Hi All,
This is an interesting discussion. I'll draw your attention to two
papers, one new and the other old. This is the new one:
Grandcolas, P., R. Nattier, F. Legendre, and R. Pellens. 2011. Mapping
extrinsic traits such as extinction risks or modelled bioclimatic niches on
phylogenies: does it make sense at all? Cladistics 27:181-185.
It is written from a somewhat different perspective than we usually have on
this list.
This is the old one, and I am taking the liberty of pasting in the
relevant passage:
Garland, T., Jr., P. H. Harvey, and A. R. Ives. 1992. Procedures for the
analysis of comparative data using phylogenetically independent contrasts.
Systematic Biology 41:18-32.Pages 29-30:WHAT KINDS OF TRAITSCAN BE ANALYZED?
The independent contrasts approach isdesigned to investigate the correlated
evolutionof traits that are inherited from ancestors,whatever the cause of that
heritability.Thus, the phenotypic data for tipspecies are generally assumed to
reflect underlyinggenetic differences among species,as could be verified
through common-garden experiments (Garland and Adolph,1991). The tip species
for one set of contrastscan even be different from those forthe other set, as
long as the phylogenetictrees are isomorphic. This realization makesit possible
to use independent contrasts toexamine coevolution of phenotypic traitssuch as
body size and life span in coevolvedhost-parasite systems (see Harveyand
Keymer, 1991). In addition to the usual phenotypic traits(e.g., body size,
metabolic rate), cultural(see Cavalli-Sforza and Feldman, 1981),
environmental(e.g., soil or water pH, meanannual temperature), and other traits
thatare difficult to categorize (e.g., home rangearea) can be studied as long
as they arepassed on from ancestral to descendentspecies (or populations) and
have a continuousdistribution. For example, many environmentalproperties, such
as latitude ormean annual rainfall, are not inherited inthe conventional
(genetic) sense. Nevertheless,they are inherited in the sense thatorganisms are
born into environmentalconditions and locations experienced bytheir parents at
the time of birth. Thus, theancestor of two species living in a desertmay also
have lived in a desert (cf. Huey,1987), or the ancestor of one high-latitudeand
one equatorial species may have livedat midlatitude. Similarly, if an
environmentalcharacteristic is determined solely(without externally imposed
constraints)through a process of habitat selection, andif species differences
in habitat selectionare genetically based, then species differencesin the
environmental trait will begenetically based as well. Alternatively,
ifvariation in some (genetically based) phenotypictrait can be used as a
precise indicatorof some environmental characteristic,then that phenotypic
trait may be usedas a surrogate for the environmental characteristic.For
example, toe fringes in lizardsmight indicate occupancy of sandyhabitats.
Unfortunately, this is not unfailinglythe case; some species that glidethrough
the air or that run across wateralso possess toe fringes (Luke, 1986).
Finally,paleoclimatological and historicalbiogeographical data might be used in
conjunctionto indicate environmental characteristicsof hypothetical ancestral
(as opposedto tip) species, but this takes us intothe realm of other
comparative methods,such as those based on minimum evolutionreconstructions of
ancestors (Huey, 1987;Harvey and Pagel, 1991; Maddison, 1991;Martins and
Garland, 1991). In any case,techniques for correlating phenotypes
withenvironmental characteristics require furtherstudy.
Cheers,Ted
Theodore Garland, Jr.
Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone: (951) 827-3524
Wet Lab Phone: (951) 827-5724
Dry Lab Phone: (951) 827-4026
Home Phone: (951) 328-0820
Facsimile: (951) 827-4286 = Dept. office (not confidential)
Email: tgarl...@ucr.edu
http://www.biology.ucr.edu/people/faculty/Garland.html
Experimental Evolution: Concepts, Methods, and Applications of Selection
Experiments
Edited by Theodore Garland, Jr. and Michael R. Rose
http://www.ucpress.edu/book.php?isbn=9780520261808
(PDFs of chapters are available from me or from the individual authors)
________________________________________
From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on
behalf of David Bapst [dwba...@uchicago.edu]
Sent: Monday, November 14, 2011 12:54 PM
To: Liam J. Revell; Joe Felsenstein; pasquale.r...@libero.it
Cc: R Sig Phylo Listserv
Subject: Re: [R-sig-phylo] Comparative Methods and Pseudo-Traits
Liam, Joe, Pasquale, all-
Thank you for your kind input.It seems that I am not the only one who
considers this issue at length.
There is just one point I'd like clarification of. Liam, in my first
example which you used, the inherited trait is the response and the
not-directly-inheritable trait the predictor, such that:
Growth Rate = beta0 + beta1*Habitat Degradation + e
What if we were to switch these? It seems to me this is the only real
difference in the extinction example. To make a neontological example,
let's say we were interested in whether larger mammals were more likely to
experience higher levels of poaching. The response here would be the
poaching intensity and body size the predictor, such that:
Poaching Intensity = beta0 + beta1*Body Size + e
Would your argument still apply? (It seems to me that it should.) If so,
then it would seem your explanation should equally apply to extinction
selectivity cases.
-Dave
On 11/10/2011 3:36 PM, David Bapst wrote:
>
>> Hello all,
>> A recent discussion set my mind thinking on a particular issue and, once
>> again, I decided to ask for the general opinion of R-Sig-Phylo denizens.
>> It
>> may be easier to start with an example.
>>
>> Let's say that there exists a worker who is measuring several different
>> traits across a number of species and then testing for correlations among
>> these traits. The first test is body size versus growth rate and they use
>> independent contrasts or PGLS to test for a the correlation, accounting
>> for
>> phylogeny. Both of these traits are inherited, evolving variables. Now
>> let's say they'd like to test for the relationship between growth rate and
>> some metric of the anthropogenic degradation of that species' habitat. Now
>> what? It is even valid to apply PIC to the habitat degradation metric even
>> though it is not an inherited, evolving trait? It's unclear to me.
>>
>> Let's consider a paleontological example, one which I have found myself
>> both strongly agreeing and disagreeing with at times. Essentially, how
>> should we test for extinction selectivity on some trait at a mass
>> extinction event? Let's say we think body size is a predictor of the risk
>> of extinction during that event and so we want to test for a correlation
>> between them (please ignore that extinction would be a discrete variable
>> for the moment). Do we treat these variable with PIC or PGLS? Is it really
>> proper to refer to the probability of going extinct during a mass
>> extinction as an evolving trait? Let's say we did and we got different
>> results than when we used an analysis which did not account for the
>> phylogenetic covariance. How should we interpret these results?
>>
>> One explanation I know of is that when we apply phylogenetic comparative
>> methods to these quasi-traits to consider their relationship to another
>> trait, we are assuming that these variables are actually the result of
>> some
>> underlying, unobserved set of traits which are evolving along the
>> phylogeny. This makes sense, maybe in the extinction event case, which
>> would mean that any PCM analysis would be testing for an evolutionary
>> relationship between body size and these unobserved traits which predict
>> extinction. Of course, if extinction risk is largely a function of
>> non-inherited traits, then the initial assumption may be incorrect (that
>> extinction risk itself is an evolving trait). Regardless, I don't see how
>> to apply that explanation to the habitat degradation example.
>>
>> So, what do people think? How should we test for correlation when
>> non-evolving quasi-traits are involved? I'm very interested to hear
>> people's thoughts on this matter.
>> -Dave Bapst, UChicago
>>
> --
David Bapst
Dept of Geophysical Sciences
University of Chicago
5734 S. Ellis
Chicago, IL 60637
http://home.uchicago.edu/~dwbapst/
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