[MORPHMET] digitizing very variable leaves

['Tina Klenovšek' via MORPHMET]

Thank you all for sharing experiences and ideas.

For the moment we decided to stick to methods based on landmarks but analyze 
simple leaves and leaves with exactly three lobes separately.
In addition, leaves from simple oval to heavily lobed will be analyzed jointly 
with outline methods as most of you suggested.
Hopefully all works out well.
Kind regards from Slovenia,
Tina


[cid:image002.jpg@01D3BF71.6B169C90]

doc. dr. Tina Klenovšek, koordinatorica doktorskega
študijskega programa Ekološke znanosti
Univerza v Mariboru | University of Maribor
Fakulteta za naravoslovje in matematiko
Faculty of Natural Sciences and Mathematics
Koroška cesta 160, 2000 Maribor, Slovenija
T: +386 41 808 366
E: tina.klenov...@um.si, 
www.fnm.um.si



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RE: [MORPHMET] digitizing very variable leaves

['Tina Klenovšek' via MORPHMET]

Thanks to all, Javier, Vincent, William, Joanna and Dr. Rohlf,

my dilemma occurred because some botanists (I work with mammal skulls) have 
asked me to help them evaluate leaf variability of two tree species from 
different localities. So, variability within and among individual trees and 
species.

In which user friendly program (like MorphoJ ☺) can I analyse outline data and 
visualize variability?

Thank you again,
Tina

From: Joanna Lenarczyk [mailto:j.kowal...@botany.pl]
Sent: Thursday, March 15, 2018 10:21 AM
To: Tina Klenovšek
Subject: Re: [MORPHMET] digitizing very variable leaves

Hello Tina,
You can try a program which does not need landmarks:

http://www.eletel.p.lodz.pl/pms/SoftwareQmazda.html

I hope it will help you :) I have not tried it yet by myself, but it can be 
useful when you cannot or do not want use landmarks :)
Best,
Joanna

2018-03-15 8:40 GMT+01:00 
<f.james.ro...@stonybrook.edu<mailto:f.james.ro...@stonybrook.edu>>:
One could do that computationally but I would worry about the homology it might 
imply for such variable leaf shapes. You might try it and then check to see if, 
for example, a lobe on one leaf might be 20% of the linear distance around the 
outline but in another it might be 30% of the way around. In such a case the 
lobe on one leaf would effectively be treated as homologous to a location 
between lobes on another leaf. If so, does that make biological sense for your 
study? If simple leaves were also included the implied homology of a point 
along its outline to that of one of the lobed leaves might be pretty arbitrary. 
Would be better if one knew something about the development of these leaves 
(which I do not!) and used that knowledge.

An alternative would be to use outline methods to group shapes for the purpose 
of say identification with little implication that groups need be biologically 
meaningful. Sorry to be rather negative but I find highly variable leaf shapes 
difficult to put in a simple standard framework. Perhaps others will have 
better suggestions.


F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution
Research Professor, Anthropology
Stony Brook University

From: Tina Klenovšek <tina.klenov...@um.si<mailto:tina.klenov...@um.si>>
Sent: Wednesday, March 14, 2018 12:28 AM
To: f.james.rohlf 
<f.james.ro...@stonybrook.edu<mailto:f.james.ro...@stonybrook.edu>>
Cc: morphmet@morphometrics.org<mailto:morphmet@morphometrics.org>
Subject: RE: [MORPHMET] digitizing very variable leaves

Thanks to everyone who answered.

Dear Dr. Rohlf,
I assumed great variability would be a problem.
I was thinking the best way of digitizing would be to draw a curve on the 
outline of each leaf (simple and lobed leaves). Resample curves by length with 
approx. 40 landmarks. Then append curves to landmarks. Two landmarks, the leaf 
tip and base, would be fixed others could be defined as semi-landmarks. Is this 
sensible?
Alternatively, we could analyse simple and lobed leaves separately.
Thank you a lot for your help.

Tina


From: f.james.rohlf [mailto:f.james.ro...@stonybrook.edu]
Sent: Wednesday, March 14, 2018 3:59 AM
To: Tina Klenovšek
Subject: Re: [MORPHMET] digitizing very variable leaves

An assumption of the usual GMM methods is that shape variation is "small". I 
think these leaves exceed this quite a bit! Another problem is landmarks. How 
to match leaves with and without lobes?

__
F. James Rohlf, Distinguished Prof. Emeritus
Dept. Anthropology and Ecology & Evolution
Stonybrook University

---- Original message 
From: 'Tina Klenovšek' via MORPHMET 
<morphmet@morphometrics.org<mailto:morphmet@morphometrics.org>>
Date: 3/12/18 10:56 AM (GMT-10:00)
To: morphmet@morphometrics.org<mailto:morphmet@morphometrics.org>
Subject: [MORPHMET] digitizing very variable leaves

Hello everyone,

we would like to digitize tree leaves that are very variable (from simple oval 
to strongly lobed on one tree).

1.)I am wondering if TpsDig can do some kind of automatic digitizing like 
the LeafAnalyser software: 
http://www.plant-image-analysis.org/software/leaf-gp, which evenly distributes 
a defined number of landmarks on the leaf outline...

LeafAnalyser does not seem flexible or precise enough. Or I can’t use it 
properly. Any experience?


2.)Is it possible/sensible to put objects that are so differently shaped 
(photos attached) into the same group or is it better to analyse simple and 
lobed leaves separately?


I apologize if similar questions have been already answered...

Kind regards,
Tina







Napaka! Ime datoteke ni navedeno.

doc. dr. Tina Klenovšek, koordinatorica doktorskega
študijskega programa Ekološke znanosti
Univerza v Mariboru | University of Maribor
Fakulteta za naravoslovje in matematiko
Faculty of Natural Sciences and Mathematics
Koroška cesta 
160<https://maps.google.com/

RE: [MORPHMET] digitizing very variable leaves

['Tina Klenovšek' via MORPHMET]

Thanks to everyone who answered.

Dear Dr. Rohlf,
I assumed great variability would be a problem.
I was thinking the best way of digitizing would be to draw a curve on the 
outline of each leaf (simple and lobed leaves). Resample curves by length with 
approx. 40 landmarks. Then append curves to landmarks. Two landmarks, the leaf 
tip and base, would be fixed others could be defined as semi-landmarks. Is this 
sensible?
Alternatively, we could analyse simple and lobed leaves separately.
Thank you a lot for your help.

Tina


From: f.james.rohlf [mailto:f.james.ro...@stonybrook.edu]
Sent: Wednesday, March 14, 2018 3:59 AM
To: Tina Klenovšek
Subject: Re: [MORPHMET] digitizing very variable leaves

An assumption of the usual GMM methods is that shape variation is "small". I 
think these leaves exceed this quite a bit! Another problem is landmarks. How 
to match leaves with and without lobes?

__
F. James Rohlf, Distinguished Prof. Emeritus
Dept. Anthropology and Ecology & Evolution
Stonybrook University

 Original message ----
From: 'Tina Klenovšek' via MORPHMET <morphmet@morphometrics.org>
Date: 3/12/18 10:56 AM (GMT-10:00)
To: morphmet@morphometrics.org
Subject: [MORPHMET] digitizing very variable leaves

Hello everyone,

we would like to digitize tree leaves that are very variable (from simple oval 
to strongly lobed on one tree).

1.)I am wondering if TpsDig can do some kind of automatic digitizing like 
the LeafAnalyser software: 
http://www.plant-image-analysis.org/software/leaf-gp, which evenly distributes 
a defined number of landmarks on the leaf outline...

LeafAnalyser does not seem flexible or precise enough. Or I can’t use it 
properly. Any experience?


2.)Is it possible/sensible to put objects that are so differently shaped 
(photos attached) into the same group or is it better to analyse simple and 
lobed leaves separately?


I apologize if similar questions have been already answered...

Kind regards,
Tina







[cid:image002.jpg@01D3BA4C.D9433EA0]

doc. dr. Tina Klenovšek, koordinatorica doktorskega
študijskega programa Ekološke znanosti
Univerza v Mariboru | University of Maribor
Fakulteta za naravoslovje in matematiko
Faculty of Natural Sciences and Mathematics
Koroška cesta 160, 2000 Maribor, Slovenija
T: +386 41 808 366
E: tina.klenov...@um.si<mailto:ime.prii...@um.si>, 
www.fnm.um.si<http://www.fnm.uni-mb.si>



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[MORPHMET] New publication on patterns of skull modularity and integration over postnatal ontogeny

['Tina Klenovšek' via MORPHMET]

Dear Morphometricians,



we wish to inform you about a publication on skull modularity and integration 
across ontogenetic stages in a long-lived vole with well-defined age stages 
conducted on wild and laboratory bred specimens from two phylogenetic groups:





Modularity and cranial integration across ontogenetic stages in Martino's vole, 
Dinaromys bogdanovi

Link: http://www.ctoz.nl/vol85/nr03/a02



Abstract: We explored modularity and morphological integration of the ventral 
cranium during postnatal ontogeny in Martino's vole (Dinaromys bogdanovi). Two 
closely related phylogenetic groups, originating from the Central and 
Southeastern part of the species range in the western Balkans, were considered. 
As expected, both phylogroups had similar patterns of ontogenetic changes in 
cranial size and shape variation, modularity and integration. At the level of 
within individual variation, the hypothesis that the viscerocranial and 
neurocranial regions are separate modules was rejected, indicating that the 
hypothesized modules are not developmental, but rather functional. At the level 
of among individual variation, the viscerocranium and the neurocranium could 
not be recognized as separate modules at the juvenile stage. The strength of 
association between the hypothesized modules becomes lower with age which 
finally results in a clear 2-module organization of the ventral cranium at the 
adult stage. On the other hand, patterns of morphological integration for the 
cranium as a whole, the viscerocranium and the neurocranium stay consistent 
across ontogenetic stages. The developmental mechanism producing integration of 
the cranium as a whole, as well as integration of the neurocranium, varies 
throughout postnatal ontogeny. In contrast, we detected the ontogenetic 
stability of the mechanism responsible for covariation of viscerocranial traits 
which could provide ongoing flexibility of the viscerocranial covariance 
structure for high functional demands during lifetime. Findings from our study 
most likely support the idea of the 'palimpsest-like' model of covariance 
structure. Moreover, similarity or dissimilarity in the patterns of within and 
among individual variation in different sets of analyzed traits and comparisons 
across ontogenetic stages demonstrate how studies on small mammals other than 
mice can give new insights into postnatal cranial development.



Kind regards,



Tina Klenovšek and Vida Jojić






[cid:image002.jpg@01CDF575.0D631B30]

doc. dr. Tina Klenovšek
Univerza v Mariboru | University of Maribor
Fakulteta za naravoslovje in matematiko
Faculty of Natural Sciences and Mathematics
Koroška cesta 160, 2000 Maribor, Slovenija
T: (00 386) 041 808 366
E: tina.klenov...@um.si,
www.fnm.um.si









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