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MBE Advance Access originally published online on March 6, 2009
Molecular Biology and Evolution 2009 26(6):1235-1243; 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 Articles

Environmental Genomics: A Tale of Two Fishes1

Giuseppe Bucciarelli*, Miriam Di Filippo*, Domenico Costagliola*, Fernando Alvarez-Valin{dagger}, Giacomo Bernardi{ddagger} and Giorgio Bernardi*

* Laboratory of Molecular Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
{dagger} Sección Biomatemática, Facultad de Ciencias, Iguá, Montevideo, Uruguay
{ddagger} Department of Ecology and Evolutionary Biology, University of California, Santa Cruz

E-mail: bernardi{at}szn.it.

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 °C, respectively, was addressed by analyzing their genomes. Compared with 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 noncoding control regions (D-loops), from which a divergence time of less than 0.66–0.75 Mya could be estimated. In the nuclear genome, 1) both AT -> GC/GC -> AT and transversion: transition ratios in coding sequences (CDSs) were relatively high; moreover, the ratios of nonsynonymous/synonymous changes (Ka/Ks) suggested that some genes were under positive selection; 2) DNA methylation showed a very significant decrease; and 3) 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 mold 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 CDSs is of special interest because it provides a model for the formation of the GC-rich and gene-rich isochores of the genomes of mammals and birds.

Key Words: body temperature • evolution • genomes • minisatellites • isochores • speciation

1 This paper is respectfully dedicated to His Majesty the Emperor of Japan, a unique scholar of gobiid fishes.

Norihiro Okada, Associate Editor


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