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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., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Annals of Botany Company.)

Premise: The Fagaceae comprise around 1000 tree species in the Northern Hemisphere. Despite an extensive fossil pollen record, reconstructing biogeographic patterns is hampered because it is difficult to achieve good taxonomic resolution with light microscopy alone. We investigate dispersed pollen of Fagaceae from the Miocene Søby flora, Denmark. We explore the latitudinal gradient in Fagaceae distribution during the Miocene Climatic Optimum (MCO) in Europe and the Northern Hemisphere to compare it with the Eocene Warmhouse and the present., Methods: We investigated dispersed pollen using light and scanning electron microscopy. We assessed biogeographic patterns in Fagaceae during two warm periods in Earth history (MCO, Eocene) and the present., Results: Eight species of Fagaceae were recognized in the Søby flora. Of these, Fagus had a continuous Mediterranean to subarctic distribution during MCO; Quercus sect. Cerris and castaneoids had northern limits in Denmark, and evergreen Quercus sect. Ilex in Central Europe. In a northern hemispheric context, Fagus and sections of Quercus had more northerly distribution limits during Eocene and MCO with maximum northward extensions during Eocene (Fagus, castaneoids) or Oligo-Miocene (Quercus sects. Cerris and Ilex). The known distribution of the extinct Tricolporopollenites theacoides during MCO included Central Europe and East China, while this taxon thrived in South China during Eocene., Conclusions: More northerly distributions during MCO and Eocene probably were determined by temperature. In contrast, fossil occurrences in areas that are arid or semi-humid today were determined by maritime conditions in these areas (western North America, Central Asia) during the Cenozoic., (© 2021 The Authors. American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

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., (© 2020 John Wiley & Sons Ltd.)

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., (© 2019 The Authors. New Phytologist © 2019 New Phytologist Trust.)

Wilf et al (Research Articles, 7 June 2019, eaaw5139) claim that Castanopsis evolved in the Southern Hemisphere from where it spread to its modern distribution in Southeast Asia. However, extensive paleobotanical records of Antarctica and Australia lack evidence of any Fagaceae, and molecular patterns indicate shared biogeographic histories of Castanopsis , Castanea , Lithocarpus , and Quercus subgenus Cerris , making the southern route unlikely., (Copyright © 2019, American Association for the Advancement of Science.)

The Late Oligocene to Early Miocene flora of the Ban Pa Kha Subbasin (Li Basin, northern Thailand) provides a record of montane dry tropical oak-pine forests. The rich ensemble of Fagaceae typical of these forests might have existed in the wider region of Southeast Asia since Eocene times and various fossil plant assemblages represented both lowland (Fagaceae, Dipterocarpaceae) and upland (Fagaceae, Pinaceae) tropical forests. These findings are in conflict with previous interpretations of vegetation development in northern Thailand, which stressed that stratigraphically older (possibly Late Oligocene) spore and pollen assemblages in northern Thailand were markedly different from the modern tropical flora and had a distinct northern temperate character. A major change in climate would have caused a dramatic shift to tropical conditions since the Mid-Miocene. Considering palaeobotanical data from adjacent regions in Southeast Asia, we suggest that differences in spore and pollen assemblages in intermontane basins in northern Thailand are more likely to represent different facies and lowland/upland settings. Assembly of these forest ecosystems, typically comprising Quercus sections Cyclobalanopsis , Ilex and Quercus , pollen of Castaneoideae with affinities to Castanopsis and Lithocarpus , and extinct fagaceous genera such as Eotrigonobalanus , most probably dates back to the Eocene. The absence of oaks of Quercus section Cerris in the spore and pollen assemblage of the Ban Pa Kha Subbasin, despite this group being part of the modern vegetation, might reflect the late arrival (secondary radiation) of this chiefly temperate group in tropical Southeast Asia. [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]

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]

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]