Genealogical structure changes as range expansions transition from pushed to pulled

Birzu, Gabriel; Hallatschek, Oskar; Korolev, Kirill S.

doi:10.1073/pnas.2026746118

Cited by 13 publications

(12 citation statements)

References 84 publications

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“…Long-distance dispersal events are capable of breaking down these regional patterns and maintaining local diversity, though the behavior of these systems is dependent on the extent of long-distance dispersal, i.e., the tails of the dispersal kernel [ 65 ]. The offspring distribution of alleles at the wave front is also overdispersed due to the occurrence of these chance events, violating the assumptions of standard population genetics models (see [ 66 , 67 ] for recent work in this area). Allele surfing dynamics are potentially relevant to quickly expanding viral populations, such as SARS-CoV-2 VOCs [ 68 , 69 ], and introduce further complexities to the interpretation of mutation frequency data.…”

Section: Complications In Adaptive Evolution: Spatially Heterogeneous...mentioning

confidence: 99%

Population genetic models for the spatial spread of adaptive variants: A review in light of SARS-CoV-2 evolution

Steiner

Novembre²

2022

PLoS Genet

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Theoretical population genetics has long studied the arrival and geographic spread of adaptive variants through the analysis of mathematical models of dispersal and natural selection. These models take on a renewed interest in the context of the COVID-19 pandemic, especially given the consequences that novel adaptive variants have had on the course of the pandemic as they have spread through global populations. Here, we review theoretical models for the spatial spread of adaptive variants and identify areas to be improved in future work, toward a better understanding of variants of concern in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) evolution and other contemporary applications. As we describe, characteristics of pandemics such as COVID-19—such as the impact of long-distance travel patterns and the overdispersion of lineages due to superspreading events—suggest new directions for improving upon existing population genetic models.

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Section: Complications In Adaptive Evolution: Spatially Heterogeneous...mentioning

confidence: 99%

Population genetic models for the spatial spread of adaptive variants: A review in light of SARS-CoV-2 evolution

Steiner

Novembre²

2022

PLoS Genet

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“…Intricate phase transitions in front propagations have been observed in previous works [5,33,42,20]. One interesting example is a population whose large scale behavior is described by the noisy F-KPP equation with Allee effect [4,5]…”

Section: Pushed and Pulled Wavesmentioning

confidence: 71%

Relative vs absolute fitness in a population genetics model. How stronger selection may promote genetic diversity

Schertzer¹,

Wences²

2023

Preprint

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Since the foundation of population genetics, it is believed that directional selection should reduce genetic diversity. We present an exactly solvable population model which contradicts this intuition. The population is modelled as a cloud of particles evolving in a 1-dimensional fitness space (fitness wave). We show the existence of a phase transition which separates the parameter space into a weak and a strong selection regimes. We find that genetic diversity is highly non-monotone in the selection strength and, in contrast with the common intuition, our model predicts that genetic diversity is typically higher in the strong selection regime. This apparent paradox is resolved by observing that a higher selection strength increases the absolute fitness of the wave, but typically generate lower relative fitness between individuals within the wave. These findings entail that inferring the magnitude of natural selection from genetic data may raise some serious conceptual issues.Along the way, we uncover a new phase transition in front propagation. Namely, we show that the transition from weak to strong selection can be reformulated in terms of a transition from fully-pulled to semi-pulled waves. This transition is the pulled analog to the semi-pushed to fully-pushed regimes observed in noisy-FKPP travelling waves in the presence of Allee effect.

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“…a slight variant of it) emerges in a variety of models with rapid selection [BD13, NH13, DWF13, BBS13, Sch17]. The Beta-coalescent has also been associated with range expansions [BHK21]. In addition, Psi n -coalescents have been successfully used as proxy models for detecting regions experiencing positive selection [HJ20].…”

Section: Discussionmentioning

confidence: 99%

“…[BD13, NH13, DWF13, BBS13, Sch17]. Importantly, other biological factors can also lead to MMC-like genealogies, including large rapid demographic deviations [BBM + 09], seed banks [CCSWB22], extinction-recolonisation in metapopulations [TV09] and range expansions [BHK21]. Yet, the frequency of MMC genealogies in nature, and more generally whether MMC models ought to be employed as a more appropriate null for certain species, remains an open question.…”

Section: Introductionmentioning

confidence: 99%

Interpreting the pervasive observation of U-shaped Site Frequency Spectra

Freund

Kerdoncuff

Matuszewski³

et al. 2022

Preprint

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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.

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Genealogical structure changes as range expansions transition from pushed to pulled

Cited by 13 publications

References 84 publications

Population genetic models for the spatial spread of adaptive variants: A review in light of SARS-CoV-2 evolution

Population genetic models for the spatial spread of adaptive variants: A review in light of SARS-CoV-2 evolution

Relative vs absolute fitness in a population genetics model. How stronger selection may promote genetic diversity

Interpreting the pervasive observation of U-shaped Site Frequency Spectra

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