Exploring the causes of small effective population sizes in cyst nematodes using artificial<i>Globodera pallida</i>populations

Montarry, Josselin; Bardou‐Valette, Sylvie; Mabon, Romain; Jan, Pierre‐Loup; Fournet, Sylvain; Grenier, Éric; Petit, Éric

doi:10.1098/rspb.2018.2359

Cited by 14 publications

(14 citation statements)

References 82 publications

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“…The intensity of genetic drift is still unknown for many plant parasites, but two recent studies have estimated the effective population size in cyst nematodes. Using H. schachtii populations from the wild (Jan et al, 2016) or using artificial G. pallida populations (Montarry et al, 2019), both studies highlighted very low effective population sizes, resulting in a strong intensity of genetic drift in these species. Therefore, both characteristics, gene flow due to the passive dispersal of cysts and strong genetic drift, could lead to the weak pattern of local adaptation we reported here.…”

Section: Discussionmentioning

confidence: 99%

Plant–parasite coevolution: A weak signature of local adaptation between Peruvian Globodera pallida populations and wild potatoes

Gautier

Fournet

Piriou

et al. 2020

Ecology and Evolution

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Plant–parasite coevolution has generated much interest and studies to understand and manage diseases in agriculture. Such a reciprocal evolutionary process could lead to a pattern of local adaptation between plants and parasites. Based on the phylogeography of each partner, the present study tested the hypothesis of local adaptation between the potato cyst nematode Globodera pallida and wild potatoes in Peru. The measured fitness trait was the hatching of cysts which is induced by host root exudates. Using a cross‐hatching assay between 13 populations of G. pallida and root exudates from 12 wild potatoes, our results did not show a strong pattern of local adaptation of the parasite but the sympatric combinations induced better hatching of cysts than allopatric combinations, and there was a negative relationship between the hatching percentage and the geographical distance between nematode populations and wild potatoes. Moreover, a strong effect of the geographic origin of root exudates was found, with root exudates from south of Peru inducing better hatching than root exudates from north of Peru. These results could be useful to develop new biocontrol products or potato cultivars to limit damages caused by G. pallida.

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Section: Discussionmentioning

confidence: 99%

Plant–parasite coevolution: A weak signature of local adaptation between Peruvian Globodera pallida populations and wild potatoes

Gautier

Fournet

Piriou

et al. 2020

Ecology and Evolution

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“…In this case, the amount and the direction of bias as well as the precision of estimates are highly dependent on life history traits, thus species‐specific, but also on the sampling fraction (Marandel et al, ; R. S. Waples et al, ). Other factors such as unequal sex ratio, high level of inbreeding and high variance in family sizes have also been found to bias N e estimates(Montarry et al, ).…”

Section: Introductionmentioning

confidence: 99%

“…Other factors such as unequal sex ratio, high level of inbreeding and high variance in family sizes have also been found to bias N e estimates (Montarry et al, 2019).…”

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confidence: 99%

Estimating effective population size using RADseq: Effects of SNP selection and sample size

Marandel

Charrier

Lamy

et al. 2020

Ecology and Evolution

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Effective population size (Ne) is a key parameter of population genetics. However, Ne remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site‐associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on Ne estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient FIS was positively correlated with the amount of missing data, implying data were missing nonrandomly. The precision of Neestimates decreased with the number of SNPs. Mean Ne estimates (averaged across 50 random data sets with2000 SNPs) ranged between 237 and 1784. Increasing the percentage of missing data from 25% to 50% increased Ne estimates between 82% and 120%, while increasing the minor allele frequency (MAF) threshold from 0.01 to 0.1 decreased estimates between 71% and 75%. Considering these effects is important when interpreting RADseq data‐derived estimates of effective population size in empirical studies.

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“…At this state, the avr allele cannot be selected, and variations in its frequency are only driven by genetic drift, which induces high stochasticity among replicates. This effect should be strengthened in species with small effective population sizes, such as in cyst nematodes (Gracianne et al 2016; Montarry et al 2019).…”

Section: Discussionmentioning

confidence: 99%

Impact of ploidy and pathogen life cycle on resistance durability

Saubin

Mita

Zhu

et al. 2021

Preprint

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The breeding of resistant hosts based on the gene-for-gene interaction is crucial to address epidemics of plant pathogens in agroecosystems. Resistant host deployment strategies are developed and studied worldwide to decrease the probability of resistance breakdown and increase the resistance durability in various pathosystems. A major component of deployment host strategies is the proportion of resistant hosts in the landscape. However, the impact of this proportion on resistance durability remains unclear for diploid pathogens with complex life cycles. In this study, we modelled pathogen population dynamics and genetic evolution at the virulence locus to assess the impact of the ploidy (haploid or diploid) and the pathogen's life cycle (with or without host alternation) on resistance durability. Ploidy has a strong impact on evolutionary trajectories, with much greater stochasticity and delayed times of resistance breakdown for diploids. This result emphasizes the importance of genetic drift in this system: as the virulent allele is recessive, positive selection on resistant hosts only applies to homozygous (virulent) individuals, which may lead to population collapses at low frequencies of the virulent allele. We also observed differences in the effect of host deployment depending on the pathogen's life cycle. With host alternation, the probability that the pathogen population collapses strongly increases with the proportion of resistant hosts in the landscape. Therefore, resistance breakdown events occurring at high proportions of resistant hosts frequently amount to evolutionary rescue. Last, life cycles correspond to two selection regimes: without host alternation (soft selection) the resistance breakdown is mainly driven by the migration rate. Conversely, host alternation (hard selection) resembles an all-or-nothing game, with stochastic trajectories caused by the recurrent allele redistributions on the alternate host.

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Exploring the causes of small effective population sizes in cyst nematodes using artificialGlobodera pallidapopulations

Cited by 14 publications

References 82 publications

Plant–parasite coevolution: A weak signature of local adaptation between Peruvian Globodera pallida populations and wild potatoes

Plant–parasite coevolution: A weak signature of local adaptation between Peruvian Globodera pallida populations and wild potatoes

Estimating effective population size using RADseq: Effects of SNP selection and sample size

Impact of ploidy and pathogen life cycle on resistance durability

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