Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography

Matuszewski, Sebastian; Hildebrandt, Marcel; Achaz, Guillaume; Jensen, Jeffrey D.

doi:10.1534/genetics.117.300499

Cited by 50 publications

(53 citation statements)

References 74 publications

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“…• The other N − U N (z) have one offspring each, Specific modified Moran models leading to Dirac n-coalescents as genealogy limits have been introduced as population models with skewed offspring distributions, see Eldon and Wakeley (2006) and Matuszewski et al (2017), for fixed and variable population sizes. For any Λ-n-coalescent with Λ([0, 1]) = 1 (denoted by Λ ∈ M[0, 1]), Huillet and Möhle (2013, Prop.…”

Section: Models and Main Resultsmentioning

confidence: 99%

“…While some care has to be taken to not change coalescence probabilities (see Remark 4.4 for an example), there will be different possibilities to choose A N,r . For Dirac-n-coalescents with exponential growth (on the coalescent time scale), Matuszewski et al (2017) used A n,r = d N,r . A reasonable approach may also be to set A n,r (close to) proportional to the fraction U Nr /N r of offspring coming from the multiplying parent: Each of the d N,r added individuals are added to the multiplying parent with probability U Nr /N r (with the obvious constraint that after U Nr − 1 individuals are added as offspring of non-reproducing parents, all further individuals need to be added to the multiplying parent).…”

Section: Models and Main Resultsmentioning

confidence: 99%

“…Huillet and Möhle (2013), and the Cannings models introduced in Schweinsberg (2003). The main tool to establish the convergence to the time-changed Λ-ncoalescent is, as in Matuszewski et al (2017), applying Möhle (2002, Thm. 2.2).…”

Section: Introductionmentioning

confidence: 99%

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Cannings models, population size changes and multiple-merger coalescents

Freund

2020

J. Math. Biol.

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Multiple-merger coalescents, e.g. Λ-n-coalescents, have been proposed as models of the genealogy of n sampled individuals for a range of populations whose genealogical structures are not captured well by Kingman's n-coalescent. Λ-n-coalescents can be seen as the limit process of the discrete genealogies of Cannings models with fixed population size, when time is rescaled and population size N → ∞. As established for Kingman's n-coalescent, moderate population size fluctuations in the discrete population model should be reflected by a time-change of the limit coalescent. For Λ-n-coalescents, this has been explicitly shown for only a limited subclass of Λ-n-coalescents and exponentially growing populations. This article gives a general construction of time-changed Λ-n-coalescents as limits of specific Cannings models with rather arbitrary time changes.

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Section: Models and Main Resultsmentioning

confidence: 99%

Section: Models and Main Resultsmentioning

confidence: 99%

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Cannings models, population size changes and multiple-merger coalescents

Freund

2020

J. Math. Biol.

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“…We have demonstrated here that 344 performing inference under the assumptions of the Wright-Fisher model and the 345 Kingman coalescent leads to an incorrect understanding of both population size and 346 selection coefficients in such organisms. Matuszewski et al (2018) have also shown the 347 same to be true for the demographic history of the population. Fortunately, the 348 theoretical details are in place to develop similar inference of demography and selection 349 under biologically appropriate alternative coalescent models (Wakeley, 2013).…”

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confidence: 79%

Inferring demography and selection in organisms characterized by skewed offspring distributions

Sackman

Harris

Jensen

2018

Preprint

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The recent increase in time-series population genomic data from experimental, natural, and ancient populations has been accompanied by a promising growth in methodologies for inferring demographic and selective parameters from such data. However, these methods have largely presumed that the populations of interest are well-described by the Kingman coalescent. In reality, many groups of organisms, including viruses, marine organisms, and some plants, protists, and fungi, typified by high variance in progeny number, may be best characterized by multiple-merger coalescent models. Estimation of population genetic parameters under Wright-Fisher assumptions for these organisms may thus be prone to serious mis-inference. We propose a novel method for the joint inference of demography and selection under the Ψ-coalescent model, termed Multiple-Merger Coalescent Approximate Bayesian Computation, or MMC-ABC. We first quantify mis-inference under the Kingman and then demonstrate the superior performance of MMC-ABC under conditions of skewed offspring distribution. In order to highlight the utility of this approach, we re-analyzed previously published drug-selection lines of influenza A virus. We jointly inferred the extent of progeny-skew inherent to viral replication and identified putative drug-resistance mutations.

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“…(2015) demonstrated that population growth may be distinguished from multiple-merger coalescent events owing to progeny-skew, given differing expectations in the SFS. Second, Matuszewski et al . (2018) derived analytical expectations for the SFS under a multiple merger coalescent model with changing population size and further demonstrated that these parameters can indeed be accurately inferred jointly within a likelihood framework.…”

Section: Introductionmentioning

confidence: 99%

Within-host Mycobacterium tuberculosis evolution: a population genetics perspective

Morales‐Arce

Harris

Stone

et al. 2019

Preprint

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12The within-host evolutionary dynamics of TB remain unclear, and underlying biological 13 characteristics render standard population genetic approaches based upon the Wright-Fisher 14 model largely inappropriate. In addition, the compact genome combined with an absence of 15 recombination is expected to result in strong purifying selection effects. Thus, it is imperative to 16 establish a biologically-relevant evolutionary framework incorporating these factors in order to 17 enable an accurate study of this important human pathogen. Further, such a model is critical for 18 inferring fundamental evolutionary parameters related to patient treatment, including mutation 19 rates and the severity of infection bottlenecks. We here implement such a model and infer the 20 underlying evolutionary parameters governing within-patient evolutionary dynamics. Results 21 demonstrate that the progeny skew associated with the clonal nature of TB severely reduces 22 polymorphic sites per patient genome-wide. In addition, the observed site frequency spectrum 56 (SFS) is generally characterized by an abundance of rare variants (i.e., it is strongly left-skewed). 57These patterns have partly led to the suggestion that purifying selection effects may be wide-58 spread in the M.TB genome (Brown et al. 2016; Phelan et al. 2016; Mortimer et al. 2018). 59 60 Additional evolutionary factors likely contribute to these genomic patterns as well. For 61 example, population bottlenecks may reduce genetic variation and alter the shape of the SFS 62 (see review Thornton et al. 2007). Previous M.TB studies have investigated these effects 63 3 separately in both the deep-time view of the population bottleneck and subsequent growth 64 experienced by the host human population (Hershberg et al. 2008, Liu et al. 2018, as well as the 65 shallow-time view of the population bottleneck and subsequent growth characterizing each novel 66 transmission event and treatment (e.g., Trauner et al. 2017). Additionally, in fitting the left-67 skewed SFS, Pepperell et al. (2013) found that such a demographic history combined with a mix 68 of both deleterious and neutrally-evolving sites produced the nearest fit to the observed SFS. 69Finally, given the lack of recombination in M.TB, related linkage effects (i.e., background 70 selection (Charlesworth et al. 1993)) have similarly been discussed within these contexts 71 (Pepperell et al. 2010; Copin et al. 2016). 72 73 While these studies have provided many important insights, there remains a relatively 74 unexplored, though potentially highly significant, effect: clonality. Indeed, clonality and the 75 related progeny distribution represents an important violation of commonly used evolutionary 76 inference approaches based upon the Wright-Fisher (WF) model and the related Kingman 77 coalescent (Eldon et al. 2006; Dos Vultos et al. 2008; Huillet et al. 2011; Lapierre et al. 2016). 78 Specifically, progeny distributions under the WF model are Poisson distributed with a mean and 79 variance of 1. Therefore, when an ind...

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Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography

Cited by 50 publications

References 74 publications

Cannings models, population size changes and multiple-merger coalescents

Cannings models, population size changes and multiple-merger coalescents

Inferring demography and selection in organisms characterized by skewed offspring distributions

Within-host Mycobacterium tuberculosis evolution: a population genetics perspective

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