[Taxacom] Molecular data in mycology/systematics

[Robinwbruce at aol.com]

Is it too late to go back to Haeckel's antithesis and choose the  other 
neologism of his making as the basis of our classifications. What would  
ontogenetic systematics look like? I think it might well be more biological and  
less ideological, and pondering  phylogenetic inference,  why-questions and 
the like would disperse like the morning  mist through sunlight breaking 
through..................one can but  dream.
 
Robin
 
 
 
 
 
In a message dated 5/4/2013 1:42:29 A.M. GMT Daylight Time,  
kfitzhugh at nhm.org writes:
 
The  paper refers to an often-stated issue that has intrigued me for a 
while,  "it is widely accepted that [maximum likelihood & Bayesianism] 
are  better able to correct for spurious effects caused by long-branch  
attraction, which is a problem of major concern in phylogenetic  inference."

If one knows /a priori/ that their observation statements  of shared 
similarities are in fact not shared similarities, then wouldn't  the 
solution be to rename those characters as different prior to inferring  
phylogenetic hypotheses, rather than implementing an algorithm that  
assumes not-similarity for observations one claims are shared  
similarities? It goes to the matter that if cladograms are explanatory  
vehicles, then they are answers to particular why-questions, and  
why-questions regarding shared similarities presume the truth of those  
observations.

Kirk

--  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
J. Kirk Fitzhugh, Ph.D.
Curator  of Polychaetes
Invertebrate Zoology Section
Research & Collections  Branch
Natural History Museum of Los Angeles County
900 Exposition  Blvd
Los Angeles CA 90007
Phone: 213-763-3233
FAX:  213-746-2999
e-mail:  kfitzhug at nhm.org
http://www.nhm.org/site/research-collections/polychaetous-annelids
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


On  5/3/2013 4:29 PM, Henrik Nilsson wrote:
> Dear Taxacom  readers,
>
> We just published an introduction to the use of  molecular data in fungal 
systematics and taxonomy. In the article we also take  the opportunity to 
discuss some of the challenges that systematics/taxonomy  face at present.
>
> Hyde et al. 2013. Incorporating molecular  data in fungal systematics: a 
guide for aspiring researchers. Current Research  in Applied & Environmental 
Mycology 3: 1-32.
>
> Open access:  http://www.creamjournal.org/vol-3-issue1.php#article1
>
> Although  the focus is on fungi, much of the text is general in nature as 
to apply, we  feel, to systematics/taxonomy at large.
>
> Yours  sincerely,
>
> Henrik Nilsson
>
> --
>
>  http://www2.dpes.gu.se/staff/hennil/
>
>
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Celebrating 26 years of Taxacom in  2013.