What a load of bollocks. The tree of life as a concept emerging from the idea of common ancestry has no problems with molecular genetics processes such as duplication or fusion, and what about "unknown mechanisms"? How the fuck could the tree of life have a problem with an "unknown mechanism"? The two are simply not in conflict and seem to me entirely unrelated.

The problem is horizontal gene-transfer, but this doesn't require a fucking rewrite or rejection of the entire theory of evolution(the modern one, the one proposed by Darwin has been replaced a long time ago). Life still evolved, largely through processes like natural selection and genetic drift, and the tree concept is still largely valid for large multicellular eucaryotes (such as animals). There are a few rare cases of horizontal gene transfer between distantly related lineages through viral infections, but these are extremely rare exceptions. The phenomenon is rampant in procaryotes and other single-celled organisms though. This destroyes the idea of a true tree and replaces it with a more net-like structure.

Instead of watching that load of hyped snot you should start here if you want competent insights on challenges to the tree of life: [link to www.biology-direct.com]