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Phylogeographic inference with microsatellites vs SNPs: a case of two frogs from the Iberian Peninsula
Add to bottom half a similar plot for the Hyla data, though for H. molleri the SSC will have to be calculated on the average of the localities.
Hand draw lines englobing the clusters.
Silvia suggested to plot diversity on a map.
check clumpp does the job
build assertion for rownames from qclumpak
rownames from results of Pelobates are different from structure respect to gen because I changed them-> solve that
run clumpp with dapc results as well
200 SNPs have roughly the same info that the microsatellite dataset. In order to compare the behaviour of the curves at the plot dnp/dnr Craig suggested to subsample 200 snps instead of using the whole dataset.
The metrics Dnp and Dnr are done over standarized tree distances. However, in the plots "DnrDnp_ggplot_bw.pdf" it is possible to see that metric for both markers do not have the same highest value. This could be caused by the fact that the lengths of the branches supporting the trees are different between usats and SNPs. For that reason, in the meeting from Sept 13th 2019, it was suggested to normalize the the distances using the maximum distance from any internal node (non-tip nodes) instead of normalizing as I have it now:
maxd <- ape::cophenetic.phylo(tr1) %>% max()
tr1$edge.length <- tr1$edge.length / maxd
Craig suggested to change the order of the sections in the manuscript. As it is now:
Craig suggested:
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