-------- Original Message --------
Subject: RE: population-level non-independence
Date: Thu, 8 Dec 2011 20:50:10 -0500
From: Ivan Perez <[email protected]>
To: <[email protected]>
Dear all
Here there are some recent papers modeling the non-independence among
human populations by using spatial and mtDNA covariance matrices.
Although the non-independence may be approximated by a migration matrix
among populations, as has been suggested by Felsenstein (2002),
the use of spatial covariance matrices is a more general solution for
the lack of independence among observations
These methods are widely used in ecology and biogeography.
Best
ivan.
Perez, S.I., J.A.F. Diniz-Filho, V. Bernal, and P.N. Gonzalez. 2010.
Alternatives to partial Mantel test in the study the environmental
factors shaping the human morphological variation. Journal of Human
Evolution 59: 689-703.
Bernal, V., S.I. Perez, and P.N. Gonzalez, José Alexandre Felizola
Diniz-Filho. 2010. Ecological and evolutionary factors in dental
morphological diversification among modern human populations from
southern South America. Proceedings of Royal Society B. Biological
Sciences 277: 1107-1112.
Gonzalez, P.N., S.I. Perez and V. Bernal. 2011. Evolutionary and
ontogenetic allometry in cranial diversification of human populations
from South America. The Anatomical Record 294: 1864–1874.
Perez, S.I., V. Lema, J.A.F. Diniz-Filho, V. Bernal, P. Gonzalez, D.
Gobbo, and H.M. Pucciarelli. 2011. The role of diet and temperature in
shaping cranial diversification of South American human populations: an
approach based on spatial regression and rate tests. Journal of
Biogeography 38: 148–163.
--
S. Ivan Perez
División Antropología
Museo de La Plata
Paseo del Bosque s/n
La Plata, Buenos Aires, Argentina.
http://www.evomorfologica.com.ar/
<https://sites.google.com/site/laboratoriolaplata1>
> Date: Thu, 8 Dec 2011 15:50:34 -0500
> From: [email protected]
> To: [email protected]
> Subject: Fwd: population-level non-independence
>
>
>
> -------- Original Message --------
> Subject: population-level non-independence
> Date: Thu, 1 Dec 2011 15:09:27 -0500
> From: Dean Adams <[email protected]>
> To: [email protected] <[email protected]>
>
> Andrea,
>
> Indeed, the lack of independence among observations needs to be handled
> differently at different levels of biological organization. For
> comparative analyses across species, the phylogenetic relationships
> among taxa best describe the non-independence. Thus methods of
> independent contrasts (ala Felsenstein 1985) or PGLS (ala Martins and
> Hansen 1996) allow one to assess the association of phenotype vs. some
> other variable while accounting for non-independence due to shared
> evolutionary history.
>
> When populations across the landscape are of interest, one might
> consider using an analog from spatial statistics. Here the
> non-independence among observations can be captured by a spatial
> covariance matrix, which could be held constant in the analyses in much
> the same manner in GLS (see Cressie 1993 for estimating spatial
> covariance matrices).
>
> Yet another way of accounting for covariance among populations stems
> from population genetics. Here a population-level phylogeny is not
> appropriate, because this assumes that all of the non-independence is
> captured by a branching pattern as seen in the phylogeny. However,
> differential migration among populations may follow more of a network
> pattern. As such, non-independence may be better approximated by a
> migration matrix among populations. Felsenstein described the initial
> approach in a book chapter in 2002 (cited in the Stone et al 2011 paper
> you mentioned). However, while logical and rather straightforward, to my
> knowledge, no one has implemented this procedure to account for
> non-independence among populations.
>
> Best,
>
> Dean
>
> --
> Dr. Dean C. Adams
> Associate Professor
> Department of Ecology, Evolution, and Organismal Biology
> Department of Statistics
> Iowa State University
> Ames, Iowa
> 50011
> www.public.iastate.edu/~dcadams/
> phone: 515-294-3834
>
>
> On 12/1/2011 1:30 PM, morphmet wrote:
> >
> > -------- Original Message --------
> > Subject: Re: [Past] cva question
> > Date: Thu, 1 Dec 2011 05:15:48 -0500
> > From: andrea cardini<[email protected]>
> > To: Manabu Sakamoto<[email protected]>
> > CC: Jordan Mallon<[email protected]>,
[email protected],
> > PAST<[email protected]>
> >
> > 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: [email protected]
> >>
> >> 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 dealt
> >>> with it?
> >>>> Thanks,
> >>>>
> >>>> Jordan
> >>>>
> >>>>
> >>>>
> >>> Dr. 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: [email protected], [email protected],
> >>> [email protected], [email protected]
> >>>
> >>> 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/
> >>>
> >>>
> >>>
>
>
