Thomas Denk

• Swedish Museum of Natural History

We propose a long-overdue subgeneric classification of Fagus and revision of its western Eurasian taxa based on population- level sampling of morphological and molecular data. The molecular sequence data bolstering this classification derive from nuclear-encoded genetic markers. Fagus subg. Fagus comprises twelve species, of which two occur in Nort...

Despite often being referred to as a ‘coolhouse climate’, the climate during the Miocene (23.03–5.33 Ma) was overall humid, warm and temperate. It was paced by orbitally driven cooler periods (the Oligocene–Miocene Transition and Mi-events) overprinted by a climatic optimum. Global cooling during the Late Miocene brought more arid conditions with c...

We describe a new species of Ampelopsideae (Vitaceae), Nekemias mucronata sp. nov., from the Rupelian of Cervera (Spain) and revise another fossil species, Ampelopsis hibschii, originally described from Germany. Comparison with extant Ampelopsideae suggests that the North American species Nekemias arborea is most similar to Nekemias mucronata while...

Oriental plane tree ( Platanus orientalis ) is native to the East Mediterranean region and sister to three western North American species, together forming the Pacific North American–European (PNA‐E) clade. Its sister clade, comprising several eastern North American–Mexican species, has been termed the Atlantic North American (ANA) clade. The origi...

Middle Eocene interbasaltic deposits of Hareø, West Greenland, have yielded a rich leaf and fruit record, which was described in the second half of the nineteenth century. In this study, we describe dispersed spores and pollen from the Aumarûtigssâ Member of the Hareøen Formation in order to obtain a more comprehensive picture of the late middle Eo...

Plant‐insect interactions play a crucial role in shaping terrestrial ecosystems, influencing abundance and distribution of plant species. In the present study, we investigated leaf‐mining patterns on fossil leaves from Pliocene strata of the Mahuadanr Valley, Jharkhand, eastern India, deposited under a seasonal tropical climate, and reported comple...

Standard models of speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality is more complex: plant species can evolve from other species via isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and a...

We report a new type of fossil margin galls arranged in a linear series on dicot leaf impressions from the latest Neogene (Pliocene) sediments of the Chotanagpur Plateau, Jharkhand, eastern India. We collected ca. 1500 impression and compression leaf fossils, of which 1080 samples bear arthropod damage referable to 37 different damage types (DT) in...

Notes S1 Assessment of diagnostic leaf characters in Vauquelinia and Kageneckia and of previous paleobotanical records. Notes S2 Biome occupancy and climatic characterization of modern taxa of Vauquelinia and Kageneckia. Notes S3 Fossil used for FBD chronograms and effect of different placements of fossil-taxa on clade age.

Background and Aims Cork oaks (Quercus sect. 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 effec...

Previous paleobotanical work concluded that Paleogene elements of the sclerophyllous subhumid vegetation of western Eurasia and western North America were endemic to these disjunct regions, suggesting that the southern areas of the Holarctic flora were isolated at that time. Consequently, molecular studies invoked either parallel adaptation to dry...

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 lowlan...

An increasing body of palaeobotanical data demonstrates a series of Pliocene and Pleistocene extirpations and extinctions of plant lineages in western Eurasia, which are believed to have been determined by the climatic properties of their related East Asian and North American sister lineages. We investigated the diversity of a widespread northern h...

The Gleisdorf Formation (Fm.) deposits in the clay pit at Gratkorn, Styria, Austria, are dated to 12.2–12 Ma, and are of late middle Miocene age (late Serravallian or Sarmatian). To reconstruct the paleovegetation and estimate the paleoclimate at this important vertebrate site, the palynoflora close to the boundary between the vertebrate-bearing la...

The late Early Pleistocene was the last time of equable climate in northern Central Italy, reflected in its large mammal fauna and numerous palynological records. Reliably dated leaf fossils from this time are rare, but provide crucial information on local and regional vegetation, biogeographic relationships, and species turnover coinciding with th...

Details about reasoning for using HTS data, sampling, 5S-IGS identification, pre-processing, amplicon length/GC content diversity within each sample/major type, and description of most prominent length-polymorphic patterns. Includes three supplement tables, 15 supplementary figures and two appendices: Appendix A gives a summary of Data S2; Append...

This file is part of the figshare data collection associated to the main paper. When using these data, please cite: Simeone, Cardoni et al. (2021): High-Throughput Sequencing of 5S-IGS in Fagus L. - Updated. figshare. Online resource. https://doi.org/10.6084/m9.figshare.16803481.v1

Basic information about samples, obtained HTS reads, and completely annotated lists for the 4,693 variants with an abundance of ≥ 4, as-is and summarised as Pivot tables. Uses auto-filter, auto-generating and auto-formatting functionality; up-to-date version of EXCEL® is recommended to properly view the file. This file is part of the figshare data...

Details about downstream in-depth analysis of 38 selected variants, including selection process and a fully annotated alignment in tabulated, graphically enhanced form. This file is part of the figshare data collection associated to the main paper. When using these data, please cite: Simeone, Cardoni et al. (2021): High-Throughput Sequencing of 5S...

Tabulation and characterization of gene incongruence seen in, and phylogenetic information that can be extracted from, the 28-gene data of Jiang et al. (2021); including tree inference, bootstrapping and gene-wise model statistics. The file makes extensive use of colouring and auto-filter functionality not available in pre-view mode. Up-to-date ve...

Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind‐pollinated trees with long evolutionary histories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give r...

The position of Turkey between Europe and Asia makes this region interesting for palaeobotanical investigations. We investigated plant macrofossils from early Miocene deposits of W Turkey (Soma, Manisa) and compiled a catalog of revised and new plant taxa. We documented 100 fossil-taxa, of which several are new for Turkey (Mahonia aff. pseudosimple...

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....

Diospyros is a large genus of woody flowering plants with a predominantly subtropical and tropical modern distribution. Fossils attributed to Diospyros are mainly leaf impressions from Cretaceous and Cenozoic strata across the Northern Hemisphere. However, it is difficult to assign such fossils to Diospyros because genus-diagnostic leaf characteris...

This chapter reviews Cenozoic plant assemblages from the sub-arctic North Atlantic region and their biogeographic implications. Engler's hypothesis about the ‘Arcto-Tertiary element’ remains a fundamental hypothesis about the origin of northern temperate tree genera. The book reviews previous work on the plant fossil record from Paleocene to Pleist...

Standard models of speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality is more complex: plant species can evolve from other species via isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and a...

Ecosystems are defined by the community of living organisms and how they interact together and with their environment. Insects and plants are key taxa in terrestrial ecosystems and their network determines the trophic structure of the environment. However, what drives the interactions between plants and insects in modern and fossil ecosystems is no...

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 ta...

Eocene Baltic amber forms the largest amber deposit worldwide; however, its source vegetation and climate are much debated. Representatives of the oak family (Fagaceae) were abundant in the Baltic amber source area based on numerous inclusions of staminate inflorescences or individual florets, previously assigned to Castanea and Quercus. However, t...

Species distribution models can help predicting range shifts under climate change. The aim of this study is to investigate the late Quaternary distribution of Oriental beech (Fagus orientalis) and to project future distribution ranges under different climate change scenarios using a combined palaeobotanical, phylogeographic, and modelling approach....

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 sequenc...

The late Miocene is marked by pronounced environmental changes and the appearance of strong temperature and precipitation seasonality. Although environmental heterogeneity is to be expected during this time, it is challenging to reconstruct palaeoenvironments using plant fossils. We investigated leaves and dispersed spores/pollen from 6.4 to 6 Ma s...

The former family Taxodiaceae is currently treated as nine genera in five subfamilies of the family Cupressaceae. Pollen of the ‘taxodiaceous’ Cupressaceae typically has a papilla in the leptoma area and is common in Cenozoic strata because some of its genera were key elements in lignite forming swamp forests. Dispersed fossil pollen of this group...

The late Miocene is marked by pronounced environmental changes and the appearance of strong temperature and precipitation seasonality. Although environmental heterogeneity is to be expected during this time, it is challenging to reconstruct palaeoenvironments using plant fossils. We investigated leaves and dispersed spores/pollen from 6.4-6 Ma stra...

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 Ca...

The Pliocene flora of Frankfurt am Main described by Karl Mädler during the first half of the twentieth century is a key flora for the European Pliocene. In the present study, we revised the leaf fossil taxa described by Mädler and investigated plant material collected after Mädler’s publication. The revised and augmented floral list comprises seve...

In this presentation, the distributions of Oriental beech (Fagus orientalis Lipsky) under present, past (Last Glacial Maximum, LGM; 21 ka and mid-Holocene, MH; 6 ka) and future climates (Representative Concentration Pathway (RCP) 2.6, 4.5, 8.5 scenarios) were modeled using five different species distribution modeling algorithms. Output of Maxent an...

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 infor...

The International Symposium on "Major refugia of relict trees" was a high-level scientific collaboration event co-sponsored by Shanghai Chenshan Botanical Garden (China) and University of Fribourg (Switzerland), which aimed to promote scientific exchange and international cooperation. This symposium in Shanghai is to provide a platform for sharing...

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 t...

The early Miocene was a period of major palaeogeographic reorganization in the eastern Mediterranean region, during which time the Anatolian Plateau became subaerial and several intracontinental basins intermittently became connected to the Paratethys and Mediterranean seas. In this paper, we analyse early Miocene vegetation and climate using leaf...

The tree of life is highly reticulate, with the history of population divergence buried amongst phylogenies deriving from introgression and lineage sorting. In this study, we test the hypothesis that there are regions of the oak ( Quercus , Fagaceae) genome that are broadly informative about phylogeny and investigate global patterns of oak diversit...

Premise of the study: The Eocene Baltic amber deposit represents the largest accumulation of fossil resin worldwide, and hundreds of thousands of entrapped arthropods have been recovered. Although Baltic amber preserves delicate plant structures in high fidelity, angiosperms of the "Baltic amber forest" remain poorly studied. We describe a pistill...

Reconstruction of palaeobiomes, ancient communities that exhibit a physiognomic and functional structure controlled by their environment, depends on proxies from different disciplines. Based on terrestrial mammal fossils, the late Miocene vegetation from China to the eastern Mediterranean and East Africa has been reconstructed as a single cohesive...

The middle Miocene climate transition (MMCT) was a phase of global cooling possibly linked to decreasing levels of atmospheric CO2. The MMCT coincided with the European Mammal Faunal Zone MN6. From this time, important biogeographic links between Anatolia and eastern Africa include the hominid Kenyapithecus. Vertebrate fossils suggested mixed open...

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. Her...

The middle Miocene climate transition (MMCT) was a phase of global cooling possibly linked to decreasing levels of atmospheric CO2. The MMCT coincided with the European Mammal Faunal Zone MN6. From this time, important biogeographic links between Anatolia and eastern Africa include the hominid Kenyapithecus. Vertebrate fossils suggested mixed open...

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 15 species, a dozen of which are confined to western Eurasia. This section has not been comprehensively studied using molecular tools. Here,...

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 15 species, a dozen of which are confined to western Eurasia. This section has not been comprehensively studied using molecular tools. Here,...

The early Burdigalian (MN3) plant assemblage of the Güvem area (northwestern Central Anatolia) is preserved in lacustrine sediments of the Dereköy pyroclastics. Its age is well constrained by radiometric dates of basaltic rocks bracketing the pyroclastics, making the Güvem flora one of the extremely few precisely dated early Miocene floras in the M...

In this chapter, we review major classification schemes proposed for oaks by John Claudius Loudon, Anders Sandøe Ørsted, William Trelease, Otto Karl Anton Schwarz, Aimée Antoinette Camus, Yuri Leonárdovich Menitsky, and Kevin C. Nixon. Classifications of oaks (Fig. 2.1) have thus far been based entirely on morphological characters. They differed pr...

Plant macrofossils from the lignite mines of Eskihisar, Tinaz, and Salihpaşalar (Yataǧan Basin, southwestern Anatolia) were investigated. The fossils were collected from marls overlying the exploited lignite seams and represent three subbasins within the main Yataǧan Basin. The age of the Eskihisar lignite seam is well constrained by vertebrate fos...

The historical collection of the Sarmatian flora of Leše, Slovenia, housed in the LMK, is revised. The flora is derived from lignite-bearing deposits. The fossil assemblage is dominated by Glyptostrobus europaeus, Sequoia vel Taxodium, Byttneriophyllum tiliifolium, Carpinus grandis and Quercus gigas. A characteristic element of the flora is a varie...

In this paper, we review major classification schemes proposed for oaks by John Claudius Loudon, Anders Sandøe Ørsted, William Trelease, Otto Karl Anton Schwarz, Aimée Antoinette Camus, Yuri Leonárdovich Menitsky, and Kevin C. Nixon. Classifications of oaks (Fig. 1) have thus far been based entirely on morphological characters. They differed profou...

In an ongoing palaeobotanical study of the lignite mines of the Yatağan Basin, Muğla province, Turkey, the fossil leaves of the Eskihisar lignite mine were analysed using the Climate Leaf Analysis Multivariate Program (CLAMP). The investigated fossil leaves derive from the marls and clayey limestones (Sekköy Member) overlying the exploited lignite...

Middle Miocene deposits belonging to the Eskihisar Formation exposed at the Tınaz lignite mine, Yatağan Basin, Muğla, southwestern Turkey, were investigated palynologically. Nine spores, aplanospores/zygospores and cysts of fungi and algae, seven moss and fern spores, 12 gymnosperm pollen types, and more than 80 angiosperm pollen taxa were recovere...

Sclerophyllous oaks (genus Quercus) play important roles in Neogene ecosystems of south-western Eurasia. Modern analogues (‘nearest living relatives’) for these oaks have been sought among five of six infrageneric lineages of Quercus, distributed across the entire Northern Hemisphere. A revision of leaf fossils from lower Miocene to Pliocene deposi...

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 Fagace...

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 di...

In an ongoing study, focussing on the plant fossils and palynofloras of the lignite strip mines of the Yatağan basin (Muğla province), a number of pollen taxa, previously not reported from middle Miocene terrestrial sediments of Anatolia were encountered.

The fossilized birth–death (FBD) model can make use of information contained in multiple fossils representing the same clade, and we here apply this model to infer divergence times in beeches (genus Fagus), using 53 fossils and nuclear sequences for all nine species. We also apply FBD dating to the fern clade Osmundaceae, with about 12 living speci...

We investigated a palynological section from middle Miocene sediments at Eskihisar (south-western Anatolia) to establish biogeographic links of the palynoflora and to infer the palaeoenvironment. Four algal palynomorphs, nine spore taxa, eight gymnosperms, three monocots and 67 dicot pollen types were encountered and investigated using the ‘single...

The excavated main lignite seams and overlying lacustrine sediments of the opencast mines Eskihisar, Salihpaşalar, and Tınaz, Muğla Province, south-western Turkey were investigated using a high taxonomic resolution palynological approach. The Eskihisar section comprises 47m and 56 samples of which 30 were usable for palynological analysis. The Tına...

Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in...

Plastome divergence in Fagales Intra- and intertaxonomic minimum and maximum pairwise genetic distances in Fagales based on the used plastid markers.

RbcL and trnK-matK haplotype networks haplotype networks of the investigated dataset based on rbcL and trnK-matK markers.

List of specimens investigated

Online Supplementary Archive: primary data and analyses

The uppermost Eocene Florissant Formation, Rocky Mountains, Colorado, has yielded numerous insect, vertebrate and plant fossils. Three previous comprehensive palynological studies investigated sections of lacustrine deposits of the Florissant Formation and documented the response of plant communities to volcanic eruptive phases but overall found li...

Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreem...

Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreem...

In their recent contribution, Sun et al. 1 used a fossil leaf to infer the elevation of northern Tibet during the early Miocene (ca 17 Ma). The authors compared the fossil leaf to a particular species of barberries, Berberis asiatica Roxb. ex DC., which today occurs in Nepal and the Tibetan Plateau 2 at elevations between 914 and 2,450 m 1 or 1,000...

The subject of this study is the palynology (biostratigraphic and taxonomic) and the plant remains of the lignite strip mines of Eskihisar, Salihpaşalar, and Tınaz (Muğla province, western Turkey). In the Yatağan basin two Miocene to Pliocene formations are present, the Eskihisar Formation (early to middle Miocene) and the Yatağan Formation (late M...

The “Coexistence Approach” is a mutual climate range (MCR) technique combined with the nearest-living relative (NLR) concept. It has been widely used for palaeoclimate reconstructions based on Eurasian plant fossil assemblages, most of them palynofloras (studied using light microscopy). The results have been surprisingly uniform, typically convergi...

• 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...

In this paper we document Fagaceae pollen from the Eocene of western Greenland. The pollen record suggests a remarkable diversity of the family in the early Cenozoic of Greenland. Extinct Fagaceae pollen types include Eotrigonobalanus, which extends at least back to the Paleocene, and two ancestral pollen types with affinities to the Eurasian Querc...

• 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 diffi cult to assign foss...

It has been suggested that pollen ornamentation can be used to distinguish infrageneric groups in Quercus. Here, we document pollen morphology of nearly all species of Quercus Group Ilex and show that they share distinctive microrugulate pollen ornamentation. Furthermore, pollen ultrastructure of all six infrageneric groups of Quercus was studied c...