Wednesday, April 25, 2007

Whiting et al. 2004 / Trueman et al. 2004

Whiting, M.F., S. Bradler and T. Maxwell. 2004. Loss and recovery of wings in stick insects. Nature. 421: 264-267.

This paper has been commented upon in three different reading/discussion groups that I have attended so I thought I should post some of my comments of the paper here. I will also add notes on some of the rebuttals that have been published.

Whiting et al. used phylogeny to demonstrate that the first Phasmatodea was wingless and that wings evolved secondarily and on numerous occasions in this group. They suggest that wing developmental pathways are conserved in wingless stick bugs.

Data used: 1) 18S rDNA; 2) 28S rDNA; 3) portion of Histone 3.
-sequenced 22 outgroup specimens (representing all Polyneoptera)
-sequenced 37 ingroup taxa (representing 14 out of 19 subfamily groups)

Analyses: -used bootstrap and bremer support
-used POY for optimization alignment analysis and compared this to MP, ML and bayesian methods

[Notes: Acctran = Accelerated transformation -changes are assigned as close to the root of the cladogram (where the outgroups and ingroups diverge) as possible. Favours reversals.
Deltran = Delayed transformation -puts the character change as far from the root as possible. Favours parallelisms.]

Some of the problems that I had with this paper are:

1) what about fossil phasmids that have wings?
2) why did they use POY? This seems to be very rarely used and unfortunately I have never used it so I can't really comment on this program. Why didn't they publish their ML or Bayesian trees?

Another point that seems to be important and that is a direct quote from this paper is: "re-evolution of wings in insects is thought to be impossible because functional wings require complex interactions among multiple structures, and the associated genes would be free to accumulate mutations in wingless lineages, effectively blocking the path for any future wing reacquisition."

Trueman, J.W.H., B.E. Pfeil, S.A. Kelchener and D.K. Yeates. 2004. Did stick insects really regain their wings? Systematic Entomology. 29: 138-139.

Points that the authors make in this paper are:

1) two lines of evidence are necessary for the Whiting et al. hypothesis to hold true:
1) topology of phylogenetic tree
2) distribution of wing/wingless transformations on tree

2) Whiting et al. have overstated significantly the probability of wing re-evolution in stick
insects

3) reconstruction of the phasmid ancestor is not the relevant issue

4) support for each hypothesis needs to be compared when alternative ancestral states are
assumed to be true

The authors then do some easy math to show how the ratio of lost wings to gained wings is a mere 2.5:1.

Whiting, M.F. and A.S. Whiting. 2004. Systematic Entomology. 29: 140-141.

Whiting and Whiting then published a reply to Trueman et al. I found the tone very whiny. We did this and you didn't. We had super computers and you didn't, so there. It's really not even worth commenting on.

2 comments:

David Marjanović said...

why did they use POY?

They used POY?

Ouch.

POY has a very good idea: rather than doing the alignment based on phenetic criteria and then using that for the phylogenetic analysis, it does alignment and phylogenetic analysis at once.

The problem is that the alignment doesn't work. Earlier versions didn't even show you the alignment. More recent ones allow you to see it... and I'm told it's flabbergasting in every instance.

There was a Syst. Biol. paper a few months ago that clobbered POY.

Cashlin said...

You write very well.