Il 01/11/22 18:02, Han Xiao ha scritto:
Dear morpho people,
I am writing to ask a rarely discussed question, which is to test
associations between genomic data and shape variation.
Dear Han,
yes, this is a topic that is perhaps less frequently discussed than
others. As a participant to one of the editions of my geometric
morphometric course, you may recall we covered this general topic to
some extent.
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?
Presumably, if this is your main question and by "shape variation" you
mean "individual shape", you would be performing the analysis mainly on
the only introgressed morph (whose individuals I have to assume based on
your text have varying levels of introgression), using information from
the two "parental" morphs.
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.
About the genetic measures, if the question is about the degree of
introgression (of one morph into another when producing the third
morph), it is doubtful that any of the measures you mention would
adequately capture that. For instance, within your introgressed morph
genetic variation among individuals may not be produced exclusively by
varying levels of introgression. So FST would be a poor choice because
it would capture genetic variation produced by other causes (e.g.,
neutral variation). There are other reasons why FST may be a poor
choice, but let's keep it at that.
Perhaps a semi-decent solution to quantify the degree of introgression
would be to subset your SNP panel to only those SNPs (if any) which are
fixed between "parental" morphs (and which are biallelic in the
introgressed morph), code them to reflect their "polarity" (e.g., 0 the
allele in one parental morph, 1 the allele in the other parental morph)
rather than using the actual nucleotides, and then use the data scored
this way for your individuals from the introgressed morph to do tests
with morphology.
The above is just a very rough solution, with ample margins of
improvement depending on the details of your system (e.g., ongoing gene
flow between the two "parental" morphs, with most of alleles not being
fixed between them). But, as you may imagine, this goes well beyond this
brief reply and would require more in-depth knowledge of your specific
situation (notice how I had to make several assumptions about how
genetic variation is distributed among your morphs).
Notice also that if the level of introgression is all you care about
(regardless of which loci it comes from) you may obtain a much better
and "faster" (i.e., less work for you) solution by using individual
estimates of levels of admixture between morphs from one of the software
used for analysis of genetic admixture (which you have probably used
anyway).
So my questions are:
1. Do you all agree that sb-PLS should also make sense for such a
comparison?
PLS may be a good solution to identify how the shape and levels of
introgression co-vary. Tests based on a measure of association (e.g.,
Escoufier RV) may be used to test the null hypothesis that they are
independent.
If your estimate of level of introgression is univariate (notice that in
the rough solution I suggested above this may not be the case), you may
also consider general linear models (and associated tests of
significance) using the level of introgression as a predictor.
2. What you will suggest for the input files? (I do have some
considerations to discuss)
See above. I suppose the main issue is a bit beyond input files per se
and more about how you quantify/represent introgression.
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).
This is absolutely correct. But, more fundamentally, GWAS' goal is quite
distinct from the hypothesis you want to test.
Also, the potential transgressive shape of
hybrids may be a confounding factor, especially there is different
allometry observed.
Yes. But transgressive segregation may not be a concern if you are just
interested in whether and how levels of introgression scored within a
single "introgressed" morph is associated to shape variation.
Best,
Carmelo
--
==================
Carmelo Fruciano
Italian National Research Council (CNR)
IRBIM Messina
http://www.fruciano.org/
==================
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