Interpreting the pervasive observation of U-shaped Site Frequency Spectra

Abstract

The standard neutral model of molecular evolution has traditionally been used as the null model for population genomics. We gathered a collection of 45 genome-wide site frequency spectra from a diverse set of species, most of which display an excess of low and high frequency variants compared to the expectation of the standard neutral model, resulting in U-shaped spectra. We show that multiple merger coalescent models often provide a better fit to these observations than the standard Kingman coalescent. Hence, in many circumstances these under-utilized models may serve as the more appropriate reference for genomic analyses. We further discuss the underlying evolutionary processes that may result in the widespread U-shape of frequency spectra.

Long-term evolution ofStreptococcus mitisandStreptococcus pneumoniaeleads to higher genetic diversity within rather than between human populations

“…Within-host deep-sequencing showed transmission bottlenecks sizes between donor and recipient to be higher than one [44], the within-host diversity of one colonization event (defined from cultured isolates) is consistent with N e ranging from 1 to 72 bacterial cells [43], and mice colonization experiments allowed to estimate within-host N e s of ∼100 [78]. In fact, a multiple merger coalescent genealogy was previously inferred for S. pneumoniae [79], which is concordant with range expansion [80]. It would be interesting to understand how horizontal transmission affects Ne over a great number of generations.…”

Weak genetic draft and the Lewontin’s paradox

“…Intuitively, if one assumes that beneficial mutations arise frequently and are scattered throughout the genome, the average genomic pattern will likely be the result of a mix of the different scenarios, where the strongly affected regions likely encompass only a small proportion of the genomes. It is then tempting to postulate that the average patterns of diversity such as genome-wide SFS would be better fitted by Multiple Merger Coalescent models than by a pure Kingman coalescent model, an observation recently supported for a wide range of organisms (F reund , et al ., 2023; Á rnason et al ., 2023).…”

Simultaneous Inference of Past Demography and Selection from the Ancestral Recombination Graph under the Beta Coalescent

“…However, to adjust the SM β C approach would be somewhat more cumbersome (but doable), since we would need to extend the underlying HMM to account for simultaneous multiple mergers. We emphasise that while there is growing evidence that MMC models produce better fitting genealogies for various species [32], there is ongoing discussions about which mathematical models are better suited to which species (for example see [3] for cod). We advocate that the life-cycle and various ecological factors determine whether a haploid or diploid MMC model can be chosen.…”

“…As genome sequence data become available for a wide variety of species with different biological traits and/or life cycles, the applicability of the Kingman coalescent relying on the WF model can be questioned [91,2,3,71,47,68,94,65,33]. Indeed, for some species, such as fish, with high fecundity and high juveniles mortality (type III survivorship, [24]), it is expected that the variance in reproduction between parents can be much larger than under the Poisson distribution [94].…”