morphmet
Thu, 01 Dec 2011 11:31:49 -0800
-------- Original Message -------- Subject: Re: [Past] cva question Date: Thu, 1 Dec 2011 05:15:48 -0500 From: andrea cardini <alcard...@interfree.it> To: Manabu Sakamoto <m.sakam...@bristol.ac.uk>CC: Jordan Mallon <jordan.mal...@gmail.com>, morphmet@morphometrics.org, PAST <past-us...@nhm.uio.no>
Dear Manabu, thanks for your message. I could not yet find time to read it, unfortunately, but this could be interesting for your question: 2011 Phil. Trans. R. Soc. B 366 1410-1424 Graham N. Stone, Sean Nee and Joseph Felsenstein Controlling for non-independence in comparative analysis of patterns across populations within species I doubt that in many cases a within species (or subspecies) phylogeny would be really 'star-like'. Using appropriate genetic markers for that level, it is, I suspect, likely that one finds some kind of hierarchical or network structure. This is at the end of the day much of what's behind phylogeographic studies. Besides, there might be other (extrinsic) sources of autocorrelation that one might have to consider to adress possible issues of non-independence among observations. The biogeographical literature and studies of spatial data might be a good source of references on this. This is not my field, however, and these are issues that I find truly difficult in terms of both the theory and the applications. Others on the lists will make much more competent comments. Cheers Andrea At 09:08 01/12/2011 +0000, Manabu Sakamoto wrote:
Dear Andrea, This probably veers off from the original question (sorry Jordan) but I am
curious how you and others feel about specimen-level ordination. For instance, if Jordan (or I) want to test for separation in morphospace of specimens belonging to subspecies Ai from subspecies Aii, then how would we take into account the phylogenetic non-independence? Surely a specimen-level phylogeny would be pretty meaningless (i.e., pretty much a star-phylogeny with a basal dichotomy)?
Manabu Manabu Sakamoto, PhD Postdoctoral Research Associate School of Earth Sciences University of Bristol Bristol, UK, BS8 1RJ Tel: +44 (0) 117 954 5421 Fax: +44 (0)117 925 3385 Email: m.sakam...@bristol.ac.uk On 1 Dec 2011, at 07:55, andrea cardini wrote:Dear Jordan, this is not an answer to your specific question. It's more of a general comment. The hierarchical nature of variation may have some other consequences: your observations are not independent because of phylogeny. Comparative methods try to address this issue in statistical analysis but I've never seen any application to DA/CVA. DA/CVA ordinations are done in a statistical space which maximize between to within group differences. This has some interesting implications and with small samples and large number of variables you can get a perfect discrimination of random numbers split in arbitrary groups. I'd be very careful with interpretations of those plots. For ordinations, a few people (including a recent paper by Mitteroecker & Bookstein and another one by Kovarovic, myself et al. - should be in my webpage and in the paper you'll find the ref. to M&B and other refs) have suggested between group PCA as an alternative for ordinations which maximize group differences without distortions of the original morphometric space of your data. Good luck. Cheers Andrea At 19:34 30/11/2011 -0700, Jordan Mallon wrote:Dear all, I've reached a bit of a dilemma with my morphometrics studies lately, stemming from the hierarchical nature of variation. I've been studying ecomorphology and how it varies within and between three dinosaur families (each family contains two subfamilies). I've been using canonical variates analysis to examine which variables best discriminate the various taxa. The three families are perfectly discriminated in CVA space. Next, I would like to examine how the subfamilies differ, particularly those that belong within the same family (i.e., looking at intra-family variation). As far as I can tell, I have two options: 1) Place all six subfamilies into a single CVA and look for intra-family clustering. The problem I see here is that most of the variance captured by the CV axes will comprise inter-family differences, rather than intra-family differences, because the families are much more separate in space than sister subfamilies. In other words, if families A and C are well-separated along axis 2, and subfamilies Ai and Aii are only slightly separated along the same axis, the loadings on that axis will tell me more about the separation of families A and C than about subfamilies Ai and Aii. Right? Hopefully I'm making myself clear. 2) Just run separate discriminant function analyses on all sister subfamilies. I suppose this negates the problem above, but it otherwise involves more work. Has anyone run into a similar problem before? If so, how have you dealtwith it?Thanks, JordanDr. Andrea Cardini Researcher in Animal Biology Dipartimento di Biologia, Universitá di Modena e Reggio Emilia, via Campi 213, 41100, Modena, Italy tel: 0039 059 2055017 ; fax: 0039 059 2055548 Honorary Fellow Functional Morphology and Evolution Unit, Hull York Medical School University of Hull, Cottingham Road, Hull, HU6 7RX, UK University of York, Heslington, York YO10 5DD, UK Adjunct Associate Professor Centre for Forensic Science , The University of Western Australia 35 Stirling Highway, Crawley WA 6009, Australia E-mail address: alcard...@interfree.it, andrea.card...@unimore.it, andrea.card...@hyms.ac.uk, andrea.card...@uwa.edu.au Webpage: http://sites.google.com/site/hymsfme/drandreacardini Datasets: http://ads.ahds.ac.uk/catalogue/archive/cerco_lt_2007/overview.cfm#metadata Editorial board for: Zoomorphology: http://www.springer.com/life+sciences/animal+sciences/journal/435 Journal of Zoological Systematics and Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1 Hystrix, the Italian Journal of Mammalogy: http://www.italian-journal-of-mammalogy.it/