2017 

Hillen, J. E. J., et al. "Estimates of genetic variability and inbreeding in experimentally selected populations of European sea bass." Aquaculture. 479 (2017): 742–749.
Résumé: The aquaculture industry has increasingly aimed at improving economically important traits like growth, feed efficiency and resistance to infections. Artificial selection represents an important window of opportunity to significantly improve production. However, the pitfall is that selection will reduce genetic diversity and increase inbreeding in the farmed stocks. Genetic tools are very useful in this context as they provide accurate measures of genetic diversity together with many additional insights in the stock status and the selection process. In this study we assessed the level of genetic variability and relatedness over several generations of two lines of experimentally selected European sea bass (Dicentrarchus labrax L.). The first line was selected for growth over three generations and the second line for both high and low weight loss under a starvation regime over two generations. We used a genomic approach (2549 single nucleotide polymorphism markers derived from double digest restriction site associated DNA sequencing) in combination with eight microsatellites to estimate genetic variation, relatedness, effective population size and genetic differentiation across generations. Individual heterozygosity estimates indicated that the selected lines showed no significant reduction in diversity compared with wild populations. There was, however, a decreasing trend in allelic richness, suggesting the loss of low frequency alleles. We compared the estimates of effective population size from genetic markers with pedigree information and found good correspondence between methods. This study provides important insights in the genetic consequences of selective breeding and demonstrates the operational use of the latest genomic tools to estimate variability, inbreeding and at a later stage domestication and artificial selection.
MotsClés: Artificial selection; ddRAD; fish; genetic diversity; Genomics; Inbreeding


2016 

Reichel, K., et al. "Rare sex or out of reach equilibrium? The dynamics of FIS in partially clonal organisms." BMC Genet.. 17 (2016): 76.
Résumé: 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 (FIS) over bar < 0. Yet in partially clonal species, both FIS < 0 and FIS > 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 stateandtime discrete Markov chain model to describe the dynamics of FIS over time under increasing rates of clonality. Results: Results of the mathematical model and simulations show that partial clonality slows down the asymptotic convergence to FIS = 0. Thus, although clonality alone does not lead to departures from HardyWeinberg expectations once reached the final equilibrium state, both negative and positive FIS values can arise transiently even at intermediate rates of clonality. More importantly, such “transient” departures from Hardy Weinberg proportions may last long as clonality tunes up the temporal variation of FIS and reduces its rate of change over time, leading to a hyperbolic increase of the maximal time needed to reach the final mean (FIS,Finfinity) over bar value expected at equilibrium. Conclusion: Our results argue for a dynamical interpretation of FIS in clonal populations. Negative values cannot be interpreted as unequivocal evidence for extremely scarce sex but also as intermediate rates of clonality in finite populations. Complementary observations (e.g. frequency distribution of multiloci genotypes, population history) or time series data may help to discriminate between different possible conclusions on the extent of clonality when mean (FIS) over bar values deviating from zero and/or a large variation of FIS over loci are observed.
