Hi Philipp, Thanks a lot, although the phenotypic traits measured in the paper were not shape variation or multi-dimensional based, it is good to check how they build up the analyses!
Best, Han 在2022年11月4日星期五 UTC 14:42:17<[email protected]> 写道： > Hi, > > Maybe this is of interest in this context: > > Mitteroecker P, Cheverud JM, Pavlicev M (2016) Multivariate analysis of > genotype-phenotype association. *Genetics *202(4), 1345-1363 > > It is about multivariate methods to explore associations between genetic > variation and shape/form variation. > > Best, > > Philipp > > [email protected] schrieb am Mittwoch, 2. November 2022 um 02:24:31 > UTC+1: > >> Dear morpho people, >> >> I am writing to ask a rarely discussed question, which is to test >> associations between genomic data and shape variation. >> >> To describe my system and bit first, I am working with four sympatric >> fish morphs in a lake. I have both genetic data (SNP generated by ddRADSeq, >> around 12000 SNPs) and shape data (landmarks and semilandmarks-based GM for >> the head shape) of the same fish samples. The genetics indicate that three >> morphs are genetically distinct, while one is of hybridization origin >> between two morphs with different degrees of introgression. I like to ask >> the question: for the three related morphs (two parental morphs and one >> hybrid morph) there any correlation between the degree of genetic >> introgression and the shape variation? >> >> I was suggested to apply a 2b-PLS to test it. Then I searched for some >> literature and find a few cases. However, the studies vary for the input >> data of both genetics and morphometrics. For genetics, people have used >> genetic distances (calculated as Fst/(1-Fst), Fst is a measurement of >> genetic differentiation), Prevosti distance, allele frequencies (a few >> microsatellites), and expression results (numeric and continuous). For the >> shape data, people used Eucidean distances, GPA coordinates, centroid >> sizes, etc. >> >> So my questions are: >> 1. Do you all agree that sb-PLS should also make sense for such a >> comparison? >> 2. What you will suggest for the input files? (I do have some >> considerations to discuss) >> 3. Is there any other analysis you will recommend? >> >> I know normally people will use GWAS to search for associations, however, >> I am looking for something that can tolerate a smaller sample size (30 fish >> per morph). Also, the potential transgressive shape of hybrids may be a >> confounding factor, especially there is different allometry observed. >> >> I appreciate all kinds of suggestions and comments. >> >> Best regards, >> Han Xiao >> > -- 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/morphmet2/7379de0e-4d73-4f0d-9a03-4592b87ce231n%40googlegroups.com.
