What lies beneath? Molecular evolution during the radiation of caecilian amphibians

BMC Genomics

Diego San Mauro¹  María Torres-Sánchez²  David J. Gower³  Mark Wilkinson³  Christopher J. Creevey⁴  David Alvarez-Ponce⁵ 

[1] 0000 0001 2157 7667, grid.4795.f, Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, 28040, Madrid, Spain;0000 0001 2157 7667, grid.4795.f, Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, 28040, Madrid, Spain;0000 0004 1936 8438, grid.266539.d, Present address: Department of Neuroscience, Spinal Cord and Brain Injury Research Center & Ambystoma Genetic Stock Center, University of Kentucky, 40536, Lexington, KY, USA;0000 0001 2270 9879, grid.35937.3b, Department of Life Sciences, The Natural History Museum, SW7 5BD, London, UK;0000 0004 0374 7521, grid.4777.3, Institute for Global Food Security, Queen’s University Belfast, University Road, BT7 1NN, Belfast, Northern Ireland, UK;0000 0004 1936 914X, grid.266818.3, Department of Biology, University of Nevada, 89557, Reno, NV, USA;

关键词: Ecological opportunity;    Gene ontology;    Gymnophiona;    Positive selection signatures;    Vertebrate evolution;   

DOI  :  10.1186/s12864-019-5694-1

来源: publisher

【 摘 要 】

BackgroundEvolution 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.ResultsA 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.ConclusionsThe 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.

【 授权许可】

CC BY