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ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps ArchiMer
Becheler, Ronan; Masson, Jean-pierre; Arnaud-haond, Sophie; Halkett, Fabien; Mariette, Stephanie; Guillemin, Marie-laure; Valero, Myriam; Destombe, Christophe; Stoeckel, Solenn.
Partial clonality is commonly used in Eukaryotes and has large consequences for their evolution and ecology. Assessing accurately the relative importance of clonal versus sexual reproduction matters for studying and managing such species. Here, we proposed a Bayesian approach, ClonEstiMate, to infer rates of clonality c from populations sampled twice over a short time interval, ideally one generation time. The method relies on the likelihood of the transitions between genotype frequencies of ancestral and descendent populations, using an extended Wright-Fisher model explicitly integrating reproductive modes. Our model provides posterior probability distribution of inferred c, given the assumed rates of mutation, as well as inbreeding and selfing when...
Tipo: Text Palavras-chave: Inbreeding; Instantaneous inference; Population genetics model; Rate of asexuality; Selfing.
Ano: 2017 URL: https://archimer.ifremer.fr/doc/00390/50187/50810.pdf
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Rare sex or out of reach equilibrium? The dynamics of F-IS in partially clonal organisms ArchiMer
Reichel, Katja; Masson, Jean-pierre; Malrieu, Florent; Arnaud-haond, Sophie; Stoeckel, Solenn.
Background: Partially clonal organisms are very common in nature, yet the influence of partial asexuality on the temporal dynamics of genetic diversity remains poorly understood. Mathematical models accounting for clonality predict deviations only for extremely rare sex and only towards mean inbreeding coefficient (F-IS) over bar < 0. Yet in partially clonal species, both F-IS < 0 and F-IS > 0 are frequently observed also in populations where there is evidence for a significant amount of sexual reproduction. Here, we studied the joint effects of partial clonality, mutation and genetic drift with a state-and-time discrete Markov chain model to describe the dynamics of F-IS over time under increasing rates of clonality. Results: Results of the...
Tipo: Text Palavras-chave: Partial asexuality; Parthenogenesis; Mating system; Inbreeding coefficient; Heterozygote excess; Genetic diversity.
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00344/45474/45019.pdf
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The Combined Effect of Haplodiplonty and Partial Clonality on Genotypic and Genetic Diversity in a Finite Mutating Population ArchiMer
Stoeckel, Solenn; Arnaud-haond, Sophie; Krueger-hadfield, Stacy A; Orive, Maria.
Partial clonality is known to affect the genetic composition and evolutionary trajectory of diplontic (single, free-living diploid stage) populations. However, many partially clonal eukaryotes exhibit life cycles in which somatic development occurs in both haploid and diploid individuals (haplodiplontic life cycles). Here, we studied how haplodiplontic life cycles and partial clonality structurally constrain, as immutable parameters, the reshuffling of genetic diversity and its dynamics in populations over generations. We assessed the distribution of common population genetic indices at different proportions of haploids, rates of clonality, mutation rates, and sampling efforts. Our results showed that haplodiplontic life cycles alone in finite populations...
Tipo: Text Palavras-chave: Mating system; Asexuality; Genetic and genotypic diversity; Life cycle; Linkage disequilibrium; FIS.
Ano: 2021 URL: https://archimer.ifremer.fr/doc/00684/79593/82282.pdf
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