whole or part of an individual's DNA, provided a powerful means to dig into past human demographic history. Notably, the coalescent theory posits that individuals in a population share genetic variants that originated from a common ancestor. This powerful theory is the basis for a number of bioanalytical innovations that utilize genetic data to reconstruct human movements around the world.

scholarly journals Effects of recent population bottlenecks on reconstructing the demographic history of prairie-chickens

2007 ◽  
Vol 16 (11) ◽  
pp. 2203-2222 ◽  
Author(s):  
JEFF A. JOHNSON ◽  
PETER O. DUNN ◽  
JUAN L. BOUZAT
Keyword(s):  
Demographic History ◽  
Population Bottlenecks ◽  
History Of

scholarly journals Applicability of the Mutation–Selection Balance Model to Population Genetics of Heterozygous Protein-Truncating Variants in Humans

2019 ◽  
Vol 36 (8) ◽  
pp. 1701-1710 ◽  
Author(s):  
Donate Weghorn ◽  
Daniel J Balick ◽  
Christopher Cassa ◽  
Jack A Kosmicki ◽  
Mark J Daly ◽  
...  
Keyword(s):  
Population Genetics ◽  
De Novo ◽  
Demographic History ◽  
Purifying Selection ◽  
Population History ◽  
Balance Model ◽  
Data Set ◽  
Stochastic Force ◽  
Drift Estimation ◽  
Human Genes

Abstract The fate of alleles in the human population is believed to be highly affected by the stochastic force of genetic drift. Estimation of the strength of natural selection in humans generally necessitates a careful modeling of drift including complex effects of the population history and structure. Protein-truncating variants (PTVs) are expected to evolve under strong purifying selection and to have a relatively high per-gene mutation rate. Thus, it is appealing to model the population genetics of PTVs under a simple deterministic mutation–selection balance, as has been proposed earlier (Cassa et al. 2017). Here, we investigated the limits of this approximation using both computer simulations and data-driven approaches. Our simulations rely on a model of demographic history estimated from 33,370 individual exomes of the Non-Finnish European subset of the ExAC data set (Lek et al. 2016). Additionally, we compared the African and European subset of the ExAC study and analyzed de novo PTVs. We show that the mutation–selection balance model is applicable to the majority of human genes, but not to genes under the weakest selection.

Domestication and human demographic history in South America

2017 ◽  
Vol 163 (1) ◽  
pp. 44-52 ◽  
Author(s):  
S. Ivan Perez ◽  
María Bárbara Postillone ◽  
Diego Rindel
Keyword(s):  
South America ◽  
Demographic History ◽  
Human Demographic History

Detecting past population bottlenecks using temporal genetic data

2005 ◽  
Vol 14 (10) ◽  
pp. 2915-2922 ◽  
Author(s):  
UMA RAMAKRISHNAN ◽  
ELIZABETH A. HADLY ◽  
JOANNA L. MOUNTAIN
Keyword(s):  
Genetic Data ◽  
Population Bottlenecks ◽  
Past Population

scholarly journals A novel DNA sequence database for analyzing human demographic history

2008 ◽  
Vol 18 (8) ◽  
pp. 1354-1361 ◽  
Author(s):  
J. D. Wall ◽  
M. P. Cox ◽  
F. L. Mendez ◽  
A. Woerner ◽  
T. Severson ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Demographic History ◽  
Sequence Database ◽  
Human Demographic History

Abstracts of papers from the discussion meeting on mathematical genetics

1983 ◽  
Vol 390 (1798) ◽  
pp. 217-220
Keyword(s):  
Population Genetics ◽  
Restriction Endonuclease ◽  
Natural Populations ◽  
Genetic Data ◽  
Genetic Constitution ◽  
Genetic Process ◽  
Major Trend ◽  
Deductive Theory

A major trend of population genetics theory in the 1970s was the increased emphasis on inductive arguments, based on observed genetic data, rather than on deductive arguments based on theory and models. This occurred in part because the deductive theory had largely fulfilled its role of describing evolution as a genetic process, and in part because of the increasing amounts of data available on the genetic constitution of natural populations. Inference procedures raise difficulties not present in the deductive theory. Often conditional arguments are necessary since the data often must fulfil some condition to be observed. Different inference procedures, having different efficiencies, apply for data from different apparatuses. Care must be taken in deciding what it is that the inference concerns. These problems are illustrated by reference to restriction endonuclease techniques and ascertainment sampling.

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