Hi Carmelo, Thank you for those answers. One more question please: I know that the number of specimens should exceed the number of the total landmarks (fixed-landmarks + semi-landmarks). Is there a rule of thumb of by how much or what ratio between specimens to semi-landmarks one should keep?
Thank you, Avi On Sunday, March 11, 2018 at 5:15:24 PM UTC+2, Carmelo Fruciano wrote: > > > > 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. > > Best, > Carmelo > > -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.