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*To*: <augustoharo@gmail.com>, <keenir@hotmail.com>*Subject*: RE: Pneumaticity in Triassic pterosaurs*From*: "ralphchapman" <ralphchapman@earthlink.net>*Date*: Sun, 17 May 2009 16:04:11 -0600*Authentication-results*: msg-ironport0.usc.edu; dkim=neutral (message not signed) header.i=none*Cc*: <davidpeters@att.net>, <david.marjanovic@gmx.at>, <dinosaur@usc.edu>*In-reply-to*: <78eb35330905171102l530b033frcd0198def5fb2152@mail.gmail.com>*References*: <98D12D0D28C947628BDCA9E7668A8B30@LENOVO> <926832.17824.qm@web83710.mail.sp1.yahoo.com> <78eb35330905171102l530b033frcd0198def5fb2152@mail.gmail.com>*Reply-to*: <ralphchapman@earthlink.net>*Sender*: owner-DINOSAUR@usc.edu

In the early days of numerical taxonomy, the term covered both phenetic and cladistic-style approaches, although NT has since often been used to refer mostly to phonetic ones. Phenetic approaches can indeed use continuous data and, in fact, are most often done with such - specifically very often with actual measurement data and generating typically Euclidean distance (or another related metric) matrices which are then subjected to clustering (if a tree is really wanted - typically the UPGMA clustering algorithm is used although there are a zillion clustering methods). For binary data there are fewer options but many of the standard distance/similarity metrics can and have been used. The simple matching coefficient was a biggie and is mathematically more pure than others, such as the jaccard or dice, that are more often used with ecological or biogeographic analyses. The distance metric used early with more cladistic related methods was/is the manhattan or city-block metric. Where Euclidean distance is the direct distance from A to B, manhattan distance is the distance equivalent of a taxicab driving in manhattan, with each block change roughly equivalent to a character change. If there are 3 differences in one variable in four in another, for example, Euclidean distance will give a distance of 5 and the manhattan distance will be 3+4=7. There is a nice book for geeks on taxicab geometry which is fun (like flatland is fun) It is a great exercise for any evolutionary biologist to experiment with phenetic and other approaches, as well as clustering, preferably all by hand. When I've taught classes in data analysis, multivariate analysis, or ecological ordinations I have had students do this and the good ones leave really comfortable with the strengths/weaknesses of all methods played with. I cannot stress strongly enough the importance of NOT doing stuff in a black box way and, instead, knowing why you take each step. Probably more than you wanted to know... Ralph Chapman -----Original Message----- From: owner-DINOSAUR@usc.edu [mailto:owner-DINOSAUR@usc.edu] On Behalf Of Augusto Haro Sent: Sunday, May 17, 2009 12:03 PM To: keenir@hotmail.com Cc: davidpeters@att.net; david.marjanovic@gmx.at; dinosaur@usc.edu Subject: Re: Pneumaticity in Triassic pterosaurs As far as I know, you can submit asame matrix with binary characters to perform either phenetic or phylogenetic algorythms. Phenetic and phylogenetic analyses are obviously different, based on different phylosophies and implementing different algorythms, and generally leading to topologically different trees, but this does not mean that the same matrices can not be used for both. I am not aware if in phenetics step-matrix and continuous characters can be employed, but all these can be made binary, so I guess that phenetic algorythms can be applied to all data matrices. In case someone wants to do so, of course, for the utility of phenetics have been discredited not only in phylogenetics.

**References**:**Re: Pneumaticity in Triassic pterosaurs***From:*"David Marjanovic" <david.marjanovic@gmx.at>

**Re: Pneumaticity in Triassic pterosaurs***From:*David Peters <davidpeters@att.net>

**Re: Pneumaticity in Triassic pterosaurs***From:*Augusto Haro <augustoharo@gmail.com>

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