Morphometrics - Science topic

Hello, Is this ARCGIS workflow for Stream Gradient Index Calculation is Correct? I tried it, some time I found the SL Index through it smoothly but sometime I found 5 to 6 time more L values thn Delta L & Delta H in numbers.

Hassan Nait-Si You're correct that the Line Density tool in ArcGIS doesn't directly calculate drainage density (Dd) as defined by Horton (1932). The tool only considers the length of segments, not the surface area of the watershed.

Your approach to create a grid, calculate Dd for each cell, and interpolate the results is a good workaround. This method allows you to account for the surface area and accurately represent the drainage density.

To further validate your methodology, consider the following:

1. Cell size: Ensure the grid cell size is appropriate for your analysis. Smaller cells can provide more detailed results but may increase processing time.

2. Data quality: Verify the accuracy of your stream network data and watershed boundary.

3. Interpolation method: Choose an appropriate interpolation technique (e.g., inverse distance weighting, kriging) that suits your data and study area.

4. Comparison: Compare your results with other studies or field observations to confirm the accuracy of your methodology.

5. Consultation: Discuss your approach with experts in GIS, hydrology, and geomorphology to gather feedback and improve your methodology.

Regarding the Line Density tool, it's essential to understand its limitations and potential biases. You may want to:

1. Contact Esri support: Reach out to Esri's technical support to clarify the tool's functionality and limitations.

2. Consult documentation: Review the tool's documentation and research articles to understand its intended use and potential applications.

3. Discuss with experts: Engage with specialists in GIS and hydrology to discuss the tool's suitability for calculating drainage density.

Yes, the signs of some elliptic Fourier coefficients will change after the polyline change its direction: cv <--> ccv

Thank you very much Muhammad Abrar Yousaf and Lorenzo Halasan for your much-appreciated help.

Sorry but I do not know other packages.

please send me your email id I will send one excel sheet for all analyses.

Generally, it is not recommended to make permanent mounts for large nematodes. Nematodes should be studied between a slide and a cover glass with little pressure (in glycerin or another medium) and you should be able to move gently the cover slip to see all sides of the nematode body.

Hello Claudia; I've used a picnic ice chest to create a cold place. Cooling the butterflies to some low temperature will immobize them for a little while. Try it in the lab so you can tell how long it takes to cool them and how long they stay immobile. Good luck with your project; Jim Des Lauriers

Thankyou @Mainak choudhuri

thank you!

Best wishes

It depends on what your goal for the job is. If you have the morphometric data during the months, a comparison test can be done for a single species during the months of collection. However, I say and I repeat, it depends on your goal.

Hi, this article Cells | Free Full-Text | A Universal Approach to Analyzing Transmission Electron Microscopy with ImageJ | HTML (mdpi.com) is interesting in using ImageJ to measure mitochondrial morphology, you might want to give it a try, good luck,

See the attached screenshot for a great book available in the z-library. The R package cluster contains all the programs. Best wishes, David Booth

Hunt, D.J., Palomares-Rius, J.E., Manzanilla-L´opez, R.H., 2018. Identification,

morphology and biology of plant parasitic nematodes. In: Sikora, R.A., Coyne, D.,

Hallmann, J., Patricia, T. (Eds.), Plant parasitic Nematodes in Subtropical and

Tropical Agriculture. CABI Publishing, Wallingford, UK, pp. 20–61.

Composition and diversity of larval fish in the Indian Ocean using morphological and molecular methods

Specifically what kind of analysis you have in mind? You can use any kind of general morphometry software like MorphoJ (https://morphometrics.uk/MorphoJ_page.html) or R package like geomorph (https://cran.r-project.org/web/packages/geomorph/geomorph.pdf).

The measurements themselves can be done in a variety of ways (micrometric eyepiece, software like Digimizer, etc), and the analyses can be performed with any kind of statistical software.

Dear Jobin Thomas

We also faced a similar problem in the Jhelum basin. In larger basins, you are very much right that natural drainage is not always available for stream burning. Further in our case, the pseudo drainage occurred in flat surfaces and over the lakes. For lakes, we had the lake polygon layer to burn. I think increasing the threshold is one of the viable options that does reduce such spurious drainage lines.

The solution lies in between the opinions provided by W. J. van Verseveld Richard Gloaguen Neelakantan Sajikumar

Thank you all for this wonderful knowledgeable discussion.

Regards

Gowhar Meraj

Is there a certain point in the procedure where you are getting stuck? Or maybe an error message ?

I know you may have already tried these, but they were helpful to me when I got stuck with a similar problem -

If ANOVA fails to signify stats correlation I think that the raw data sampling is defective . Plese repeat the data collection as per SOP .

Dear Ivica, here a chapter regarding guly monitoring (geomorphic changes) based on HR DEMs: DOI:10.1016/B978-0-444-64177-9.00010-2, In book: Remote Sensing of Geomorphology

Dear Muhammad

Yes, of course. This approach can be used for any stable shape such as skulls, insect wings, molluscs shells, leaves, etc.

Be aware that the truss network is not theoretically equivalent to geometric morphometrics.

Cheers,

Kiavash

Morpometric analysis

Watershed delineation for the Amazon sub-basin system using GTOPO30 DEM and a drainage network extracted from JERS SAR images

Dear Alina Davis

I am currently doing microcomputer (_mCT) tomography of beetles. The owners of these tomogrofofs have websites where you can find the morphological characteristics of the objects under study. If interested, I will post links to you

Regards, Sergey Viktorovich Pushkin

Dear colleague, Mechanical degradation related to brittle shear zones may lead to linear patterns of the drainage system due to morphoselection or passive control of an underlying shear zone.

But many other geological contacts may also lead to this situation (lithol. contacts, etc.). Also, local morphoclimatic environment controls how well imposed a shear zone might be in the landscape. For instance, an interplate structure with high slip rate such as the Alpine Fault in N Zealand exhibits a discrete linear imprint, whereas you can follow long-lived inactive shear zones in cratonic areas throghout hundreds of kms.

So I´ll look for rectilinear depressions, fault saddles, etc, as potential indicators of shears zones, but I doubt if you can isolate specific diagnostic morphologies.

Hope this helps. Best

No difference clinically. Manage symptomatically.

I think it depends on the type and the degree of pollution. Different results have been reported:

We exactly CANNOT identity new species based on barcoding! Barcoding data could have a signal for existing of a new species, it's true. Barcodind identifies some BINs, nobody known what is it, and they change all the times after adding new sequences. Regading these strange products as something species-like is clearly contradicting to the main approach declared in the Preambule to the International Code of Zoological Nomenclature created for STABILITY.

It may be desirable to have DNA with morphology when describing a new species, but it is not required. After all and for practicality, species are recognized morphologically, not by molecular analysis. On the other hand I would strongly recommend not to describe a new species on molecular data alone if they cannot be shown to also be defined by morphological data.

Dear Muhammad:

Your'e welcome. Good luck in your research!

Best regards

Pablo.

You are using the wrong methods. See this post about logistic regression:

Best, D. Booth

Combination of softwares like tpsUtil, tpsDig, PAST are useful for landmark based TRUSS morphometrics. However, landmark based Geometric Morphometrics (GM) assess the shape and compare shape. Softwares for GM analysis are R package Geomorph, past and MorphoJ. Manuals of these softwares are easily available online.

I would not try to interpret the pattern of loadings by reading the numbers. Instead, I would plot the results. The function returns the shapes at the extreme values for each PC, so you can use the plotRefToTarget function to show the difference between the two extremes (or you could show the change from the mean to an extreme. In this example, the shape data are coordinates of landmarks, in a 3D array, in a file called "niger.shape". This returns a plot of the scores and the changes along the first two PCs, from the shape with the minimum to the maximum score along each.

niger.gm<-gm.prcomp(niger.shape)

plot(niger.gm,pch=21,cex=1.5,bg="black")

plotRefToTarget(niger.gm$shapes$shapes.PC1$min,

niger.gm$shapes$shapes.PC1$max,method="vector")

title("PC1")

plotRefToTarget(niger.gm$shapes$shapes.PC2$min,

niger.gm$shapes$shapes.PC2$max,method="vector")

title("PC2")

Dear Melanie Baker

To my knowledge neither PAST nor MorphoJ can estimate missing landmarks, in fact in theory MorphoJ does not allow the use of semilandmarks. From your question I understand you are using 2D landmarks obtained from 2D pictures using TPSDig. Thus, my recommendation is use two packages available in R which allow estimate missing landmarks. In the first one Geomorph there are two algorithms that can be used using the function estimate.missing:

The first approach (method="TPS") uses the thin-plate spline to interpolate landmarks on a reference specimen to estimate the locations of missing landmarks on a target specimen. Here, a reference specimen is obtained from the set of specimens for which all landmarks are present, Next, each incomplete specimen is aligned to the reference using the set of landmarks common to both. Finally, the thin-plate spline is used to estimate the locations of the missing landmarks in the target specimen (Gunz et al. 2009).

The second approach (method="Reg") is multivariate regression. Here each landmark with missing values is regressed on all other landmarks for the set of complete specimens, and the missing landmark values are then predicted by this linear regression model. Because the number of variables can exceed the number of specimens, the regression is implemented on scores along the first set of PLS axes for the complete and incomplete blocks of landmarks (see Gunz et al. 2009).

Please check the help file https://cran.r-project.org/web/packages/geomorph/geomorph.pdf

The second one named Morpho also uses two functions to estimate missing landmarks. The function fixLMmirror allow estimate missing landmarks from their bilateral counterparts and in the fixLMtps function the missing landmarks are estimated by deforming a sample average or a weighted estimate of the configurations most similar onto the deficient configuration. The deformation is performed by a Thin-plate-spline interpolation calculated by the available landmarks.

Please check the help file https://cran.r-project.org/web/packages/Morpho/Morpho.pdf

Please note that these methods have different requirements.

Both packages allow use files derived from TPSDig, thus you can use your files. These functions allow you read landmarks into R in Geomorph readland.tps and in Morpho readallTPS

I hope this helps!

Cheers,

Miguel

Dear Jobst, thank you!

It seems like an inspiring study.

J.

Please go through the following RG links and PDF attachments.

Andriy; Of course you can core a branch and it will give you only the age of the branch. You must be reluctant to core the trunk of the tree. If you are reluctant, why is that?

I've never seen a paper that had a method of reliably aging a standing tree without counting rings. It's a puzzle! Jim Des Lauriers

I don't know there is one. I would like to participate if you decide to create one

You can find that data in the on-line book "Gadiformes" of A.N. Svetovidov. 1948. Fauna SSSR. Pisces. Vol. IX (4).

Well,

Streams High orders (5 and above) indicate that the streams run down streams in soft rocks or in steep areas such as floodplains.

  The intermediate orders (third and fourth) are found in areas with medium slope and their increasing number indicates the rigidity of the drainage rocks.

Low orders (first and second) are found in high-sloping rocky cliffs due to the speed of stream water. The first ranks are short in proportion to the rest.

The normal bifurcation rate in basins ranges between (3-5) and is a natural reflection of climatic, terrain and geological conditions.

Their values close to (3-5) are indicative of the similarity of the pond's climatic and structural properties.

  Any rise or fall of the ratio above the threshold is evidence of pond asymmetry and terrain.

It is evidence of normal anomalies in the pelvis or of tectonic activity in the basin area.

Regards

Tristan D. Schramer I haven't, but I will now! Thanks!

Here are a couple of papers to look at for PGLS, one that introduces the method for shape data---if you've already done PGLS, this may not be very helpful, but the second one should be useful and the first is useful background reading for PGLS, in general. I don't know what you are questioning about your PGLS; there are lots of issues (conceptual and statistical) and some of those are addressed in the second of these papers. If it's just a matter of not knowing whether you ran the analysis correctly, then the first of these papers should clarify that.

Adams, D. C. 2014. A method for assessing phylogenetic least squares models for shape and other high-dimensional multivariate data. Evolution 9:2675-2688.

Adams, D. C. and M. L. Collyer. 2018. Phylogenetic ANOVA: Group-clade aggregation, biological challenges, and a refined permutation procedure. Evolution 72:1204-1215.

Yes, it looks like a straightforward ANOVA question. A couple of further thoughts. You ask 'which of the 25 variables differ significantly' so you will need to account for colinearity and multiple testing, and more importantly to decide what you mean by 'significant'. I don't recommend fishing for a method that gives a p value, but rather that you decide what you want to know and find a method that answers that specific question. If the question is more general, i.e. whether the fish in the different rivers in in some way different, then you may want to try a more multivariate approach in which you consider all the variables together. I would probably use PERMANOVA (to get around the assumptions underpnning classical MANOVA) for testing, and something like SIMPER to understand which variables are contributing to observed differences.

Before you get too far into the literature, I'd strongly recommend reading this critical evaluation of methods:

Adams, D. C. and M. L. Collyer. 2018. Multivariate phylogenetic comparative methods: Evaluations, comparisons, and recommendations. Systematic Biology 67:14-31.

It's main focus is on the methods for analyzing the evolutionary dynamics of shape (and it explains why not to use some of the methods used in Davis and Betancur-R). I would also wait on using the methods introduced by Catalano and Goloboff until you understand the theory underlying Procrustes-based geometric morphometrics thoroughly.

While you are learning the theory, you might look at the software for conducting the analyses to see what methods are now available and how to use them, as well as reading empirical studies that use them. The R package geomorph (by Adams, Collyer and Kaliontzopoulou) provides all those methods. The main method for analyzing the evolutionary relationships between ecology and morphology is phylogenetic generalized least squares (PGLS):

Adams, D. C. 2014. A method for assessing phylogenetic least squares models for shape and other high-dimensional mutlivariate data. Evolution 68:2675-2688, and

Adams, D. C. and M. L. Collyer. 2018b. Phylogenetic ANOVA: Group-clade aggregation, biological challenges, and a refined permutation procedure. Evolution 72:1204-1215.

There is a large empirical literature on the evolutionary relationship between ecology and shape, but much of it predates the methods that can analyze that relationship rigorously. However, those methods do now exist. At present, there are no generally accepted methods that incorporate shape data into phylogenetic analyses.

Hi Rafaela. Actually as far I know, the tpsdig does not estimates missing landmarks. When you use the option "next landmark is missing", it computes "-1.00000 -1.00000" as coordinates of that missing landmark in your .tps file. Then, when you load your file in R (for example) you can use the function "estimate.missing" of the geomorph package. In that case, you can use two different approaches to estimate as described in the help function.

I do not know if you still are struggling with the same issue, here are some help. What are the critical parameters you wish to compare and extract from those DEMs? Elevation, slope, aspect, hydrology, ruggedness are just a few of them. The actual ground verification you will compare the DEMs with are from toposheets. How accurate are those toposheets. You can go with RMSE comparison, but you will need quite a lot of points strewn across your region of interest. You can dissect the slope to classes and look for the compliance of the data points falling in those slope classes independently. Look for the attached papers of mine, you will get the idea. Good luck.

The angle between the vectors is a measure of the difference in the directions of shape change. If the two vectors point in the same direction, the angle between them is zero. So (in geomorph) the statistical test determines whether that angle exceeds what would be expected by chance. There are two functions that perform the analysis in geomorph, depending on whether the vectors are trajectories between means or regression coefficients (slopes). The functions that did the analyses up until this most recent version of geomorph (3.10) are two of the major changes The function for comparing trajectories between means is trajectory.analysis, which is now in the RRPP package (but geomorph depends on RRPP so this is a minor change except in the manual and in the arguments for the function). The function that compares slopes is now procDlm used in conjunction with anova.lm.rrpp, and pairwise (in the previous version, you'd use trajectory.analysis and advanced.procD.lm) You can see examples of these analyses in the vignette for the newest version of geomorph.

Thre are a number of methods and it depends on the type of species you want to study

Jonathan Wagner thank you very much. You helped me a lot ! I think i got this. =)

If, and it seems so, these analyzes are post-mortem, you can fix the fish and stain the scales or the pores. There is a variety of stains that you can use, protocols are fairly simple so that should not be a problem. In this way, you should be able to determine the scales number and position easier. Hope that helps.

Some interesting reading about color matching vs mathematical projection and perceived color vs color sensation by following:

hi,

I believe that typically DBM, or tensor-based morphometry, estimates how much deformation is needed to make a brain fit into a certain template (an average brain). This would indirectly return an atrophy value.

You can visit the SIENA's fslwiki page (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/SIENA) or the papers attached below:

best,

J

You could go "all out", although this would entail switching strategies: if you digitize standardized pictures of your species of interest, taking care to include those features which you hypothesize will differentiate them based upon geographic location, you could use the resulting coordinates (entire morphology) as the variables of your investigation, using Procrustes analysis and PCA. The resulting variables can be made amenable to multivariate statistics, or subjected to ordination techniques to see whether you can separate the (geographic) groups based upon morphology. Not a quick fix though...

Unfortunately, till now I did not have a study in this field.

I use comments. Thanks

With the best wishes

Mr Rezaei Ahvanooei.

Estimates of effective population sizes and, related to this, estimates of genetic variation within and amongst populations might be interesting. If you have enough markers you might also be able to estimate relatedness among fish and from this infer quantitative genetic parameters (e.g. h2). There are many possibilities! Good luck!

Alternatively, you can break your directions into a north-south and an east-west aspect component.You require assignation of angles or compass directions in degrees. Depending on your study system, one of these slope aspect components might be of greatest interest (for example if working at a temperate latitude, most likely you would expect the degree of N-S orientation to matter more biologically, due to the difference in solar incidences). If you take the cos (angle) this will give you the N-S component as a numeric form ranging from 1 to -1, with 1 being N (0 or 360 degrees) and -1 being S (180), zero indicates a compete east or west exposition. The Sin(angle) is the E-W component, again ranging from 1 (East) to -1 (West). Then you can run correlations and linear regressions with your data.

In Arc GIS you can calculate the length of the main stream and the perimeter/basin length. Yoe have to open the attribute table of the stream layer. click on the "Table Options" tab then select the "Add Field" option there. Then in the "Add Field" dialogue box u may provide the name, type (double) and precision and click "OK". then the name provide u can bee seen in the attribute table as a column.Then go to editor tool bar and click on editor and select "start editing" and select the stream layer that u are going to edit. Then again open the attribute table of the stream and right click on the new column heading u created. Select the Calculate geometry from the drop down list. Then u may calculate the length of the stream by units u select there. Then click OK button and u may see the actual length of the strem in the column u created. Do the same for the Basin length.

Hi,

I am not a zooarcheologist, so may be my answer would not fit your needs but it my help you.

Here is some interesting stuff to read/follow:

- you have to identify clearly to which taxon is your bones

- you have to know which methods or measurement techniques to use and its bias

- you have than to check it through the Virtual Zooarchaeology of the Arctic Project (VZAP) : http://vzap.iri.isu.edu/ViewPage.aspx?id=230, direct access to the project database is here: http://bones.iri.isu.edu/ (in the classification field you choose mammalian than rodentia)

- check these links/papers:

+ Animal Bones and Archaeology Guidelines for best practice: https://content.historicengland.org.uk/images-books/publications/animal-bones-and-archaeology/animal-bones-and-archaeology.pdf/

+ Animal Bone Specimens Preparation Method: http://www.nara.accu.or.jp/elearning/2011/animal.pdf

+ Identifying and Interpreting Animal Bones: A Manual (Texas A&M University Anthropology Series): https://www.amazon.com/Identifying-Interpreting-Animal-Bones-Anthropology/dp/162349026X/ref=pd_sim_14_2?_encoding=UTF8&pd_rd_i=162349026X&pd_rd_r=WTGSHCJN8W6SJKWGYHWX&pd_rd_w=9WPzI&pd_rd_wg=WraQI&psc=1&refRID=WTGSHCJN8W6SJKWGYHWX

+ Integrating Zooarchaeology and Paleoethnobotany: A Consideration of Issues, Methods, and Cases (Springer) : http://www.springer.com/la/book/9781441909343

Best.

Sure, I have all of those. Please check the direct message I sent you.

Apparently this elusive work has additional information on crocodilian proportions, but I have not been able to find it so far:

Junprasert, S. and Youngprapakorn, P. (1994) Head length proportion and predictable equation of Siamese crocodile’s body length at Samutprakan Crocodile Farm and Zoo. Journal of the Thai Association for Trade in Reptiles and Amphibians 1 (1), 45–46.

Jorge.

Dear Debottam,

the software developed by Montani (2001) can be useful for your research. However you must take pictures from diffenrent angles.

Best,

Cristna

Elena

The sample size depends on the research question or objective:

If you want to describe a morphometric character in a follow-up study or in two generation of insects, you can calculate your sample size for a statistical estimation of a population parameter (generally, the mean), then you need to stablish the expected variability of the morphometric measure, the confidence level and the precision that you will do the estimation. This sample size will be the same for each generation of insects.

But if you want to compare the morphometric character in the same population in two stages or generations, then you will perform an hypothesis test for two independent populations, then you need to stablish the expected difference between the mean of the two populations and the expected variability about this mean, the significance level and the power expected of the statistical test.

Like you can see, the sample size is given by the morphometric measure that you want to evaluate, and for this calculus, the expected values can be estimated previously with a pilot study or experiment like Pieter said.

Never use a convenience selected sample size and try to apply then inferencial statistics (estimations or hypothesis tests), something will be going wrong.

Best regards

Federico

If the underlying algorithm was linear, 'regress-out' approach would be somewhat applicable, yet, since this is ML and deep-learning, linear decomposition doesn't really make sence - because, if the relationship between, say, age, and Morphometry metrics is not linear, your regression would basically corrupt the data, when without the regression the non-linar algorithm would probably identify the relationship quine nicely.

So why not just incorporate age into the model? Add another input into your model, and pass age into it. Same with gender and any other characteristic of the subjects. With deep learning it's reasonable to assume the model would make appropriate use of additional inputs, if given enough samples. But, well, the same goes for any ML algorithm

Since this incorporation is a bit different than, say, adding several more voxels, and carries a more 'modulation-like' sence, I would assume that the NN would require more layers/neurons to 'build' the underlying relationship. However I do not know the starting point so the structure used (or planned for use) may easily be enough already.

Significant between-group difference isn't perfect, but is not a deal breaker, in my opinion

Thank you Michelle for the update.

I do not really understand your question but maybe the following might help:

Co-registration of point clouds or meshes can be done with a free tool called CloudCompare: http://www.danielgm.net/cc/

Cloudcompare has an ICP (+ scaling) algorithm to co-register two 3D objects (meshes or point clouds) and you can choose from various algorithms to compute and visualise the differences between them.

Also, the free Meshlab can do point cloud comparison: http://www.meshlab.net/

Cheers, Geert

In the case of geometric morphometrics, you can also use MorphoJ

doi: 10.1111/j.1755-0998.2010.02924.x.

I would refer to them as morphotypes. It is not unusual to find different morphs within seeds of the same species - what is interesting is why? When you say different forms, are you refering to size, shape?  

In addition to MorphoJ, you could also use PAST for analysis. It has several tools for morphometrics analysis and it is easy to use, just like MorphoJ. The other thing is you could just enroll for one of Klingenberg's GMM courses. He wrote the MorphoJ software plus he is an excellent teacher!

I agree with the answers of both Dr. William and Dr. Kevin. Considering all the other parameters being the same, it is quite a general rule that the occurrence of  flash floods is more in circular watersheds and there is extended time for the peak discharge in the elongated watersheds. There are class books written by the greats like Horton, Strahler and Schumm.

I agree with Sedat on the articles.  In my opinion the size means very little clinically 

These two articles study baboons in the wild and have a measurement for body condition that they use:

Strum, SC (2005). Measuring success in primate translocation: A baboon case study. Am. J. Primatol., 65: 117–140. doi:10.1002/ajp.20103

Silk JB, Strum SC (2010). Maternal Condition Does Not Influence Birth Sex Ratios in Anubis Baboons (Papio anubis). PLoS ONE 5(9): e12750. doi:10.1371/journal.pone.0012750

hi, here some publications you may interest.

Dear Yassar,

Your questions can only be addressed/answered AFTER a morphological statistics investigation. Procrustes analysis is the method of choice. However, you will need to define landmarks and measure their coordinates (preferably in 3D). If you look at Warp Analysis, etc. you will get a signal as to which regions (defined by your landmarks) will be variable within a species (and therefore: which will not be).

Kind Regards, Hermann

Hello Virginie Plot 

please check the attachment

There is a lot of free software for morphometric analyses.  Some programs are more useful for analyzing size measurements, others for shape. Some are point-and-click programs, others are packages for morphometrics that run in R; R gives you much greater flexibility and it is far easier to repeat the same kind of analysis many times, as well as to keep a complete record of what you did, but it does take time to learn enough about R before it is easy to use. I have written a general overview of free software for geometric morphometrics, but it is seriously outdated in the sections on doing morphometrics in R (it can be downloaded from ResearchGate). If you want to use measurements of size instead, you could do your analyses in R anyway, but as mentioned above, PAST is a reasonable alternative. It does the standard analyses and it is not that difficult to learn. If you plan to analyze shape, I would strongly recommend doing your analyses in R because the most comprehensive program for shape analysis is the R package geomorph. It has an excellent manual and a very complete Users Guide. It is also excellent for graphics. The first step in any morphometric analysis is collecting the data, and the tps program, tpsDig remains my favorite for that (it is for collecting data from photographs by clicking on landmarks and outlining curves). I've digitizing several thousand photographs using it and although I've experimented with other programs I have not found one as easy to use or as complete. That one you can get at www.life.bio.sunysb.edu/morph/. That is the Stony Brook morphometrics website and it has links to many programs (just follow the link to software). 

As mentioned earlier, the TPS software suite very useful and user-friendly in placing landmarks and performing basic analyses. http://life.bio.sunysb.edu/morph/

My former adviser has also worked on computer-based species identification. This may be of interest to you.

Best of luck with your work

I just found a study of leporid lagomorphs that tackles a similar problem and uses 3D landmarks for morphometrics and phylo-morphospace plots:

Kraatz B, Sherratt E. 2016. Evolutionary morphology of the rabbit skull. PeerJ 4:e2453 https://doi.org/10.7717/peerj.2453

Dear Dominique Ponton,

I have sent my project to your email. 

Thanks

Rongrong Li