Re: "Common ancestor" in cladistics

[Christopher Taylor <ck.taylor@auckland.ac.nz>]

    Actually, there are many ways that a phylogeny of a single gene may
differ from the phylogeny of the organism, even in eukaryotes. (Warning:
long theoretical example ahead)
    Many genes are present in multiple copies in a single genome (ribosomal
genes, for instance), and each of those copies may have its own evolutionary
history. If phylogenies are constructed using sequences that actually come
from a mixture of copies from different species, the resulting tree will be
quite different from the 'true' tree.
    Even assuming that you are not mistaken in your selection of genes,
there can still be a conflict between gene and organism if the gene is
polymorphic in the population. Take an organismal phylogeny:

    |--A
    `--+--B
       `--C

    Imagine that in this example, speciation has occurred by 'budding off'
of small peripheral populations from a large, central population (like has
been mentioned on the list recently for Canada geese). B in the tree above
represents the central population as it currently stands, from which A
diverged earlier than C.
    Now imagine that we are trying to track this phylogeny using gene 1. Two
(selectively neutral) alleles of this gene diverged in the central
population prior to the divergence of A. One of these alleles became fixed
in A as a result of drift, the other became fixed in C, B has a larger
population and so retains both alleles. The gene tree is then:

Ancestral 1
    |--1
    |   |--1 in B
    |   `--1 in A
    `--1'
        |--1' in B
        `--1' in C

    (As an aside, selective neutrality is not vital for this example.
Perhaps the different alleles are each more advantageous in different parts
of the widespread population that is now B, and A and C each arose from
widely separated parts of the population)
    Now, if we only sample allele 1 in species B (either 1' was simply
missed when sampling, or it has gone extinct in B subsequent to the
divergence of C), we get a gene tree:

    |--C
    `--+--A
       `--B

    which is totally different from the organismal tree.
    Moral of the story: Use as many genes as possible (because hopefully
they can't all express such polymorphism in exactly the same way, and the
more recently divergent population will share more alleles overall than the
older population). And for added relevance, the same scenario I've used here
applies to dealing with polymorphic morphological characters :-).

    And as a final pointer, ribosomal genes have generally been used in
prokaryotic phylogentics because it was imagined that they are so vital and
integral to the function of the organism that lateral transfer was not
possible, but some researchers now suspect that this is not necessarily the
case. The hyperthermophilic eubacteria Thermotoga and Aquifex, for example,
which appear quite close to Archaebacteria in rDNA trees, may do so because
they've picked up genes from Archaebacteria - non-ribosomal genes often put
them much higher among the eubacteria (Cavalier-Smith, 2002, in the IJSEM).

    Cheers,

        Christopher Taylor

On 30/7/04 6:16 am, "Tim Williams" <twilliams_alpha@hotmail.com> wrote:

> 
> Ribosomal RNA sequences are usually used as the datasets when investigate
> the relatedness of bacterial and archaeal 'species'.  When we construct a
> phylogeny based on ribosomal sequences of bacteria or archaea, we are not
> recovering a phylogeny of the actual species, but of a solitary gene.  By
> contrast, when we investigate relationships within a group of vertebrates or
> plants or arthropods, we can be fairly sure that the phylogeny of a certain
> gene does reflect the phylogeny of its owner.  (Of course, there are
> important exceptions, since multicellular organisms may acquire genes from
> elsewhere.)
> 
>> For instance, we know that rheiformes (like ostriches) and a closely
>> related
>> group are most distantly related to all other living birds, that chickens,
>> geese and ducks are next most related to all other groups of living birds,
>> and somehow passeriformes end up at the other end of the spectrum.    Some
>> researchers find rheiformes to be the oldest group, some find chickens,
>> geese and ducks to be the oldest group, and some actually insist that
>> passeriformes are the oldest group!
> 
> By 'Rheiformes' you probably mean Palaeognathae (ratites and tinamous); but
> I take your point.  Many phylogenies have the Palaeognathae branching off
> first, followed by the Galloanserae (chickens, geese, ducks, &c), then all
> other birds, with the Passeriformes the last clade to branch off.  The idea
> that passeriforms are the oldest group of modern birds was based on one or
> two molecular studies, and never had much support; newer analyses appear to
> have killed off this idea.
> 
> 
> 
> Tim
> 
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