Yes, to some extent genes are mobile and do get shuffled around, but if this hypothesis were true, it would be obvious. Whole genomes don't just merge on the ti

Yes, to some extent genes are mobile and do get shuffled around, but if this hypothesis were true, it would be obvious. Whole genomes don't just merge on the time scales we're talking here. If this hypothesis were true, there would be clear genomic anomalies indicating it (e.g. biases of genes used at the same developmental stage tending to cluster in similar genomic regions); no such anomalies have been found.