@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.} } @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 {144, title = {Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations}, journal = {PLoS ONEPLoS ONE}, volume = {7}, number = {10}, year = {2012}, pages = {e47268}, publisher = {Public Library of Science}, abstract = {

The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis) is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands) was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (NST = 0.751\> GST = 0.690, P\<0.05). Q. variabilis displayed high interpopulation and low intrapopulation genetic diversity across the distribution range. Both unimodal mismatch distribution and significant negative Fu{\textquoteright}s FS indicated a demographic expansion of Q. variabilis populations in East Asia. A fossil calibrated phylogenetic tree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s), a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia.

}, author = {Chen, Dongmei and Zhang, Xianxian and Kang, Hongzhang and Sun, Xiao and Yin, Shan and Du, Hongmei and Yamanaka, Norikazu and Gapare, Washington and Wu, Harry X. and Liu, Chunjiang} } @article {131, title = {Exploring Species Limits in Two Closely Related Chinese Oaks}, journal = {PLoS ONEPLoS ONE}, volume = {5}, number = {11}, year = {2010}, pages = {e15529}, publisher = {Public Library of Science}, abstract = {Background

The species status of two closely related Chinese oaks, Quercus liaotungensis and Q. mongolica, has been called into question. The objective of this study was to investigate the species status and to estimate the degree of introgression between the two taxa using different approaches.

Methodology/Principal Findings

Using SSR (simple sequence repeat) and AFLP (amplified fragment length polymorphism) markers, we found that interspecific genetic differentiation is significant and higher than the differentiation among populations within taxa. Bayesian clusters, principal coordinate analysis and population genetic distance trees all classified the oaks into two main groups consistent with the morphological differentiation of the two taxa rather than with geographic locations using both types of markers. Nevertheless, a few individuals in Northeast China and many individuals in North China have hybrid ancestry according to Bayesian assignment. One SSR locus and five AFLPs are significant outliers against neutral expectations in the interspecific FST simulation analysis, suggesting a role for divergent selection in differentiating species.

Main Conclusions/Significance

All results based on SSRs and AFLPs reached the same conclusion: Q. liaotungensis and Q. mongolica maintain distinct gene pools in most areas of sympatry. They should therefore be considered as discrete taxonomic units. Yet, the degree of introgression varies between the two species in different contact zones, which might be caused by different population history or by local environmental factors.

}, author = {Zeng, Yan-Fei and Liao, Wan-Jin and Petit, R{\'e}my J. and Zhang, Da-Yong} }