Grusea, S. | bioRxiv Science

bioRxiv2024

Extending the IICR to multiple genomes and identification of limitations of some demographic inferential methods

Reconstructing the demographic history of populations and species is one of the greatest challenges facing population geneticists. [50] introduced, for a sample of size k = 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 on Tk, the time to the first coalescence event in a haploid sample of size k where k [≥] 2. We define the IICRk as the Inverse Instantaneous Coalescence Rate among k lineages. We show that (i) under a panmictic population [Formula] is equivalent to Ne, (ii) the IICRk can be obtained by either simulating Tk values or by using the Q-matrix approach of [61] and we provide the corresponding Python and R scripts. We then study the properties of the [Formula] under a limited set of n-island and stepping-stone models. We show that (iii) in structured models the [Formula] is dependent on the sample size and on the sampling scheme, even when the genomes are sampled in the same deme. For instance, we find that [Formula] plots for individuals sampled in the same deme will be shifted towards recent times with a lower plateau as k increases. We thus show that (iv) the [Formula] cannot be used to represent "the demographic history" in a general sense, (v) the [Formula] can 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 [Formula], but are close to the [Formula] in 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 the [Formula] to identify the signature of population structure, and to develop new strategies for model choice.

evolutionary biology↗

bioRxiv2018

The IICR and the Non-Stationary Structured Coalescent: demographic inference with arbitrary changes in population structure

In the last years, a wide range of methods allowing to reconstruct past population size changes from genome-wide data have been developed. At the same time, there has been an increasing recognition that population structure can generate genetic data similar to those produced under models of population size change. Recently, Mazet et al. (2016) showed that, for any model of population structure, it is always possible to find a panmictic model with a particular function of population size changes, having exactly the same distribution of T2 (the coalescence time for a sample of size two) to that of the structured model. They called this function IICR (Inverse Instantaneous Coalescence Rate) and showed that it does not necessarily correspond to population size changes under non panmictic models. Besides, most of the methods used to analyse data under models of population structure tend to arbitrarily fix that structure and to minimise or neglect population size changes. Here we extend the seminal work of Herbots (1994) on the structured coalescent and propose a new framework, the Non-Stationary Structured Coalescent (NSSC) that incorporates demographic events (changes in gene flow and/or deme sizes) to models of nearly any complexity. We show how to compute the IICR under a wide family of stationary and non-stationary models. As an example we address the question of human and Neanderthal evolution and discuss how the NSSC framework allows to interpret genomic data under this new perspective.\n\nAuthor summaryGenomic data are becoming available for a rapidly increasing number of species, and contain information about their recent evolutionary history. If we wish to understand how they expanded, contracted or admixed as a consequence of recent and ancient environmental changes, we need to develop general inferential methods. Currently, demographic inference is either done assuming that a species is a single panmictic population or using arbitrary structured models. We use the concept of IICR (Inverse of the Instantaneous Coalescence Rate) together with Markov chains theory to develop a general inferential framework which we call the Non-Stationary Structured Coalescent and apply it to explain human and Neanderthal genomic data in a single structured model.

evolutionary biology↗