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

• Main Authors: Liu, Shenglin, Hansen, Michael M.
• Format: Dataset
• Language: unknown
• Published: Dryad Digital Repository 2016
• Subjects: Demographic history; Pairwise Sequential Markovian Coalescent (PSMC); RAD sequencing; threespine stickleback; whole genome sequencing; Life sciences; medicine and health care; envir; geo; Greenland; Hudson
• Online Access: https://doi.org/10.5061/dryad.0618v

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. empirical data(psmcfa files)The zip file contains the input files for PSMC from the empirical data of threespine sticklebacks in the study. Seventeen of them are from RAD data, and one of them is from whole genome sequencing data.Generating PSMC input files from simulated dataThe file contains a function written in R. This function randomly samples RAD loci from chromosomes simulated by ms (Hudson 2002), ...