Il 6/03/2018 4:44 PM, Avi Koplovich ha scritto:
Hi Carmelo,
Thank you for your answer.
My project tests for the influence of kairomones of a predator fish on the morphology of Salamander larvae during its development. To do this, I take pictures every other week of larvae spawned from six different females and assigned to 3 treatments: No fish, 3 caged fish, 6 caged fish.

Hi Avi,
it sounds like an interesting experiment. I will try to answer to your questions but keeping in mind that I'm not very knowledgeable on salamander development.

 1. I intend to use landmark 1 (dorsal connection of the tail fin) as a
    fixed factor. But I thought I may be able to use the tail tip
    (landmark 20) and head tip (landmark 48) as fixed landmarks as well.
    Do you think it's ok in an ontogeny experiment?

I guess it will depend on how long into ontogeny you will track the larvae and whether or not that point will "disappear" over ontogeny and/or slide unreasonably (depends also on your question). You, being knowledgeable on their biology, are the best judge on that.

If not, do you think
    it's ok to slide all semi-landmarks of the tail on landmark 1, and
    all head semi-landmarks on an eye landmark? Since the eye isn't part
    of the head contour, is it ok if I slide one semi-landmark to the
    eye and all rest semi-landmarks of the head one to each other as a
    closed shape?

The point(s) slid relative to the eye won't be sliding along the direction tangent to the curve you want to approximate (i.e., the curvature of the head). A good starting point on the method could be
Gunz & Mitteroecker 2013 - Hystrix

 2. Is it ok if landmarks 1 and 39 slid relative to each other as well
    as 41 and 55, since both describe a closed shape?

It's not particularly desirable (see answer above).

 3. Another worry I have is that landmark 40 which I used to create the
    comb fan for both the tail and the head is too far from both of them
    so it doesn't bypass the bending.
 4. I'm affraid I don't fully understand why landmark 40 can not be
    treated as a fixed landmark. In the book of Zelditch 2004, she says
    that one of the basic differences between fixed-landmark and
    semi-landmark is the degree of freedom, while fixed has two because
    it is docked on both X and Y axes while semi only on one of them
    (depending on the nature of the specific fan). Please correct me if
    I'm wrong, but what if I use the side line of the larvae (which is
    an anatomical/homologous feature) as my X axis and use the Y
    component of landmark 1 (dorsal connection of the tail fin) to dock
    landmark 40 on the Y axis? Is it wrong because of the dependency of
    landmark 40 on landmark 1 regarding the Y coordinate?

I think Don has covered these two very well.

 5. Emma Sherratt told me she straightened the bent tail-body using TPS
    software in her paper Sherratt et al. 2017 - Nature ecology &
    evolution. In the supplementary material of her paper she wrote:
    "To correct for dorso-ventral bending in the landmark configurations
    (caused by the joint of the tail with the head/body), we used the
    ‘unbend specimens’ function of tpsUtil v.1.86 (Rohlf 2015). The
    landmark configurations for each specimen were transformed using the
    quadratic approach, straightening from the eye (1) along the
    notochord landmarks (46 to 55) to the tip of the tail (8)."
    Jim mentioned this unbending function here before. I read the help
    about unbending specimens and thought I can use landmarks 20 (tail
    tip), 48 (head tip) and several semi-landmarks I can digitize using
    the comb fan (equally spaced) along the side line of the larvae, in
    order to create the quadratic curve (while the side line "helper"
    semi-landmarks can be later omitted from the dataset - I saw
    Fruciano et al. 2016). Does this sound good?
    I bet that this can basically solve the problems I mentioned in 3 &
    4, since then I can digitized the whole body contour.

That function is great but, as everything, relies on a set of assumptions (see also Fruciano 2016 - Development Genes and Evolution for a brief discussion). In your case: - that you can consistently identify those points along an hypothetical line (which you would remove after the unbending)
- that your arching is well represented by the chosen function

You are the best judge on whether these assumptions are satisfied in your case or not. I suggested the Valentin et al. (2008 - Journal of Fish Biology) approach because it's more flexible (less stringent assumptions, which obviously doesn't mean assumption-free) and therefore more generally applicable. But, of course, the approach in tpsUtil can be a great solution if it's appropriate to your data.


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