Re: Underlying basis of classification (Was: Re Dinobirds)

[chris brochu <cbrochu@fmppr.fmnh.org>]

I'm not entirely sure I understand what you're saying, so if I
misinterpret, accept my apologies.

Philidor11@aol.com wrote:
> 

> Trying to lay this out simply, certain characters are chosen to connect a set
> of animals. 

In principle, *all* relevant characters are considered.  I understand
that some analyses are more "selective" than others, but that's the
fault of the analysis, not the method.


 Under cladistics, this relationship is explicitly stated to be
> an evolutionary relationship; that because these animals share these
> characters they therefore share a single common ancestor.  Animals are
> considered closer to (basal) or farther from (derived) this ancestor based on
> the degree to which they have these characters.


I'm not sure "degree" is the appropriate word here, as the number of
characters, by itself, is not an arbiter of closeness of relationship.  

Phylogenetic analyses - cladistic or otherwise - recover an internested
hierarchical set.  Terminal taxa are close to each other if they share a
more recent common ancestor than they do with something else.  This is
true whether they are joined by lots of characters or only one at a
given node.



  The basal connection can be
> quite small; there are basal ornithiscians which do not have the diagnostic
> ornithiscian hip.
> The problem for me is the fact that the ancestor is hypothetical.  Without an
> evolutionary progression from documented source to descendant I can't
> distinguish between the diagnostic character and the definition of the clade.


Definition and diagnosis are entirely different operations, regardless
of whether an ancestor is inferred or documented.  Dinosauria is the
last common ancestor of ornithischians and saurischians and all of its
descendents.  Whether we actually have that last common ancestor in hand
is irrelevant - after all, we don't have all of the descendents,
either.  The diagnosis is the set of characters at that node in a given
analysis - again, regardless of whether the state is actually known in
all members; taxa for which the hip is unknown cannot be coded for the
presence or absence of a perforate acetabulum, but other features
support their placement in subgroups within Dinosauria.

Diagnoses are not stable - and we have no expectation that they should
be.  Any new discovery will change them.



>  Essentially, parsimony says it makes a simpler story if one evolutionary
> progression is postulated rather than any other progression which can be
> hypothesized.  Once that progression has been asserted, though, what evidence
> is relevant to see if it is consistent with known fact? 

Any and all biotic evidence - morphology, molecules (when available),
behavior (when available), etc.

Some would argue for the utility of stratigraphy or biogeography to
overturn a phylogeny - this might work with marine invertebrates, but
for most terrestrial vertebrates, sampling levels are way too low and
way to biased.


 How much evidence is
> necessary to say that the hypothesis has been supported or even proven?

Proven?  Can't be done.  But as scientists, we're not in the business of
proving anything - its disproof we're after.

But support is a relevant issue - and there are several approaches out
there for assessing it.  Sadly, these are rarely applied to analyses of
fossil vertebrates.  Bootstrapping is the most common method among
neontologists, but there are others.

In molecular analyses, a bootstrap proportion of 70 is used as a
benchmark for robustness, but this is problematic.  




> >From the fact that stratocladistics gets a different name from cladistics it
> seems that including the time when the animal lived is a controversial part
> of hypothesis testing. 

It can be.  The problem with stratocladistics is that it assumes
uniform, unbiased sampling among analyzed lineages - the recent paper in
Science found that it outperforms standard parsimony, but only with this
assumption intact.  I am unaware of any terrestrial vertebrate lineage
in which this assumption can be safely made.

Stratigraphy can be used as internal evidence, i.e. used in the
tree-building algorithm (such as stratocladistics).  Or it can be used
as external evidence, to compare competing trees built from biological
information.  How this is used can be problematic, as the stratigraphic
signal is not likely to be an unbiased measure of phylogeny.



 Only the characters, it seems,  are essential to the
> analysis, and though character significance has been referred to as 'robust',
> I do wonder about how temporary decorative differences within a group (which
> could be lost in subsequent generations) are distinguished from necessarily
> ongoing functional (evolution being based on functional advantage)

As far as phylogenetics is concerned, only two factors are important -
that the characters be heritable and independent.  If they're passed on
from parent to offspring, they can preserve a phylogenetic signal,
regardless of subjective assumptions of "importance."





> differences and how a continuing new evolutionary direction can be
> distinguished from simple coincidence in all its various forms (from
> convergence to the sort of repetition which causes certain lizards to become
> legless frequently; might not, for example, a certain group of dinos have a
> tendency to evolve feathers from dinofuzz repeatedly and independantly?).

Detailed morphological analyses can highlight differences questioning
assumptions of homology.  Otherwise, we can't know two identical
features are nonhomologous without a phylogeny.

chris

-- 
----------------------
Christopher A. Brochu
Department of Geology
Field Museum of Natural History
Roosevelt Road at Lake Shore Drive
Chicago, IL 60605

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electronic:  cbrochu@fmppr.fmnh.org