[Taxacom] dinosaurs and wolves (was: another putative arthropod outgroup)

Ken Kinman kinman at hotmail.com
Tue Oct 2 22:58:39 CDT 2012


  Stephen,          
      I didn't say anything about reversals requiring reactivation of genes.  I certainly know of no snakes or marine mammals reactivating leg genes and the reinvention of legs.  And I didn't say anything about secondarily simplified parasitic taxa regaining lost morphologies.                 -----------------Ken

Date: Tue, 2 Oct 2012 20:39:06 -0700
From: stephen_thorpe at yahoo.co.nz
Subject: Re: [Taxacom] dinosaurs and wolves (was: another putative arthropod outgroup)
To: kinman at hotmail.com; taxacom at mailman.nhm.ku.edu

Seems to me that 5 issues may be conflated here:
(1) secondary simplification
(2) vestigial remnants
(3) reversal
(4) homeoplasy
(5) deactivated genes.
I don't see any direct relevance, in the present context, of (5) to (1) or (2)
Reversal presumably does require reactivation of genes, though it is difficult to distinguish from reinvention of the same morphology, and I'm not sure how widespread a phenomenon it is? Certainly, I do not know of any examples of secondarily simplified parasitic taxa which have regained anything that they lost morphologically.
 
Stephen




From: Ken Kinman <kinman at hotmail.com>
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>; "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu> 
Sent: Wednesday, 3 October 2012 4:21 PM
Subject: RE: [Taxacom] dinosaurs and wolves (was: another putative arthropod outgroup)







Hi Stephen,
       Well, not the "entire evolutionary history" of species, but still important when it comes to evolutionary reversals.  Perhaps the best known result of deactivated genes is the loss of legs in vertebrates (such as snakes and various marine mammals and reptiles).  It also explains why humans don't have a tail.  HOWEVER, what we do know about deactivated genes in evolutionary history is probably just the tip of the iceberg and much remains to be discovered, especially when it comes to invertebrates.   If we keep putting various "worms" at the base of invertebrate taxa just because they look "simple", I think future generations of biologists are going to wonder why we were stuck in such a rut for so long.  
                    -------------------Ken




Date: Tue, 2 Oct 2012 19:59:13 -0700
From: stephen_thorpe at yahoo.co.nz
Subject: Re: [Taxacom] dinosaurs and wolves (was: another putative arthropod outgroup)
To: kinman at hotmail.com; taxacom at mailman.nhm.ku.edu



Wow, Ken, maybe the entire evolutionary history of species is preserved in deactivated genes? Are there many convincingly established examples of this sort of thing?
 
The only thing that is turned on in my genes right now is ...
 
S :)



From: Ken Kinman <kinman at hotmail.com>
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>; "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu> 
Sent: Wednesday, 3 October 2012 3:46 PM
Subject: RE: [Taxacom] dinosaurs and wolves (was: another putative arthropod outgroup)








Hi All, 
     I am very hopeful that many such pentastomid genes have not actually been lost, but merely "deactivated" (if you will).  If certain regulatory genes have mutated in such a way that many genes downstream are no longer turned on (and thus resulted in morphological simplifications or total losses), then it is regulatory gene sequences which are most likely to give us much needed information on the ancestral group.  The "deactivated" genes downstream may also be helpful, if they haven't been eliminated over long periods of time.                     
      
       The point is that we know very little about the pentastomid genome, and yet such taxa still seem to take a back seat to intensive sequencing of taxa that don't really advance our knowledge of biodiversity or evolutionary history very much (like individual wolves or polar bears, which have been studied ad nauseum decade after decade after decade).  And I suspect that the cost of one flight of a helicopter hunting down wolves or polar bears once again (for diminishing returns) could fund some really interesting research (including pentastomid sequencing).  Wolves and polar bears are probably sick of being darted, weighed, measured, etc., by another generation of biologists who could be working on poorly studied taxa.  Although I am a mammalogist, if I see another PBS special advertised on the subject of wolves, I think I am going to scream.  Especially if it is funded by governmental agencies.  If
 the public wants more specials on wolves or dinosaurs, let private groups fund it completely.  Governments and universities should be in the business of balance, NOT feeding the public's fascination with certain taxa (especially dinosaurs).  If kids are fascinated by dinosaurs, fine, but their parents should support dinosaur research privately (easily done if they divert a mere 1% of what they readily pump into professional and college sports).  Of course, government could fund FAR greater amounts of conservation and taxonomic research if it just reduced payments into the corporate welfare system.         
                 -------------Ken  




Date: Fri, 28 Sep 2012 20:50:23 -0700
From: stephen_thorpe at yahoo.co.nz
Subject: Re: [Taxacom] another putative arthropod outgroup
To: kinman at hotmail.com; taxacom at mailman.nhm.ku.edu



but that is still very "hopeful" ... if pentastomids have lost genes, then we still won't know what they lost exactly, so we can't reconstruct the "groundplan" any more than we can with lost morphology! MAYBE we will find some very specific genetic material shared with a crustacean ingroup, but maybe not ...
 
Stephen





From: Ken Kinman <kinman at hotmail.com>
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>; "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu> 
Sent: Saturday, 29 September 2012 3:24 PM
Subject: RE: [Taxacom] another putative arthropod outgroup






        I actually think that reduced molecularities (lost genes) will eventually prove more informative than reduced morphologies in such cases.  The trouble is that a small molecular change can result in a cascade yielding a number of morphological changes, so it can be like looking for a needle in a molecular haystack.  If so, what the morphologists call parsimonious in this case may be deceptive.  Not that I am always swayed by molecularists (even when they have lots more data).  I look at each case individually, and weigh morphology vs. molecularity data when they don't agree.  In this case, there is so little molecular data that it seems ridiculous to even invoke parsimony at this stage.       
                  -------------------Ken




Date: Fri, 28 Sep 2012 19:59:08 -0700
From: stephen_thorpe at yahoo.co.nz
Subject: Re: [Taxacom] another putative arthropod outgroup
To: kinman at hotmail.com; taxacom at mailman.nhm.ku.edu



at any rate, is there any sound basis for thinking that the DNA associated with reduced morphologies won't itself be reduced/absent, so, unless there is some very specific other DNA shared with a crustacean ingroup (might be, but might not), we are no better off?





From: Ken Kinman <kinman at hotmail.com>
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>; "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu> 
Sent: Saturday, 29 September 2012 2:47 PM
Subject: RE: [Taxacom] another putative arthropod outgroup






Hi Stephen, 
      Well, just to be fair, I wouldn't call the morphological data in this case "extremely" limited.  It is actually quite impressive how much detail they can see in these Orsten fossils.  My concern in this case is not so much in how limited the morphological data is (even though much of it is from such fossils), but rather how limited the molecular data is on pentastomids.  Sometimes amazing that grant money can be found for sequencing very large numbers of specimens of some species (or even subspecies or populations) of certain taxa, but extremely little on a much higher level taxon like Pentastomida.


                      --------------Ken




Date: Fri, 28 Sep 2012 19:05:25 -0700
From: stephen_thorpe at yahoo.co.nz
Subject: Re: [Taxacom] another putative arthropod outgroup
To: kinman at hotmail.com; taxacom at mailman.nhm.ku.edu



>The paleontological morphologists insist that it is unparsimonous to assume that pentastomids have secondarily lost so many crustacean morphologies<
 
It is a general problem with obligate parasite groups, that they are so derived and have lost so many characters that their relationships are obscure. Given that paleontological morphological data is extremely limited (both by the patchiness of the fossil record, and the fact that you can't see much on a fossil specimen), I would look to molecular data on this one (though there is still no guarantee of success). Whether it is "unparsimonious" or not depends on a whole phylogeny, not just part of it taken out of context ...
 
Stephen





From: Ken Kinman <kinman at hotmail.com>
To: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu> 
Sent: Saturday, 29 September 2012 1:47 PM
Subject: [Taxacom] another putative arthropod outgroup


Dear All,      Beside tardigrades and onychophorans, another taxon (Pentastomida) has also long been put forward as an outgroup to euarthropods (or arthropods in general, including fossil
 taxa).  However, molecular data (18S rRNA and mitochondrial data), along with very limited morphological data, indicates that pentastomids are actually highly modified (morphologically "simplified") maxillopodan crustaceans.        
      Anyone want to weigh in on whether morphologists (especially paleontologists) or molecularists are right on this one?  The paleontological morphologists insist that it is unparsimonous to assume that pentastomids have secondarily lost so many crustacean morphologies, even though they are highly derived due to their parasitic life styles (see weblink below).  The question is whether they are right, or whether the molecularists are just sorely in need of far more molecular data on the pentastomids.  Anyway, if pentastomids are secondarily simplified crustaceans, will tardigrades turn out to also be secondarily simplified arthropods (although perhaps from another
 branch of arthropods such as chelicerates)?  The debate continues.                      
              ---------------------Ken Kinman                        
http://www.core-orsten-research.de/Publications/PDF_Paper/ulm_team/2011%20CASTELLANI_ETAL.pdf                         
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