Researchers from the University of Manchester, the University of Tennessee and Harvard Medical School in a 15 year study also identified several genetic loci that control the size of different brain parts.
The study aimed to find out if different parts of the brain can respond independently of each other to evolutionary stimulus (mosaic evolution) or whether the brain responds as a whole (concerted evolution).
Unlike previous studies the researchers compared the brain measurements within just one species.
The brains of approximately 10,000 mice were analysed. Seven individual parts of each brain were measured by volume and weight.
The entire genome, except the Y chromosome, was scanned for each animal and the gene set for each brain part identified.
Dr Reinmar Hager from MU compared variation in the size of the brain parts to variation in the genes. He found that the variation in the size of brain parts is controlled by the specific gene set for that brain part and not a shared set of genes.
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He also compared the measurements for each mouse to the overall size of its brain. Surprisingly, he found very little correlation between the sizes of the brain parts and the overall size of the brain.
"If all the different brain parts evolved as a whole we would expect that the same set of genes influences size in all parts. However, we found many gene variations for each different part of the brain supporting a mosaic scenario of brain evolution," Hager said in a statement.
"We also found very little correlation between the size of the brain parts and the overall size of the brain. This again supports the mosaic evolutionary hypothesis," Hager added.
They study found that the size of the brain is governed by an independent gene set to the one that controls the size of the body and there was very little correlation between variations in the size of the body and the brain.
The evidence means that overall brain size can evolve independently of body size, researchers said.
The findings have been published in the journal Nature Communications.