[Taxacom] Disappointing "Deep Arthropod Phylogeny"

[Derek Sikes]

Ken,

No reason to be so disappointed...

If the outgroups Regier et al. chose actually belong nested deeper inside
the arthropods then this would have been uncovered in the analysis (they did
not "force" tardigrades & onychophorans to be external to the arthropods;
such analyses are rooted after the optimal trees are found and choosing the
root as they did doesn't change anything else in the tree - it merely
orients the tree for viewing).  Your criticism might be valid if they hadn't
included tardigrades & onychophorans in the analysis but had simply "tacked
them on" to some randomly chosen base of the tree afterwards - but this is
not what they did.

Their results support a monophyletic Arthropoda that does not include
tardigrades & onychophorans (unless one were to widen the definition of the
phylum to include these basal lineages currently excluded; but their basal
position is well supported regardless of their membership).

Also, Regier et al. indicate that they included an expanded outgroup
analysis (supplementary fig 7.) which included nematodes, priapulids,
molluscs, and even Homo! Same results.

Their analysis was superb.  Your criticism seems to stem from a
misunderstanding of how such analyses are performed.

Out of curiosity, where do you think the tardigrades & onychophorans belong?
And what outgroups would you suggest they have included instead?

Derek

PS - text from the caption of their supp. fig 7:
Commentary on Supplementary Figure 7:  In this likelihood analysis of amino
acids, the outgroup
shown in Figure 1 of the main text (namely, 3 spp. Onychophora and 2 spp.
Tardigrada) was
supplemented with two Nematoda, one Priapulida, one Mollusca and one
Deuterostomia species to test
whether an expansion of the outgroup would dramatically affect node support
values within
Arthropoda, particularly for the more inclusive groups such as Mandibulata.
It did not. Indeed, the
expanded outgroup resulted in no topological changes within Arthropoda
relative to the 80-taxon
analysis except for one weakly supported node (BP <50%) within Euchelicerata
(see “-”).


On Fri, Feb 12, 2010 at 6:01 PM, Kenneth Kinman <kennethkinman at webtv.net>wrote:

> Dear All,
>      I am EXTREMELY disappointed by he initial results of project "Deep
> Arthropod Phylogeny" published this week in the journal Nature.  I'm
> sure they are building an excellent molecular database, but whether it
> is getting them any closer to actually resolving arthropod
> interrelationships is very doubtful in my opinion.
>       The main problem is probably a FALSE ASSUMPTION.  Namely that
> they should be using tardigrades and onychophorans as their outgroup
> taxa.  They did actually have enough sense not to include pentastomids
> in the outgroup, because that group has been shown to be derived from
> crustaceans, and therefore an example of what I have called
> DEARTHROPODIZATION.
>       Unfortunately, tardigrades and onychophorans are probably ALSO
> dearthropodized arthropods, and therefore are also DEFINITELY NOT
> appropriate outgroups to arthropods as a whole.  No wonder they continue
> to get remipedes in a relatively primitive position.   Also no surprise
> that chelicerate phylogeny remains unresolved.
>        There is thus very little new in this new study, and what is new
> is questionable.  Until they are more creative and test a number of
> other possible outgroups to arthropods, they are just going to spin
> their wheels and get little in the way new results.  They confirmed
> Pancrustacea (insects evolved from crustaceans)---big deal.  We've known
> that for years now.  Anyway, I am confident that molecular data is the
> main key to answering most questions about deep arthropod phylogeny, but
> without being more creative about what outgroups to use, their computers
> will continue to spew out very questionable results.  It's not the
> computers fault---just the humans restricting the results with
> questionable assumptions of what taxa are appropriate outgroups.  Other
> than faulty data (which is probably not a big problem here), nothing is
> more damaging to scientific results than false assumptions.
>           ----------Kenneth Kinman
>
>
> _______________________________________________
>
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
> The Taxacom archive going back to 1992 may be searched with either of these
> methods:
>
> (1) http://taxacom.markmail.org
>
> Or (2) a Google search specified as:  site:
> mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>



-- 
PLEASE NOTE NEW EMAIL ADDRESS: dssikes at alaska.edu

+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Assistant Professor of Entomology
University of Alaska Museum
907 Yukon Drive
Fairbanks, AK   99775-6960

dssikes at alaska.edu
http://users.iab.uaf.edu/~derek_sikes/sikes_lab.htm

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum  -
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++