This is what you promised on the last round and it turned out to be apples and oranges. The chart is meaningless without knowing the organisms. You also had no external evidence of common descent but had a better shot due to prokaryotic HGT.
Lets get back to why you think the mechanisms you listed account for the pattern. Can you support it without assuming common descent?
I think you need to take a step back at this point and read Winstons paper. Seeing both sides of an argument objectively is a good thing.
How the animals reproduce is relevant to the pattern. How the animals transfer genetic material is relevant to the pattern. Frequent HGT in bacteria may have been a causal factor in the e coli pattern. Less likely in the vertebrate pattern. Genetic recombination maybe a cause in the vertebrate pattern less likely in the bacterial pattern.
We still don’t know what caused the pattern in e coli at this point.
Sorry, but HGT would only obscure the pattern, not create a false one. (Though in fact HGT is most common among close relatives, so that would tend to resist noise.) And genetic recombination within species would not affect the pattern between species. So none of that is important.
You don’t know. I do. HGT doesn’t create a nested hierarchy.
Each belongs to one of two different lineages derived from clonal cultures of a single strain of Plasmodium falciparum (Pf) called NF54, a malaria parasite. The lineages are “E5” and “3D7”. NF54 is an isolate from a single malaria patient in the Netherlands.
As the clonal lineages evolved in the lab, they lost and gained genes. For example, after passaging for while, E5 had 62 var genes, but 3D7 has 61. This means E5 gained a new var gene. The researchers figured out the mechanism for this and its, drumrolls, recombination:
Again we see common descent reproducing the Howe diagram pattern. We also observe gene gain and loss. In addition, recombination was found to be the mechanism for the formation of one of the genes in E5.
They are not single eukaryotic cells and reproduce differently. The experiment is a different animal with different reproduction. Why would you expect this type of result in vertebrates?
Stop saying nonsense. Don’t you know malaria parasites reproduce sexually and asexually? In fact, the paper I got the Venn diagram figured out that recombination that produced the novel var gene was formed during the sexual reproductive stage of the parasite’s life cycle.
Since you are ignorant of the malaria parasite life cycle, this CDC introduction should help you out:
To further hit the point home, you can look at the same Howe-type diagram (fig A) generated for several rice species which are all multicellular, sexually reproducing eukaryotes. The diagram on the right (fig B) shows the lineage-specific gene loss and gene gain events following common descent. So whether we deal with prokaryotes or eukaryotes, we still get the same Howe-type diagram.
The nested hierarchy pattern observed in all the Venn diagrams I have shown, and others like Howe’s, echoes an important conclusion: there was common descent, and there were mechanisms like recombination and duplication (see below) that drove the formation of novel genes as lineages diverged. Selection and drift also acted on these changing repertoire of gene families, keeping some and purging the others.
PS: some new genes in the various rice families evolved via duplication and even single amino acid substitutions. For duplications:
Recombination happens in all life forms and can contribute to the generation of new genes, as I showed in the case of the malaria parasite lineages.
A Howe-type diagram can be constructed for any set of organisms and it will show orthologs and species-specific genes in all cases. There is just nothing special about Howe’s diagram in particular.
The Howe diagram is vertebrates. Its not rice and not eukaryotic parasites. You have done some good research here but it’s not done. You need to show that recombination like this occurs in vertebrates to the extent we can explain the pattern.
This is true but not new news. Can recombination create lungs flight feathers etc? Or were they the result of a separate starting point?
We’ve been using recombination to map genes in vertebrates for decades. There are literally tens, probably hundreds, of thousands of papers demonstrating vertebrate recombination. I have even authored a few of them.
Flight feathers keeps coming up. Why are you so impressed with them? To me, they look like not so much a problem as rather a prime exhibit of a selectable feature which evolved by way of plenty of intermediate functionality.
And let us remember, which Bill will not, that flight feathers evolved from non-flight feathers, and those from more primitive protofeathers, for quite a while before the stage that Bill is thinking of. Of course, Bill doesn’t believe in common descent of chickens and turkeys, so none of that would work on him. He doesn’t even think that birds are a real group.
Such basic knowledge can be found in undergraduate-level genetics textbooks and some high-school level ones. Your request appears to be vapid sealioning.
