Re: Chimeras and Horizontal Gene Transfer

On May 23, 5:44 pm, Unholy Joe <transcendento...@xxxxxxxxx> wrote:
My posts are not showing up,What the hell?

I replied to this once already, and it didn't show up.

Anyway...

Check out this:http://www.pnas.org/content/105/29/10039/F3.large.jpg(figurefrom the
paper I cited)
and tell me that's a tree!Obviously we need to think on this a bit.Or
can it be that I am missing something?Can figure D in my link prove
that HGT overrides any signal by pure virtue of abundance?

Next..

The pnas paper acknowledges mosaics can be found in
prokaryotes.Thus,chimeras do exist.We do have to modify ToE because of
HGT.

Next...

*For that specific gene.*  It is typically single genes that get
transferred in procaryotes, not half genomes.  In eucaryotes, you do
get hybridization transfer before the two incipient species are
completely reproductively isolated, allowing some gene transfer.  But
that just makes the speciation boundary fuzzy.

So at a particular node,the HGT is light but overall it is
extreme.This means that we can still make relationships and trees?

Again, because horizontal transfers are rarer than vertical changes
even in procaryotes (that is an empirical fact, not a guess) *and*,
like eucaryotes, most modes of horizontal transfer in procaryotes are
limited to spreading to *relatively* genetically close species (in
addition to being limited to species in its local environment),

Cite papers that support your claim?

Every paper that describes the limitations of hybridization in
eucaryotes. We know, for example, that humans are currently
reproductively isolated from even chimps and may well have been
isolated from the humans who were called neanderthals or only engaged
in a very small amount of HGT with them by hybridization. This is
quite the norm for eucaryotic hybridization. When it occurs, it tends
to be between organisms that are closely related. The chances of
humans hybridizing to a whale or dog or tunicate or sea urchin or
mollusc or insect or marigold or mushroom or paramecium is nil.

The other mode of HGT in eucaryotes, transfer by symbiosis or
infection, has occurred in the case of plasmids like mitochondria and
chloroplasts. In fact, it is likely to have occurred independently
several times historically. Viral transfer also can occur, but viruses
tend to be limited in host ranges and most eucaryotic viruses tend not
(unlike the transducing bacteriophage) have replicative mechanisms
that lead to the accidental packaging of one host's DNA and transfer
to another. They tend to only transfer copies of themselves or (and I
am thinking of certain plant viruses) transfer DNA from symbiotic
bacteria to the plant.

In bacteria, the three mechanisms of HGT are conjugation (sometimes
called bacterial sex), transduction, and transformation. Conjugation
is really a mechanism for plasmid transfer, with plasmids acting like
an internal virus that can only spread by contact. Something like an
STD. When the plasmid becomes integrated into the bacterial
chromosome, it transfers sections of the donor chromosome to the newly
"infected" recipient. This can transfer fairly large chunks of the
donor chromosome and is the only mechanism that can do so in bacteria
(eucaryotes use meiotic sex to do so). But the recognition of a
recipient is a function of a pilin protein produced by the plasmid in
the donor and its ability to recognize a surface protein on the
recipient's surface. Thus conjugation tends to only be able to engage
in the transfer process between relatively closely related bacteria.
The need to have the protein-protein interaction prevents promiscuity
of transfer.

Transduction is the passage of DNA because it accidently gets packaged
into a viral capsid. This can only transfer a limited amount of DNA
(a virus-length worth) and also tends to be limited in its
promiscuity. Like conjugation, bacteriophage tend to recognize hosts
by more or less specific protein-protein interactions. Some viruses
are more promiscuous than others and can infect a wider range of
hosts, but most tend to be able to infect only closely related
bacteria.

Transformation *in nature* also tends to transfer only relatively
small chunks of DNA. In the lab, transformation is artificially
induced by treating bacteria with chemicals or even shooting them with
nanoparticles. But in nature, only some bacteria can "naturally"
transform (and, even then, often only under certain conditions). They
do so by producing a surface enzyme that recognizes a specific DNA
sequence and then initiates a process to 'ingest' one strand
(hydrolyzing the other strand for energy). Naturally, it tends to be
closely related species that have significant number of sites with the
necessary DNA sequence. So transformation in nature too tends to be
limited to closely related species.

identifying the rare deviation from expected vertical change is
relatively easy by seeing the *weight* of evidence from a number of
genes at any level of relationship you want.

Even when,y'know,the deviation becomes the norm.Lemme relink:http://www.pnas.org/content/105/29/10039/F3.large.jpg

Vertical transmission of genetic information (mutated or not) occurs
*every time* an organism reproduces itself. Horizontal transmission
of genetic information (the same or different) is extremely rare
relative to instances of vertical transmission, although not so rare
that it doesn't *ever* happen. On geological time frames HGT could
easily happen to produce a fixed novelty in sequence once or twice for
each gene, but the vast and overwhelming of fixed novelties in
sequence will be due to mutation and either selection or neutral
fixation of vertically transmitted genes. The latter is what produces
the consistent tree. The former is rare enough to be identifiable as
exceptions from the tree (as in the genes of mitochondria and
chloroplast, which were certainly *originally* obtained by HGT, but
have been vertically transmitted ever since).

.

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