R_PopGen_answers

FILE FORMATS

FASTA (seqinr)

• Why do we observe the two square blocks in the table?

These square blocks are the two species that we have replicates for, and they show up because the replicates of individuals within the same species are more similar to each other than to the replicates of the other species.

Data filtering

Questions

• How many diagnostic markers do I have?

75

• How many non-diagnostic markers do I have?

506

• Does it add up to the total of markers in the input file?

No

• Where did the other markers go?

The other markers had too much missing data, which would suggest they are null alleles, and they were excluded in the first lines of the code.

Challenge

write a code that takes one SNP per RAD locus randomly

Principal Component Analysis

• What is the variance explained per axis?

Projected inertia (%): Ax1 Ax2 Ax3 Ax4 Ax5 26.841 2.779 1.302 1.166 1.043

Hardy Weinberg equilibrium

Questions:

• Why do we have rows with no output?

Because we have too much missing data:

• Why do we have only 43 loci?

We had selected for the first 100 SNPs, but those contain multiple SNPs per marker. Since Hardy Weinberg is calculated per marker, and not per SNP, we only get 43 loci. See also the header of the table above; L0001 has 3 SNPs (L0001.02, L0001.00, L0001.01).

THE END