The time unfolding of the embryo development computation is NOT dependent on the genome's layout. In fact, what drives its unfolding are the GeNets and the PRs among them, as represented in the BioPert, and not the physical positions of individual genes & coding sequences on the genome. This is why shuffled genomes, such as those seen in the human vs. mouse case, are each capable of generating well formed & functioning phenotypes.
An interesting question is:" Why related species' genomes are distinct shuffles of the genomic card deck?". It seems that such shuffling is useful to reproductively separate budding sub-species from each other by interfering with interspecies lining up & matching of coding sequences in the zygote. This will, initially, reduce interbreeding success and eventually eliminate it altogether. Thus, eventually, as explained in Homo Pan divergence, the gene pool will split into separate gene pools free to follow independent evolutionary trajectories maximizing adaptation to distinct emerging niches.
On May 17, 2006 a number of press articles reported Prof. David Reich of Harvard Medical School startling findings concerning the divergence of the DNA for the Homo and Pan species. The articles being journalistic accounts are inaccurate and confused.
The evidence considered in Prof. Reich study is the number of different base pairs (BPs) in the corresponding segments of the two species DNA. The number of differences being proportional to the elapsed time from the two segments divergence in the speciation process. In fact, the rate with which successful structural or architectural DNA changes accumulate is linear or proportional to elapsed time (for example, see the data in predictions on the quasi linearity of the relation between evolutionary & embryogenetic milestones). In other words, the number of different BPs can be considered a molecular clock for the evolution of the two related species.
What Prof. Reich found is that different DNA segments yield different elapsed time figures, with the earliest separation occurring somewhere between 6.3 MYA and 5.4 MYA and the most recent being only 1.2 MYA for X, the female sex chromosome. In other words, the separation of the human from the chimpanzee species occurred over a period of about 4 million years in a rather complex process involving a number of cross species hybridizations.
Here are some press reports re Prof. Reich findings:
We can also speculate that at a given time a species' gene pool may contain a number of such shuffles affecting different regions of the genome. In other words, the species may sport a number of "buds". In the event that the species' niche is stable and not splitting up in a number of sub-niches such buds would not afford adaptive advantages and they would, over time, disappear due to their inherent reproductive disadvantage. However, if the original niche segments due to, for example, a splitting of a land mass, then some or all such buds may result in a budding adaptive advantage. The latter may compensate for the reproductive disadvantage of heterozygous individual. In such case the bud(s) could prosper and rapidly evolve into one or more emerging species pursuing differential evolutionary trajectories. In other words, such buds, in the presence of an ecological challenge could evolve into a biological radiation.
It is clear that the study of emerging genomic shuffles in our and other species is very likely to yield crucial insights on the mechanisms of speciation, that is, evolution "in the large" or macro evolution.