Figure 3.

CGH analyses. A) For each species, genomic DNAs from each animal (n = 4) were hybridized on separate arrays against a reference DNA from pooled zebra finches. Histograms are shown of the resulting mean log2 ratios (zebra finch:test species) for all gene targets, by test species. Note that when samples from individual zebra finches were hybridized versus the pooled zebra finch reference, the log2 signal ratios cluster closely around 0 as expected. The curve becomes shorter and broader with cross-hybridization to the kingbird and the chicken. B) Histograms of log2 ratios (zebra finch:test species) for a subset of 200 spots found significantly different on multi-species analysis of CGH data. Significant spots were determined by multi-class SAM Analysis using TIGR TMEV software with a median number of false significant genes set at 0. Note the large shift of the distribution to the right with increasing phylogenetic distance. C) Hierarchical tree of all CGH arrays, in a multiclass analysis using the Euclidean distance metric with average linkage clustering [82]. Arrays from the same species are clustered together, and the hierarchy is consistent with phylogenetic species relationships. The autologous hybridization (zebra finch – zebra finch, not shown) is effectively the outgroup in this analysis. D) The distribution of log2 ratios (test species:zebra finch reference) for one spot across 28 arrays (7 species).