Causes and consequences of large clonal assemblies in a poplar hybrid zone.

Asexual reproduction is a common and fundamental mode of reproduction in plants. Although persistence in adverse conditions underlies most known cases of clonal dominance, proximal genetic drivers remain unclear, in particular for populations dominated by a few large clones. In this paper, we studied a clonal population of the riparian tree Populus alba in the Douro river basin (northwestern Iberian Peninsula) where it hybridizes with P. tremula, a species that grows in highly contrasted ecological conditions. We used 73 nuclear microsatellites to test whether genomic background (species ancestry) is a relevant cause of clonal success, and to assess the evolutionary consequences of clonal dominance by a few genets. Additional Genotyping-by-Sequencing (GBS) data were produced to estimate the age of the largest clones. We found that a few ancient (over a few thousand years old) and widespread genets dominate the population, both in terms of clone size and number of sexual offspring produced. Interestingly, large clones possessed two genomic regions introgressed from P. tremula, which may have favored their spread under stressful environmental conditions. At the population level, the spread of large genets was accompanied by an overall ancient (>0.1 Myr) but soft decline of effective population size. Despite this decrease, and the high clonality and dominance of sexual reproduction by large clones, the Douro hybrid zone still displays considerable genetic diversity and low inbreeding. This suggests that, even in extreme cases as in the Douro, asexual and sexual dominance of a few large, geographically-extended individuals does not threaten population survival. This article is protected by copyright. All rights reserved

TECHNICAL NOTE - Single embryoid body formation in a multi-well plate

Embryoid bodies (EB) formed from murine embryonic stem (ES) cells recapitulate many aspects of a developing embryo. Of specific importance, synchronous differentiation of EB recapitulates organ-specific development and is achieved in culture by formation of uniformly sized EB. The method described here demonstrates a simple and cost-effective way of generating EB from murine ES cells. Single EB are formed in a multi-well plate format and large numbers of EB are generated using a 96-well multi-well plate. Uniform single-sized EB formed in the multi-well are an ideal system for screening compounds and determining differentiation effects. Since EB contain all three germ layers, they are appropriate for studying small molecule effects on differentiation of ES such as is performed in high-throughput screening protocols

A parentage study of closely related Ukrainian wine grape varieties using microsatellite markers

Four bred grapevine varieties released for commercial cultivation in Ukraine, namely ‘Antey Magarachskii’, ‘Rubinovyi Magaracha’, ‘Granatovyi Magaracha’ and ‘Rubin Golodrigi’, and their putative parental forms were genotyped using six microsatellite loci.Четыре селекционных сорта винограда Антей Магарачский, Рубиновый Магарача, Рубин Голодриги и Гранатовый Магарача, которые культивируются в Украине для приготовления сухих и крепленых вин, и их предполагаемые родительские формы были генотипированы с использованием шести микросателлитных локусов.Чотири селекційних сорти винограду Антей Магарацький, Рубіновий Магарача, Рубін Голодриги та Гранатовий Магарача, що культивують в Україні для приготування сухих і десертних вин, та їх потенційні батьківські форми були генотиповані з використанням шести мікросателітних локусів

Exploration et conservation des ressources génétiques du pin maritime au Maroc

Cet article présente une intéressante synthèse sur les ressources génétiques du pin maritime au Maroc, où il est fréquemment utilisé dans les reboisements. Cette espèce a fait l'objet d'un programme d'aménagement, d'amélioration et de conservation génétique depuis 1970. Cet article présente quelques résultats synthétiques sur la description et l'organisation des ressources génétiques du pin maritime au Maroc, ainsi que des données sur l'état de conservation de ces populations. Des informations utiles dans une optique de conservation des ressources génétiques

High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland

Nucleotide polymorphism at 12 nuclear loci was studied in Scots pine populations across an environmental gradient in Scotland, to evaluate the impacts of demographic history and selection on genetic diversity. At eight loci, diversity patterns were compared between Scottish and continental European populations. At these loci, a similar level of diversity (θsil=~0.01) was found in Scottish vs mainland European populations, contrary to expectations for recent colonization, however, less rapid decay of linkage disequilibrium was observed in the former (ρ=0.0086±0.0009, ρ=0.0245±0.0022, respectively). Scottish populations also showed a deficit of rare nucleotide variants (multi-locus Tajima's D=0.316 vs D=−0.379) and differed significantly from mainland populations in allelic frequency and/or haplotype structure at several loci. Within Scotland, western populations showed slightly reduced nucleotide diversity (πtot=0.0068) compared with those from the south and east (0.0079 and 0.0083, respectively) and about three times higher recombination to diversity ratio (ρ/θ=0.71 vs 0.15 and 0.18, respectively). By comparison with results from coalescent simulations, the observed allelic frequency spectrum in the western populations was compatible with a relatively recent bottleneck (0.00175 × 4Ne generations) that reduced the population to about 2% of the present size. However, heterogeneity in the allelic frequency distribution among geographical regions in Scotland suggests that subsequent admixture of populations with different demographic histories may also have played a role

Within-population genetic structure in beech (Fagus sylvatica L.) stands characterized by different disturbance histories: does forest management simplify population substructure?

The fine-scale assessment of both spatially and non-spatially distributed genetic variation is crucial to preserve forest genetic resources through appropriate forest management. Cryptic within-population genetic structure may be more common than previously thought in forest tree populations, which has strong implications for the potential of forests to adapt to environmental change. The present study was aimed at comparing within-population genetic structure in European beech (Fagus sylvatica L.) plots experiencing different disturbance levels. Five plot pairs made up by disturbed and undisturbed plots having the same biogeographic history were sampled throughout Europe. Overall, 1298 individuals were analyzed using four highly polymorphic nuclear microsatellite markers (SSRs). Bayesian clustering within plots identified 3 to 11 genetic clusters (within-plot hST ranged from 0.025 to 0.124). The proportion of within-population genetic variation due to genetic substructuring (FCluPlot = 0.067) was higher than the differentiation among the 10 plots (FPlotTot = 0.045). Focusing on the comparison between managed and unmanaged plots, disturbance mostly explains differences in the complexity of within-population genetic structure, determining a reduction of the number of genetic clusters present in a standardized area. Our results show that: i) genetic substructuring needs to be investigated when studying the within-population genetic structure in forest tree populations, and ii) indices describing subtle characteristics of the within-population genetic structure are good candidates for providing early signals of the consequences of forest management, and of disturbance events in general

Ancient and historical DNA in conservation policy

Although genetic diversity has been recognized as a key component of biodiversity since the first Convention on Biological Diversity (CBD) in 1993, it has rarely been included in conservation policies and regulations. Even less appreciated is the role that ancient and historical DNA (aDNA and hDNA, respectively) could play in unlocking the temporal dimension of genetic diversity, allowing key conservation issues to be resolved, including setting baselines for intraspecies genetic diversity, estimating changes in effective population size (N-e), and identifying the genealogical continuity of populations. Here, we discuss how genetic information from ancient and historical specimens can play a central role in preserving biodiversity and highlight specific conservation policies that could incorporate such data to help countries meet their CBD obligations.Peer reviewe

TRY plant trait database - enhanced coverage and open access

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Paternity analysis of pollen-mediated gene flow for Fraxinus excelsior L. in a chronically fragmented landscape

Paternity analysis based on microsatellite marker genotyping was used to infer contemporary genetic connectivity by pollen of three population remnants of the wind-pollinated, wind-dispersed tree Fraxinus excelsior, in a deforested Scottish landscape. By deterministically accounting for genotyping error and comparing a range of assignment methods, individual-based paternity assignments were used to derive population-level estimates of gene flow. Pollen immigration into a 300ha landscape represents between 43% and 68% of effective pollination, mostly depending on assignment method. Individual male reproductive success is unequal, with 31 of 48 trees fertilising one seed or more, but only three trees fertilising more than ten seeds. Spatial analysis suggests a fat-tailed pollen dispersal curve with 85% of detected pollination occurring within 100m, and 15% spreading between 300m and 1900m from the source. Identification of immigrating pollen sourced from two neighbouring remnants indicates further effective dispersal at 2900m. Pollen exchange among remnants is driven by population size rather than geographic distance, with larger remnants acting predominantly as pollen donors, and smaller remnants as pollen recipients. Enhanced wind dispersal of pollen in a barren landscape ensures that the seed produced within the catchment includes genetic material from a wide geographic area. However, gene flow estimates based on analysis of non-dispersed seeds were shown to underestimate realised gene immigration into the remnants by a factor of two suggesting that predictive landscape conservation requires integrated estimates of post-recruitment gene flow occurring via both pollen and seed