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Background and Aims Cork oaks (Quercus section Cerris) comprise 15 extant species in Eurasia. Despite being a small clade, they display a range of leaf morphologies comparable to the largest sections (>100 spp.) in Quercus. Their fossil record extends back to the Eocene. Here, we explore how cork oaks achieved their modern ranges and how legacy effects might explain niche evolution in modern species of section Cerris and its sister section Ilex , the holly oaks. Methods We inferred a dated phylogeny for cork and holly oaks using a reduced-representation next-generation sequencing method, restriction site-associated DNA sequencing (RAD-seq), and used D- statistics to investigate gene flow hypotheses. We estimated divergence times using a fossilized birth–death model calibrated with 47 fossils. We used Köppen profiles, selected bioclimatic parameters and forest biomes occupied by modern species to infer ancestral climatic and biotic niches. Key Results East Asian and Western Eurasian cork oaks diverged initially in the Eocene. Subsequently, four Western Eurasian lineages (subsections) differentiated during the Oligocene and Miocene. Evolution of leaf size, form and texture was correlated, in part, with multiple transitions from ancestral humid temperate climates to mediterranean, arid and continental climates. Distantly related but ecologically similar species converged on similar leaf traits in the process. Conclusions Originating in temperate (frost-free) biomes, Eocene to Oligocene ranges of the primarily deciduous cork oaks were restricted to higher latitudes (Siberia to north of Paratethys). Members of the evergreen holly oaks (section Ilex) also originated in temperate biomes but migrated southwards and south-westwards into then-(sub)tropical southern China and south-eastern Tibet during the Eocene, then westwards along existing pre-Himalayan mountain ranges. Divergent biogeographical histories and deep-time phylogenetic legacies (in cold and drought tolerance, nutrient storage and fire resistance) thus account for the modern species mosaic of Western Eurasian oak communities, which are composed of oaks belonging to four sections. [ABSTRACT FROM AUTHOR]

Late Oligocene leaf assemblages from four sites in Southwestern Siberia (Kurgan, Tyumen, Omsk oblasts) are described. Twenty-three leaf taxa and 3 reproductive structures represent local vegetation of a lake (Salvinia, Typha, Phragmites, Nelumbo, Hemitrapa, Liquidambar, Pterocarya, Alnus, Populus, Salix, Nyssa). Additionally, 57 spore and pollen taxa were recorded from one site (Shish River). Gymnosperms dominate the assemblage with ~30% Pinaceae and ~25% taxodiaceous (papillate) Cupressaceae pollen. Ferns and peat mosses (Sphagnaceae) comprised ~6%. Angiosperms were dominated by Fagaceae, Betulaceae, Juglandaceae and Ulmus and comprised a few exotic elements (Liquidambar, Eucommia, Nyssa, Symplocos); scarce herbaceous plants reflect lakeshore vegetation. The flora of the Turgay type comprised old elements (Nelumbo protospeciosa, Liquidambar europaea, taxodiaceous/papillate Cupressaceae, Quercus sect. Protobalanus) and taxa present in Siberia/Kazakhstan during the Paleogene with later arrivals in Europe (Ulmus pyramidalis, Quercus pseudocastanea, Alnus julianiformis, Byttneriophyllum tiliifolium). A few taxa were endemic in the late Oligocene of western Siberia (Trapa praeconocarpa, Platycrater iljinskajae sp. nov.). Combined macrofossil and palynological evidence places the Shish River site flora into the late Oligocene Zhuravka (Turtas) Formation. Floras of similar composition from western Eurasia are commonly middle Miocene or younger in age highlighting the dynamic spatiotemporal evolution of temperate Eurasian floras during the Cenozoic. [ABSTRACT FROM AUTHOR]

The piggyback basin of Bezhan, southeastern Albania, was formed during the late Neogene and contains Pliocene/Pleistocene deposits. These continental deposits consist of marls, siltstones and clays separated by a thin series of lignite-seams alternating with clays (Bezhan formation). We investigated leaf fossils and dispersed pollen from marls of the upper portion of this formation. Fifty-two plant taxa comprising algae, gymnosperms, and angiosperms were recovered. Of these, at least 19% belong to extant species and less than 16% belong to taxa today extinct in western Eurasia. Tsuga is represented by three pollen taxa with affinities to modern Chinese, Japanese, and North American species. Herbaceous taxa indicative of steppe (Artemisia, Amaranthaceae) occur in low quantities (≤1%) suggesting an interglacial setting. Four vegetation units are recognised: Wet riparian and aquatic vegetation, mesic oak forest, dry sub-Mediterranean woodland, and montane conifer forest. A comparison of the Bezhan flora with well-dated Pliocene and Pleistocene floras of Italy suggests a Calabrian (late early Pleistocene) age for the upper unit. This estimate is based on the abundance of extant taxa, the absence of subtropical taxa, and threshold values of particular taxa (Tsuga, Carya). The findings are in agreement with age estimates for extant tree species from molecular studies. [ABSTRACT FROM AUTHOR]

Measuring biological diversity is a crucial but difficult undertaking, as exemplified in oaks where complex patterns of morphological, ecological, biogeographical and genetic differentiation collide with traditional taxonomy, which measures biodiversity in number of species (or higher taxa). In this pilot study, we generated high‐throughput sequencing amplicon data of the intergenic spacer of the 5S nuclear ribosomal DNA cistron (5S‐IGS) in oaks, using six mock samples that differ in geographical origin, species composition and pool complexity. The potential of the marker for automated genotaxonomy applications was assessed using a reference data set of 1,770 5S‐IGS cloned sequences, covering the entire taxonomic breadth and distribution range of western Eurasian Quercus, and applying similarity (blast) and evolutionary approaches (maximum‐likelihood trees and Evolutionary Placement Algorithm). Both methods performed equally well, allowing correct identification of species in sections Ilex and Cerris in the pure and mixed samples, and main lineages shared by species of sect. Quercus. Application of different cut‐off thresholds revealed that medium‐ to high‐abundance (>10 or 25) sequences suffice for a net species identification of samples containing one or a few individuals. Lower thresholds identify phylogenetic correspondence with all target species in highly mixed samples (analogous to environmental bulk samples) and include rare variants pointing towards reticulation, incomplete lineage sorting, pseudogenic 5S units and in situ (natural) contamination. Our pipeline is highly promising for future assessments of intraspecific and interpopulation diversity, and of the genetic resources of natural ecosystems, which are fundamental to empower fast and solid biodiversity conservation programmes worldwide. [ABSTRACT FROM AUTHOR]

Summary: The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny.We utilize fossil data and restriction‐site associated DNA sequencing (RAD‐seq) for 632 individuals representing nearly 250 Quercus species to infer a time‐calibrated phylogeny of the world's oaks. We use a reversible‐jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among‐clade sampling biases. We then map the > 20 000 RAD‐seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity.The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome. See also the Editorial on this article by Plomion & Martin, 226: 943–946. [ABSTRACT FROM AUTHOR]

Oaks (Quercus) comprise more than 400 species worldwide and centres of diversity for most sections lie in the Americas and East/Southeast Asia. The only exception is the Eurasian sect. Cerris that comprises about 15 species, most of which are confined to western Eurasia. This section has not been comprehensively studied using molecular tools. Here, we assess species diversity and provide a first comprehensive taxonomic and phylogeographic scheme of western Eurasian members of sect. Cerris using plastid (trnH-psbA) and nuclear (5S-IGS) DNA variation with a dense intra-specific and geographic sampling. Chloroplast haplotypes primarily reflected phylogeographic patterns originating from interspecific cytoplasmic gene flow within sect. Cerris and its sister section Ilex. We identified two widespread and ancestral haplotypes, and locally restricted derived variants. Signatures shared with Mediterranean species of sect. Ilex, but not with the East Asian Cerris oaks, suggest that the western Eurasian lineage came into contact with Ilex only after the first (early Oligocene) members of sect. Cerris in Northeast Asia had begun to radiate and move westwards. Nuclear 5S-IGS diversification patterns were more useful for establishing a molecular-taxonomic framework and to reveal hybridization and reticulation. Four main evolutionary lineages were identified. The first lineage is comprised of Q. libani, Q. trojana and Q. afares and appears to be closest to the root of sect. Cerris. These taxa are morphologically most similar to the East Asian species of Cerris, and to both Oligocene and Miocene fossils of East Asia and Miocene fossils of western Eurasia. The second lineage is mainly composed of the widespread Q. cerris and the narrow endemic species Q. castaneifolia, Q. look, and Q. euboica. The third lineage comprises three Near East species (Q. brantii, Q. ithaburensis and Q. macrolepis), well adapted to continental climates with cold winters. The forth lineage appears to be the most derived and comprises Q. suber and Q. crenata. Q. cerris and Q. trojana displayed high levels of variation; Q. macrolepis and Q. euboica, previously treated as subspecies of Q. ithaburensis and Q. trojana, likely deserve independent species status. A trend towards inter-specific crosses was detected in several taxa; however, we found no clear evidence of a hybrid origin of Q. afares and Q. crenata, as currently assumed. [ABSTRACT FROM AUTHOR]

Oaks of Quercus Group Ilex are emblematic components of the Mediterranean landscapes and the full extent of their diversity in a geographic context is still poorly assessed. In order to detail differentiation patterns within Group Ilex and to illuminate causes and circumstances that underlie the distribution of its lineages, we examined plastome differentiation in the four species currently representing this oak group across the Mediterranean Basin ( Quercus ilex, Quercus coccifera, Quercus aucheri, Quercus alnifolia). Plastid DNA variation was explored with three markers on 124 individuals and spatial analyses were performed with phylogenetic and landscape genetics approaches. A strong geographic sorting, entirely decoupled from species boundaries, was found. Spatial coincidences with phylogenetic splits highlights the presence of four geographic regions (the Middle East, the Aegean region, the central and the western Mediterranean) characterised by different degrees of isolation. Distinct sub-regional structures were identified. Inter- and intra-lineage divergence patterns appear to reflect the complex orogeny of the Mediterranean region and Pleistocene climatic oscillations, while a few widespread haplotypes might represent the remnants of the ancestral Group Ilex range. Regional differentiation in this group is recognised to be triggered by a number of factors, including disruption of the original range, incomplete lineage sorting, repeated phases of asymmetrical introgression and isolation. The key role played by some Mediterranean regions on the range establishment and dynamics of this oak group is discussed. [ABSTRACT FROM AUTHOR]

Modern lineages of the beech family, Fagaceae, one of the most important north-temperate families of woody flowering plants, have been traced back to the early Eocene. In contrast, molecular differentiation patterns indicate that the Fagus lineage, Fagoideae, with a single modern genus, evolved much earlier than the remaining lineages within Fagaceae (Trigonobalanoideae, Castaneoideae, Quercoideae). The minimum age for this primary split in the Fagaceae has been estimated as 80 ± 20 Ma (i.e. Late Cretaceous) in recently published, time-calibrated phylogenetic trees including all Fagales. Here, we report fagaceous fossils from the Campanian of Wyoming (82-81 Ma; Eagle Formation [Fm]), the Danian of western Greenland (64-62 Ma; Agatdal Fm), and the middle Eocene of British Columbia (ca 48 Ma; Princeton Chert), and compare them to the Fagaceae diversity of the recently studied middle Eocene Hareøen Fm of western Greenland (42-40 Ma). The studied assemblages confirm that the Fagus lineage (= Fagoideae) and the remainder of modern Fagaceae were diverged by the middle Late Cretaceous, together with the extinct Fagaceae lineage(s) of Eotrigonobalanus and the newly recognised genus Paraquercus, a unique pollen morph with similarities to both Eotrigonobalanus and Quercus. The new records push back the origin of (modern) Fagus by 10 Ma and that of the earliest Fagoideae by 30 Ma. The earliest Fagoideae pollen from the Campanian of North America differs from its single modern genus Fagus by its markedly thicker pollen wall, a feature also seen in fossil and extant Castaneoideae. This suggests that a thick type 1 foot layer is also the plesiomorphic feature in Fagoideae although not seen in any of its living representatives. The Danian Fagus pollen of Greenland differs in size from those of modern species but is highly similar to that of the western North American early Eocene F. langevinii, the oldest known beech so far. Together with the Quercus pollen record, absent in the Campanian and Danian formations but represented by several types by the middle Eocene, this confirms recent dating estimates focussing on the genera Fagus and Quercus, while rejecting estimates from all-Fagales-dated trees as too young. The basic Castaneoideae pollen type, still found in species of all five extant genera of this putatively paraphyletic subfamily, represents the ancestral pollen type of most (modern) Fagaceae (Trigonobalanoideae, Castaneoideae, Quercoideae). [ABSTRACT FROM AUTHOR]

* Premise of the study: Recent molecular studies provide a phylogenetic framework and some dated nodes for the monocot genus Smilax. The Caribbean Havanensis group of Smilax is part of a well-supported "New World clade" with a few disjunct taxa in the Old World. Although the fossil record of the genus is rich, it has been difficult to assign fossil taxa to extant groups based on their preserved morphological characters. * Methods: Leaf fossils from Europe and Asia Minor were studied comparatively and put into a phylogenetic and biogeographic context using a molecular phylogeny of the genus. * Key results: Fossils from the early Miocene of Anatolia represent a new species of Smilax with systematic affinities with the Havanensis group. The leaf type encountered in the fossil species is exclusively found in species of the Havanensis group among all modern Smilax. Scattered fossils of this type from the Miocene of Greece and Austria, previously referred to Quercus (Fagaceae), Ilex (Aquifoliaceae), and Mahonia (Berberidaceae) also belong to the new species. * Conclusions: The new Smilax provides first fossil evidence of the Havanensis group and proves that this group had a western Eurasian distribution during the Miocene. The age of the fossils is in good agreement with the (molecular-based) purported split between the Havanensis and Hispida groups within Smilax. The Miocene Smilax provides evidence that all four subclades within the "New World clade" had a disjunct intercontinental distribution during parts of the Neogene involving trans-Atlantic crossings (via floating islands or the North Atlantic land bridge) and the Beringia land bridge. [ABSTRACT FROM AUTHOR]

It has been suggested that pollen ornamentation can be used to distinguish infrageneric groups inQuercus. Here, we document pollen morphology of nearly all species ofQuercusGroup Ilex and show that they share distinctive microrugulate pollen ornamentation. Furthermore, pollen ultrastructure of all six infrageneric groups ofQuercuswas studied comparatively and evaluated using a phylogenetic framework for Fagaceae. Characteristics of the foot layer, such as its thickness and continuity, and the ratio foot layer to tectum are not stable within infrageneric groups ofQuercus. The foot layer in derived groups (Groups Cerris, Quercus, Lobatae) is irregular, discontinuous and thin (type 2 foot layer). Members of Groups Cyclobalanopsis and Ilex either have a regular, continuous, and comparatively thick foot layer (type 1), or a type 2 foot layer. Only Group Protobalanus consistently has a type 1 foot layer and is similar toTrigonobalanusandColombobalanusamong trigonobalanoids, and to castanoids. Because (I) all except for one species ofCastaneaandNothofagushave a type 1 foot layer and (II) basal groups inQuercusmay have a type 1 foot layer, we suggest that this is the ancestral state in Fagaceae, and that the type 2 foot layer ofFagusis derived. [ABSTRACT FROM AUTHOR]

* Premise of the study: The early Cenozoic was a key period of evolutionary radiation in Fagaceae. The common notion is that species thriving in the modern summer-dry climate of California originated in climates with ample summer rain during the Paleogene. * Methods: We investigated in situ and dispersed pollen of Fagaceae from the uppermost Eocene Florissant fossil beds, Colorado, United States, using a combined light and scanning electron microscopy approach. * Key results: Pollen types of Castaneoideae with affinities to modern Castanea, Lithocarpus, and Castanopsis were recognized. Pollen of the extinct genus Fagopsis represents a derived type of Castaneoideae pollen. Infrageneric groups of Quercus were well represented, including pollen of Group Protobalanus. The taxonomic diversity of Fagaceae and of the total plant assemblage indicates a mosaic of microclimates, that range from pronounced to weakly seasonal climates and depend on slope aspect and elevation. Continental climatic conditions may have triggered the evolution of sclerophyllous leaves and adaptive radiation in Quercus and other taxa thriving today under distinctly summer-dry and winter-dry climates. * Conclusions: Vegetation types similar to modern vegetation belts of the Coastal Ranges (chaparral, nemoral conifer forest) were established in the Front Range in the late Eocene. Coeval plant assemblages from the Coastal Ranges of California indicate distinctly subtropical, moist climates. Hence, characteristic elements found today in the summer-dry and winter-dry climates of Pacific North America (Quercus Group Protobalanus, Notholithocarpus) may opportunistically have dispersed into their modern ranges later in the Cenozoic. This scenario is in contrast to the evolution and migration patterns of their western Eurasian Mediterranean counterparts (Quercus Group Ilex). [ABSTRACT FROM AUTHOR]

Trichome characters are often considered to be taxonomically important in oak species. In this article, we investigate a group of Mediterranean oaks, Quercus subsection Galliferae and Q. pubescens, using a large dataset and covering the entire distribution range of the group. As a result of the different interpretations of terms in previous studies, trichome terminology was re-assessed aiming to obtain a practicable nomenclature. In contrast with previous studies, we found that acicular, bifurcate, fasciculate, stellate, uniseriate and capitate trichomes are represented in all taxa. One exception is the lack of bifurcate trichomes in Q. canariensis. This suggests that seemingly taxonomically informative presence/absence data for trichome types, as reported previously, may be the result of too small a sample size, and this may be unrepresentative. In combination with other morphological characters (leaf shape, size and texture), features of the indumentum, such as the floccose, easily removable trichomes in Q. canariensis, can be important in species delimitation. The use of trichome characteristics in Quercus subsection Galliferae requires exhaustive sampling of all taxa in order to extract a reproducible taxonomic signal from quantitative characters. This is the prerequisite for building datasets that can be used for phylogenetic analyses, investigations of character evolution and comparative morphological studies. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169, 611-644. [ABSTRACT FROM AUTHOR]

Phylogenetic relationships among species of Quercus (oaks) from western Eurasia including the western part of the Himalayas are examined for the first time. Based on ITS and 5S-IGS data three major infrageneric groups are recognized for western Eurasia: the cerroid, iliciod, and roburoid oaks. While individuals of the cerroid and ilicoid groups cluster according to their species, particularly in the 5S-IGS analyses, individuals of species of roburoid oaks do not cluster with exception of Quercus pontica. The Cypriot endemic Quercus alnifolia belongs to the ilicoid oaks, in contrast to traditional views placing it within the cerroid oaks. Based on all ITS data available, the groups identified for western Eurasia can be integrated into a global infrageneric framework for Quercus. The Ilex group is resurrected as a well-defined group that comprises taxa traditionally placed into six subsections of Q. sects. Cerris and Lepidobalanus (white oaks) sensu Camus. Phylogenetic reconstructions suggest two major lineages within Quercus, each consisting of three infrageneric groups. Within the first lineage, the Quercus group (roburoid oaks in western Eurasia) and the Lobatae group evolved by "budding" as is reflected by incomplete lineage sorting, high variability within groups, and low differentiation among groups. The groups of the second lineage, including the Cyclobalanopsis, Cerris (cerroid oaks in western Eurasia), and Ilex (ilicoid oaks in western Eurasia) groups, evolved in a more tree-like fashion. [ABSTRACT FROM AUTHOR]

Dating the subsidence history of the North Atlantic Land Bridge (NALB) is crucial for understanding intercontinental disjunctions of northern temperate trees. Traditionally, the NALB has been assumed to have functioned as a corridor for plant migration only during the early Cenozoic, but recent findings of plant fossils and inferences from molecular studies are challenging this view. Here, we report dispersed pollen of Quercus from Late Miocene sediments in Iceland that shows affinities with extant northern hemispheric white oaks and North American red oaks. Older (15 to 10 Ma) sediments do not contain pollen of Quercus suggesting it arrived after that time. Pollen from the 9-8 Ma Hrátagil locality is indistinguishable from morphotypes common among white and red oaks. In contrast, pollen from the 5.5 Ma Selárgil locality has a tectum that is at present confined to North American white and red oaks, indicating a second episode of migration to Iceland. These findings suggest that transatlantic migration of temperate plant taxa may not have been limited by vast areas of sea or by cold climates during the Miocene. Furthermore, our results offer a plausible explanation for the remarkably low degree of genetic differentiation between modern disjunct European and North American oaks. [ABSTRACT FROM AUTHOR]

Patterns of tectum ornamentation in pollen of Quercus (oak trees, Fagaceae) are investigated using high-resolution scanning electron microscopy.Tectumornamentation is highly consistent at the infrageneric level and can be used to polarize character states within Quercus by comparison with other genera in Fagaceae. In particular, pollen data strongly suggest the recognition of an infrageneric Ilex group and, for the first time, allow definition of the set of taxa that comprise this group. The infrageneric Ilex group displays a relatively simple tectum ornamentation exclusively found in this group of oaks, in Fagus, and in extinct lineages related to Trigonobalanus, Colombobalanus, andFormanodendron. Such a simple type of tectumornamentation is also knownto represent an early developmental stage in infrageneric groups ofQuercus that have otherwise complex ornamentation (Quercus and Lobatae). Ornamentation of the tectum in the infrageneric Cyclobalanopsis group can be derived from the plesiomorphic Ilex type showing little accumulation of secondary sporopollenin. In the infrageneric Cerris, Protobalanus, Quercus, and Lobatae groups, accumulation of secondary sporopollenin masks the basic Ilex pattern. The five distinct types of tectum ornamentation are in perfect agreement with published molecular phylogenies of Quercus. Thus, pollen ornamentation is a most valuable tool to identify members of the major infrageneric groups in Quercus and provides the basis for a reevaluation of the fossil record of Quercus. [ABSTRACT FROM AUTHOR]