[Taxacom] Molecular data in mycology/systematics

[Kirk Fitzhugh]

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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