The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice

Abstract

Several inferential methods using genomic data have been proposed to quantify and date population size changes in the history of species. At the same time an increasing number of studies have shown that population structure can generate spurious signals of population size change. Recently, Mazet et al. (2016) introduced, for a sample size of two, a time-dependent parameter, which they called the IICR (inverse instantaneous coalescence rate). The IICR is equivalent to a population size in panmictic models, but not necessarily in structured models. It is characterised by a temporal trajectory that suggests population size changes, as a function of the sampling scheme, even when the total population size was constant. Here, we extend the work of Mazet et al. (2016) by (i) showing how the IICR can be computed for any demographic model of interest, under the coalescent, (ii) applying this approach to models of population structure (1D and 2D stepping stone, split models, two- and three-island asymmetric gene flow, continent-island models), (iii) stressing the importance of the sampling strategy in generating different histories, (iv) arguing that IICR plots can be seen as summaries of genomic information that can thus be used for model choice or model exclusion (v) applying this approach to the question of admixture between humans and Neanderthals. Altogether these results are potentially important given that the widely used PSMC (pairwise sequentially Markovian coalescent) method of Li and Durbin (2011) estimates the IICR of the sample, not necessarily the history of the populations.

Genomic patterns in the widespread Eurasian lynx shaped by Late Quaternary climatic fluctuations and anthropogenic impacts

“…Lynx lynx shows a long period of soft decline from 3 million years ago (Mya) to 600 thousand years ago (kya), and then declining more steeply to around 200 kya. This steep decline is followed by an apparent recovery of the population until 70 kya, although this could instead indicate the emergence of population structure (Chikhi et al, ; Mazet, Rodríguez, Grusea, Boitard, & Chikhi, ). From that point on, the demographic trajectories of European and Asian lynxes start diverging, with the European populations experiencing a sharper decline in N e than the Asian ones (Figure a; bootstraps presented in Figure ).…”

“…To infer the divergence time between populations we built pseudodiploids by randomly combining haplotypes of two individuals sampled in different populations (Cahill, Soares, Green, & Shapiro, 2016;Chikhi et al, 2018). To do so, we used the fasta files generated from the bam files during the PSMC pipeline.…”

“…From 200 to 70 kya, PSMC shows an apparent increase in population size, after which the species entered a continuous population decline (Figure 2a). This transient population size increase probably instead indicates the emergence of population structure (Chikhi et al, 2018;Mazet et al, 2016), as suggested by the departure of demographic trajectories of pseudodiploids in PSMC, and by the deepest divergence of mitochondrial haplogroups around 100 kya (Figures 2b and 3b). The isolation between eastern and western populations became complete around 22-15 kya, coinciding with the LGM (20-15 kya), and with the time of the most recent split that is registered in both nuclear and mitogenomic data (Figures 2 and 3).…”

A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data

“…Coalescent theory shows that the inverse of this rate, sometimes called the inverse instantaneous coalescence rate (Mazet et al, ), can be used as a proxy for population size under certain assumptions. However, if the study population does not meet these assumptions, then other factors can affect the coalescence rate and must be taken into account when we attempt to interpret apparent changes in population size (Chikhi et al, ; Mazet, Rodríguez, & Chikhi, ; Mazet et al, ). For example, the relationship between coalescence times and population sizes can be confounded by natural selection and by nonrandom mating (Mazet et al, ).…”

Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses

“…() by also carrying out psmc analysis of a pseudodiploid genome made by randomly sampling an allele at each site from each of the individual genome assemblies using seqtk (https://github.com/lh3/seqtk; see Figure for details). The pseudodiploid analysis provides information on changes in the rate of coalescence between two individual genomes through time, and therefore the timing of changes in population structure relative to the changes in Ne inferred by the single‐genome psmc analyses (see Cahill, Soares, Green, & Shapiro, ; Chikhi et al., ).…”