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Unique human psychological and cultural characteristics were present in our distant hunter gatherer past, but in terms of the biophysical impact of our species, agricultural represented an unequivocal and decisive evolutionary break.
Our analysis on evolutionary break points shows that the regional regulation of gene transcription is relatively conserved between chicken and human.
In comparing evolutionary break points between RIDGEs and anti-RIDGEs, we found a higher number of break points within RIDGEs than anti-RIDGEs in both the chicken and the human genome.
Although RIDGEs clearly show an increase in the number of evolutionary break points, we also showed a significantly higher number of RIDGE-to-RIDGE break points between the chicken and human genomes.
Although we cannot ask if origins existed at evolutionary break sites prior to rearrangements, we can examine breakpoints generated in systems where origin location is known prior to the break event.
Because the identification of these synteny blocks was based on chicken genome assembly WASHUC1 (Dec. 2004), we mapped the ends of these syntenic blocks to the current chicken genome assembly (WASHUC2, May 2006) (Additional file 4), and considered each end as an evolutionary break point.
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Others have attempted to address this by correlating the evolutionary breaks with other genomic landmarks as well as with breaks in cancer cells [ 5, 24].
Inherent to the latter model is the prediction that evolutionary breaks will frequently overlap with fragile sites and cancer-associated breakpoints [ 9, 66, 69, 70].
We use a novel approach to assert independence among the evolutionary breaks, while minimizing the role of negative selection as an underlying cause.
Recent findings indicate that evolutionary breaks in the genome are not randomly distributed, and that certain regions, so-called fragile regions, are predisposed to breakages.
An association between evolutionary breaks and segmental duplications has been previously reported [ 8, 12] suggesting that specific regions within the genome have been predisposed to small duplications as well as large evolutionary rearrangements.
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