Estimating effective population size of large marine populations,is it feasible?

Sustainable exploitation of marine populations is a challenging task relying on information about their current and past abundance. Fisheries‐related data can be scarce and unreliable making them unsuitable for quantitative modelling. One fishery independent method that has attracted attention in this context consists in estimating the effective population size (N_e), a concept founded in population genetics. We reviewed recent empirical studies on N_e and carried out a simulation study to evaluate the feasibility of estimating N_e in large fish populations with the currently available methods. The detailed review of 26 studies found that published empirical N_e values were very similar despite differences in species and total population sizes (N). Genetic simulations for an age‐structured fish population were carried out for a range of population and samples sizes, and N_e was estimated using the Linkage Disequilibrium method. The results showed that already for medium‐sized populations (1 million individuals) and common sample sizes (50 individuals), negative estimates were likely to occur which for real applications is commonly interpreted as indicating very large (infinite) N_e. Moreover, on average, N_e estimates were negatively biased. The simulations further indicated that around 1% of the total number of individuals might have to be sampled to ensure sufficiently precise estimates of N_e. For large marine populations, this implies rather large samples (several thousands to millions of individuals). If however such large samples were to be collected, many more population parameters than only N_e could be estimated.     

Quantitative resistance to Plum pox virus in Prunus davidiana P1908 linked to components of the eukaryotic translation initiation complex

A complex, polygenic resistance to Plum pox virus (PPV) was previously described in a wild peach-related species, Prunus davidiana clone P1908. In the current study, an analysis of quantitative trait loci (QTL) was performed on an F₂ population comprising 99 individuals obtained by selfing the F₁ individual #40 of an interspecific cross between susceptible nectarine cv. Summergrand and the resistant P. davidiana clone P1908. Six QTL were identified using both parametric and non-parametric methods of detection, individually explaining 5–28% of the phenotypic variance. The total phenotypic variation explained ranged from 29 to 58%. Alignment of the genetic map of the F₂ cross with the P. davidiana parent map showed consistency of QTL over generations, with three of the six QTL co-localizing at the 1-LOD interval and another one at the 2-LOD interval. Two of the QTL were mapped onto linkage group one, where resistance to PPV was previously mapped in apricot. Development and mapping of new microsatellite markers linked to candidate genes revealed a striking co-localization of three of the detected QTL with gene copies coding for eukaryotic translation initiation factors eIF4E and eIF(iso)4G. As co-localization of one QTL with candidate gene eIF(iso)4E was previously reported in the F₁ population, the results reported here strongly reinforce the idea that components of the eukaryotic translation initiation complex are correlated with resistance to PPV in P. davidiana P1908.     

Determining long‐term changes in a skate assemblage with aggregated landings and limited species data

Sustainable fisheries management requires assessment of exploited populations and communities. Traditional fisheries stock assessment methods need species‐specific input data, which for skates have only recently become available in Europe. To overcome this limitation, a Bayesian multispecies biomass production model was developed. In addition to aggregated landings, input data are short time series with species‐specific information (landings and biomass indices). Applying the approach to four main skate species and a group of two skate species, all managed together in the Bay of Biscay (Northeast Atlantic), long‐term changes in the skate assemblage composition were identified. Since the 1990s, Leucoraja naevus became increasingly dominant, while the contributions of the other three species (Raja brachyura, Raja clavata and Raja montagui) declined. The abundance of the grouped Leucoraja fullonica and L. circularis has also strongly decreased, suggesting long‐term overexploitation. All species except this species group are expected to increase over the next decade under current harvest rates. Currently, the species considered here are managed under a single fishing quota making it unlikely that the group of the two most depleted species will recover soon. The multispecies modelling approach bears promise for other harvested assemblages for which only grouped harvest information is available for certain periods.