Building evolutionary trees from genomes is challenging, in part because of the difficulties inferring trees when different parts of the genome may be evolving

Building evolutionary trees from genomes is challenging, in part because of the difficulties inferring trees when different parts of the genome may be evolving at very different rates, but also because of the wide dynamic range of genome quality. Human and mouse genomes have far fewer errors (missing regions) than rat and cow, and many of the other several hundred genomes will be of much much lower quality. At this scale, it is difficult to know whether surprising results reflect biology or inaccuracy.