Longitudinal clines in the frequency distribution of ‘super-clones’ in an aphid crop pest

Gilabert, Aude; Dedryver, C. A.; Stoeckel, Solenn; Plantegenest, Manuel; Simon, Jean‐Christophe

doi:10.1017/s0007485315000619

Cited by 13 publications

(17 citation statements)

References 43 publications

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“…In fact, departure from HWE in this study confirms the complementarity of genotypic and genetic parameters by supporting the prevalence of clonal reproduction across the cycle, with mean FIS values of -0.21 and -0.24 in the earlier and later season, respectively, suggesting a more important influence of clonality in the later season, with a lower mean and larger variance. Similar patterns have been found in multiple studies on cyclical parthenogenetic species (e.g., Gilabert et al, 2015;Loxdale et al 2011). Another example is a highly clonal root-sucking nematode, Xiphinema index, which shows mid-range R values (0.16 to 0.39); however, negative mean FIS values with large variance in agreement with LD values suggest a rates of clonality exceeding 0.95 in all these populations, which had better agree with a naturalistic knowledge (Villate et al 2010).…”

Section: Quantifying Clonality or Merely Evaluating Its Extent: How Wsupporting

confidence: 83%

The discernible and hidden effects of clonality on the genotypic and genetic states of populations: improving our estimation of clonal rates

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Partial clonality is widespread across the tree of life, but most population genetics models are designed for exclusively clonal or sexual organisms. This gap hampers our understanding of the influence of clonality on evolutionary trajectories and the interpretation of population genetics data. We performed forward simulations of diploid populations at increasing rates of clonality (c), analysed their relationships with genotypic (clonal richness, R, and distribution of clonal sizes, Pareto β) and genetic (FIS and linkage disequilibrium) indices, and tested predictions of c from population genetics data through supervised machine learning. Two complementary behaviours emerged from the probability distributions of genotypic and genetic indices with increasing c. While the impact of c on R and Pareto β was easily described by simple mathematical equations, its effects on genetic indices were noticeable only at the highest levels (c>0.95). Consequently, genotypic indices allowed reliable estimates of c, while genetic descriptors led to poorer performances when c<0.95. These results provide clear baseline expectations for genotypic and genetic diversity and dynamics under partial clonality.Worryingly, however, the use of realistic sample sizes to acquire empirical data systematically led to gross underestimates (often of one to two orders of magnitude) of c, suggesting that many interpretations hitherto proposed in the literature, mostly based on genotypic richness, should be reappraised. We propose future avenues to derive realistic confidence intervals for c and show that, although still approximate, a supervised learning method would greatly improve the estimation of c from population genetics data.

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Section: Quantifying Clonality or Merely Evaluating Its Extent: How Wsupporting

confidence: 83%

The discernible and hidden effects of clonality on the genotypic and genetic states of populations: improving our estimation of clonal rates

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“…Aphid populations are sometimes composed of a small number of dominant clones and many rare genotypes (Harrison and Mondor, 2011). “Superclones” are highly abundant clones distributed over a large geographical scale and persisting over time (Gilabert et al, 2015). The combination of asexual reproduction and high reproduction rates in aphids can lead to superclones (Piffaretti et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

Microsatellite Markers Reveal a Predominant Sugarcane Aphid (Homoptera: Aphididae) Clone is Found on Sorghum in Seven States and One Territory of the USA

Harris‐Shultz

Wadl

et al. 2017

Crop Science

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The sugarcane aphid (Melanaphis sacchari) has become a serious pest causing severe economic losses to sorghum [Sorghum bicolor (L.) Moench] grown in the southern United States. Since its original detection in four states in 2013, M. sacchari on sorghum has now, in 2016, spread to 19 states. The presence of one or multiple genotypes on sorghum in the United States has not yet been established. In this study, genome sequencing of M. sacchari was used to develop microsatellite markers. A total of 8,665,267 reads and 1.44 Gb of nucleotide sequences were generated, and 79.6% of the reads were from M. sacchari. Melanaphis sacchari DNA from 46 samples from 17 locations across seven states and one US territory was polymerase chain reaction (PCR) amplified using 38 newly created microsatellite markers, as well as 14 published microsatellite markers. Genotyping with the 52 microsatellite markers indicated that the samples of M. sacchari on sorghum were all one genotype, with the exception of a single sample collected from Sinton, TX, which had the predominant genotype as well as another genotype. Genotyping of the aphid samples with 12 microsatellite markers for Buchnera aphidicola, the obligate aphid symbiont, had nearly identical results. The invasive M. sacchari on sorghum appears to be spreading in the United States on sorghum as primarily one asexual clone.

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“…Although migration appears to be the main driver of the genetic distribution, the selection is also a relevant force that shapes the distribution of the different genotypes (e.g. Kasprowicz et al, 2008;Gilabert et al, 2015). Understanding the processes underlying the genetic distribution of aphids will allow us to monitor them better.…”

Section: Understanding the Distribution Dynamics Of Insect Pestsmentioning

confidence: 99%

Molecular ecology of insect pests of agricultural importance: the case of aphids

Morales‐Hojas

2017

Ecological Entomology

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Abstract. 1. Ongoing environmental change is predicted to have a strong impact on biodiversity. Studies have already noted a range shift in many species as they track their favoured environments. A key challenge entomologists are facing is to understand how insect pest species are responding to this rapid environmental change, and molecular ecology has a central role to play in this task. In the present paper, I argue that molecular ecology has much relevance in relation to the monitoring of insect pests of agricultural importance, with a focus on aphids.2. First, I examine how the combination of phylogeography and species distribution modelling can be a powerful approach to understanding species responses to climate change and to forecasting future distributions. Despite such a joint approach being increasingly used to understand these questions (e.g. in conservation biology), there are still very few studies that concern pest species of agricultural importance.3. I then discuss how the use of samples from natural history collections represent an opportunity to directly observe the evolution of species, enhancing our knowledge of the evolutionary processes occurring at ecological time scales. I introduce the Rothamsted Insect Survey (RIS) sample archive and the central role it plays in the studies of pest species of agricultural importance.4. Lastly, I assess how the advances in DNA sequencing technologies have allowed us to investigate genetic variation at the genome-wide level. Thus, they provide us with the opportunity of studying a variety of questions about the dynamics of pest insects that were previously impossible as well as unmanageable.

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Longitudinal clines in the frequency distribution of ‘super-clones’ in an aphid crop pest

Cited by 13 publications

References 43 publications

The discernible and hidden effects of clonality on the genotypic and genetic states of populations: improving our estimation of clonal rates

The discernible and hidden effects of clonality on the genotypic and genetic states of populations: improving our estimation of clonal rates

Microsatellite Markers Reveal a Predominant Sugarcane Aphid (Homoptera: Aphididae) Clone is Found on Sorghum in Seven States and One Territory of the USA

Molecular ecology of insect pests of agricultural importance: the case of aphids

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