Data from: Mixed-model reanalysis of primate data suggests tissue and species biases

An emerging issue in evolutionary genetics is whether it is possible to
use gene expression profiling to identify genes that are associated with
morphological, physiological, or behavioral divergence between species and
whether these genes have undergone positive selection. Some of these
questions were addressed in a recent study (Enard et al. 2002) of the
difference in gene expression among human, chimp, and orangutan, which
suggested an accelerated rate of divergence in gene expression in the
human brain relative to liver. Reanalysis of the Affymetrix data set using
analysis of variance methods to quantify the contributions of individuals
and species to variation in expression of 12,600 genes indicates that as
much as one-quarter of the genome shows divergent expression between
primate species at the 5% level. The magnitude of fold change ranges from
1.2-fold up to 8-fold. Similar conclusions apply to reanalysis of Enard et
al. 2002 parallel murine data set. However, biases inherent to short
oligonucleotide microarray technology may account for some of the tissue
and species effects. At high significance levels, more differences were
observed in the liver than in the brain in each of the pairwise species
comparisons, so it is not clear that expression divergence is accelerated
in the human brain. Further, there is an apparent bias toward upregulation
of gene expression in the brain in both primates and mice, whereas genes
are equally likely to be up- or downregulated in the liver when these
species diverge. A small subset of genes that are candidates for adaptive
divergence may be identified on the basis of a high ratio of interspecific
to intraspecific divergence.