Gene flow as a simple cause for an excess of high‐frequency‐derived alleles

Marchi, Nina; Excoffier, Laurent

doi:10.1111/eva.12998

Cited by 16 publications

(14 citation statements)

References 129 publications

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“…The site frequency spectra estimated in populations G1 and T were U-shaped, indicating an excess of high-frequency derived alleles (Figure 2; population G2 was excluded because of too small a sample size), consistent with ongoing episodes of positive selection, mis-assignment of ancestral alleles or gene flow (Marchi & Excoffier 2020). Estimates of Tajima’s D were positive but close to zero in clusters T and G1 (T: D=0.309; G1: D=0.167), indicating a slight deficit of low frequency variants (Table 2; Supplementary Table 2), consistent with balancing selection or population contraction.…”

Section: Resultsmentioning

confidence: 81%

Population Genomics Reveals Molecular Determinants of Specialization to Tomato in the Polyphagous Fungal PathogenBotrytis cinereain France

Mercier

Simon

Lapalu

et al. 2020

Preprint

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Many fungal plant pathogens encompass multiple populations specialized on different plant species. Understanding the factors underlying pathogen adaptation to their hosts is a major challenge of evolutionary microbiology, and it should help preventing the emergence of new specialized pathogens on novel hosts. Previous studies have shown that French populations of the grey mould pathogen Botrytis cinerea parasitizing tomato and grapevine are differentiated from each other, and have higher aggressiveness on their host-of-origin than on other hosts, indicating some degree of host specialization in this polyphagous pathogen. Here, we aimed at identifying the genomic features underlying the specialization of B. cinerea populations to tomato and grapevine. Based on whole genome sequences of 32 isolates, we confirmed the subdivision of B. cinerea pathogens into two genetic clusters on grapevine and another, single cluster on tomato. Levels of genetic variation in the different clusters were similar, suggesting that the tomato-specific cluster has not recently emerged following a bottleneck. Using genome scans for selective sweeps and divergent selection, tests of positive selection based on polymorphism and divergence at synonymous and non-synonymous sites and analyses of presence/absence variation, we identified several candidate genes that represent possible determinants of host specialization in the tomato-associated population. This work deepens our understanding of the genomic changes underlying the specialization of fungal pathogen populations.

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Section: Resultsmentioning

confidence: 81%

Population Genomics Reveals Molecular Determinants of Specialization to Tomato in the Polyphagous Fungal PathogenBotrytis cinereain France

Mercier

Simon

Lapalu

et al. 2020

Preprint

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“…Second, to explore population structure, we performed a PCA analysis of all datasets, followed by a k -means clustering (results in Table H in S1 Appendix ). We acknowledge the possibility that unsampled “ghost” demes can exist and could potentially result in U-shaped SFS [ 10 ], and that some cases of metapopulation dynamics results in MMC trees [ 41 , 42 ]. Assessing the presence of ghost demes from genetic data is challenging.…”

Section: Discussionmentioning

confidence: 99%

“…Many possible factors may result in such a pattern of variation. These include recent migration from non-sampled populations [ 10 ], population structure [ 11 ], misorientation of ancestral and derived alleles [ 12 ], biased gene conversion [ 13 ], recent positive selection at many targets across the genome [ 14 ], background selection [ 15 , 16 ], temporally-fluctuating selection [ 17 ], and various reproductive strategies [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

Interpreting the pervasive observation of U-shaped Site Frequency Spectra

Freund

Kerdoncuff

Matuszewski³

et al. 2023

PLoS Genet

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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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“…Many possible factors may result in such a pattern of variation. These include recent migration from non-sampled populations [ME20], population structure [LBL + 16], misorientation of ancestral and derived alleles [BD03], biased gene conversion [PATE18], recent positive selection at many targets across the genome [BWSH01], background selection [CGD18], [JCJ20], temporally-fluctuating selection [HSDB08], and various reproductive strategies [TL14].…”

Section: Introductionmentioning

confidence: 99%