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).