@article {162, title = {Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus}, journal = {Systematics and BiodiversitySystematics and Biodiversity}, year = {2014}, pages = {1-19}, publisher = {Taylor \& Francis}, abstract = {Phylogenetic relationships among 108 oak species (genus Quercus L.) were inferred using DNA sequences of six nuclear genes selected from the existing genomic resources of the genus. Previous phylogenetic reconstructions based on traditional molecular markers are inconclusive at the deeper nodes. Overall, weak phylogenetic signals were obtained for each individual gene analysis, but stronger signals were obtained when gene sequences were concatenated. Our data support the recognition of six major intrageneric groups Cyclobalanopsis, Cerris, Ilex, Quercus, Lobatae and Protobalanus. Our analyses provide resolution at deeper nodes but with moderate support and a more robust infrageneric classification within the two major clades, the ?Old World Oaks? (Cyclobalanopsis, Cerris, Ilex) and ?New World Oaks? (Quercus, Lobatae, Protobalanus). However, depending on outgroup choice, our analysis yielded two alternative placements of the Cyclobalanopsis clade within the genus Quercus. When Castanea Mill. was chosen as outgroup, our data suggested that the genus Quercus comprised two clades corresponding to two subgenera as traditionally recognized by Camus: subgenus Euquercus Hickel and Camus and subgenus Cyclobalanopsis ?ersted (Schneider). However, when Notholithocarpus Manos, Cannon and S. Oh was chosen as an outgroup subgenus Cyclobalanopsis clustered with Cerris and Ilex groups to form the Old World clade. To assess the placement of the root, we complemented our dataset with published data of ITS and CRC sequences. Based on the concatenated eight gene sequences, the most likely root position is at the split between the ?Old World Oaks? and the ?New World Oaks?, which is one of the alternative positions suggested by our six gene analysis. Using a dating approach, we inferred an Eocene age for the primary divergences in Quercus and a root age of about 50?55 Ma, which agrees with palaeobotanical evidence. Finally, irrespective of the outgroup choice, our data boost the topology within the New World clade, where (Protobalanus + Quercus) is a sister clade of Lobatae. Inferred divergence ages within this clade and the Cerris?Ilex clade are generally younger than could be expected from the fossil record, indicating that morphological differentiation pre-dates genetic isolation in this clade.}, isbn = {1477-2000}, author = {Hubert, Fran{\c c}ois and Grimm, Guido W. and Jousselin, Emmanuelle and Berry, Vincent and Franc, Alain and Kremer, Antoine} } @article {160, title = {High Rates of Gene Flow by Pollen and Seed in Oak Populations across Europe}, journal = {PLoS ONEPLoS ONE}, volume = {9}, number = {1}, year = {2014}, pages = {e85130}, publisher = {Public Library of Science}, abstract = {

Gene flow is a key factor in the evolution of species, influencing effective population size, hybridisation and local adaptation. We analysed local gene flow in eight stands of white oak (mostly Quercus petraea and Q. robur, but also Q. pubescens and Q. faginea) distributed across Europe.

Adult trees within a given area in each stand were exhaustively sampled (range [239, 754], mean 423), mapped, and acorns were collected ([17,147], 51) from several mother trees ([3], [47], 23). Seedlings ([65,387], 178) were harvested and geo-referenced in six of the eight stands. Genetic information was obtained from screening distinct molecular markers spread across the genome, genotyping each tree, acorn or seedling. All samples were thus genotyped at 5{\textendash}8 nuclear microsatellite loci. Fathers/parents were assigned to acorns and seedlings using likelihood methods. Mating success of male and female parents, pollen and seed dispersal curves, and also hybridisation rates were estimated in each stand and compared on a continental scale.

On average, the percentage of the wind-borne pollen from outside the stand was 60\%, with large variation among stands (21{\textendash}88\%). Mean seed immigration into the stand was 40\%, a high value for oaks that are generally considered to have limited seed dispersal. However, this estimate varied greatly among stands (20{\textendash}66\%). Gene flow was mostly intraspecific, with large variation, as some trees and stands showed particularly high rates of hybridisation.

Our results show that mating success was unevenly distributed among trees. The high levels of gene flow suggest that geographically remote oak stands are unlikely to be genetically isolated, questioning the static definition of gene reserves and seed stands.

}, author = {Gerber, Sophie and Chad{\oe}uf, Jo{\"e}l and Gugerli, Felix and Lascoux, Martin and Buiteveld, Joukje and Cottrell, Joan and Dounavi, Aikaterini and Fineschi, Silvia and Forrest, Laura L. and Fogelqvist, Johan and Goicoechea, Pablo G. and Jensen, Jan Svejgaard and Salvini, Daniela and Vendramin, Giovanni G. and Kremer, Antoine} } @article {142, title = {Comparative mapping in the Fagaceae and beyond with EST-SSRs}, journal = {BMC Plant BiologyBMC Plant Biology}, volume = {12}, number = {1}, year = {2012}, pages = {153}, abstract = {BACKGROUND:Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species.RESULTS:We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n=2x=24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype.CONCLUSIONS:This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.}, isbn = {1471-2229}, author = {Bodenes, Catherine and Chancerel, Emilie and Gailing, Oliver and Vendramin, Giovanni and Bagnoli, Francesca and Durand, Jerome and Goicoechea, Pablo and Soliani, Carolina and Villani, Fiorella and Mattioni, Claudia and Koelewijn, Hans and Murat, Florent and Salse, Jerome and Roussel, Guy and Boury, Christophe and Alberto, Florian and Kremer, Antoine and Plomion, Christophe} } @article {143, title = {Genetic Diversity Increases Insect Herbivory on Oak Saplings}, journal = {PLoS ONEPLoS ONE}, volume = {7}, number = {8}, year = {2012}, pages = {e44247}, publisher = {Public Library of Science}, abstract = {

A growing body of evidence from community genetics studies suggests that ecosystem functions supported by plant species richness can also be provided by genetic diversity within plant species. This is not yet true for the diversity-resistance relationship as it is still unclear whether damage by insect herbivores responds to genetic diversity in host plant populations. We developed a manipulative field experiment based on a synthetic community approach, with 15 mixtures of one to four oak (Quercus robur) half-sib families. We quantified genetic diversity at the plot level by genotyping all oak saplings and assessed overall damage caused by ectophagous and endophagous herbivores along a gradient of increasing genetic diversity. Damage due to ectophagous herbivores increased with the genetic diversity in oak sapling populations as a result of higher levels of damage in mixtures than in monocultures for all families (complementarity effect) rather than because of the presence of more susceptible oak genotypes in mixtures (selection effect). Assemblages of different oak genotypes would benefit polyphagous herbivores via improved host patch location, spill over among neighbouring saplings and diet mixing. By contrast, genetic diversity was a poor predictor of the abundance of endophagous herbivores, which increased with individual sapling apparency. Plant genetic diversity may not provide sufficient functional contrast to prevent tree sapling colonization by specialist herbivores while enhancing the foraging of generalist herbivores. Long term studies are nevertheless required to test whether the effect of genetic diversity on herbivory change with the ontogeny of trees and local adaptation of specialist herbivores.

}, author = {Castagneyrol, Bastien and Lagache, L{\'e}lia and Giffard, Brice and Kremer, Antoine and Jactel, Herv{\'e}} } @article {146, title = {Genomics of Fagaceae}, journal = {Tree Genetics \& GenomesTree Genetics \& Genomes}, volume = {8}, year = {2012}, pages = {583-610}, publisher = {Springer Berlin / Heidelberg}, abstract = {An overview of recent achievements and development of genomic resources in the Fagaceae is provided, with major emphasis on the genera Castanea and Quercus . The Fagaceae is a large plant family comprising more than 900 species belonging to 8{\textendash}10 genera. Using a wide range of molecular markers, population genetics and gene diversity surveys were the focus of many studies during the past 20 years. This work set the stage for investigations in genomics beginning in the early 1990s and facilitated the application of genetic and quantitative trait loci mapping approaches. Transferability of markers across species and comparative mapping have indicated tight macrosynteny between Quercus and Castanea . Omic technologies were more recently developed and the corresponding resources are accessible via electronic and physical repositories (expressed sequence tag sequences, single-nucleotide polymorphisms, candidate genes, cDNA clones, bacterial artificial chromosome (BAC) libraries) that have been installed in North America and Europe. BAC libraries and physical maps were also constructed in Castanea and Quercus and provide the necessary resources for full nuclear genome sequencing projects that are currently under way in Castanea mollissima (Chinese chestnut) and Quercus robur (pedunculate oak).}, keywords = {Biomedical and Life Sciences}, isbn = {1614-2942}, author = {Kremer, Antoine and Abbott, Albert and Carlson, John and Manos, Paul and Plomion, Christophe and Sisco, Paul and Staton, Margaret and Ueno, Saneyoshi and Vendramin, Giovanni} }