We used fineStructure to look for fine-scale patterns of population structure based on our phased genotype data.
For this analysis we used the phased haps format files from shapeit.
These were converted into chromopainter format with
impute2chromopainter.pl per scaffold. To use linked mode, we generated
uniform recombination rate map files using makeuniformrecfile.pl.
These steps are captured in the snakemake script
0.prepare_chromopainter.smk
In the chromopainter EM parameter estimation step we used 30% of samples (20). Next, fineStructure was run with 2000000 iterations of which half were assigned to burn in iteration and half to sampling iteration. These steps are captured in 1.fs_computation.sh
This process produces a finestructure tree xml file which we parsed
using the R code provided as part of the fineStructure program to
produce a standard phylo object. This was then plotted using ggtree to
produce the finestructure tree shown below.
All nodes in this tree had bootstrap support of 0.99 or better. The tree clearly distinguishes our three locations as distinct clades, but also identifies some structure within these clades. Two small clades (RS1_M11_840, RS1-2_422) and (BR-4-088, BR-4-077) were identified which contained samples with relatively low sequencing depth and presumably reflect small biases due to genotyping error that fineStructure is able to identify as structure. Within the inshore samples however there did seem to be a genuine split between the two inshore locations AI (Adele Island) and BR (Beagle Reef).
Although this split was clearly evident from the fineStructure tree it was not evident in PCA analyses (smartpca, PCAngsd), nor was it visible in patterns of IBD sharing. Since these differences between AI and BR were evidently small relative to the differences between major geographically defined populations (IN, NO, SO) we chose to ignore them for our other analyses.