[Taxacom] Disappointing "Deep Arthropod Phylogeny"

[Kenneth Kinman]

Hi Derek, 
          Well, I wouldn't include nematodes as an
outgroup, since I suspect nematodes could just be legless descendants of
primitive tardigrades, and therefore also dearthropodized descendants of
what are currently included in Panarthropoda (Panarthropoda could
actually be cladistically equivalent to Ecydyozoa, unless you want a
paraphyletic Panarthropoda for just the taxa that have not undergone
dearthropodization).  Same probably goes for clitellate annelids. I'm
not sure about polychaetes (which I am not convinced is holophyetic
anyway).  
       In any case, I would be more inclined to suggest outgroups such
as bryozoans and/or primitive bivalves.  Or even more distant outgroups
like cnidarians might provide some insight compared to what they are
doing now.  I don't know if deuterostomes would be helpful or not
(certainly NOT a derived form like Homo).
          Tonight, I found a fairly recent paper
which tends to support what I have been saying for many years now.
Proper outgroup selection is critical to a real understanding of
evolutionary relationships. Especially note their criticism that
nematodes and onychophorans have "G 
+ C content and strand specific biases which are very different from
those of arthropods". Such biases have long been keeping us from
discovering true arthropods relationships. But the biggest bias of all,
in my opinion, is the failure to recognize DEARTHROPODIZATION as having
given rise to a number of phylum or class-level taxa not normally
associated with arthropods!!!!  Anyway, this is from the abstract from
one relevant, recent paper: 

  Mol Phylogenet Evol (2008). 
A multi criterion approach for the selection of optimal outgroups in
phylogeny: Recovering some support for Mandibulata over Myriochelata
using mitogenomics. 
O Rota-Stabelli, MJ Telford 
The choice of an appropriate outgroup is a fundamental prerequisite when
the difference between two conflicting phylogenetic hypotheses depends
on the position of the root. This is the case for the myriapods that may
group either with Pancrustacea forming a clade called Mandibulata, in
accordance with morphological characters, or with chelicerates to form
Myriochelata (also called Paradoxopoda) as has recently been proposed by
mitochondrial and ribosomal RNA gene phylogenies. In order to understand
the impact that outgroup choice may have on phylogenetic reconstruction,
we have investigated compositional heterogeneity and genetic distance in
mtDNA sequences of several different outgroups to the arthropods,
selected from deuterostomes, lophotrochozoans and ecdysozoans, and have
used them to root a phylogenetically balanced and compositionarily
homogeneous arthropod dataset. Results indicate that some outgroups, in
particular from lophotrochozoans, nematodes and an onychophoran have G+C
content and strand specific biases which are very different from those
of arthropods, suggesting that the use of such outgroups may interfere
with the stationarity of the model to create a random outgroup effect.
We suggest a multi criterion approach for the selection of optimal
outgroup species on the basis of (1) low substitution rate, (2)
ingroup-like G+C composition, (3) a new strand bias estimator called the
skew index, (4) the ability of the outgroup to avoid a "random branching
effect" and (5) phylogenetic proximity to arthropods. Inference of
phylogeny using various outgroups shows that use of phylogenetically
distant and compositionally distinct lophotrochozoans as outgroups
strongly supports Myriochelata and use of more closely related, but fast
evolving nematodes supports Mandibulata. A dataset comprising multiple
ecdysozoan outgroups also supports Mandibulata, unless the
compositionally distant Onychophora are included. A group of the best
outgroups selected according to our multi criteria selection, and
including the most closely related, least genetically distant and most
compositionally similar outgroup, a priapulid worm, supports
Mandibulata. We conclude that support for the Myriochelata hypothesis
from mitochondrial sequences may depend on the nature of the outgroup
sequences rather than a true phylogenetic signal.   Finally, we
advocate a careful analysis and an objective choice of outgroup when
dealing with derived sequences, such as mitochondrial genomes.