Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China.

Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex evolutionary relationships in closely related species and to observe variations in species relationships across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution in southwest China and probably constitute a syngameon. In this study, we mapped resequencing data from different species in this group to the Quercus aquifolioides reference genome to obtain a high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. We reconstructed their phylogenetic relationships, explored the level and pattern of introgression among these species and investigated gene tree variation in the genomes of these species using sliding windows. The same or closely related plastomes were found to be shared extensively among different species within a specific geographical area. Phylogenomic analyses of genome-wide SNP data found that most oaks in the Himalayan-Hengduan subalpine clade showed genetic coherence, but several species were found to be connected by introgression. The gene trees obtained using sliding windows showed that the phylogenetic relationships in the genomes of oaks are highly heterogeneous and therefore highly obscured. Our study found that all the oaks of the Himalayan-Hengduan subalpine clade from southwest China form a syngameon. The obscured phylogenetic relationships observed empirically across the genome are best explained by interspecific gene flow in conjunction with incomplete lineage sorting.

Interspecific Variation between the American Quercus virginiana and Mediterranean Quercus Species in Terms of Seed Nutritional Composition, Phytochemical Content, and Antioxidant Activity.

This study aimed to evaluate a complete nutritional composition in the seeds Quercus virginiana to compare this nutritional composition with three Mediterranean Quercus species. We analyzed the seed morphometry, proximate composition, phytochemicals, and antioxidant capacity. The seed of Q. virginiana presented the smaller seed size and weight, while Q. suber presented the highest values. Moreover, Q. virginiana seeds showed the highest amounts of sugar and total lipids, digestibility, energy, palmitic acid, and stearic acid. On the other hand, Q. virginiana seeds showed the lowest values of linoleic acid. Moreover, Q. coccifera seeds presented the highest total phenolics and flavonoids contents and antioxidant activity. The clustering analysis revealed a significant similarity in seed morphometry and nutritional composition between the Mediterranean Q. ilex and Q. suber, grouping with the American Q. virginiana, but to a considerable distance; by contrast, the Mediterranean Q. coccifera was the most distant in the clustering analysis. The content of phenolics and flavonoids and digestibility value were the variables that contributed to the separation to a greater extent in the clustering of the four species. The nutritional and biological activity assessment of plant seed may be considered as an essential mission to find new sustainable sources and novel chemical agents. In this sense, Quercus seeds may be an alternative and a competitive food source for the agri-food industry.

Variation in the Phenolic Composition of Cork Stoppers from Different Geographical Origins.

Cork stopper granulates from five geographical origins from Portugal and six from Spain were analyzed regarding polyphenol composition by HPLC-DAD/ESI-MS and geographical discrimination studied by near-infrared spectroscopy (NIRS). The phenolic composition of the eleven origins ranged from 30 to 52 mg/g cork granulates, with vescavaloninic acid, castalagin, sanguisorbic acid dilactone, vescalagin, castavaloninic acid, dehydrated tergallic-C-Glc, and ellagic acid being the major compounds. NIRS revealed to be a powerful tool to discriminate origins and predict the concentration of polyphenols. However, polyphenols do not fully explain the discrimination of geographical origins. Variability in the polyphenol composition of cork stoppers is not significantly influenced by geographical location but probably may be more related to the plant genetics, tree age, and phytosanitary and edaphoclimatic conditions.

A Disjunctive Marginal Edge of Evergreen Broad-Leaved Oak (Quercus gilva) in East Asia: The High Genetic Distinctiveness and Unusual Diversity of Jeju Island Populations and Insight into a Massive, Independent Postglacial Colonization.

Jeju Island is located at a marginal edge of the distributional range of East Asian evergreen broad-leaved forests. The low genetic diversity of such edge populations is predicted to have resulted from genetic drift and reduced gene flow when compared to core populations. To test this hypothesis, we examined the levels of genetic diversity of marginal-edge populations of Quercus gilva, restricted to a few habitats on Jeju Island, and compared them with the southern Kyushu populations. We also evaluated their evolutionary potential and conservation value. The genetic diversity and structure were analyzed using 40 polymorphic microsatellite markers developed in this study. Ecological Niche Modeling (ENM) has been employed to develop our insights, which can be inferred from historical distribution changes. Contrary to our expectations, we detected a similar level of genetic diversity in the Jeju populations, comparable to that of the southern Kyushu populations, which have been regarded as long-term glacial refugia with a high genetic variability of East Asian evergreen trees. We found no signatures of recent bottlenecks in the Jeju populations. The results of STRUCTURE, neighbor-joining phylogeny, and Principal Coordinate Analysis (PCoA) with a significant barrier clearly demonstrated that the Jeju and Kyushu regions are genetically distinct. However, ENM showed that the probability value for the distribution of the trees on Jeju Island during the Last Glacial Maximum (LGM) converge was zero. In consideration of these results, we hypothesize that independent massive postglacial colonization from a separate large genetic source, other than Kyushu, could have led to the current genetic diversity of Jeju Island. Therefore, we suggest that the Jeju populations deserve to be separately managed and designated as a level of management unit (MU). These findings improve our understanding of the paleovegetation of East Asian evergreen forests, and the microevolution of oaks.

Use of ultrasound at a pilot scale to accelerate the ageing of sherry vinegar.

In the present work, the accelerated ageing process of sherry vinegar has been studied at pilot scale by means of the joint application of ultrasound, micro-oxygenation and wood chips (American oak, French oak and Spanish oak). The CIELab parameters have been studied as well as the polyphenolic and volatile content of the aged vinegar samples. Vinegars aged with American oak presented different chromatic characteristics to those aged with French and Spanish oak and a lower polyphenolic and volatile content than the latter ones. On the other hand, Spanish oak generated vinegars with a higher content of volatile compounds and an intermediate polyphenolic profile between those obtained using French and American oak. In addition, the use of ultrasound for a period between 4 and 21 days, generated vinegars with similar characteristics to others that were aged in the traditional way for between 2 and 6 months. It has been demonstrated that the use of ultrasound, combined with micro-oxygenation and chip addition, is a technique which can accelerate the ageing process of vinegars at a pilot scale, so it could be a viable alternative to obtain sherry vinegars aged in a shorter time.

Diversidad florística y captura de carbono en robledales y pasturas con árboles en Santa Isabel, Tolima, Colombia / Floristic diversity and carbon capture in oak groves and pastures with trees in Santa Isabel, Tolima, Colombia

Introducción: La acelerada transformación de los usos del suelo en los Andes colombianos han afectado la diversidad y la provisión de servicios ecosistémicos. Objetivo: Se caracterizó la estructura y composición florística, junto a la estimación del carbono almacenado en biomasa de bosques primarios intervenidos y pasturas con árboles en Santa Isabel, Tolima. Métodos: En cada sistema, se establecieron cinco parcelas de muestreo: rectangulares de 1 000 m2 cada una en bosques y circulares de 707 m2 en pasturas, para medir todos los individuos con diámetro a 1.30 m de altura, ≥10 cm. La biomasa se estimó a partir de modelos alométricos multi-especies y un modelo genérico en el caso de biomasa abajo del suelo. Resultados: En el bosque se registró una abundancia promedio de 642 ± 125 individuos/ha, se encontraron 25 familias, 39 géneros, 43 especies y morfoespecies en 0.5 ha de muestreo. Quercus humboldtii y Ladenbergia macrocarpa fueron las especies con el mayor Índice de Valor de Importancia (IVI = 32.5 y 11.2, respectivamente) en los bosques. En pasturas se encontraron 175.0 ± 21.3 individuos/ha, pertenecientes a 8 familias, 9 géneros, 10 especies y morfoespecies en 0.35 ha de muestreo. Eugenia spp. y Weinmannia pubescens tuvieron la mayor importancia ecológica (19.5 y 17.6 %, respectivamente) en pasturas. El bosque almacenó en promedio 125.0 ± 30.0 t C/ha, comparado con 18.4 ± 1.8 t C/haen pasturas. Conclusiones: Estos hallazgos muestran alta capacidad de almacenamiento de carbono en estos usos del suelo, lo cual contribuye a mantener o disminuir la concentración de gases de efecto invernadero en la atmósfera, y por ende, son un referente que permite desarrollar estrategias de conservación, con miras a mitigar el cambio climático.

Introduction: The accelerated transformation of land uses in the Colombian Andes has affected diversity and the provision of ecosystem services. Objective: The structure and floristic composition and the estimation of the carbon stored in biomass of intervened primary forests and pastures with trees in Santa Isabel, Tolima, was described. Methods: In each system, five sampling plots were established: rectangular of 1 000 m2 each in forests and circular of 707 m2 in pastures to measure all individuals with a diameter of 1.30 m in height, ≥10 cm. The biomass was estimated from multi-species allometric models and a generic model in the case of below-ground biomass. Results: In the forest, an average abundance of 642 ± 125 individuals / ha was recorded, finding 25 families, 39 genera, 43 species and morphospecies in 0.5 ha of sampling. Quercus humboldtii and Ladenbergia macrocarpa were the species with the highest Importance Value Index (IVI = 32.5 and 11.2, respectively) in the forests. In pastures, 175.0 ± 21.3 individuals / ha were found, belonging to 8 families, 9 genera, 10 species and morphospecies in 0.35 ha of sampling. Weinmannia pubescens and Eugenia spp. had the greatest ecological importance (19.5 and 17.6 %, respectively) in pastures. The forest stored an average of 125.0 ± 30.0 t C/ ha, compared to 18.4 ± 1.8 t C/ha in pastures. Conclusions: These findings show high carbon storage capacity in these land uses, which contributes to maintain or decrease the concentration of greenhouse gases in the atmosphere, and therefore, are a benchmark that allows to develop conservation strategies, with a view to mitigate climate change.

Species Identification of Oaks (Quercus L., Fagaceae) from Gene to Genome.

Species identification of oaks (Quercus) is always a challenge because many species exhibit variable phenotypes that overlap with other species. Oaks are notorious for interspecific hybridization and introgression, and complex speciation patterns involving incomplete lineage sorting. Therefore, accurately identifying Quercus species barcodes has been unsuccessful. In this study, we used chloroplast genome sequence data to identify molecular markers for oak species identification. Using next generation sequencing methods, we sequenced 14 chloroplast genomes of Quercus species in this study and added 10 additional chloroplast genome sequences from GenBank to develop a DNA barcode for oaks. Chloroplast genome sequence divergence was low. We identified four mutation hotspots as candidate Quercus DNA barcodes; two intergenic regions (matK-trnK-rps16 and trnR-atpA) were located in the large single copy region, and two coding regions (ndhF and ycf1b) were located in the small single copy region. The standard plant DNA barcode (rbcL and matK) had lower variability than that of the newly identified markers. Our data provide complete chloroplast genome sequences that improve the phylogenetic resolution and species level discrimination of Quercus. This study demonstrates that the complete chloroplast genome can substantially increase species discriminatory power and resolve phylogenetic relationships in plants.

Elucidating Drought Stress Tolerance in European Oaks Through Cross-Species Transcriptomics.

The impact of climate change that comes with a dramatic increase of long periods of extreme summer drought associated with heat is a fundamental challenge for European forests. As a result, forests are expected to shift their distribution patterns toward north-east, which may lead to a dramatic loss in value of European forest land. Consequently, unraveling key processes that underlie drought stress tolerance is not only of great scientific but also of utmost economic importance for forests to withstand future heat and drought wave scenarios. To reveal drought stress-related molecular patterns we applied cross-species comparative transcriptomics of three major European oak species: the less tolerant deciduous pedunculate oak (Quercus robur), the deciduous but quite tolerant pubescent oak (Q. pubescens), and the very tolerant evergreen holm oak (Q. ilex). We found 415, 79, and 222 differentially expressed genes during drought stress in Q. robur, Q. pubescens, and Q. ilex, respectively, indicating species-specific response mechanisms. Further, by comparative orthologous gene family analysis, 517 orthologous genes could be characterized that may play an important role in drought stress adaptation on the genus level. New regulatory candidate pathways and genes in the context of drought stress response were identified, highlighting the importance of the antioxidant capacity, the mitochondrial respiration machinery, the lignification of the water transport system, and the suppression of drought-induced senescence - providing a valuable knowledge base that could be integrated in breeding programs in the face of climate change.

Anatomical features of Fagaceae wood statistically extracted by computer vision approaches: Some relationships with evolution.

The anatomical structure of wood is complex and contains considerable information about its specific species, physical properties, growth environment, and other factors. While conventional wood anatomy has been established by systematizing the xylem anatomical features, which enables wood identification generally up to genus level, it is difficult to describe all the information comprehensively. This study apply two computer vision approaches to optical micrographs: the scale-invariant feature transform algorithm and connected-component labelling. They extract the shape and pore size information, respectively, statistically from the whole micrographs. Both approaches enable the efficient detection of specific features of 18 species from the family Fagaceae. Although the methods ignore the positional information, which is important for the conventional wood anatomy, the simple information on the shape or size of the elements is enough to describe the species-specificity of wood. In addition, according to the dendrograms calculated from the numerical distances of the features, the closeness of some taxonomic groups is inconsistent with the types of porosity, which is one of the typical classification systems for wood anatomy, but consistent with the evolution based on molecular phylogeny; for example, ring-porous group Cerris and radial-porous group Ilex are nested in the same cluster. We analyse which part of the wood structure gave the taxon-specific information, indicating that the latewood zone of group Cerris is similar to the whole zone of group Ilex. Computer vision approaches provide statistical information that uncovers new aspects of wood anatomy that have been overlooked by conventional visual inspection.

Ion Torrent and lllumina, two complementary RNA-seq platforms for constructing the holm oak (Quercus ilex) transcriptome.

Transcriptome analysis is widely used in plant biology research to explore gene expression across a large variety of biological contexts such as those related to environmental stress and plant-pathogen interaction. Currently, next generation sequencing platforms are used to obtain a high amount of raw data to build the transcriptome of any plant. Here, we compare Illumina and Ion Torrent sequencing platforms for the construction and analysis of the holm oak (Quercus ilex) transcriptome. Genomic analysis of this forest tree species is a major challenge considering its recalcitrant character and the absence of previous molecular studies. In this study, Quercus ilex raw sequencing reads were obtained from Illumina and Ion Torrent and assembled by three different algorithms, MIRA, RAY and TRINITY. A hybrid transcriptome combining both sequencing technologies was also obtained in this study. The RAY-hybrid assembly generated the most complete transcriptome (1,116 complete sequences of which 1,085 were single copy) with a E90N50 of 1,122 bp. The MIRA-Illumina and TRINITY-Ion Torrent assemblies annotated the highest number of total transcripts (62,628 and 74,058 respectively). MIRA-Ion Torrent showed the highest number of shared sequences (84.8%) with the oak transcriptome. All the assembled transcripts from the hybrid transcriptome were annotated with gene ontology grouping them in terms of biological processes, molecular functions and cellular components. In addition, an in silico proteomic analysis was carried out using the translated assemblies as databases. Those from Ion Torrent showed more proteins compared to the Illumina and hybrid assemblies. This new generated transcriptome represents a valuable tool to conduct differential gene expression studies in response to biotic and abiotic stresses and to assist and validate the ongoing Q. ilex whole genome sequencing.

Phenolic and volatile compounds in Quercus humboldtii Bonpl. wood: effect of toasting with respect to oaks traditionally used in cooperage.

BACKGROUND: The most frequent renewal of barrels of different origins and species is a current trend, but this demand does not match the current availability of wood. An alternative could be the use of Quercus humboldtii wood. However, there is little information about its composition. Because of this, the aim was to study low-molecular-weight phenols (LMWP), ellagitannins and volatile compounds in untoasted and toasted Q. humboldtii oak, and compare these with the species traditionally used in cooperage: Q. petraea (French and Romanian) and Q. alba (American). RESULTS: The LMWPs in Q. humboldtii were comparable to those in Q. petraea and Q. alba. Ellagitannin composition in Q. humboldtii was similar to that in Q. alba. The toasting process improved volatile composition, mainly in Q. humboldtii, presenting the highest concentration of several volatile compounds. CONCLUSION: The results indicate that Q. humboldtii could be considered suitable for aging wine, although it is necessary to continue the study of this wood species to confirm its potential use in oenology. © 2018 Society of Chemical Industry.

Identification of odorous compounds in oak wood using odor extract dilution analysis and two-dimensional gas chromatography-mass spectrometry/olfactometry.

Over the centuries, oak wood has been used in the maturation process of alcoholic beverages imparting aroma and flavor notes. Whereas several studies have dealt with the impact of oak wood on the chemical composition of, for example, wine aroma, only limited information is available on the odorant composition of unmodified and raw oak wood itself. To close this gap, a combination of human sensory and chemo-analytical techniques was applied for the elucidation of the chemical composition of oak odor, comprising extraction of the volatile fraction of oak wood by means of solvent-assisted flavor evaporation (SAFE) and subsequent mild concentration of the distillate. Odor extract dilution analysis (OEDA), which is based on gas chromatography-olfactometry (GC-O), was then applied for the targeted characterization of the odor-active compounds. Overall, a total of 97 odorants was identified via gas chromatography-mass spectrometry/olfactometry (GC-MS/O) and heart-cut two-dimensional gas chromatography-mass spectrometry/olfactometry (2D-GC-MS/O). The majority of these odorants comprised a series of terpenes, mainly mono- and sesquiterpenes, aldehydes, acids, and lactones, as well as a number of odorants containing a phenolic core moiety. Several odorants are reported here for the first time as volatile organic compounds in oak wood. Identification of the molecular composition of oak wood odor helps to establish a better understanding of the distinctive smell of oak wood, and offers the basis for unveiling its potential effects on humans when being exposed to oak wood smell in daily life. Graphical abstract ᅟ.

Contrasting Patterns of Population History and Seed-mediated Gene Flow in Two Endemic Costa Rican Oak Species.

Lower Central America is an important area to study recent population history and diversification of Neotropical species due to its complex and dynamic geology and climate. Phylogeographic studies in this region are few in comparison with other regions and even less for tree species. The aim of the present study was to characterize the phylogeographic structure in 2 partially co-distributed endemic oak species (Quercus costaricensis and Q. bumelioides) of the Costa Rican mountains using chloroplast short sequence repeats (cpSSRs), and to test for the effect of geological and palaeoclimatic processes on their population history. Genetic diversity and structure, haplotype networks, patterns of seed-mediated gene flow and historical demography were estimated for both species. Results suggested contrasting patterns. Quercus costaricensis exhibited high values of genetic diversity, a marked phylogeographic structure, a north-to-south genetic diversity gradient and evidence of a demographic expansion during the Quaternary. Quercus bumelioides did not show significant genetic structure and the haplotype network and historical demography estimates suggested a recent population expansion probably during the Pleistocene-Holocene transition. The phylogeographic structure of Q. costaricensis seems to be related to Pleistocene altitudinal migration due to its higher altitudinal distribution. Meanwhile, historical seed-mediated gene flow through the lower altitudinal distribution of Q. bumelioides may have promoted the homogenization of genetic variation. Population expansion and stable availability of suitable climatic areas in both species probably indicate that palaeoclimatic changes promoted downwards altitudinal migration and formation of continuous forests allowing oak species to expand their distribution into the Panamanian mountains during glacial stages.

Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus).

Here we study hybridization, introgression and lineage diversification in the widely distributed canyon live oak (Quercus chrysolepis) and the relict island oak (Q. tomentella), two Californian golden cup oaks with an intriguing biogeographical history. We employed restriction-site-associated DNA sequencing and integrated phylogenomic and population genomic analyses to study hybridization and reconstruct the evolutionary past of these taxa. Our analyses revealed the presence of two cryptic lineages within Q. chrysolepis. One of these lineages shares its most recent common ancestor with Q. tomentella, supporting the paraphyly of Q. chrysolepis. The split of these lineages was estimated to take place during the late Pliocene or the early Pleistocene, a time corresponding well with the common presence of Q. tomentella in the fossil records of continental California. Analyses also revealed historical hybridization among lineages, high introgression from Q. tomentella into Q. chrysolepis in their current area of sympatry, and widespread admixture between the two lineages of Q. chrysolepis in contact zones. Our results support that the two lineages of Q. chrysolepis behave as a single functional species phenotypically and ecologically well differentiated from Q. tomentella, a situation that can be only accommodated considering hybridization and speciation as a continuum with diffuse limits.

Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): Insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia.

The evolutionary history of Quercus section Cyclobalanopsis, a dominant lineage in East Asian evergreen broadleaved forests (EBLFs), has not been comprehensively studied using molecular tools. In this study, we reconstruct the first comprehensive phylogeny of this lineage using a genomic approach (restriction-site associated DNA sequencing, RAD-seq), sampling 35 of the ca. 90 species currently recognized, representing all main morphological groups of section Cyclobalanopsis. In addition, 10 other species of Quercus and two outgroups were also sampled. Divergence times were estimated using a relaxed clock model and two fossil calibrations. Ancestral areas and dispersal routes were inferred using statistical dispersal-vicariance analysis and the dispersal-extinction-cladogenesis (DEC) model. The phylogeny of Quercus section Cyclobalanopsis demonstrates the section to be monophyletic, comprising two main lineages and six subclades that are well supported by anatomical traits. Biogeographical reconstructions indicate that the wide northern hemisphere distribution of Quercus was disrupted in the Late Eocene, leading to the main extant groups at about 33 Ma. The earliest divergences in section Cyclobalanopsis correspond to the phased uplift of the Himalayas and lateral extrusion of Indochina at the transition of the Oligocene and Miocene, where the highest rate of diversification occurred in the late Miocene. Dispersal from Sino-Himalaya and the Palaeotropics to Sino-Japan in the Miocene was facilitated by the increased intensity of East Asian summer monsoons and by the Middle Miocene Climatic Optimum. Our results highlight the importance of climatic changes and Indo-Eurasian collision-induced tectonic activities from the Neogene onward to the spatial-temporal diversification patterns of Asian EBLF lineages.

Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations.

Phylogenetic analysis by maximum likelihood (PAML) has become the standard approach to study positive selection at the molecular level, but other methods may provide complementary ways to identify amino acid replacements associated with particular conditions. Here, we compare results of the decision tree (DT) model method with ones of PAML using the key photosynthetic enzyme RuBisCO as a model system to study molecular adaptation to particular ecological conditions in oaks (Quercus). We sequenced the chloroplast rbcL gene encoding RuBisCO large subunit in 158 Quercus species, covering about a third of the global genus diversity. It has been hypothesized that RuBisCO has evolved differentially depending on the environmental conditions and leaf traits governing internal gas diffusion patterns. Here, we show, using PAML, that amino acid replacements at the residue positions 95, 145, 251, 262 and 328 of the RuBisCO large subunit have been the subject of positive selection along particular Quercus lineages associated with the leaf traits and climate characteristics. In parallel, the DT model identified amino acid replacements at sites 95, 219, 262 and 328 being associated with the leaf traits and climate characteristics, exhibiting partial overlap with the results obtained using PAML.

Leaf morphological variability and intraspecific taxonomic units for pedunculate oak and grayish oak (genus Quercus L., series Pedunculatae Schwz.) in Southern Carpathian Region (Romania).

Even though pedunculate oak (Quercus robur L.) and grayish oak (Quercus pedunculiflora K. Koch) have different ecological requirements, they have been considered as having low differentiation at the level of morphological traits and genetic variation. The leaf morphology for 862 trees has been assessed in 16 natural populations, seven of Q. robur, eight of Q. pedunculiflora and a mixed forest were both taxa coexist. In total, fifteen descriptors have been analysed by using discriminant analysis, while it was found that with only four out of the fifteen leaf traits (abaxial pubescence, abaxial colour of the leaf, petiole length and basal shape of lamina) the two taxa could be clearly differentiated. A dendrogram has been constructed on the basis of these traits, where the populations of each taxon have been clustered together. PU and CL traits of Q. pedunculiflora were discussed for their adaptive value for drought resistance in the steppe habitats occupied by this taxon. Using the leaves' morphological descriptors and data from the literature, intra-taxonomic units (varieties, forms and sub-forms) have been identified in all analysed populations. Eight intraspecific units for Q. robur and six for Q. pedunculiflora have been identified in the investigated area. An analysis of spatial distribution of the two taxa and of their intraspecific units has been performed using maps of ecoregions for the study area.

Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America.

Species within the genus Quercus (oak) hybridize in complex patterns that have yet to be fully explored with phylogenomic data. Analyses to date have recovered reasonable divergent patterns, suggesting that the impact of introgression may not always be obvious in inferred oak phylogenies. We explore this phenomenon using RADseq data for 136 samples representing 54 oak species by conducting phylogenetic analyses designed to distinguish signals of lineage diversification and hybridization, focusing on the lobed-leaf species Quercus gambelii, Q. lobata, and Q. garryana in the context of a broad sampling of allied white oaks (Quercus section Quercus), and particularly the midwestern Q. macrocarpa. We demonstrate that historical introgressive hybridization between once sympatric species affects phylogeny estimation. Historical range expansion during periods of favorable climate likely explains our observations; analyses support genetic exchange between ancestral populations of Q. gambelii and Q. macrocarpa. We conclude that the genomic consequences of introgression caused the attraction of distant lineages in phylogenetic tree space, and that introgressive and divergent signals can be disentangled to produce a robust estimate of the phylogenetic history of the species.

Chemical characterization and extractives composition of heartwood and sapwood from Quercus faginea.

Heartwood and sapwood of Quercus faginea were evaluated in relation to summative chemical composition and non-polar and polar extracts composition, including an assessment of antioxidant properties (DPPH and FRAP). Twenty trees from two sites in Portugal were analysed. Heartwood had approximately two times more solvent extractible compounds than sapwood (on average 19.0% and 9.5%). The lipophilic extractible compounds were below 1%, and most of them were polar e.g. ethanol-soluble compounds corresponded to 65% of total extractives in heartwood and 43% in sapwood. Lignin content was similar in sapwood and heartwood (28.1% and 28.6% of extractive-free wood respectively) as well as the sugar composition. Site did not influence the chemical composition. The lipophilic extractible compounds from both sapwood and heartwood included mainly saturated fatty acids (23.0% and 36.9% respectively) and aromatic compounds were also abundant in sapwood (22.9%). The ethanol-water extractibles had a high content of phenolic substances (558.0 and 319.4 mg GAE/g extract, respectively of heartwood and sapwood). The polyphenolic composition was similar in heartwood and sapwood with higher content of ellagitannins (168.9 and 153.5 mg tannic acid/g of extract in sapwood and heartwood respectively) and very low content of condensed tannins. The antioxidant activity was very high with IC50 of 2.6 µg/ml and 3.3 µg/ml for sapwood and heartwood respectively, as compared to standard antioxidants (IC50 of 3.8 µg/ml for Trolox). The ferric reducing ability was 2.8 and 2.0 mMol Trolox equivalents/g extract of heartwood and sapwood respectively. The variability between trees was low and no differences between the two sites were found. Q. faginea showed a very good potential for cooperage and other applications for which a source of compounds with antioxidant properties is desirable.

A genetic legacy of introgression confounds phylogeny and biogeography in oaks.

Oaks (Quercus L.) have long been suspected to hybridize in nature, and widespread genetic exchange between morphologically defined species is well documented in two- to six-species systems, but the phylogenetic consequences of hybridization in oaks have never been demonstrated in a phylogenetically diverse sample. Here, we present phylogenomic analyses of a ca 30 Myr clade that strongly support morphologically defined species and the resolution of novel clades of white oaks; however, historical hybridization across clade boundaries is detectable and, undiagnosed, would obscure the imprint of biogeographic history in the phylogeny. Phylogenetic estimation from restriction-site-associated DNA sequencing data for 156 individuals representing 81 species supports two successive intercontinental disjunctions of white oaks: an early vicariance between the Eurasian and American white oaks, and a second, independent radiation represented by two relictual species. A suite of subsampled and partitioned analyses, however, supports a more recent divergence of the Eurasian white oaks from within the American white oaks and suggests that historic introgression between the Eurasian white oaks and a now-relictual lineage biases concatenated phylogenetic estimates. We demonstrate how divergence and reticulation both influence our understanding of the timing and nature of diversification and global colonization in these ecologically and economically important taxa.