In the light of evolution IX: Clonal reproduction: Alternatives to sex

Tibayrenc, Michel; Avise, John C.; Ayala, Francisco J.

doi:10.1073/pnas.1508087112

Cited by 10 publications

(8 citation statements)

References 24 publications

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“…The hemiclonality should be viewed as an evolutionary destination with a positive effect on species continuum. Species with clonal traits are increasingly being identified in different kinds of living organisms (Neaves and Baumann, 2011) and clonal biology has recently gained a great momentum in several laboratories considering the adaptive potential of clonal organisms in extreme environments (Johnson et al, 2010; Klimesova and Pysek, 2011; Tibayrenc et al, 2015). It may be possible that, when genetic recombination becomes at a premium due to the genetic constraints imparted by ecological and climatic factors such as habitat fragmentation or global warming, plants may trigger asexual methods in order to carefully preserve genotypes with adaptive fitness.…”

Section: Resultsmentioning

confidence: 99%

Analyses between Reproductive Behavior, Genetic Diversity and Pythium Responsiveness in Zingiber spp. Reveal an Adaptive Significance for Hemiclonality

et al. 2016

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Mode of reproduction is generally considered to have long-range evolutionary implications on population survival. Because sexual reproduction produces genetically diverse genotypes, this mode of reproduction is predicted to positively influence the success potential of offspring in evolutionary arms race with parasites (Red queen) whereas, without segregation and recombination, the obligate asexual multiplication may push a species into extinction due to the steady accumulation of deleterious mutations (Muller’s ratchet). However, the extent of linearity between reproductive strategies, genetic diversity and population fitness, and the contributions of different breeding strategies to population fitness are yet to be understood clearly. Genus Zingiber belonging to the pan-tropic family Zingiberaceae represents a good system to study contributions of different breeding behavior on genetic diversity and population fitness, as this genus comprises species with contrasting breeding systems. In this study, we analyzed breeding behavior, amplified fragment length polymorphism diversity and response to the soft-rot pathogen Pythium aphanidermatum in 18 natural populations of three wild Zingiber spp.: Z. neesanum, Z. nimmonii, and Z. zerumbet, together with the obligately asexual cultivated congener, ginger (Z. officinale). Ginger showed an exceptionally narrow genetic base, and adding to this, all the tested cultivars were uniformly susceptible to soft-rot. Concordant with the postulates of Muller’s ratchet, the background selection may be continuously pushing ginger into the ancestral state, rendering it inefficient in host-pathogen coevolution. Z. neesanum and Z. nimmonii populations were sexual and genetically diverse; however, contrary to Red Queen expectations, the populations were highly susceptible to soft-rot. Z. zerumbet showed a hemiclonal breeding behavior. The populations inhabiting forest understory were large and continuous, sexual and genetically diverse, but were susceptible, whereas populations inhabiting the revenue land were fragmented and monoclonal, but were resistant. It may be possible that, when genetic recombination becomes at a premium due to the genetic constraints imparted by habitat fragmentation or pathogen pressure, Z. zerumbet

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Section: Resultsmentioning

confidence: 99%

Analyses between Reproductive Behavior, Genetic Diversity and Pythium Responsiveness in Zingiber spp. Reveal an Adaptive Significance for Hemiclonality

et al. 2016

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“…Due to its impact on taxonomy and epidemiology of bacterial, viral and eukaryotic pathogens, understanding parasite population structure(s) has been the subject of intense research and controversy (Ramírez and Llewellyn, 2014;Tibayrenc et al, 2015). It should be recalled that clonality does not imply a lack of recombination, but rather a strongly restrained recombination on an evolutionary scale, and that the main consequences of clonality on pathogen population structure are linkage disequilibrium and stable genetic clustering (Tibayrenc et al, 2015). What could be the advantage of clonality for D. fragilis?…”

Section: Discussionmentioning

confidence: 99%

Multilocus sequence typing of Dientamoeba fragilis identified a major clone with widespread geographical distribution

Cacciò

Sannella

Bruno

et al. 2016

International Journal for Parasitology

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The flagellated protozoan Dientamoeba fragilis is often detected in humans with gastrointestinal symptoms, but it is also commonly found in healthy subjects. As for other intestinal protozoa, the hypothesis that genetically dissimilar parasite isolates differ in their ability to cause symptoms has also been raised for D. fragilis. To date, only two D. fragilis genotypes (1 and 2) have been described, of which genotype 1 largely predominates worldwide. However, very few markers are available for genotyping studies and therefore the extent of genetic variation among isolates remains largely unknown. Here, we performed metagenomics experiments on two D. fragilis-positive stool samples, and identified a number of candidate markers based on sequence similarity to the phylogenetically related species Trichomonas vaginalis. Markers corresponding to structural genes and to genes encoding for proteases were selected for this study, and PCR experiments confirmed their belonging to the D. fragilis genome; two previously described markers (small subunit ribosomal DNA and large subunit of RNA polymerase II) were also included. Using this panel of markers, 111 isolates of human origin were genotyped, all of which, except one, belonged to genotype 1. These isolates had been collected at different times from symptomatic and asymptomatic persons of different age groups in Italy, Denmark, Brazil and Australia. By sequencing approximately 160kb from 500 PCR products, a very low level of polymorphism was observed across all the investigated loci, suggesting the existence of a major clone of D. fragilis with a widespread geographical distribution.

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“…Clonality occurs across the entire tree of life, including all kingdoms of Eukaryota (Avise & Nicholson, 2008; Schön et al, 2009; Tibayrenc et al, 2015). Most, if not all, clonal eukaryotic species alternate between clonal and sexual reproduction at the population scale over a few generations (see Box 1 for the definitions used in this work).…”

Section: Introductionmentioning

confidence: 99%

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

Stoeckel

Porro

Arnaud‐Haond

2021

Molecular Ecology Resources

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Partial clonality is widespread across the tree of life, but most population genetic 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 genetic 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 genetic 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 genetic data.

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In the light of evolution IX: Clonal reproduction: Alternatives to sex

Cited by 10 publications

References 24 publications

Analyses between Reproductive Behavior, Genetic Diversity and Pythium Responsiveness in Zingiber spp. Reveal an Adaptive Significance for Hemiclonality

Analyses between Reproductive Behavior, Genetic Diversity and Pythium Responsiveness in Zingiber spp. Reveal an Adaptive Significance for Hemiclonality

Multilocus sequence typing of Dientamoeba fragilis identified a major clone with widespread geographical distribution

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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