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What lies beneath? Molecular evolution during the radiation of caecilian amphibians
BACKGROUND: Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptiv...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6507065/ https://www.ncbi.nlm.nih.gov/pubmed/31072350 http://dx.doi.org/10.1186/s12864-019-5694-1 |
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author | Torres-Sánchez, María Gower, David J. Alvarez-Ponce, David Creevey, Christopher J. Wilkinson, Mark San Mauro, Diego |
author_facet | Torres-Sánchez, María Gower, David J. Alvarez-Ponce, David Creevey, Christopher J. Wilkinson, Mark San Mauro, Diego |
author_sort | Torres-Sánchez, María |
collection | PubMed |
description | BACKGROUND: Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality). This enigmatic order of amphibians are very distinct phenotypically from other extant amphibians and likely from the ancestor of Lissamphibia, but little to nothing is known about the molecular changes underpinning their radiation. We hypothesised that colonization of various depths of tropical soils and of freshwater habitats presented new ecological opportunities to caecilians. RESULTS: A total of 8540 candidate groups of orthologous genes from transcriptomic data of five species of caecilian amphibians and the genome of the frog Xenopus tropicalis were analysed in order to investigate the genetic machinery behind caecilian diversification. We found a total of 168 protein-coding genes with signatures of positive selection at different evolutionary times during the radiation of caecilians. The majority of these genes were related to functional elements of the cell membrane and extracellular matrix with expression in several different tissues. The first colonization of the tropical soils was connected to the largest number of protein-coding genes under positive selection in our analysis. From the results of our study, we highlighted molecular changes in genes involved in perception, reduction-oxidation processes, and aging that likely were involved in the adaptation to different soil strata. CONCLUSIONS: The genes inferred to have been under positive selection provide valuable insights into caecilian evolution, potentially underpin adaptations of caecilians to their extreme environments, and contribute to a better understanding of fossorial adaptations and molecular evolution in vertebrates. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5694-1) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6507065 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-65070652019-05-13 What lies beneath? Molecular evolution during the radiation of caecilian amphibians Torres-Sánchez, María Gower, David J. Alvarez-Ponce, David Creevey, Christopher J. Wilkinson, Mark San Mauro, Diego BMC Genomics Research Article BACKGROUND: Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality). This enigmatic order of amphibians are very distinct phenotypically from other extant amphibians and likely from the ancestor of Lissamphibia, but little to nothing is known about the molecular changes underpinning their radiation. We hypothesised that colonization of various depths of tropical soils and of freshwater habitats presented new ecological opportunities to caecilians. RESULTS: A total of 8540 candidate groups of orthologous genes from transcriptomic data of five species of caecilian amphibians and the genome of the frog Xenopus tropicalis were analysed in order to investigate the genetic machinery behind caecilian diversification. We found a total of 168 protein-coding genes with signatures of positive selection at different evolutionary times during the radiation of caecilians. The majority of these genes were related to functional elements of the cell membrane and extracellular matrix with expression in several different tissues. The first colonization of the tropical soils was connected to the largest number of protein-coding genes under positive selection in our analysis. From the results of our study, we highlighted molecular changes in genes involved in perception, reduction-oxidation processes, and aging that likely were involved in the adaptation to different soil strata. CONCLUSIONS: The genes inferred to have been under positive selection provide valuable insights into caecilian evolution, potentially underpin adaptations of caecilians to their extreme environments, and contribute to a better understanding of fossorial adaptations and molecular evolution in vertebrates. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5694-1) contains supplementary material, which is available to authorized users. BioMed Central 2019-05-09 /pmc/articles/PMC6507065/ /pubmed/31072350 http://dx.doi.org/10.1186/s12864-019-5694-1 Text en © The Author(s). 2019 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 Torres-Sánchez, María Gower, David J. Alvarez-Ponce, David Creevey, Christopher J. Wilkinson, Mark San Mauro, Diego What lies beneath? Molecular evolution during the radiation of caecilian amphibians |
title | What lies beneath? Molecular evolution during the radiation of caecilian amphibians |
title_full | What lies beneath? Molecular evolution during the radiation of caecilian amphibians |
title_fullStr | What lies beneath? Molecular evolution during the radiation of caecilian amphibians |
title_full_unstemmed | What lies beneath? Molecular evolution during the radiation of caecilian amphibians |
title_short | What lies beneath? Molecular evolution during the radiation of caecilian amphibians |
title_sort | what lies beneath? molecular evolution during the radiation of caecilian amphibians |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6507065/ https://www.ncbi.nlm.nih.gov/pubmed/31072350 http://dx.doi.org/10.1186/s12864-019-5694-1 |
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