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Calculating the distance to the most recent common ancestor (dMRCA) and the mutation type

SH Shi Huang
SJ Shuaiming Jiang
DH Dongxue Huo
CA Celeste Allaband
ME Mehrbod Estaki
VC Victor Cantu
PB Pedro Belda-Ferre
YV Yoshiki Vázquez-Baeza
QZ Qiyun Zhu
CM Chenchen Ma
CL Congfa Li
AZ Amir Zarrinpar
YL Yang-Yu Liu
RK Rob Knight
JZ Jiachao Zhang
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To calculate dMRCA for each model at each time point, we counted the number of positions at which the called allele was different from the ancestral allele for each isolate, assessing only SNP positions that were polymorphic among isolates from the particular time point, and averaged the results. SNPs were categorized into 6 types, based on the chemical nature of the single nucleotide changes. We computed the mutation spectrum for each model and then computed the mean and standard deviation of each of the 6 types. The frequency of G-C to A-T mutation was the most abundant in all three models. The frequency of A-T to G-C mutation was significantly higher in the zebrafish model than that in the other two models.

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