@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 {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 {145, title = {Stabilizing selection for within-season flowering phenology confirms pollen limitation in a wind-pollinated tree}, journal = {Journal of EcologyJournal of Ecology}, volume = {100}, number = {3}, year = {2012}, pages = {758-763}, publisher = {Blackwell Publishing Ltd}, abstract = {1. We examined the fitness consequences of pollen limitation in the valley oak (Quercus lobata N{\'e}e, Fagaceae), a wind-pollinated, predominantly outcrossing tree endemic to California, by examining the relationship between within-year phenology and acorn production over an 8~year period. 2. We predicted that pollen limitation should result in trees flowering relatively early and late in the season, when fewer trees are in flower, to experience reduced reproductive success compared to trees flowering during the middle of the season. 3. Despite considerable variation in acorn production from year to year, analyses confirmed this prediction and indicated that there was significant overall stabilizing selection on budburst date consistent with the pollen limitation hypothesis. 4. Analyses including herbivory and pre-budburst temperatures at individual trees revealed significant correlations with acorn production, but we still found significant stabilizing selection on budburst date even when considering these variables. 5.Synthesis. Pollen limitation, as indicated by stabilizing selection on within-year flowering phenology, significantly affects acorn production by individual trees in Q.~lobata and has the potential to influence other key life-history features including masting behaviour and spatial synchrony.}, keywords = {acorn production, herbivory, mast-fruiting, phenology, pollen limitation, Quercus lobata, reproductive ecology, wind-pollination}, isbn = {1365-2745}, author = {Koenig, Walter D. and Funk, Kyle A. and Kraft, Thomas S. and Carmen, William J. and Barringer, Brian C. and Knops, Johannes M. H.} } @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} } @article {147, title = {Fine-scale environmental control of hybridization in oaks}, journal = {Molecular EcologyMolecular Ecology}, year = {2012}, pages = {n/a-n/a}, abstract = {Natural hybridization is attracting much interest in modern speciation and conservation biology studies, but the underlying mechanisms remain poorly understood. In particular, it is unclear why environmental changes often increase hybridization rates. To study this question, we surveyed mating events in a mixed oak stand and developed a spatially explicit individual-based hybridization model. This model, where hybridization is frequency-dependent, pollen is nonlimiting and which allows immigrant pollen to compete with local pollen, takes into account species-specific pollen dispersal and sexual barriers to hybridization. The consequences of pollen limitation on hybridization were studied using another simple model. The results indicate that environmental changes could increase hybridization rates through two distinct mechanisms. First, by disrupting the spatial organization of communities, they should decrease the proportion of conspecific pollen available for mating, thus increasing hybridization rates. Second, by decreasing the density of conspecifics, they should increase pollen limitation and thus hybridization rates, as a consequence of chance pollination predominating over deterministic pollen competition. Altogether, our results point to a need for considering hybridization events at the appropriate level of organization and provide new insights into why hybridization rates generally increase in disturbed environments.}, keywords = {disturbance, immigration, mass action model, paternity analysis, pollen limitation, Quercus petraea, Quercus robur}, isbn = {1365-294X}, author = {Lagache, L{\'e}lia and Klein, Etienne K. and Guichoux, Erwan and Petit, R{\'e}my J.} } @article {148, title = {Genetic evidence for hybridization in red oaks (Quercus sect. Lobatae, Fagaceae)}, journal = {American Journal of BotanyAmerican Journal of Botany}, volume = {99}, number = {1}, year = {2012}, month = {January 1, 2012}, pages = {92-100}, abstract = {{\textbullet} Premise of the study: Hybridization is pervasive in many plant taxa, with consequences for species taxonomy, local adaptation, and management. Oaks (Quercus spp.) are thought to hybridize readily yet retain distinct traits, drawing into question the biological species concept for such taxa, but the true extent of gene flow is controversial. Genetic data are beginning to shed new light on this issue, but red oaks (section Lobatae), an important component of North American forests, have largely been neglected. Moreover, gene flow estimates may be sensitive to the choice of life stage, marker type, or genetic structure statistic.{\textbullet} Methods: We coupled genetic structure data with parentage analyses for two mixed-species stands in North Carolina. Genetic structure analyses of adults (including FST, RST, G{\textquoteright}ST, and structure) reflect long-term patterns of gene flow, while the percentage of seedlings with parents of two different species reflect current levels of gene flow.{\textbullet} Key results: Genetic structure analyses revealed low differentiation in microsatellite allele frequencies between co-occurring species, suggesting past gene flow. However, methods differed in their sensitivity to differentiation, indicating a need for caution when drawing conclusions from a single method. Parentage analyses identifed >20\% of seedlings as potential hybrids. The species examined exhibit distinct morphologies, suggesting selection against intermediate phenotypes.{\textbullet} Conclusions: Our results suggest that hybridization between co-occurring red oaks occurs, but that selection may limit introgression, especially at functional loci. However, by providing a source of genetic variation, hybridization could influence the response of oaks and other hybridizing taxa to environmental change.}, author = {Moran, Emily V. and Willis, John and Clark, James S.} } @article {149, title = {Mitochondrial barcodes are diagnostic of shared refugia but not species in hybridizing oak gallwasps}, journal = {Molecular EcologyMolecular Ecology}, year = {2012}, pages = {no-no}, publisher = {Blackwell Publishing Ltd}, abstract = {Mitochondrial DNA barcodes provide a simple taxonomic tool for systematic and ecological research, with particular benefit for poorly studied or species-rich taxa. Barcoding assumes genetic diversity follows species boundaries; however, many processes disrupt species-level monophyly of barcodes leading to incorrect classifications. Spatial population structure, particularly when shared across closely related and potentially hybridizing taxa, can invalidate barcoding approaches yet few data exist to examine its impacts. We test how shared population structure across hybridizing species impacts upon mitochondrial barcodes by sequencing the cytochrome b gene for 518 individuals of four well-delimited Western Palaearctic gallwasp species within the Andricus quercuscalicis species group. Mitochondrial barcodes clustered individuals into mixed-species clades corresponding to refugia, with no difference in within- and between-species divergence. Four nuclear genes were also sequenced from 4 to 11 individuals per refugial population of each species. Multi-locus analyses of these data supported established species, with no support for the refugial clustering across species seen in mitochondrial barcodes. This pattern is consistent with mitochondrial introgression among populations of species sharing the same glacial refugium, such that mitochondrial barcodes identify a shared history of population structure rather than species. Many taxa show phylogeographic structure across glacial refugia, suggesting that mitochondrial barcoding may fail when applied to other sets of co-distributed, closely related species. Robust barcoding approaches must sample extensively across population structure to disentangle spatial from species-level variation. Methods incorporating multiple unlinked loci are also essential to accommodate coalescent variation among genes and provide power to resolve recently diverged species.}, keywords = {DNA barcoding, introgression, multi-locus, spatial population structure}, isbn = {1365-294X}, author = {Nicholls, James A. and Challis, Richard J. and Mutun, Serap and Stone, Graham N.} } @article {150, title = {Ontogenetic conflicts and rank reversals in two Mediterranean oak species: implications for coexistence}, journal = {Journal of EcologyJournal of Ecology}, volume = {100}, number = {2}, year = {2012}, pages = {467-477}, publisher = {Blackwell Publishing Ltd}, abstract = {1. In heterogeneous environments, species segregate spatially in response to selective abiotic and biotic filters occurring throughout plant ontogeny. Ontogenetic conflicts in recruitment may lead to spatially discordant patterns of regeneration among microhabitats with different plant cover. In addition, species differing in seed size may be subjected to opposing ecological and evolutionary pressures throughout the life cycle of the plant. 2. We used a multi-stage demographic approach aimed at characterizing the main stage-specific probabilities of recruitment (seed survival, seed germination, seedling emergence and survival during the first 3~years of life) in two Mediterranean oak species coexisting at southern Spain. We calibrated linear and nonlinear likelihood models for each of these consecutive life history stages and calculated overall probabilities of recruitment along a wide range of plant cover and seed size variation. 3. Seed predation and seedling mortality over the dry season were the most limiting processes for the two studied oak species. However, species ranking diverged substantially through the life history stages considered in this study due to different ontogenetic trends among species. 4. At the intraspecific level, recruitment-driving processes during the seed and the seedling stages showed opposing tendencies along the explored range of plant cover and seed size. Thus, small-sized acorns and open areas were favoured for the seed stage, whereas large acorns and dense microhabitats did for the seedling stage. 5. The existence of opposing selective pressures on seed mass and their differential influence on the two studied oak species determined the occurrence of species-specific optimal seed sizes (small acorns for Quercus canariensis vs. acorns of large or intermediate size for Quercus suber). 6. The spatial patterns predicted by our overall-recruitment models provided some evidence of regeneration niche partitioning in the two coexisting oak species, supporting their current distribution patterns as saplings and adults at the study area. 7. Synthesis. We conclude that within- and among-species differences through plant ontogeny, arising from species differential response to microhabitat heterogeneity and seed size variation, could be of great importance for oak species niche segregation, driving stand dynamics and spatial pattern distribution along the landscape. The information provided by this study could be also applied to optimize management and restoration programmes since it has enabled us to identify the most favourable conditions and traits for recruitment in oak species that exhibit serious constraints for natural regeneration.}, keywords = {Mediterranean forest, plant cover, Quercus canariensis, Quercus suber, regeneration niche, reproductive ecology, seed size, seed{\textendash}seedling conflict}, isbn = {1365-2745}, author = {P{\'e}rez-Ramos, Ignacio M. and Urbieta, Itziar R. and Zavala, Miguel A. and Mara{\~n}{\'o}n, Teodoro} } @article {151, title = {A landscape genetics approach reveals ecological-based differentiation in populations of holm oak (Quercus ilex L.) at the northern limit of its range}, journal = {Biological Journal of the Linnean SocietyBiological Journal of the Linnean Society}, year = {2012}, pages = {n/a-n/a}, abstract = {The holm oak plays a relevant role in the functioning of Mediterranean forests. In the area north of Garda Lake, Italian Prealps, holm oak populations are at the northernmost edge of their distribution. Being peripheral, these populations are of particular interest for ecological, evolutionary and conservation studies. Through an explicit individual-based landscape genetics approach, we addressed the following questions: (1) are levels of genetic variation reduced in these marginal populations compared with central populations?; (2) despite the narrow geographical scale, do individual-based analyses have some power to detect genetic differentiation?; (3) do environmental and/or climatic factors exert a role in shaping patterns of genetic variation and differentiation? Through a Bayesian method, we identified three clusters whose genetic variability can be considered to be of the same order as that recorded in central Quercus ilex populations. Although being geographically very close (< 20 km), the differentiation was statistically significant (P < 0.05) with global F st and ΦPt values of 0.019 and 0.038, respectively. Geography and phylogeography could not be invoked to explain this differentiation. A redundancy discriminant analysis revealed that relevant eco-pedological and climatic features, such as soil depth, aspect, elevation and humidity, were correlated with the observed pattern of differentiation. Toblino was ecologically separated from the other clusters, as it lies on deep soil with subhumid conditions. The differentiation of the Brione{\textendash}Ranzo{\textendash}Val Busa cluster appeared to be related to superficial soils and drier conditions, whereas the Nanzone{\textendash}Padaro cluster was differentiated mainly according to its mid-elevation. Coupling spatial and genetic information on a local scale proved to be effective to investigate the evolutionary and demographic history of peripheral populations.~{\textcopyright} 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, {\textbullet}{\textbullet}, {\textbullet}{\textbullet}{\textendash}{\textbullet}{\textbullet}.}, keywords = {Bayesian computation, Geneland, Italian Prealps, microsatellites}, isbn = {1095-8312}, author = {Vernesi, Cristiano and Rocchini, Duccio and Pecchioli, Elena and Neteler, Markus and Vendramin, Giovanni G. and Paffetti, Donatella} }