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Re: Dino farts



Mitochondria and chloroplasts are undoubtedly derived from Eubacteria 
(Alphaproteobacteria and Cyanobacteria respectively)
Mitochondria are found in all branches of Eukaryotes (though I think some 
groups have lost them).
They have highly degenerate genomes, it seems much of their genome has been 
incorporated into the nucleus of the "host cell"

Therefore, there was clearly lateral gene transfer from Eubacteria to 
Eukaryotes. As this is a clear case of symbiosis, you could argue Eukaryotes 
are part Eubacteria.

So the question is, where did the ancestral Eukaryotic cell come from that 
engulfed an Alphaproteobacteria?

There are some features which link Eukaryotes and Archea.
For example, histone proteins which package DNA and are found in the nucleus, 
are homologous to archaea histone proteins (interestingly enough, the group of 
archaea that have histones are mostly methanogens). Eubacteria lack homologs of 
these proteins.
Similar arguments about cholestoral usage and proteasomes are used to support 
Archaea and Eukaryotes as sister groups (or even place Eukaryotes within 
Archaea, much as the mitochondria falls within Eubacteria).

IMHO, the best explanation is that Eukaryotes resulted from symbiosis between 
Archaea and Eubacteria.
Such a situation doesn't fit well on a typical branching cladogram, and there 
was undoubtedly a lot of lateral gene transfer back then (as there still is 
across disparate "species" within most Eubacteria)

Presumably, there were stem-Eukaryotes proto-Eukaryotes containing a nucleus 
and such, that had not yet acquired mitochondria. It seems crown Eukaryotes all 
come after this symbiosis event (and plants/algae had yet another symbiosis 
event with cyanobacteria)

Representing it as a trichotomy seems the simplest way to portray a complex and 
unclear origin.

--- On Mon, 5/7/12, Dan Chure <danchure@easilink.com> wrote:

> From: Dan Chure <danchure@easilink.com>
> Subject: Re: Dino farts
> To: tijawi@gmail.com
> Cc: dinosaur@usc.edu
> Date: Monday, May 7, 2012, 11:06 PM
> I have seen some ph
 where Eubacteria is the sister group to
> Eukaryota, and 
> others where there is a trichotomy between the three
> groups.  However, I 
> think the latter is most often a byproduct of using ranks,
> i.e. each is 
> a Domain so they must be equal. Not sure which of the first
> two 
> phylogenies is the best supported but there are characters
> supporting 
> each arrangement and my guess would be that there is a
> nested sister 
> group phylogeny rather than a trichotomy.
> 
> Dan
> 
> 
> 
> 
> On 5/7/2012 8:55 PM, Tim Williams wrote:
> > Dann Pigdon<dannj@alphalink.com.au> 
> wrote:
> >
> >
> >> Surely in order to determine the amount of methane
> sauropods produced globally, we'd need to
> >> know:
> >>
> >> - Whether or not they utilised methanogenic
> bacteria (not all modern herbivores do).
> >
> > The authors used non-ruminant herbivores to derive
> their estimates.
> >
> >
> > BTW, a pedantic but important correction: methanogenic
> microbes are
> > archaea, not bacteria.  Archaea are the so-called
> Third Domain of Life
> > (after Bacteria and Eukaryota).  Phylogenetically
> speaking, archaea
> > are no more closely related to bacteria than we are.
> >
> >
> >> - The total biomass of sauropods in the world at
> any one time.
> >> - The rate at which digestion took place.
> >>
> >> Pinning any of these factors down with any degree
> of accuracy would seem to be a tall order.
> >
> > The authors do show their working.  Although there
> are certainly a lot
> > of assumptions made along the way.
> >
> >
> > As you imply, the range of methane production among
> herbivorous
> > mammals is highly variable.  For example,
> herbivorous marsupials
> > produce far less methane than ruminants, in part
> because of the
> > different anatomies of their respective digestive
> systems, and in part
> > because of the microbes themselves (lower numbers of
> methanogenic
> > archaea in marsupials, plus different metabolic
> interactions with
> > fermentative bacteria).
> >
> >
> >
> >> I'm also puzzled as to why the amount o
ased by sauropods
> >> compared to the amount estimated for modern
> domestic livestock is of any statistical importance.
> >> There are more herbivores currently in the world
> than just human livestock.
> >
> > Yes, but ruminants (including livestock) are
> notoriously high emitters
> > of methane.
> >
> >
> >
> >
> >
> >
> > Cheers
> >
> > Tim
> >
> >
> >> I'm also puzzled as to why the amount of methane
> estimated to have been released by sauropods
> >> compared to the amount estimated for modern
> domestic livestock is of any statistical importance.
> >> There are more herbivores currently in the world
> than just human livestock.
> >>
> >> And even if sauropods did produce that much
> methane, wouldn't decomposing plant matter still
> >> produce similar amounts whether it got eaten by
> herbivores or not?
> >>
> >> --
> >>
> _____________________________________________________________
> >>
> >> Dann Pigdon
> >> Spatial Data Analyst       
>        Australian Dinosaurs
> >> Melbourne, Australia       
>        http://home.alphalink.com.au/~dannj
> >>
> _____________________________________________________________
> >>
> >
> >
> > -----
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> >
> >
> 
> 
>