[Taxacom] Reproducibility of phylogenetic analysis

Stephen Thorpe s.thorpe at auckland.ac.nz
Wed Jan 27 18:15:48 CST 2010

Realistically, not many people give a damn if some millipedes or whatever go extinct without having even been discovered, and I don't just mean "ordinary people" - I mean managers and politicians ...

From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Bob Mesibov [mesibov at southcom.com.au]
Sent: Thursday, 28 January 2010 12:21 p.m.
Subject: Re: [Taxacom] Reproducibility of phylogenetic analysis

Hi, all.

I'm humbled that my post started such a fascinating thread! It's gone off in several different directions, and I'd like to comment on two of the new ones.

(1) Richard Pyle's post reminds us that salvaging what we can from the burning library would be a good idea. As old-hand Taxacomers know, I've been promoting biodiversity salvage for years. Unfortunately, the near-universal response to that plea has been the shoulder-shrug of the small child as Homer and Dante get chucked in the flames. I've therefore given up the promotion, pulled my biodiversity salvage blog off the Web and promised myself not to publish any more salvage papers. Instead, I plan to just continue salvaging invertebrates from 'at-risk' remnants in developed areas. (Something I'd recommend to Mike Ivie.) Some of these salavaged specimens make it into my taxonomic papers, but most begin their long sleep anonymously on museum shelves. The world's human population has increased by a quarter - almost another China - since Rio 1992. This growth can easily be correlated with increasingly intensive use of existing agricultural land, and the 'bringing of land into prod
 uction' (i.e., habitat destruction). There is simply no way to stop or slow down biodiversity loss in a pro-natalist world. Even the most biodiversity-friendly politicians and strategists aim only at finding a balance between conserving nature and 'achieving economic growth and sound social outcomes' (quote from a recent biodiversity white paper). This balance point is continually moving in the direction of Humans 1, Other species 0. Such is life.

(2) The pattern-process issue is reflected in the history of classification. Classifications started out (say, with Aristotle) as character-based, i.e. pattern-based. Following Darwin, classifications moved towards being relationship-based, i.e. organised according to the evolutionary process as we infer it. The current classification of living things is a pattern-process mix. Most of the structure comes from character-based investigation, while revisions and many fine-scale details come from process-based studies, by which I mean attempts to reconstruct phylogenies. Many modern systematists think that character-based classification is scientifically deficient in some way, but that comes, I think, from wanting classifications to be strictly phylogenetic. While I agree that's a good idea, I wonder whether it's worth the time, effort and money (not to mention all the methodological argument) to get classifications 100% Correct in the process sense, given that most of the world'
 s life still hasn't been fitted into the pattern.
Dr Robert Mesibov
Honorary Research Associate
Queen Victoria Museum and Art Gallery, and
School of Zoology, University of Tasmania
Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
(03) 64371195; 61 3 64371195
Website: http://www.qvmag.tas.gov.au/mesibov.html


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