@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 {163, title = {Evidence for selection on a CONSTANS-like gene between two red oak species}, journal = {Annals of BotanyAnnals of Botany}, year = {2014}, month = {March 10, 2014}, abstract = {Background and Aims Hybridizing species such as oaks may provide a model to study the role of selection in speciation with gene flow. Discrete species{\textquoteright} identities and different adaptations are maintained among closely related oak species despite recurrent gene flow. This is probably due to ecologically mediated selection at a few key genes or genomic regions. Neutrality tests can be applied to identify so-called outlier loci, which demonstrate locus-specific signatures of divergent selection and are candidate genes for further study.Methods Thirty-six genic microsatellite markers, some with putative functions in flowering time and drought tolerance, and eight non-genic microsatellite markers were screened in two population pairs (n = 160) of the interfertile species Quercus rubra and Q. ellipsoidalis, which are characterized by contrasting adaptations to drought. Putative outliers were then tested in additional population pairs from two different geographic regions (n = 159) to support further their potential role in adaptive divergence.Key Results A marker located in the coding sequence of a putative CONSTANS-like (COL) gene was repeatedly identified as under strong divergent selection across all three geographically disjunct population pairs. COL genes are involved in the photoperiodic control of growth and development and are implicated in the regulation of flowering time.Conclusions The location of the polymorphism in the Quercus COL gene and given the potential role of COL genes in adaptive divergence and reproductive isolation makes this a promising candidate speciation gene. Further investigation of the phenological characteristics of both species and flowering time pathway genes is suggested in order to elucidate the importance of phenology genes for the maintenance of species integrity. Next-generation sequencing in multiple population pairs in combination with high-density genetic linkage maps could reveal the genome-wide distribution of outlier genes and their potential role in reproductive isolation between these species.}, author = {Lind-Riehl, Jennifer F. and Sullivan, Alexis R. and Gailing, Oliver} } @article {164, title = {Is there a species spectrum within the world-wide leaf economics spectrum? Major variations in leaf functional traits in the Mediterranean sclerophyll Quercus ilex}, journal = {New PhytologistNew Phytologist}, year = {2014}, pages = {n/a-n/a}, abstract = {The leaf economics spectrum is a general concept describing coordinated variation in foliage structural, chemical and physiological traits across resource gradients. Yet, within this concept, the role of within-species variation, including ecotypic and plastic variation components, has been largely neglected. This study hypothesized that there is a within-species economics spectrum within the general spectrum in the evergreen sclerophyll Quercus ilex which dominates low resource ecosystems over an exceptionally wide range. An extensive database of foliage traits covering the full species range was constructed, and improved filtering algorithms were developed. Standardized data filtering was deemed absolutely essential as additional variation sources can result in trait variation of 10{\textendash}300\%, blurring the broad relationships. Strong trait variation, c. two-fold for most traits to up to almost an order of magnitude, was uncovered. Although the Q.~ilex spectrum is part of the general spectrum, within-species trait and climatic relationships in this species partly differed from the overall spectrum. Contrary to world-wide trends, Q.~ilex does not necessarily have a low nitrogen content per mass and can increase photosynthetic capacity with increasing foliage robustness. This study argues that the within-species economics spectrum needs to be considered in regional- to biome-level analyses.}, keywords = {bioclimatic niche, climatic drivers, dry mass per unit area, leaf economics spectrum, leaf physiognomy, nitrogen, photosynthesis, trait relationships}, isbn = {1469-8137}, author = {Niinemets, {\"U}lo} } @article {165, title = {KISSMig {\textendash} a simple model for R to account for limited migration in analyses of species distributions}, journal = {EcographyEcography}, year = {2014}, pages = {n/a-n/a}, publisher = {Blackwell Publishing Ltd}, abstract = {Detecting the legacy of time-lagged migration in species ranges is an urgent matter for understanding range dynamics. KISSMig is a simple migration model which generates maps of accessibility from areas of origin and allows the generation and testing of hypotheses about the influence of specific spread patterns on species distributions. KISSMig has important applications: 1) uncovering the influence of limited migration relative to other drivers, 2) detecting areas of origin and their importance as sources of migration, and 3) accounting for limited migration in modeling species distributions. Here we introduce KISSMig and use the oak species Quercus cerris to illustrate these applications.}, isbn = {1600-0587}, author = {Nobis, Michael P. and Normand, Signe} } @article {166, title = {Influence of climatic niche suitability and geographical overlap on hybridization patterns among southern Californian oaks}, journal = {Journal of BiogeographyJournal of Biogeography}, year = {2014}, pages = {n/a-n/a}, abstract = {Aim Information on the association between geographical patterns of hybridization and the climatic niche requirements and co-occurrence of the species involved can provide important insights that further our understanding of the factors promoting the formation of hybrid zones. Here, we test whether climatic niche suitability explains patterns of hybridization beyond spatial overlap in distributions of the geographically restricted Engelmann oak (Quercus engelmannii) and the widespread scrub oak species complex (Quercus spp.). Location Southern California, USA. Methods We sampled Engelmann and scrub oaks across 31 localities and genotyped 343 individuals at nine microsatellite loci. We used climatic niche modelling to assess the suitability of habitats for each parental species and hybrids and to analyse whether climatic niche suitability in addition to co-occurrence are associated with observed spatial patterns of hybridization. Results Our data indicated that hybrid zones are located in areas that are geographically constrained by the presence of scattered patches of Engelmann oak within a matrix broadly occupied by scrub oaks. However, the climatic niche of hybrids differed from that occupied by both Engelmann and scrub oaks, suggesting the importance of climate on their establishment and persistence beyond the simple role of geographical overlap of parental species distributions. We also found that even moderate levels of introgression contributed to increased genetic diversity in Engelmann oak but not in scrub oaks. Main conclusions These results show that hybrid zones follow a mosaic pattern constrained by the presence of scattered patches occupied by Engelmann oak and climatically suitable~areas that favour the establishment of hybrids. The low rates of ongoing hybridization and the bimodal distribution of parental genotypes found here suggest that hybridization is not threatening Engelmann oak and this phenomenon could instead be promoting the acquisition of favourable alleles that may increase the adaptive potential of this vulnerable species.}, keywords = {Ecological niche modelling, extinction through hybridization, genetic diversity, HYBRIDIZATION, introgression, Maxent, microsatellite markers, peripheral populations, Quercus engelmannii, southern California}, isbn = {1365-2699}, author = {Ortego, Joaqu{\'\i}n and Gugger, Paul F. and Riordan, Erin C. and Sork, Victoria L.} } @article {167, title = {Climatically stable landscapes predict patterns of genetic structure and admixture in the Californian canyon live oak}, journal = {Journal of BiogeographyJournal of Biogeography}, year = {2014}, pages = {n/a-n/a}, abstract = {Aim We studied which factors shape contemporary patterns of genetic structure, diversity and admixture in the canyon live oak (Quercus chrysolepis). Specifically, we tested two alternative hypotheses: (1) that areas with high habitat suitability and stability since the Last Glacial Maximum (LGM) sustain higher effective population sizes, resulting in increased levels of genetic diversity; and (2) that populations from areas with lower habitat stability show higher levels of genetic admixture due to their recurrent colonization by individuals originating from genetically differentiated populations. Furthermore, we analysed the relative importance of past and current habitat suitability and their additive effects on contemporary patterns of genetic structure. Location California, USA. Methods We sampled 160 individuals from 33 localities across the distribution range of the canyon live oak in California and then combined information from 13 nuclear microsatellite DNA markers and climate niche modelling to study patterns of genetic variation in this species. We used Bayesian clustering analyses to analyse geographical patterns of genetic structure and admixture, and circuit theory to generate isolation-by-resistance (IBR) distance matrices. Results We found that the degree of genetic admixture was higher in localities with lower inferred population stability, but that genetic diversity was not associated with habitat suitability or stability. Landscape genetic analyses identified habitat stability as the primary driver of population genetic differentiation. Main conclusions This study shows that habitat stability can be a major factor shaping genetic variation in wind-pollinated trees and supports the idea that stable regions contribute to genetic connectivity across different climatic periods. To our knowledge, this study is the first to report an association between patterns of genetic admixture and stability of local habitat.}, keywords = {California, climatic stability, Ecological niche modelling, gene flow, genetic diversity, genetic structure, interglacial refugia, palaeodistribution modelling, Quercus chrysolepis}, isbn = {1365-2699}, author = {Ortego, Joaqu{\'\i}n and Gugger, Paul F. and Sork, Victoria L.} } @article {168, title = {Morphological and physiological divergences within Quercus ilex support the existence of different ecotypes depending on climatic dryness}, journal = {Annals of BotanyAnnals of Botany}, volume = {114}, number = {2}, year = {2014}, month = {August 1, 2014}, pages = {301-313}, abstract = {Background and Aims Several studies show apparently contradictory findings about the functional convergence within the Mediterranean woody flora. In this context, this study evaluates the variability of functional traits within holm oak (Quercus ilex) to elucidate whether provenances corresponding to different morphotypes represent different ecotypes locally adapted to the prevaling stress levels.Methods Several morphological and physiological traits were measured at leaf and shoot levels in 9-year-old seedlings of seven Q. ilex provenances including all recognized morphotypes. Plants were grown in a common garden for 9 years under the same environmental conditions to avoid possible biases due to site-specific characteristics.Key Results Leaf morphometry clearly separates holm oak provenances into {\textquoteleft}ilex{\textquoteright} (more elongated leaves with low vein density) and {\textquoteleft}rotundifolia{\textquoteright} (short and rounded leaves with high vein density) morphotypes. Moreover, these morphotypes represent two consistent and very contrasting functional types in response to dry climates, mainly in terms of leaf area, major vein density, leaf specific conductivity, resistance to drought-induced cavitation and turgor loss point.Conclusions The {\textquoteleft}ilex{\textquoteright} and {\textquoteleft}rotundifolia{\textquoteright} morphotypes correspond to different ecotypes as inferred from their contrasting functional traits. To the best of our knowledge, this is the first time that the combined use of morphological and physiological traits has provided support for the concept of these two holm oak morphotypes being regarded as two different species.}, author = {Peguero-Pina, Jos{\'e} Javier and Sancho-Knapik, Domingo and Barr{\'o}n, Eduardo and Camarero, Julio Jes{\'u}s and Vilagrosa, Alberto and Gil-Pelegr{\'\i}n, Eustaquio} } @article {169, title = {Historical patterns of oak population expansion in the Chautauqua Hills, Kansas}, journal = {Journal of BiogeographyJournal of Biogeography}, year = {2014}, pages = {n/a-n/a}, abstract = {Aim Rates of tree population expansion have increased in many North American landscapes that were mosaics of grasslands, savannas and woodlands historically. Consequences of woodland expansion include reduced economic return from grazing and changes in native biodiversity, but causes of woodland expansion are poorly understood. We address historical timing of blackjack oak (Quercus marilandica) and post oak (Quercus stellata) population expansion in tree{\textendash}grass ecosystems, roles of climate and land use in driving this expansion, and future stability of these woodlands. Location The Cross Timbers ecosystem in Kansas, USA. Methods Using increment cores, we quantified blackjack oak and post oak age structures in four woodlands on sites that were not wooded in the 1860s. We compared timing of oak regeneration with climate fluctuations (using the Palmer drought severity index) and land-use history. We quantified tree species composition within 5-m radii of sampled oaks. Results Recruitment of both oak species increased between 1925 and 1945. Modal age classes recruited from 1935 to 1960. Recruitment was associated with dry intervals at the two sites with north- or east-facing aspects. This association was driven by blackjack oak recruitment in dry intervals. Woodlands on the sites with south- and west-facing aspects contained only oaks, whereas those on the sites with north- and east-facing aspects contained saplings of fire-intolerant, shade-tolerant tree species. Main conclusions Our results contribute to growing evidence for woodland expansion in the region during dry climate intervals. The association between drought and recruitment was influenced by slope aspect and was more pronounced in the less fire-tolerant oak species. Although woodland expansion coincided with regional increases in fire frequency, drought and greater use of prescribed burning are likely to have reduced fire intensities by reducing fuel loads. These oak woodlands, which have developed during the 20th century, appear to form stable communities on xeric slopes but to be undergoing succession towards a mesophytic tree community on mesic slopes.}, keywords = {Age structure, Cross Timbers, fire ecology, Kansas, mesophication, Quercus marilandica, Quercus stellata, tree recruitment, woodland dynamics, woody plant encroachment}, isbn = {1365-2699}, author = {Rogers, Thomas R. and Russell, F. Leland} } @article {170, title = {Leaf morphological evidence of natural hybridization between two oak species (Quercus austrocochinchinensis and Q. kerrii) and its implications for conservation management}, journal = {European Journal of Forest ResearchEuropean Journal of Forest ResearchEuropean Journal of Forest Research}, year = {2014}, month = {2014/09/03}, pages = {1-13}, publisher = {Springer Berlin Heidelberg}, keywords = {Conservation, Endangered species, Hybrid zone, Leaf epidermis, Leaf morphological variation}, isbn = {1612-4669}, author = {Song, Yigang and Deng, Min and Hipp, Andrew L and Li, Qiansheng} } @article {171, title = {Factors affecting stress tolerance in recalcitrant embryonic axes from seeds of four Quercus (Fagaceae) species native to the USA or China}, journal = {Annals of BotanyAnnals of Botany}, year = {2014}, month = {October 17, 2014}, abstract = {Background and Aims Quercus species are often considered {\textquoteleft}foundation{\textquoteright} components of several temperate and/or subtropical forest ecosystems. However, the populations of some species are declining and there is considerable urgency to develop ex situ conservation strategies. In this study, the storage physiology of seeds within Quercus was explored in order to determine factors that affect survival during cryopreservation and to provide a quantitative assessment of seed recalcitrance to support future studies of this complex trait.Methods Water relations and survival of excised axes in response to water loss and cryo-exposure were compared for four Quercus species from subtropical China (Q. franchetii, Q. schottkyana) and temperate USA (Q. gambelii, Q. rubra).Key Results Seed tissues initially had high water contents and water potentials. Desiccation tolerance of the embryonic axis was not correlated with the post-shedding rainfall patterns where the samples originated. Instead, higher desiccation tolerance was observed in samples growing in areas with colder winters. Survival following cryo-exposure correlated with desiccation tolerance. Among species, plumule tissues were more sensitive than radicles to excision, desiccation and cryo-exposure, and this led to a higher proportion of abnormally developing embryos during recovery following stress.Conclusions Quercus species adapted to arid and semi-humid climates still produce recalcitrant seeds. The ability to avoid freezing rather than drought may be a more important selection factor to increase desiccation tolerance. Cryopreservation of recalcitrant germplasm from temperate species is currently feasible, whilst additional protective treatments are needed for ex situ conservation of Quercus from tropical and subtropical areas.}, author = {Xia, Ke and Hill, Lisa M. and Li, De-Zhu and Walters, Christina} } @article {159, title = {Leaf epidermal features of Quercus subgenus Cyclobalanopsis (Fagaceae) and their systematic significance}, journal = {Botanical Journal of the Linnean SocietyBotanical Journal of the Linnean Society}, volume = {176}, number = {2}, year = {2014}, pages = {224-259}, abstract = {Leaf epidermal features are important taxonomic features in Quercus. We studied leaf epidermal features of 91 species and one forma of Quercus subgenus Cyclobalanopsis using light and scanning electron microscopy. Trichome terminology in oaks was assessed and clarified, aiming to score the epidermal features accurately for genus-wide comparison. Nine trichome types, anomocytic and cyclocytic stomatal apparatus, smooth layer and platelet epicuticular wax flakes, and two trichome base types were found in subgenus Cyclobalanopsis. The epidermal features revealed three main groups in subgenus Cyclobalanopsis. The epidermal features of Quercus s.l. were uniform, supporting recognition of Cyclobalanopsis as a subgenus of Quercus rather than as a separate genus. Most leaf epidermal features show a mosaic pattern, although their numerous variations offered valuable resources for species identification. The leaf epidermal features that can be used for identification of Quercus leaves are also discussed and summarized.~{\textcopyright} 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176, 224{\textendash}260.}, keywords = {anatomy, evergreen oak, light microscope, SEM, trichome}, isbn = {1095-8339}, author = {Deng, Min and Hipp, Andrew and Song, Yi-Gang and Li, Qian-Sheng and Coombes, Allen and Cotton, Alexa} } @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.} }