Title: Exploring Schoeneae ploidy with GBS data

Name: Tammy L. Elliott

Date: February 2, 2019

R version 3.5.1

Visualize allele depth and balance

Allele depth per specimen

• I am showing a minimum depth of 25 and a maximum depth of 500

Plots showing counts compared to frequency of allele depth for dominant allele

• I am showing a minimum depth of 25 and a maximum depth of 500

Plots showing counts compared to frequency of allele depth for alternate allele

Balance between dominant and alternate allele

• the alternate allele results represent those for the allele with the second highest count at each locus

GBS2ploidy

Examine GBS data for ploidy by looking at allelic proportions using the gbs2ploidy R package

Plot estimations of ploidy with a PCA

• Diploids = BLACK
• Polyploids = Orange

Tammy’s comments

• The allelic balance plots seem to often show peaks above 3/4 and below 1/4, which is in the tails of the distribution
• Neither allele balance or gbs2ploidy appear to give any signal of diploids/triploids/polyploids similar to what is obtained by genome size estimations and chromosome counts
• This could be because the dynamic nature of holocentric chromosomes makes this signal almost possible to detect, as the genome of these species is constantly changing its arrangement.

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Examine which specimens have three alleles sequenced for a position at a loci.

• the number below the specimen shows how many times three alleles with a depth of greater than 25 were sequenced for a position at a loci

##    SchAre1    SchAre2    SchAur1    SchAur2   SchAuri1   SchAuri2 
##          0          0          0          0          0          0 
##   SchAuri3   SchAuri4   SchAuri5    SchBol1    SchBol2    SchBol4 
##          1          0          0          2          0         29 
##    SchCom1    SchCom2   SchComp1   SchComp2  SchCompA1  SchCompA2 
##          1         14          2         17          1          0 
##    SchCra1   SchCras1   SchCras2 SchCusAur1 SchCusAur2   SchCusB1 
##          6          0         26          1          4          3 
##   SchCusB2  SchCusDn1  SchCusDn2  SchCusDn3  SchCusDr1  SchCusDr2 
##          3          0          7         20          0         22 
##  SchCusDr3  SchCusEC1  SchCusEC2  SchCusEC3  SchCusEF1   SchCusJ1 
##          2         17          3          0          3          0 
##   SchCusJ2   SchCusJ3   SchCusJ4   SchCusJ5  SchCusLG2   SchCusP1 
##          0          4          1          0          0          3 
##   SchCusP2    SchEpi1   SchEpi10   SchEpi11    SchEpi2    SchEpi3 
##          1          1          2          1          1          1 
##    SchEpi4    SchEpi5    SchEpi6    SchEpi7    SchEpi8    SchEpi9 
##         18          0          1          0          0          2 
##    SchExi1    SchExi2    SchExi3    SchExi4    SchGra1    SchGra2 
##          0          4          0          1          0          0 
##    SchInc1    SchLig1    SchLim1    SchLim2    SchLim3    SchLor1 
##          4         20         51          0          0          0 
##    SchLor2    SchMeg1    SchNig1    SchPic1    SchPic2    SchPic3 
##         42          0          4          0          0          1 
##    SchPic4    SchPse1    SchPse2    SchQua1    SchQua2    SchTri1 
##          0          0          0          3         14          0 
##    SchTri2     SchUnk 
##          0         13

Tammy’s comments

• by visually looking at these values there does not seem to be an association between genome size (proxy for ploidy) and the number of times three alleles were sequences
• for example, SchBol1, SchBol2, SchBol 4 all have similar genome sizes, but SchBol4 has 29 times that three alleles were sequenced, whereas SchBol1 has two times were three alleles were sequences. SchBol2 did not have any cases were three alleles were sequences with a coverage of over 25
• SchLor2, SchComp1, and SchCusEC2 have 1 situation where four alleles were sequenced with a coverage of over 25. SchBol4 has 2 cases. No other specimens have four alleles at a position of a locus.