Data from: PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data

The pairwise sequentially Markovian coalescent (PSMC) method uses the
genome sequence of a single individual to estimate demographic history
covering a time span of thousands of generations. Although originally
designed for whole-genome data, we here use simulations to investigate its
applicability to reference genome-aligned restriction site associated DNA
(RAD) data. We find that RAD data can potentially be used for PSMC
analysis, but at present with limitations. The key factor is the
proportion (p) of the genome that the RAD data covers. In our simulations,
a proportion of 10% can still retain a substantial amount of coalescent
information, whereas for 1% estimation becomes unreliable. The performance
depends strongly on mutation rate (μ) and recombination rate (r) and is
proportional to μ*p/r. When the value of this term is low, increasing the
amount of data and number of iterations helps restoring the power of the
estimation. We subsequently analyse one whole-genome-sequenced and 17
RAD-sequenced three-spined sticklebacks (Gasterosteus aculeatus) from a
lake in Greenland. The whole-genome sequence suggests a relatively recent
expansion and decline within ca. 4000–40 000 generations ago, possibly
reflecting postglacial expansion and founding of the lake population. RAD
data, where chromosomes from 10 individuals are combined, identify a
similar pattern. Our study provides guidance about the use of PSMC
analysis and suggests measures that can improve its utility for RAD data.
Finally, the study shows that RAD loci in general contain coalescent
information that can be used for developing more targeted methods.