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MBE Advance Access published online on March 6, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp041
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Environmental genomics: a tale of two fishes

Giuseppe Bucciarelli1, Miriam Di Filippo1, Domenico Costagliola1, Fernando Alvarez-Valin2, Giacomo Bernardi3 and Giorgio Bernardi1,*

1 Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli 80121, Italy
2 Sección Biomatemática, Facultad de Ciencias, Iguá 4225, Montevideo 11400, Uruguay
3 Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 95064, California, USA

* Corresponding author. Tel.: +39 081 5833402; Fax: +39 081 2455807; e-mail address: bernardi{at}szn.it

Received for publication September 26, 2008. Revision received January 5, 2009. Accepted for publication February 6, 2009.

The influence of the environment on two congeneric fishes, Gillichthys mirabilis and Gillichthys seta, that live in the Gulf of California at temperatures of 10°- 25°C, and up to 42°- 44°, respectively, was addressed by analyzing their genomes. Compared to G. mirabilis, G. seta showed some striking features. Substitution rates in the mitochondrial genes were found to be extremely fast, in fact faster than in non-coding control regions (D-loops), from which a divergence time of less than 0.66-0.75 million years ago could be estimated. In the nuclear genome (i) both AT->GC/GC-> AT and transition/transversion ratios in coding sequences were relatively high; moreover, the ratios of non-synonymous/synonymous changes (Ka/Ks) suggested that some genes were under positive selection; (ii) DNA methylation showed a very significant decrease; and (iii) a GC-rich minisatellite underwent a 4-fold amplification in the gene-rich regions. All these observations clearly indicate that the environment (temperature and the accompanying hypoxia) can rapidly mould the nuclear as well as the mitochondrial genome. The stabilization of gene-rich regions by the amplification of the GC-rich minisatellite and by the GC increase in nuclear coding sequences is of special interest since it provides a model for the formation of the GC-rich, gene-rich isochores of the genomes of mammals and birds.

Key Words: Body temperature • Evolution • Genomes • Minisatellites • Isochores • Speciation


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