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Mickey writes:

>This question isn't directly about dinosaurs, but I think it's close
>enough that some people here might have answers.

>There's an on-going conversation in talk.origins about a protein
>sequence (for cytochrome c, I think) which indicates that humans are
>more closely related to rattlesnakes than rattlesnakes are to turtles.
>Apparently there is still some dispute about the relative affinities
>of the animals in these three groups, so it's unclear whether or not
>the sequences are consistent with what we know based on other
>information.  However, I just read an article in the June issue of
>_Natural History_ which might help.

Aaaggguuueee! (Hey Mickey that's two Aagguuee replies to posts of yours in
the same day. What are you trying to do to me? You know I'm in the delicate
write-up stage at the moment) :-)
Cytochrome c sequencing tells nothing of morphological relationships, only
time to last common ancester - see below.

>According to the NH article, turtles evolved during the Permian period
>from a group of animals known as pareiasaurs.  What I'm wondering is
>a) how secure is the conclusion that turtles arose via that lineage,

Pretty secure

>and b) given that we accept it, how much help does that give us in
>determining where the turtle/snake/mammal splits occurred?


Firstly, the Cytochrome c sequencing tells us nothing about morphological
relationships. Naturally snakes are more closely related to turtles than to
mammals - morphologically. They share far more morphological traits than
either does with mammals. The cytochrome c data is telling us a different,
but *complimentary* tale which only a moron, or . . .  (<- insert favourate
creationist here) would claim disproves evolution. In fact it is
overwhelming evidence *for* evolution.

This is what the fossil and morphological evidence suggests for turtle,
snake, mammal relationships:

   Turtles         Snakes                     Mammals
        |                   |                                  |
        |                   |                                  |
        |                   |         Dinosaurs         |
        |                   |                |                 |
        |                   |                |                 |
        |                   |                |                 |
        |                   |                |                 |
        |                   | -----------|                 |
        |               Lepidosaura |------------ |
        |                                    | Synapsida
        |-------------------------- |
                  Anapsida            |

The anapsida branched off the reptile main lineage quite early and produced
a separate reptile lineage which is characterised by having no temporal
openiongs in the skull. After this event, the synapsida branched off, at
approximately the same time or slightly earlier than the lepidosaura. The
synapsida are characterised by having two temporal openings in the skull.
The lepidosaura are most closely related to the dinosaurs. They are
diapsids, like the dinosaurs, and have two temporal openings in the skull,
but surrounded by different bones than the synapsida.

Now, the Cytochrome c data deals with the slow substitution of amino acids
within the Cytochrome c protein sequence. The theory goes something like:
unessential amino acids within a protein sequence  change randomly with
time. Over geological timescales, these substitutions become detectable.
Now assuming a group of three groups are related, the similarity in their
Cytochrome c sequences is a directly linked to the lenght of time since
they shared a common ancester. Since when they diverge their cytochrome c
sequences *will also diverge*. I.e. any sequence change occuring in one
group after divergence will not be repeated in the others. Therefore, the
number of *different* substitiutions between groups gives an indication of
in which order they separated.

B         A        C
 |           |          |
 |  y ->  |-------|
 |           |
 |--------|  <- x

In this sequence,  A represents the ancestral form and B and C two
decendant groups. Now according to the theory, since A and C diverged later
than A and B, their Cytochrome c sequences should be closer that C and B.
In other words, after B split off, A and C still shared a common ancester.
Therefore, any sequence changes that occurred between x and y would be
retained by both A and C, *but not B*. After y, the Cytochrome c sequences
of A and C will begin to diverge.
Therefore, groups which split off earlier (B) will have more differences in
their cytochrome c sequences than groups which split off later (C),
regardless of their morphological affinities.

With this in mind, lets look at the cytochrome c relationships between the
snake, turtle and mammal and see if it compares with the evolutionary model
erected using fossil and morphological data.

  Turtles         Snakes                     Mammals
        |                   |                                  |
        |                   |                                  |
        |                   |         Dinosaurs         |
        |                   |                |                 |
        |                   |                |                 |
        |                   |                |                 |
        |                   |                |                 |
        |                   | -----------|                 |
        |                                    |------------ |
        |                                    |
        |-------------------------- |


-------------------------------------> Increasing %age difference

Snake -------------------------
                           |      |
Mammal ---------       |
Turtle -----------------

The Cytochrome c data actually *supports* the evolutionary model.

Note to Mickey;

If this is still an issue on t.o. you can post this there, if you want.

Chris Nedin
Dept. of Geology and Geophysics
University of Adelaide
South Australia