It further suggests that this also happens in the prokaryotic branch of the tree - that which includes the majority of multicellular organisms, including ourselves. It points out that methods of horizontal gene transfer might occur through mediating viruses which cut and paste genetic material between hosts. It can also occur via hybridisation, where two separate species cross. This, according to Loren Riesberg, is the case for about 14% of plant species. There is also some evidence that this may have happened in early humans, between our ancestors and concurrent species, such as Homo erecutus and Neanderthals.
Personally I feel that some of this is a bit fuzzy. Firstly, the article suggests that DNA is subject to vertical transfer, but HGT can be seen in RNA. While perhaps that is just poor wording in the article, it feels from the first that the article is trying a bit too hard to make a point - and starts out almost hostile to the tree-of-life view, and so I wonder if it's trying to hide something there in order to prove a point. The article does ease up towards the end, describing the different viewpoints of scientists who feel that the tree of life needs to be 'uprooted' and those who feel that HGT just adds a new dimension to the data.
As far as the hybridisation comments, it would seem odd that where speciating groups overlapped they did not hybridise to some extent if they were able to. In fact, I am fairly sure this is what Darwin talked about in Ch. 4 or 5.
In the article it asks whether the tree-of-life view does not still apply to multicellular organisms. And replies - almost, at least - "Well, they aren't the majority, so we shouldn't bother with that view anymore". If the tree is still the way in which some genetic material is transferred, then, whatever other methods are available for its transfer, it is still a valid view.
I kept thinking "Newton...Einstein" throughout reading this, and, sure enough, right at the end he says:
If he [Michael Rose] is right, the tree concept could become biology's equivalent of Newtonian mechanics: revolutionary and hugely successful in its time, but ultimately too simplistic to deal with the messy real world.Some of the things mentioned in the article gel with my feelings about early life - knowing that single-celled organisms can only reproduce by copying made me wonder about how genetic variety worked before sexual reproduction occurred.
I guess we live in interesting times - and I am sure the Discovery Institute is going to have a field day with this. It will be interesting to watch how it all develops.