Literature DB >> 27744216

The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives.

Yuval B Simons1, Guy Sella2.   

Abstract

Over the past decade, there has been both great interest and confusion about whether recent demographic events-notably the Out-of-Africa-bottleneck and recent population growth-have led to differences in mutation load among human populations. The confusion can be traced to the use of different summary statistics to measure load, which lead to apparently conflicting results. We argue, however, that when statistics more directly related to load are used, the results of different studies and data sets consistently reveal little or no difference in the load of non-synonymous mutations among human populations. Theory helps to understand why no such differences are seen, as well as to predict in what settings they are to be expected. In particular, as predicted by modeling, there is evidence for changes in the load of recessive loss of function mutations in founder and inbred human populations. Also as predicted, eastern subspecies of gorilla, Neanderthals and Denisovans, who are thought to have undergone reductions in population sizes that exceed the human Out-of-Africa bottleneck in duration and severity, show evidence for increased load of non-synonymous mutations (relative to western subspecies of gorillas and modern humans, respectively). A coherent picture is thus starting to emerge about the effects of demographic history on the mutation load in populations of humans and close evolutionary relatives.
Copyright © 2016 Elsevier Ltd. All rights reserved.

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Year:  2016        PMID: 27744216      PMCID: PMC5161708          DOI: 10.1016/j.gde.2016.09.006

Source DB:  PubMed          Journal:  Curr Opin Genet Dev        ISSN: 0959-437X            Impact factor:   5.578


  78 in total

1.  Bottleneck effect on genetic variance. A theoretical investigation of the role of dominance.

Authors:  J Wang; A Caballero; P D Keightley; W G Hill
Journal:  Genetics       Date:  1998-09       Impact factor: 4.562

2.  Characteristics of neutral and deleterious protein-coding variation among individuals and populations.

Authors:  Wenqing Fu; Rachel M Gittelman; Michael J Bamshad; Joshua M Akey
Journal:  Am J Hum Genet       Date:  2014-10-02       Impact factor: 11.025

3.  An examination of the generation-time effect on molecular evolution.

Authors:  T Ohta
Journal:  Proc Natl Acad Sci U S A       Date:  1993-11-15       Impact factor: 11.205

4.  Evidence for recent, population-specific evolution of the human mutation rate.

Authors:  Kelley Harris
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-02       Impact factor: 11.205

5.  Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding.

Authors:  Yali Xue; Javier Prado-Martinez; Peter H Sudmant; Vagheesh Narasimhan; Qasim Ayub; Michal Szpak; Peter Frandsen; Yuan Chen; Bryndis Yngvadottir; David N Cooper; Marc de Manuel; Jessica Hernandez-Rodriguez; Irene Lobon; Hans R Siegismund; Luca Pagani; Michael A Quail; Christina Hvilsom; Antoine Mudakikwa; Evan E Eichler; Michael R Cranfield; Tomas Marques-Bonet; Chris Tyler-Smith; Aylwyn Scally
Journal:  Science       Date:  2015-04-09       Impact factor: 47.728

6.  Inference of human population history from individual whole-genome sequences.

Authors:  Heng Li; Richard Durbin
Journal:  Nature       Date:  2011-07-13       Impact factor: 49.962

7.  Homozygous loss-of-function variants in European cosmopolitan and isolate populations.

Authors:  Vera B Kaiser; Victoria Svinti; James G Prendergast; You-Ying Chau; Archie Campbell; Inga Patarcic; Inês Barroso; Peter K Joshi; Nicholas D Hastie; Ana Miljkovic; Martin S Taylor; Stefan Enroth; Yasin Memari; Anja Kolb-Kokocinski; Alan F Wright; Ulf Gyllensten; Richard Durbin; Igor Rudan; Harry Campbell; Ozren Polašek; Åsa Johansson; Sascha Sauer; David J Porteous; Ross M Fraser; Camilla Drake; Veronique Vitart; Caroline Hayward; Colin A Semple; James F Wilson
Journal:  Hum Mol Genet       Date:  2015-07-14       Impact factor: 6.150

8.  The complete genome sequence of a Neanderthal from the Altai Mountains.

Authors:  Kay Prüfer; Fernando Racimo; Nick Patterson; Flora Jay; Sriram Sankararaman; Susanna Sawyer; Anja Heinze; Gabriel Renaud; Peter H Sudmant; Cesare de Filippo; Heng Li; Swapan Mallick; Michael Dannemann; Qiaomei Fu; Martin Kircher; Martin Kuhlwilm; Michael Lachmann; Matthias Meyer; Matthias Ongyerth; Michael Siebauer; Christoph Theunert; Arti Tandon; Priya Moorjani; Joseph Pickrell; James C Mullikin; Samuel H Vohr; Richard E Green; Ines Hellmann; Philip L F Johnson; Hélène Blanche; Howard Cann; Jacob O Kitzman; Jay Shendure; Evan E Eichler; Ed S Lein; Trygve E Bakken; Liubov V Golovanova; Vladimir B Doronichev; Michael V Shunkov; Anatoli P Derevianko; Bence Viola; Montgomery Slatkin; David Reich; Janet Kelso; Svante Pääbo
Journal:  Nature       Date:  2013-12-18       Impact factor: 49.962

9.  Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans.

Authors:  Ferran Casals; Alan Hodgkinson; Julie Hussin; Youssef Idaghdour; Vanessa Bruat; Thibault de Maillard; Jean-Christophe Grenier; Jean-Cristophe Grenier; Elias Gbeha; Fadi F Hamdan; Simon Girard; Jean-François Spinella; Mathieu Larivière; Virginie Saillour; Jasmine Healy; Isabel Fernández; Daniel Sinnett; Jacques L Michaud; Guy A Rouleau; Elie Haddad; Françoise Le Deist; Philip Awadalla
Journal:  PLoS Genet       Date:  2013-09-26       Impact factor: 5.917

10.  Loss and recovery of genetic diversity in adapting populations of HIV.

Authors:  Pleuni S Pennings; Sergey Kryazhimskiy; John Wakeley
Journal:  PLoS Genet       Date:  2014-01-23       Impact factor: 5.917

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  32 in total

1.  The Effect of an Extreme and Prolonged Population Bottleneck on Patterns of Deleterious Variation: Insights from the Greenlandic Inuit.

Authors:  Casper-Emil T Pedersen; Kirk E Lohmueller; Niels Grarup; Peter Bjerregaard; Torben Hansen; Hans R Siegismund; Ida Moltke; Anders Albrechtsen
Journal:  Genetics       Date:  2016-11-30       Impact factor: 4.562

Review 2.  Evolutionary perspectives on polygenic selection, missing heritability, and GWAS.

Authors:  Lawrence H Uricchio
Journal:  Hum Genet       Date:  2019-06-14       Impact factor: 4.132

3.  The Temporal Dynamics of Background Selection in Nonequilibrium Populations.

Authors:  Raul Torres; Markus G Stetter; Ryan D Hernandez; Jeffrey Ross-Ibarra
Journal:  Genetics       Date:  2020-02-18       Impact factor: 4.562

4.  Natural selection interacts with recombination to shape the evolution of hybrid genomes.

Authors:  Molly Schumer; Chenling Xu; Daniel L Powell; Arun Durvasula; Laurits Skov; Chris Holland; John C Blazier; Sriram Sankararaman; Peter Andolfatto; Gil G Rosenthal; Molly Przeworski
Journal:  Science       Date:  2018-04-19       Impact factor: 47.728

5.  The impact of genetic modifiers on variation in germline mutation rates within and among human populations.

Authors:  William R Milligan; Guy Amster; Guy Sella
Journal:  Genetics       Date:  2022-07-30       Impact factor: 4.402

6.  Genomic consequences of a century of inbreeding and isolation in the Danish wild boar population.

Authors:  Beril Yıldız; Hendrik-Jan Megens; Christina Hvilsom; Mirte Bosse
Journal:  Evol Appl       Date:  2022-05-17       Impact factor: 4.929

Review 7.  Genetic load: genomic estimates and applications in non-model animals.

Authors:  Giorgio Bertorelle; Francesca Raffini; Hernán E Morales; Cock van Oosterhout; Mirte Bosse; Chiara Bortoluzzi; Alessio Iannucci; Emiliano Trucchi
Journal:  Nat Rev Genet       Date:  2022-02-08       Impact factor: 59.581

8.  Haplotype-based inference of the distribution of fitness effects.

Authors:  Diego Ortega-Del Vecchyo; Kirk E Lohmueller; John Novembre
Journal:  Genetics       Date:  2022-04-04       Impact factor: 4.562

9.  The Counteracting Effects of Demography on Functional Genomic Variation: The Roma Paradigm.

Authors:  Neus Font-Porterias; Rocio Caro-Consuegra; Marcel Lucas-Sánchez; Marie Lopez; Aaron Giménez; Annabel Carballo-Mesa; Elena Bosch; Francesc Calafell; Lluís Quintana-Murci; David Comas
Journal:  Mol Biol Evol       Date:  2021-06-25       Impact factor: 16.240

Review 10.  Human genetic admixture.

Authors:  Katharine L Korunes; Amy Goldberg
Journal:  PLoS Genet       Date:  2021-03-11       Impact factor: 5.917

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