Evolutionary regulation of the blind subterranean mole rat, Spalax, revealed by genome-wide gene expression - PubMed (original) (raw)

Evolutionary regulation of the blind subterranean mole rat, Spalax, revealed by genome-wide gene expression

L I Brodsky et al. Proc Natl Acad Sci U S A. 2005.

Abstract

We applied genome-wide gene expression analysis to the evolutionary processes of adaptive speciation of the Israeli blind subterranean mole rats of the Spalax ehrenbergi superspecies. The four Israeli allospecies climatically and adaptively radiated into the cooler, mesic northern domain (N) and warmer, xeric southern domain (S). The kidney and brain mRNAs of two N and two S animals were examined through cross-species hybridizations with two types of Affymetrix arrays (mouse and rat) and muscle mRNA of six N and six S animals with spotted cDNA mouse arrays. The initial microarray analysis was hypothesis-free, i.e., conducted without reference to the origin of animals. Principal component analysis revealed that 20-30% of the expression signal variability could be explained by the differentiation of N-S species. Similar N-S effects were obtained for all tissues and types of arrays: two Affymetrix microarrays using probe oligomer signals and the spotted array. Likewise, ANOVA and t test statistics demonstrated significant N-S ecogeographic divergence and region-tissue specificity in gene expression. Analysis of differential gene expression between species corroborates previous results deduced by allozymes and DNA molecular polymorphisms. Functional categories show significant N-S ecologic putative adaptive divergent up-regulation of genes highlighting a higher metabolism in N, and potential adaptive brain activity and kidney urine cycle pathways in S. The present results confirm ecologic-genomic separation of blind mole rats into N and S. Gene expression regulation appears to be central to the evolution of blind mole rats.

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Figures

Fig. 1.

Fig. 1.

PCA and cluster analysis of probe oligomer (Affymetrix arrays) and gene signals (spotted array). Profiles of the second PC of PM and MM log signals for mouse and rat Affymetrix microarray experiments and mouse spotted-array experiment. (a) PC2 reflects the general signal difference between N and S animals for two types of Affymetrix microarrays [PM (red bars) and MM (blue bars) signals] and for the spotted array experiment (green bars). This PC2 component explains 20-30% of total signal variability. (b) The dendrogram of correlation distances between Affymetrix hybridizations (average linkage) after the cleaning of artifacts. All nonpatterned probe oligomers with average signals of >300 according to all eight hybridizations were taken. Clear N-S (S. galili plus S. golani vs. S. carmeli plus S. judaei) separation is seen for both tissues as in all other evolutionary discrimination of Spalax species based on diverse molecular markers and morphological criteria (figures 16, 17, 19, 20-22, 23 a and b, 31, and 33 in ref. 7).

Fig. 2.

Fig. 2.

The estimated expression profiles of several proteins that have ecogeography-tissue specificity (see the description of proteins in the text). The log values of averaged gene expression for four factor combinations were calculated through estimated parameters of the ANOVA model according to all PM and MM probes. The same type of gene expression regulation was detected by mouse and rat array hybridizations. (a) N kidney up-regulated ferritin. The strong N up-regulation of this gene for muscle was detected by spotted array hybridizations. (b) S brain up-regulated genes: somatostatin, neuropeptide Y, and ephrin.

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