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  • 5 years programme (2012-2016)
  • 364 k€. For IGEPP & Workpackage 3, Solenn Stoeckel (108 k€)
  • Coordinator: Sophie Arnaud-Haond, Ifremer. For Igepp, Solenn Stoeckel.
  • Partners: Ifremer Brest-Sète; IAM, INRA Nancy; CNRS-UPMC Roscoff.
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Revisiting the Population Genetics and Genomics of partially clonal organisms. Influence of partial clonality on the genetic composition and evolution of natural populations Adapting population Genetics concepts and methods to partial clonality.

1. Assessing the influence of partial clonality on the genetic composition of populations of partially clonal organisms and their evolutionary trajectories.

The partial asexuality features a wide variety of organisms across the Tree of Life. Understanding their evolution and dynamics requires a good appraisal of the extent and influence of clonality versus sexual reproduction. Models hitherto available in population genetics are mainly developed for exclusively sexual, or for purely clonal organismss. Yet partial asexuals include species structuring many terrestrial and marine ecosystems, including most photosynthetic species, many human pathogens, crop or cattle pests, and a large number of invasive species. Societal issues are thus important and numerous. Clonix consortium aims at contributing to a better prediction of the consequences of clonality on the genetic structure of populations in a variety of evolutionary scenarios, in order to develop reliable inference methods of the clonal rate, c. The goal is twofold: improve the understanding of the influence of c on the clonal (i.e. genotypic) and genetic composition and thus the evolutionary trajectory of populations, and in return, develop a methodological framework that to reliably infer c from data empirical.

2. Understand the influence of partial clonality and in return, estimate its rate : models , simulations and re-analysis of empirical data sets

The core of the project is the development of analytical and predictive tools to assess the influence of clonal reproduction on the clonal (i.e. genotypic) and genetic composition of populations, and estimators conventionally used to describe it. Mathematical models and simulations are developed to describe the influence of clonality at increasing rates, and in return to compare the relevance of analytical approaches based on discrimination of clonal lineages versus genetic based approaches to estimate its rate. This step allows a radical improvement in the analysis and interpretation of empirical data. The spatial component will also be taken into account to understand the effect of the clonality on dispersal in different demographic contexts. Ultimately, the goal is to deliver analytical tools (computer programs for data analysis and simulation tools) and to test them with the diversity of datasets of Clonix partners to propose new expectations of genotypic and genetic composition under the assumption of clonality, in order to enhance our understanding of the ecological dynamics and evolutionary trajectories in partially clonal populations.


The models and simulations Clonix allowed exploring, beyond the expected equilibrium state, the evolutionary trajectories toward this state. These have shown to be so slowed by clonality that it is unrealistic to expect equilibrium state in most cases. Thus, the partial clonality profoundly affects not only the clonal structure (repeated genotypes), but also the genetic composition of populations and their evolutionary path in different demographic contexts (i.e. bottlenecks ). Although genotypic parameters remain the most relevants, genetic parameters can therefore also contribute increasing the accuracy of the estimates of clonal rates.


Improvements are planned in the coming months because the amount of information produced could still not be valorized published entirely. In view of the first empirical data analyzes interpreted in light of these theoretical advances, a clear gain is obtained in terms of understanding of the ecological and evolutionary dynamics of partially clonal species and the estimate of the rate of clonality in natural populations. However, it also appears that improvements are still necessary in order to take into account the considerable bias introduced by sampling still part of natural populations in the estimation of clonal rates. Amon other, the emergence of large scale genome scan data through NGS may contribute unlocking this still important issue.

Scientific outputs and patents

A total of 18 scientific articles have been published and nearly ten are being written. The consortium contributed to 14 communication in national or international events, produced 3 softwares for data analysis (Edenetwork, RClone et Cloneestimate), one mathematical model (Pasex) and three simulation routines (SimuClone for ‘simple’ partial asexuality, and two routines for cyclical parthenogenesis). A website was opened to disclose the main results of the consortium, that will keep on being maintained for the next few years (