2.5 | Long-term demographic history
We also assessed the long-term demographic history of eachSistrurus species using PSMC v.0.6.4 (Li & Durbin, 2011), which
infers changes in effective sizes (N e) over
extended periods of time based on the physical distance of heterozygous
genotypes across a single diploid genome. We used the highest-coverage
sample from each species (sca1038 and ste0121; Table S1) and GATK’s
(McKenna et al., 2010) best practices pipeline (www.broadinstitute.org)
to call genome-wide SNPs after excluding genomic regions containing
repetitive elements as defined by RepeatMasker v.4.0.7 (Smit, Hubley, &
Green, 2010). As such, in GATK we used DP < 8, DP
> twice the individual coverage, FS > 60.0, MQ
< 20.0, MQRankSum < −12.5, QD < 2.0, and
ReadPosRankSum < −8.0 as filtering parameters. We ran PSMC
with these data for 100 bootstrap replicates and assumed a neutral
mutation rate of 7.2 x 10−9 per generation (see
squamates in Green et al., [2014]) for each species.