2.4 Recent demographic history
The size distribution of ROH tract lengths can provide insights into the recent demographic history of individuals (Ceballos et al., 2018). Since homozygous tract length declines exponentially as a function of recombination rate and time, ROHs due to background inbreeding during an ancestral bottleneck are expected to be shorter than ROHs caused by recent inbreeding (Pool and Nielsen, 2009). ROH tract length can then be correlated with the expected number of generations since the individual’s maternal and paternal lineages shared a common ancestor. Clusters of different lengths in the overall distribution can then be used to identify and date recent populations bottlenecks due to close inbreeding and/or population declines (Pemberton et al., 2012; Saremi et al., 2019).
To identify recent demographic events in S. catenatus andS. tergeminus using this approach we used mclust v.3 in R (R Core Team, 2020) to identify distinct ROH size clusters (see Pemberton et al. [2012]) from a pooled distribution of S. catenatus samples. Schield et al. (2020) have recently documented significant differences in recombination rates on snake macro- and microchromosomes. As such, we restricted data to scaffolds that aligned to macrochromosomes identified in a prairie rattlesnake (Crotalus viridis ) genome assembly (Schield et al., 2019). We did this by mapping the 135 scaffolds ≥ 2 Mb to the C. viridis assembly using ≥ 95% sequence identity for 5-kb sliding window tracts in MashMap v.2.0 (Jain, Koren, Dilthey, Phillippy, & Aluru, 2018).
We dated the resulting ROH size clusters using the equation g = 100/(2rL ), where r is given in cM Mb−1and L in Mb (Saremi et al., 2019). Because there are no estimates of r for any reptilian species, we used a recombination rate estimate of 2.8 cM Mb−1 for chicken (Gallus gallus ) macrochromosomes (International Chicken Genome Sequencing Consortium, 2004). We used an estimated generation time of 3 years for both Sistrurus species as done previously for S. catenatusby Sovic et al. (2019).