Dear All,
many thanks for your replies and thoughts.
I'd split the problem in two (I talk about landmarks but it's similar
with semilandmarks):
1) There are things that simply cannot be done (they're wrong and deeply
misleading at least in biology): interpreting the variance of single
landmarks after a common superimposition with the aim of telling whether
this or that landmark varies more than others; computing the
evolutionary rate of single landmarks one at a time etc. etc. This is
something on which all morphometricians, who developed the methods we're
using and whom I bothered with questions since the end of '90s, agree
and have agreed for a very long time. I am glad to see there's no change
on this issue and simply one should avoid making those mistakes or
following those who keep making them (including in very prestigious
journals).
2) There might be methods that help to guess whether a specific region
(not a single landmark!) is particularly affected by change. Pietro,
Philipp and Paolo mentioned some possibilities. There might be problems
and difficulties here too, but there could be solutions or at least
approximations. I am agnostic on this (with apologies to Paolo, whose
paper has been on my reading list for quite a while: I'll get there, I
promise!).
Right now, however, my worry was about the first issue and those who
answered confirm that nothing revolutionary happened: those were and
still are big mistakes.
Carmelo raised an interesting question about whether this is more or
less common than in the past. Hard to say without a huge review of the
literature. But 30 years after the "revolution" in morphometrics, those
mistakes should not happen at all. Yet, they occur and, when made by
experienced morphometricians and published in top journals, set a very
bad example.
Thanks again for your comments.
Cheers
Andrea
On 12/05/2021 15:11, Paolo Piras wrote:
"Of course, there can be exceptions and a biological signal can be local
and be represented well by a single landmark or a single interlandmark
distance."
I think that a proper evaluation of local deformation could be effective in
interpreting the "localness" of both shape and deformation differences...
*Piras P.*, Profico A., Pandolfi L., Raia P., Di Vincenzo F., Mondanaro
A., Castiglione S., Varano V. (2020). Current options for visualization of
local deformation in modern shape analysis applied to paleobiological case
studies. *Frontiers in Earth Science*, 8:66. doi: 10.3389/feart.2020.00066
IF: 2.689
ATB
Paolo
Il giorno mer 12 mag 2021 alle ore 14:10 [email protected] <
[email protected]> ha scritto:
Dear Andrea,
In principle, I agree that one should avoid interpreting single landmarks
or shape coordinates because
- landmarks are not geometrically independent after GPA (loss of degrees
of freedom)
- landmark displacement vectors depend on the superimposition and, hence,
the other landmark positions (Pinocchio effect)
- often the shape features are not that local but involve a joint shift of
multiple landmarks; in this case, the actual shape patterns cannot be
inferred from looking at each landmark separately.
Formal statistical analyses (e.g., regressions, significance tests) of
each landmark or shape coordinate separately can hardly be interpreted and
are subject to the multiple comparison problem. This is why we have
multivariate stats and GMM. With proper visualizations, such as TPS
deformation grids or series of reconstructed shapes, the Pinocchio effect
does not apply and one can observe even complex shape or form differences.
Of course, there can be exceptions and a biological signal can be local
and be represented well by a single landmark or a single interlandmark
distance. But one cannot know about this before analyzing all the landmarks
jointly!
Best,
Philipp Mitteroecker
On Tuesday, May 11, 2021 at 6:18:33 PM UTC+2 [email protected] wrote:
Dear Dr. Andrea, Fruciano, and Pietro,
I asked a question on integration/modularity in geomorph google forum. I
benefit hugely from Mike's reply.
That post is somewhat related to the current post. So I am here to let
you aware and please feel free to comment further there if you have
interest.
Link to my question:
https://groups.google.com/u/3/g/geomorph-r-package/c/VKpAxHnVW1U
On Tuesday, May 11, 2021 at 7:52:05 PM UTC+8 Carmelo Fruciano wrote:
Dear Andrea,
I've seen this from time to time, but I am not too sure there's been a
recent increase in this.
Some of the most striking cases in my own literature searches and
reading involve genetic mapping of one coordinate at a time (post-GPA) -
as if each coordinate were a separate trait, which is (IMHO) nonsensical.
This is obviously biased because of my own research interests (i.e., I
have seen more in this area because I've read a bit more in this area
than in others, not because they are more frequent in genetic mapping
than in other areas). But these papers are fairly spread over time and I
didn't catch any particular increase in their frequency as of late.
I understand this does not exactly address what you were asking but I
still hope it helps,
Carmelo
--
==================
Carmelo Fruciano
Italian National Research Council (CNR)
IRBIM Messina
http://www.fruciano.org/
==================
On 10 May 2021 14:49, andrea cardini <[email protected]> wrote:
Dear All,
I have the impression that studies analyzing one landmark at a time
after a Procrustes superimposition (plus a possible sliding of
semilandmarks) are beginning to pop up here and there in the biological
literature.
I wonder whether there's some revolutionary evidence, which was
published and I missed, that contradicts a most basic principle of
Procrustes shape analysis: never to analyze Procrustes shape variables
one at a time, including especially the case of pairs or triplets of
2D-3D landmark Procrustes shape coordinates. This is nicely summarized
by Paul in J. Anat. (2000) 197, pp. 103–120; exemplified in Fig. 9 of
doi:10.1371/journal.pone.0025630; related to the problem of analyzing
one PW at a time discussed by Jim (Syst. Biol. 47(1):147± 158, 1998);
and most likely known since the early days of Procrustes GMM.
I would be astonished to find that this is not longer true but I am
happy to be surprised.
Many thanks in advance for refs and feedback.
Please, if you reply directly to me, let me know if I can share your
answer.
Cheers
Andrea
--
Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di
Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 4223140
Adjunct Associate Professor, Centre for Forensic Anthropology, The
University of Western Australia, 35 Stirling Highway, Crawley WA 6009,
Australia
E-mail address: [email protected], [email protected]
WEBPAGE: https://sites.google.com/view/alcardini2/
or https://tinyurl.com/andreacardini
FREE Yellow BOOK on Geometric Morphometrics:
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ESTIMATE YOUR GLOBAL FOOTPRINT:
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Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di
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tel. 0039 059 4223140
Adjunct Associate Professor, Centre for Forensic Anthropology, The
University of Western Australia, 35 Stirling Highway, Crawley WA 6009,
Australia
E-mail address: [email protected], [email protected]
WEBPAGE: https://sites.google.com/view/alcardini2/
or https://tinyurl.com/andreacardini
FREE Yellow BOOK on Geometric Morphometrics:
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ESTIMATE YOUR GLOBAL FOOTPRINT:
http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/
SUPPORT: secondwarning.org
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