@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 {161, title = {A framework phylogeny of the American oak clade based on sequenced RAD data}, journal = {PLoS ONEPLoS ONE}, volume = {9}, year = {2014}, pages = {e93975}, abstract = {Oaks (Quercus, Fagaceae) are notorious in plant systematics for the problems they pose at the species level and for higher-level phylogenetics. Previous studies based on nuclear and chloroplast DNA sequences have failed to resolve the backbone phylogeny of the genus with strong support. In this study, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23{\textendash}33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.39E06 aligned nucleotides, constituting 27,727 sequence clusters or {\textquoteleft}loci.{\textquoteright} We reran a subset of seven individuals as technical replicates and found that RAD-Seq data are readily combined across runs, with no difference in phylogenetic placement between replicates, despite the fact that a change in sequencing platforms between replicate runs resulted in data overlap between technical replicates of only 43{\textendash}64\%. 17\% (4,715) of the loci we analyzed could be matched with high confidence (BLASTN E-value < 1E{\textendash}15) to one or more expressed sequence tags (ESTs) in NCBI Genbank. A concatenated matrix of the loci that BLAST to at least one EST sequence provides approximately half as many variable or parsimony-informative characters as same-sized datasets from the non-EST loci. The EST-associated matrix is more complete (fewer missing loci) and has slightly lower homoplasy than non-EST subsampled matrices of the same size, but there is no difference in phylogenetic support or relative attribution of base substitutions to internal versus terminal branches of the phylogeny. The phylogeny we recover provides a robust estimate of the framework phylogeny for the American oak clade and demonstrates the utility of RAD-Seq data for inferring phylogeny in a 23{\textendash}33 million year-old vascular plant clade.}, keywords = {Expressed sequence tags (EST), Fagaceae, next-generation sequencing, phylogenomics, plant systematics, Quercus, restriction-site associated DNA}, author = {Hipp, Andrew L. and Eaton, Deren A. R. and Cavender-Bares, Jeannine and Fitzek, Elisabeth and Nipper, Rick and Manos, Paul S.} }