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Re: "Ratite" polyphyly and paleognathous dromornithids

David Marjanović <david.marjanovic@gmx.at> wrote:

> So, they tried 15 guide trees, got 15 alignments, and then chose the one
> that gave the shortest tree as a result?

No, they explored how the guide trees affect the final tree topology.
All the 15 alignments -- including those that were based on weird
guide tree topologies like (emu, (rheas, (tinamous, ostrich))) --
resulted in a strongly supported (bootstrap value 100% in every single
analysis) clade of non-ostrich paleognaths. A rhea/tinamou clade was
only recovered if it had already been present on a tree used to
generate the alignments. An emu/tinamou clade was recovered more
often, even without the corresponding clade on the guide trees.

> ~:-| Even with Jukes-Cantor?

Surprisingly, yes: Huelsenbeck & Hillis (1993) tested the performance
of different phylogenetic methods in the four-taxon case and found
that neighbor-joining with uncorrected (simple similarity) distances
was consistent over the same region of parameter space as parsimony,
that is, outside the Felsenstein zone. When the Jukes-Cantor
correction of distances was used and sequence evolution was also
simulated using the JC69, neighbor-joining was consistent over the
whole parameter space -- however, because of the finite size of any
real data set, a small Felsenstein zone remained where random choice
got the correct tree more often than NJ. When the JC69 correction
didn't match the underlying model of evolution, neighbor-joining was
inconsistent again, but over a smaller region than parsimony. It's
true that Huelsenbeck and Hillis only tried violating one assumption
at a time, but there is a fairly large body of literature comparing MP
and NJ and finding the latter superior to the former (Kuhner &
Felsenstein 1994; Rosenberg & Kumar 2001 and references therein).

> And in which regions of parameter space do real
> examples most often occur?

The infamous Felsenstein zone again (see above). Neighbor-joining
generally outperforms MP when rates per branch are unequal (Kuhner &
Felsenstein 1994).

> It's difficult to imagine that a phenetic method would converge on the right
> phylogeny more often than a phylogenetic method.

Well, "phenetics" is an extremely loaded word. Some people use it to
describe an approach to classification; ohers use it to describe a set
of phylogenetic methods, but don't always agree on the exact contents
of that set. They can usually agree on UPGMA, but neighbor-joining is
where it starts to get complicated: it's a distance-based clustering
algorithm, but it _does not_ cluster taxa on the basis of overall
similarity. It allows different OTUs to have different rates of
evolution, so A can be correctly linked to B even though it's more
similar to C. It gives you an unrooted tree, just like parsimony and
unlike UPGMA. And minimum evolution goes one step further by using an
optimality criterion to compare multiple trees. It's basically
parsimony for distance data: it prefers the tree with the least amount
of change, the only difference being that parsimony measures the
amount of change in character state transformations and ME in pairwise
distances. Sure, it's still possible to refer to NJ and ME as
"phenetics" and use the word as a shortcut for distance-based methods,
but then the other claims about phenetics are no longer true:
phenetics is _not_ based on overall similarity and there is certainly
nothing inherently "non-phylogenetic" about it.

(In fact, there is nothing non-phylogenetic about UPGMA. It gives you
the right tree as long as the assumptions of the method are met --
i.e., there is a clock. Parsimony... gives you the right tree as long
as the assumptions of the method are met -- i.e., rates of evolution
do not vary significantly among OTUs. It's true that the assumptions
of parsimony are met more often that the assumptions of UPGMA, but
their behavior can still be surprisingly similar in some cases: see
Swofford et al. 2001. Both are inferior to probabilistic methods such
as Bayesian inference.)


Huelsenbeck JP, Hillis DM 1993 Success of phylogenetic methods in the
four-taxon case. Syst Biol 42(3): 247-64

Kuhner MK, Felsenstein J 1994 A simulation comparison of phylogeny
algorithms under equal and unequal evolutionary rates. Mol Biol Evol
11(3): 459-68

Rosenberg MS, Kumar S 2001 Traditional phylogenetic reconstruction
methods reconstruct shallow and deep evolutionary relationships
equally well. Mol Biol Evol 18(9): 1823-7

Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers
JS 2001 Bias in phylogenetic estimation and its relevance to the
choice between parsimony and likelihood methods. Syst Biol 50(4):

David Černý