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The Skeptic wrote:One of the most prominent predictions of evolution is the nested hiearchical pattern of living organisms. Distrubitions of traits are expected to form nested hierarchies. Phylogenetic studies, both in molecular and morphological level attempt to find the correct phylogeny of life. However, despite such efforts, many parts of the 'tree' remains unsettled. These inconsistencies even caused some to question whether a phylogenetic tree exists or not. The theory, predicted almost perfect distrubitions of genetic changes. For example, if an Alu transposable element is present in the orthologous locus of humans, chimpanzees, orangutans and rhesus monkeys, even sequence based phylogeny of that element must be fully consistent with the same phylogeny as we infer from presence/absence patterns of Alu elements. Since, the Alu insertion is assumed to be accumulating random mutations, for example, the genetic distance of human-chimpanzee pair must be smaller than the genetic distance between human-orangutan and human-macaque pairs. The same is predicted for ERVs.


Evolutionary biology assumes that an ERV in the same locus, is identical by descent. If this were true, one can predict that accumulated mutational divergence must form the same tree. But this was far from facts. In 1999, some authors tried to test these predictions. Results were far from predictions. While some of the orthologous ERVs seemed a little bit consistent with phylogeny, many deviated from the pattern. According to some elements, we were closer to orangutans than to gorillas. Authors asserted that this inconsistencies were caused by gene conversion events. But this is not testable and repeatable. There is no way to check this. Also, incomplete lineage sorting of ancestral polymorphisms is expected to cause deviations from the pattern. In addition, deletion of ERVs, deletion of Alu elements, resurrection of pseudogenes are found to be very frequent. If you want to use a pseudogenization event as a phylogenetic marker, the results will be very misleading. The same authors found that one ERV was present in old world monkeys, orangutans and humans, but absent from the genomes of gorillas and chimpanzees. This means that evolution does not actually predict a nested hiearchy. Without nested hiearchy, one arm of evolution becomes broken. Theory loses its almost all testable predictions.

http://www.ncbi.nlm.nih.gov/pubmed/10468595