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Evidence for late Pleistocene origin of Astyanax mexicanus cavefish

BACKGROUND: Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They are currently assigned to two main groups, the so-called “old” and “new” lineages, which would have popu...

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Autores principales: Fumey, Julien, Hinaux, Hélène, Noirot, Céline, Thermes, Claude, Rétaux, Sylvie, Casane, Didier
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905186/
https://www.ncbi.nlm.nih.gov/pubmed/29665771
http://dx.doi.org/10.1186/s12862-018-1156-7
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author Fumey, Julien
Hinaux, Hélène
Noirot, Céline
Thermes, Claude
Rétaux, Sylvie
Casane, Didier
author_facet Fumey, Julien
Hinaux, Hélène
Noirot, Céline
Thermes, Claude
Rétaux, Sylvie
Casane, Didier
author_sort Fumey, Julien
collection PubMed
description BACKGROUND: Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They are currently assigned to two main groups, the so-called “old” and “new” lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations. RESULTS: We reanalyzed the geographic distribution of mitochondrial and nuclear DNA polymorphisms and we found that these data do not support the existence of two cavefish lineages. Using IMa2, a program that allows dating population divergence in addition to demographic parameters, we found that microsatellite polymorphism strongly supports a very recent origin of cave populations (< 20,000 years). We identified a large number of single-nucleotide polymorphisms (SNPs) in transcript sequences of pools of embryos (Pool-seq) belonging to Pachón cave population and a surface population from Texas. Based on summary statistics that can be computed with this SNP data set together with simulations of evolution of SNP polymorphisms in two recently isolated populations, we looked for sets of demographic parameters that allow the computation of summary statistics with simulated populations that are similar to the ones with the sampled populations. In most simulations for which we could find a good fit between the summary statistics of observed and simulated data, the best fit occurred when the divergence between simulated populations was less than 30,000 years. CONCLUSIONS: Although it is often assumed that some cave populations have a very ancient origin, a recent origin of these populations is strongly supported by our analyses of independent sets of nuclear DNA polymorphism. Moreover, the observation of two divergent haplogroups of mitochondrial and nuclear genes with different geographic distributions support a recent admixture of two divergent surface populations, before the isolation of cave populations. If cave populations are indeed only several thousand years old, many phenotypic changes observed in cavefish would thus have mainly involved the fixation of genetic variants present in surface fish populations and within a very short period of time. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12862-018-1156-7) contains supplementary material, which is available to authorized users.
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spelling pubmed-59051862018-04-24 Evidence for late Pleistocene origin of Astyanax mexicanus cavefish Fumey, Julien Hinaux, Hélène Noirot, Céline Thermes, Claude Rétaux, Sylvie Casane, Didier BMC Evol Biol Research Article BACKGROUND: Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They are currently assigned to two main groups, the so-called “old” and “new” lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations. RESULTS: We reanalyzed the geographic distribution of mitochondrial and nuclear DNA polymorphisms and we found that these data do not support the existence of two cavefish lineages. Using IMa2, a program that allows dating population divergence in addition to demographic parameters, we found that microsatellite polymorphism strongly supports a very recent origin of cave populations (< 20,000 years). We identified a large number of single-nucleotide polymorphisms (SNPs) in transcript sequences of pools of embryos (Pool-seq) belonging to Pachón cave population and a surface population from Texas. Based on summary statistics that can be computed with this SNP data set together with simulations of evolution of SNP polymorphisms in two recently isolated populations, we looked for sets of demographic parameters that allow the computation of summary statistics with simulated populations that are similar to the ones with the sampled populations. In most simulations for which we could find a good fit between the summary statistics of observed and simulated data, the best fit occurred when the divergence between simulated populations was less than 30,000 years. CONCLUSIONS: Although it is often assumed that some cave populations have a very ancient origin, a recent origin of these populations is strongly supported by our analyses of independent sets of nuclear DNA polymorphism. Moreover, the observation of two divergent haplogroups of mitochondrial and nuclear genes with different geographic distributions support a recent admixture of two divergent surface populations, before the isolation of cave populations. If cave populations are indeed only several thousand years old, many phenotypic changes observed in cavefish would thus have mainly involved the fixation of genetic variants present in surface fish populations and within a very short period of time. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12862-018-1156-7) contains supplementary material, which is available to authorized users. BioMed Central 2018-04-18 /pmc/articles/PMC5905186/ /pubmed/29665771 http://dx.doi.org/10.1186/s12862-018-1156-7 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Fumey, Julien
Hinaux, Hélène
Noirot, Céline
Thermes, Claude
Rétaux, Sylvie
Casane, Didier
Evidence for late Pleistocene origin of Astyanax mexicanus cavefish
title Evidence for late Pleistocene origin of Astyanax mexicanus cavefish
title_full Evidence for late Pleistocene origin of Astyanax mexicanus cavefish
title_fullStr Evidence for late Pleistocene origin of Astyanax mexicanus cavefish
title_full_unstemmed Evidence for late Pleistocene origin of Astyanax mexicanus cavefish
title_short Evidence for late Pleistocene origin of Astyanax mexicanus cavefish
title_sort evidence for late pleistocene origin of astyanax mexicanus cavefish
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905186/
https://www.ncbi.nlm.nih.gov/pubmed/29665771
http://dx.doi.org/10.1186/s12862-018-1156-7
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