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/dbf701e6-38a7-4807-be47-c94348554189n%40googlegroups.com.
