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

Abstract

A common goal of population genomics and molecular ecology is to reconstruct the demographic history of a species of interest. A pair of powerful tools based on the sequentially Markovian coalescent have been developed to infer past population sizes using genome sequences. These methods are most useful when sequences are available for only a limited number of genomes and when the aim is to study ancient demographic events. The results of these analyses can be difficult to interpret accurately, because doing so requires some understanding of their theoretical basis and of their sensitivity to confounding factors. In this practical review, we explain some of the key concepts underpinning the pairwise and multiple sequentially Markovian coalescent methods (PSMC and MSMC, respectively). We relate these concepts to the use and interpretation of these methods, and we explain how the choice of different parameter values by the user can affect the accuracy and precision of the inferences. Based on our survey of 100 PSMC studies and 30 MSMC studies, we describe how the two methods are used in practice. Readers of this article will become familiar with the principles, practice, and interpretation of the sequentially Markovian coalescent for inferring demographic history.

Demographic analyses of marine and terrestrial snakes (Elapidae) using whole genome sequences

“…Overfitting can result in large N e estimates at ancient and recent time periods and is mitigated by merging neighbouring time segments to have identical coalescent rates (Mather et al, 2020).…”

“…Sequentially Markovian coalescent models reconstruct fluctuations in N e over time from patterns of heterozygosity along a single genome. N e is estimated from the rate of coalescence events between alleles in discrete time intervals based on the principle that coalescence is more likely to occur when population size is small (and geographic population substructure is weak) (Mather et al, 2020). If the marine realm supports larger populations that experience higher connectivity (and thus weaker substructure), we would expect the PSMC plots of marine elapids to show (a) higher overall N e ; and (b) less pronounced fluctuations in N e compared to terrestrial species.…”

Contrasting Trends of Population Size Change for Two Eurasian Owlet Species—Athene brama and Glaucidium radiatum From South Asia Over the Late Quaternary

“…For this reason, it is also possible that the population decline seen in the Spotted Owlet after the LGM may also be due to changes in population structure, and this needs to be tested with more data. Disentangling the effects of population structure and demography remains challenging, particularly with sequentially Markovian Coalescent methods (Mather et al, 2020). Another technical constraint is the absence of a reference genome assembly of the study species, which would have allowed better mapping of reads.…”

Major diversification of caribou shaped by glacial cycles before the Last Glacial Maximum

“…Caution may be needed with the interpretation of some individuals given that both coverage and high levels of inbreeding can impact PSMC results (Nadachowska-Brzyska et al, 2016;Mather, Traves, & Ho, 2020), however, most individuals had coverage close to or above the 18X recommended (Table 1; Nadachowska-Brzyska et al, 2016). Itcha-Ilgachuz and Aishihik had elevated inbreeding coefficients which may impact results, and we did see large error margin predicted by the bootstrap analysis for Aishihik individuals, which have a very different demographic reconstruction than the others (Figure 4f and Figures S3a and b).…”

“…It is possible that the PSMC peak is being inflated by population structuring (Mather et al, 2020), but even so, ~120-50 kya was clearly a critical period of diversification between lineages, as shown from both the nuclear and mitochondrial DNA. Hence, prevailing theory about the evolution of caribou lineages in refugia during the LGM, followed by recolonization and a 'hybrid swarm' in the mountains (McDevitt et al, 2009;Yannic et al, 2013) is likely oversimplified, further bolstered by the evident sub-structuring within the northern mountain ecotype (Figure 6a-b), and the evidence from the mtDNA of multiple introgression events occurring before, as well as after, the LGM (Figure 2 and 3).…”