It seem strange, you used the term "professional biologist". Is there a reason for that?
I can't count the number of times I have been told to go and learn what I don't know, nor understand.
I suppose you can always apply that. Learning is fun... sometimes.
I decided though, rather than send you to find the information yourself, I'd snip out some bits on HGT (horizontal gene transfer)
Transfer of DNA from Bacteria to Eukaryotes\
...
Indeed, analyses of accumulating genomic data reveal cases of horizontal gene transfer from bacteria to eukaryotes and suggest that it represents a significant force in adaptive evolution of eukaryotic species. Specifically, recent reports indicate that bacteria other than Agrobacterium, such as Bartonella henselae (a zoonotic pathogen), Rhizobium etli (a plant-symbiotic bacterium related to Agrobacterium), or even Escherichia coli, have the ability to genetically transform their host cells under laboratory conditions.
Numerous cases of HGT from bacteria to eukaryotes have been demonstrated, although this process is assumed to be much less frequent than HGT between bacteria. The early evolution of eukaryotes was marked by endosymbiotic events leading to permanent acquisition of major organelles, e.g., mitochondria that originated from proteobacteria and plastids that originated from cyanobacteria, followed by organelle-to-nucleus gene transfer, usually referred to as endosymbiotic gene transfer (EGT) (6). Whereas the episodic gene transfer via EGT has a demonstrated evolutionary significance, the importance of HGT in the evolution of eukaryotes is still debated
Horizontal gene transfer in eukaryotes - The weak-link model
About a decade ago, Doolittle et al. raised a question about the number of bacterial genes in protists, speculating that many bacterial genes should have accumulated in genomes of protists through feeding activities 1,2. Back then,
horizontal gene transfer (HGT) had been documented widely as a mechanism to gain foreign genetic materials in prokaryotes, but remained largely an exotic concept in eukaryotes, with little substantial evidence. It is now clear that HGT has occurred in all major eukaryotic lineages. Horizontally acquired genes are not only frequent in unicellular eukaryotes 3–5, but also found in various multicellular eukaryotes, including cnidarians 6,7, mites 8, insects 9–12, nematodes 13–15, fish 16, and land plants 17–22. Although reports of HGT in eukaryotes are still frequently met with skepticism, evidence for HGT throughout eukaryotic evolution is abundant and increasing.
In this paper, I discuss issues related to HGT in eukaryotes. Because most foreign genes reported in eukaryotes thus far are from bacteria, I will focus on bacterial genes.
I argue that many bacterial genes in eukaryotes cannot be explained simply as gene transfers from mitochondria or plastids; rather, HGT in eukaryotes should be widespread and expected. Further, I propose a mechanism for integration of foreign DNA into eukaryotic genomes during unicellular or early developmental stages, when their nuclear DNA is relatively exposed to potential sources of HGT.
Horizontal gene transfer in eukaryotic evolution
Horizontal Gene Transfer and the History of Life
Microbes acquire DNA from a variety of sources.
The last decades, which have seen the development of genome sequencing, have revealed that horizontal gene transfer has been a major evolutionary force that has constantly reshaped genomes throughout evolution. However, because the history of life must ultimately be deduced from gene phylogenies, the lack of methods to account for horizontal gene transfer has thrown into confusion the very concept of the tree of life. As a result, many questions remain open, but emerging methodological developments promise to use information conveyed by horizontal gene transfer that remains unexploited today.
Evolutionary Consequences of Horizontal Transfer
The true evolutionary role and impact that horizontal gene transfer has had on the evolution of life were only realized recently with the advent of genome sequencing. The above mechanisms have relatively low specificity, and thus allow movement of genetic information even between distant species, with correspondingly profound consequences on the modes of adaptation and the concept of bacterial species (Ochman et al. 2005).
In comparison to descent with modification, horizontal gene transfer offers the possibility for quite drastic adaptation. However, far from questioning the principle of Darwinian evolution, as has been suggested, this mode of evolution underscores the importance of taking into account different levels of selection (e.g., genes vs. genomes) for understanding the evolution of genomes.
Horizontal gene transfer in evolution: facts and challenges
The contribution of horizontal gene transfer to evolution has been controversial since it was suggested to be a force driving evolution in the microbial world.
Recently, several calls have been put forward for a new evolutionary synthesis (Dean & Thornton 2007; Pigliucci 2007; Carroll 2008; Koonin 2009)
that encompasses mechanisms other than mutation, natural selection and drift to explain evolutionary changes, such as developmental constraints and epigenetic modifications among others.
Today it seems evident, from the studies discussed below, that horizontal (or lateral) gene transfer, the direct visualization of which has been achieved recently (Babić et al. 2008), is an important force driving the evolution of Bacteria and Archaea, as well as that of unicellular eukaryotes, and should therefore also be considered as part of the structure of any evolutionary synthesis.
You can always do some more research, on it.
In a nutshell, scientists don't know. They discover new things that overturn previous assumptions, and their current assumptions can be thrown out tomorrow.
Just as the tree of life was turned into a web, with new discoveries, including HGT... and I am sure there will be more webs, we can wait and see what new surprises may be in store.
However, whatever assertions scientists make, or don't make, the fact is, they don't know, and time will tell.
Did you notice that the discovery of HGT in eukaryotes, has already led to some suggesting that question the principle of Darwinian evolution?