Abstract
AbstractReconstructing the demographic history of populations and species is one of the greatest challenges facing population geneticists. [50] introduced, for a sample of sizek= 2 haploid genomes, a time- and sample-dependent parameter which they called the IICR (inverse instantaneous coalescence rate). Here we extend their work to larger sample sizes and focus onTk, the time to the first coalescence event in a haploid sample of sizekwherek≥ 2. We define the IICRkas the Inverse Instantaneous Coalescence Rate amongklineages. We show that (i) under a panmictic populationis equivalent toNe, (ii) the IICRkcan be obtained by either simulatingTkvalues or by using theQ-matrix approach of [61] and we provide the corresponding Python and R scripts. We then study the properties of theunder a limited set ofn-island and stepping-stone models. We show that (iii) in structured models theis dependent on the sample size and on the sampling scheme, even when the genomes are sampled in the same deme. For instance, we find thatplots for individuals sampled in the same deme will be shifted towards recent times with a lower plateau askincreases. We thus show that (iv) thecannot be used to represent “the demographic history” in a general sense, (v) thecan be estimated from real or simulated genomic data using the PSMC/MSMC methods [44, 65] (vi) the MSMC2 method produces smoother curves that infer something that is not the, but are close to thein the recent past when all samples are obtained from the same deme. Altogether we argue that the PSMC, MSMC and MSMC2 plots are not expected to be identical even when the genomes are sampled from the same deme, that none can be said to represent the “demographic history of populations” and that they should be interpreted with care. We suggest that the PSMC, MSMC and MSMC2 could be used together with theto identify the signature of population structure, and to develop new strategies for model choice.
Publisher
Cold Spring Harbor Laboratory