Pegada genética da seleção natural

quarta-feira, março 03, 2010

Genetic Footprint of Natural Selection

ScienceDaily (Mar. 2, 2010) — A further step has been taken towards our understanding of natural selection. CNRS scientists working at the Institut de Biologie of the Ecole Normale Supérieure (CNRS/ENS/INSERM) have shown that humans, and some of their primate cousins, have a common genetic footprint, i.e. a set of genes which natural selection has often tended to act upon during the past 200,000 years.

This study has also been able to isolate a group of genes that distinguish us from our cousins the great apes. Its findings are published in PLoS Genetics (26 February 2010 issue).

During evolution, living species have adapted to environmental constraints according to the mechanism of natural selection; when a mutation that aids the survival (and reproduction) of an individual appears in the genome, it then spreads throughout the rest of the species until, after several hundreds or even thousands of generations, it is carried by all individuals.But does this selection, which occurs on a specific gene in the genome of a species, also occur on the same gene in neighboring species?On which set of genes has natural selection acted specifically in each species?

Researchers in the Dynamique et Organisation des Génomes team at the Institut de Biologie of the Ecole Normale Supérieure (CNRS/ENS/INSERM) have studied the genome of humans and three other primate species (chimpanzee, orangutan and macaque) using bioinformatics tools.Their work consisted in comparing the entire genomes of each species in order to identify the genes having undergone selection during the past 200,000 years.The result was that a few hundred genes have recently undergone selection in each of these species.These include around 100 genes detected in man that are shared by two or three other species, which is twice as many as might be anticipated as a random phenomenon[1].Thus a not inconsiderable proportion of the genes involved in human adaptation are also present in the chimpanzee, orangutan or macaque, and sometimes in several species at the same time.Natural selection acts not only by distancing different species from each other when new traits appear.But by acting on the same gene, it can also give rise to the same trait in species that have already diverged[2], but still have a relatively similar genome.
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Human and Non-Human Primate Genomes Share Hotspots of Positive Selection

David Enard1, Frantz Depaulis2, Hugues Roest Crollius1*

1 DYOGEN Lab, CNRS UMR8541, Ecole Normale Supérieure, Paris, France, 2Laboratoire Ecologie et Evolution, CNRS UMR7625, Ecole Normale Supérieure, UPMC Paris Universitas, Paris, France

Abstract

Among primates, genome-wide analysis of recent positive selection is currently limited to the human species because it requires extensive sampling of genotypic data from many individuals. The extent to which genes positively selected in human also present adaptive changes in other primates therefore remains unknown. This question is important because a gene that has been positively selected independently in the human and in other primate lineages may be less likely to be involved in human specific phenotypic changes such as dietary habits or cognitive abilities. To answer this question, we analysed heterozygous Single Nucleotide Polymorphisms (SNPs) in the genomes of single human, chimpanzee, orangutan, and macaque individuals using a new method aiming to identify selective sweeps genome-wide. We found an unexpectedly high number of orthologous genes exhibiting signatures of a selective sweep simultaneously in several primate species, suggesting the presence of hotspots of positive selection. A similar significant excess is evident when comparing genes positively selected during recent human evolution with genes subjected to positive selection in their coding sequence in other primate lineages and identified using a different test. These findings are further supported by comparing several published human genome scans for positive selection with our findings in non-human primate genomes. We thus provide extensive evidence that the co-occurrence of positive selection in humans and in other primates at the same genetic loci can be measured with only four species, an indication that it may be a widespread phenomenon. The identification of positive selection in humans alongside other primates is a powerful tool to outline those genes that were selected uniquely during recent human evolution.

Author Summary

An advantageous mutation spreads from generation to generation in a population until individuals that carry it, because of their higher reproductive success, completely replace those that do not. This process, commonly known as positive Darwinian selection, requires the selected mutation to induce a new non-neutral heritable phenotypic trait, and this has been shown to occur unexpectedly frequently during recent human evolution. Although the exact advantageous mutation is difficult to identify, it leaves a wider footprint on neighbouring linked neutral variation called a selective sweep. We have developed an empirical method that uses whole-genome shotgun sequences of single individuals to detect selective sweeps. By doing so, we were able to extend to chimpanzee, orangutan, and macaque individuals analyses of recent positive selection that until now were only available for human. Comparisons of genes candidates for positive selection between human and non-human primates then revealed an unexpectedly high number of cases where a selective sweep at a gene in humans is mirrored by independent positive selection at the same gene in multiple other primates. This result has future implications for understanding the nature of biological changes that underlie selective sweeps in humans.

Citation: Enard D, Depaulis F, Crollius HR (2010) Human and Non-Human Primate Genomes Share Hotspots of Positive Selection. PLoS Genet 6(2): e1000840. doi:10.1371/journal.pgen.1000840

Editor: Molly Przeworski, University of Chicago, United States of America

Received: July 27, 2009; Accepted: January 6, 2010; Published: February 5, 2010

Copyright: © 2010 Enard et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: This work is funded in part by the ACI-IMPBIO program, French Ministère de l'Enseignement Supérieur et de la Recherche ACI no 045223. DE is funded by a grant from the French Ministère de l'Enseignement Supérieur et de la Recherche. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

* E-mail: hrc@ens.fr

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