Table S1 (1). Fossil species and climatic parameters of the corresponding NLR (depending on the f... more Table S1 (1). Fossil species and climatic parameters of the corresponding NLR (depending on the fossil-species and their botanical affinities, climate parameters of species, sections, subgenera, genera, or subfamilies are used as NLR). Table S1 (2). Climatic parameters of NLR.;Table S2 (1). Scored Köppen-Geiger signatures of all NLR species of the macrofossil and pollen flora of Vegora. Tables S2 (2). Köppen-Geiger signature values and diagram of the macrofossil and pollen flora of Vegora.
The authors investigated a palynological sequence from eastern North America spanning the Oligoce... more The authors investigated a palynological sequence from eastern North America spanning the Oligocene Miocene boundary in order to infer climate evolution over this time interval, possible movements of vegetation units along an altitudinal gradient, and to compare this with major glaciation events during this time. Climate reconstruction uses a nearest living relative approach and altitudinal vegetational shifts are investigated by the relative contribution of so-called "artificial vegetation units" to the entire palynoassemblage. Some pollen taxa are documented using LM and SEM.
Philosophical transactions - Royal Society. Mathematical, physical and engineering sciences, 2016
Species relationships and divergence times of beeches (Fagus): New insights from the inclusion of... more Species relationships and divergence times of beeches (Fagus): New insights from the inclusion of numerous fossil beech species in a birth-death clock approach.
Background and Aims Cork oaks (Quercus section Cerris) comprise 15 extant species in Eurasia. Des... more 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...
Abstract Ecosystems are defined by the community of living organisms and how they interact togeth... more Abstract 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 not well understood. In this study, we analyzed insect damage richness and frequency in 5000 fossil leaves deposited during the early Miocene at 20–17 Ma along a latitudinal gradient from Europe (two localities in Czech Republic) to Turkey (one locality) in a temperate climate setting. Damage frequency was mainly linked with abiotic factors (temperature, precipitation seasonality) whereas damage richness was mainly linked with biotic factors (plant richness, biome). Univariate analysis of insect damage types consistently suggested closer trophic similarity between the Mediterranean and either the one or the other Central European plant assemblage. In contrast, multivariate analysis of all insect damage types indicated closer similarity between the two Central European sites highlighting the importance of biogeographic legacy and geographic closeness to the plant-insect interaction patterns. Our results underscore the high complexity of the herbivory network and call for careful interpretations of plant-insect interaction patterns in palaeoecological studies. Finally, comparing the trophic similarity between different localities using total evidence plots as done in this work might be a promising complementary method in comparative studies of plant-insect interactions.
Species distribution models can help predicting range shifts under climate change. The aim of thi... more 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. Five species distribution modelling algorithms under the R-package `biomod2`were applied to occurrence data ofFagus orientalisto predict distributions under present, past (Last Glacial Maximum, 21 ka, Mid-Holocene, 6 ka), and future climatic conditions with different scenarios obtained from MIROC-ESM and CCSM4 global climate models. Distribution models were compared to palaeobotanical and phylogeographic evidence. Pollen data indicate northern Turkey and the western Caucasus as refugia for Oriental beech during the Last Glacial Maximum. Although pollen records are missing, molecular data point to Last Glacial Maximum refugia in northern I...
SummaryThe tree of life is highly reticulate, with the history of population divergence buried am... more SummaryThe 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 diversity.We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing ca. 250 oak species to infer a time-calibrated phylogeny of the world’s oaks. We use reversible-jump MCMC to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20,000 RAD-seq loci back to a recently published 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. Rough...
Oaks of Quercus Group Ilex are emblematic components of the Mediterranean landscapes and the full... more 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.
The palynoflora of the lignite strip mines of the Yatagan basin, located in the Mugla province of... more The palynoflora of the lignite strip mines of the Yatagan basin, located in the Mugla province of western Turkey, is the focus of this study. Samples were taken from the Eskihisar, Salihpasalar and ...
Botanical Journal of the Linnean Society, Jan 30, 2023
The Late Oligocene to Early Miocene flora of the Ban Pa Kha Subbasin (Li Basin, northern Thailand... more 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.
The Topics in Geobiology series covers the broad discipline of geobiology that is devoted to docu... more The Topics in Geobiology series covers the broad discipline of geobiology that is devoted to documenting life history of the Earth. A critical theme inherent in addressing this issue and one that is at the heart of the series is the interplay between the history of life and the changing environment. The series aims for high quality, scholarly volumes of original research as well as broad reviews. Geobiology remains a vibrant as well as a rapidly advancing and dynamic field. Given this field's multidiscipline nature, it treats a broad spectrum of geologic, biologic, and geochemical themes all focused on documenting and understanding the fossil record and what it reveals about the evolutionary history of life. The Topics in Geobiology series was initiated to delve into how these numerous facets have influenced and controlled life on Earth. Recent volumes have showcased specific taxonomic groups, major themes in the discipline, as well as approaches to improving our understanding of how life has evolved. Taxonomic volumes focus on the biology and paleobiology of organisms-their ecology and mode of life-and, in addition, the fossil record-their phylogeny and evolutionary patterns-as well as their distribution in time and space. Theme-based volumes, such as predator-prey relationships, biomineralization, paleobiogeography, and approaches to high-resolution stratigraphy, cover specific topics and how important elements are manifested in a wide range of organisms and how those dynamics have changed through the evolutionary history of life. Comments or suggestions for future volumes are welcomed.
The Topics in Geobiology series covers the broad discipline of geobiology that is devoted to docu... more The Topics in Geobiology series covers the broad discipline of geobiology that is devoted to documenting life history of the Earth. A critical theme inherent in addressing this issue and one that is at the heart of the series is the interplay between the history of life and the changing environment. The series aims for high quality, scholarly volumes of original research as well as broad reviews. Geobiology remains a vibrant as well as a rapidly advancing and dynamic field. Given this field's multidiscipline nature, it treats a broad spectrum of geologic, biologic, and geochemical themes all focused on documenting and understanding the fossil record and what it reveals about the evolutionary history of life. The Topics in Geobiology series was initiated to delve into how these numerous facets have influenced and controlled life on Earth. Recent volumes have showcased specific taxonomic groups, major themes in the discipline, as well as approaches to improving our understanding of how life has evolved. Taxonomic volumes focus on the biology and paleobiology of organisms-their ecology and mode of life-and, in addition, the fossil record-their phylogeny and evolutionary patterns-as well as their distribution in time and space. Theme-based volumes, such as predator-prey relationships, biomineralization, paleobiogeography, and approaches to high-resolution stratigraphy, cover specific topics and how important elements are manifested in a wide range of organisms and how those dynamics have changed through the evolutionary history of life. Comments or suggestions for future volumes are welcomed.
SUMMARYStandard models of plant speciation assume strictly dichotomous genealogies in which a spe... more SUMMARYStandard 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 rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi‐copy, potentially multi‐locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra‐genomic recombination. Therefore, it can provide unique insights into the dynamic speciation processes of lineages that diversified tens of millions of years ago. Here, we provide the first high‐throughput sequencing (HTS) of the 5S intergenic spacers (5S‐IGS) for a lineage of wind‐pollinated subtropical to temperate trees, the Fagus crenata – F. sylvatica s.l. lineage, and its distant re...
The internal transcribed spacers ITS1 and ITS2 of the nuclear ribosomal DNA (rDNA) have recently ... more The internal transcribed spacers ITS1 and ITS2 of the nuclear ribosomal DNA (rDNA) have recently been found to display remarkable intraspecific polymorphism, a feature suggested as limiting their value for phylogenetic reconstructions. A comparative study of oligonucleotide motives and intraindividual nucleotide variability across all species of the tree genus Fagus (beech) shows, however, that this intraspecific ITS polymorphism follows a particular pattern, which can be used to detect reticulation and ancient polymorphism within the genus. Coding ITS polymorphisms as phylogenetically informative characters, moreover, resulted in better-resolved phylogenies than traditional 'base-per-base' maximum parsimony and maximum likelihood analyses.
Table S1 (1). Fossil species and climatic parameters of the corresponding NLR (depending on the f... more Table S1 (1). Fossil species and climatic parameters of the corresponding NLR (depending on the fossil-species and their botanical affinities, climate parameters of species, sections, subgenera, genera, or subfamilies are used as NLR). Table S1 (2). Climatic parameters of NLR.;Table S2 (1). Scored Köppen-Geiger signatures of all NLR species of the macrofossil and pollen flora of Vegora. Tables S2 (2). Köppen-Geiger signature values and diagram of the macrofossil and pollen flora of Vegora.
The authors investigated a palynological sequence from eastern North America spanning the Oligoce... more The authors investigated a palynological sequence from eastern North America spanning the Oligocene Miocene boundary in order to infer climate evolution over this time interval, possible movements of vegetation units along an altitudinal gradient, and to compare this with major glaciation events during this time. Climate reconstruction uses a nearest living relative approach and altitudinal vegetational shifts are investigated by the relative contribution of so-called "artificial vegetation units" to the entire palynoassemblage. Some pollen taxa are documented using LM and SEM.
Philosophical transactions - Royal Society. Mathematical, physical and engineering sciences, 2016
Species relationships and divergence times of beeches (Fagus): New insights from the inclusion of... more Species relationships and divergence times of beeches (Fagus): New insights from the inclusion of numerous fossil beech species in a birth-death clock approach.
Background and Aims Cork oaks (Quercus section Cerris) comprise 15 extant species in Eurasia. Des... more 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...
Abstract Ecosystems are defined by the community of living organisms and how they interact togeth... more Abstract 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 not well understood. In this study, we analyzed insect damage richness and frequency in 5000 fossil leaves deposited during the early Miocene at 20–17 Ma along a latitudinal gradient from Europe (two localities in Czech Republic) to Turkey (one locality) in a temperate climate setting. Damage frequency was mainly linked with abiotic factors (temperature, precipitation seasonality) whereas damage richness was mainly linked with biotic factors (plant richness, biome). Univariate analysis of insect damage types consistently suggested closer trophic similarity between the Mediterranean and either the one or the other Central European plant assemblage. In contrast, multivariate analysis of all insect damage types indicated closer similarity between the two Central European sites highlighting the importance of biogeographic legacy and geographic closeness to the plant-insect interaction patterns. Our results underscore the high complexity of the herbivory network and call for careful interpretations of plant-insect interaction patterns in palaeoecological studies. Finally, comparing the trophic similarity between different localities using total evidence plots as done in this work might be a promising complementary method in comparative studies of plant-insect interactions.
Species distribution models can help predicting range shifts under climate change. The aim of thi... more 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. Five species distribution modelling algorithms under the R-package `biomod2`were applied to occurrence data ofFagus orientalisto predict distributions under present, past (Last Glacial Maximum, 21 ka, Mid-Holocene, 6 ka), and future climatic conditions with different scenarios obtained from MIROC-ESM and CCSM4 global climate models. Distribution models were compared to palaeobotanical and phylogeographic evidence. Pollen data indicate northern Turkey and the western Caucasus as refugia for Oriental beech during the Last Glacial Maximum. Although pollen records are missing, molecular data point to Last Glacial Maximum refugia in northern I...
SummaryThe tree of life is highly reticulate, with the history of population divergence buried am... more SummaryThe 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 diversity.We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing ca. 250 oak species to infer a time-calibrated phylogeny of the world’s oaks. We use reversible-jump MCMC to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20,000 RAD-seq loci back to a recently published 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. Rough...
Oaks of Quercus Group Ilex are emblematic components of the Mediterranean landscapes and the full... more 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.
The palynoflora of the lignite strip mines of the Yatagan basin, located in the Mugla province of... more The palynoflora of the lignite strip mines of the Yatagan basin, located in the Mugla province of western Turkey, is the focus of this study. Samples were taken from the Eskihisar, Salihpasalar and ...
Botanical Journal of the Linnean Society, Jan 30, 2023
The Late Oligocene to Early Miocene flora of the Ban Pa Kha Subbasin (Li Basin, northern Thailand... more 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.
The Topics in Geobiology series covers the broad discipline of geobiology that is devoted to docu... more The Topics in Geobiology series covers the broad discipline of geobiology that is devoted to documenting life history of the Earth. A critical theme inherent in addressing this issue and one that is at the heart of the series is the interplay between the history of life and the changing environment. The series aims for high quality, scholarly volumes of original research as well as broad reviews. Geobiology remains a vibrant as well as a rapidly advancing and dynamic field. Given this field's multidiscipline nature, it treats a broad spectrum of geologic, biologic, and geochemical themes all focused on documenting and understanding the fossil record and what it reveals about the evolutionary history of life. The Topics in Geobiology series was initiated to delve into how these numerous facets have influenced and controlled life on Earth. Recent volumes have showcased specific taxonomic groups, major themes in the discipline, as well as approaches to improving our understanding of how life has evolved. Taxonomic volumes focus on the biology and paleobiology of organisms-their ecology and mode of life-and, in addition, the fossil record-their phylogeny and evolutionary patterns-as well as their distribution in time and space. Theme-based volumes, such as predator-prey relationships, biomineralization, paleobiogeography, and approaches to high-resolution stratigraphy, cover specific topics and how important elements are manifested in a wide range of organisms and how those dynamics have changed through the evolutionary history of life. Comments or suggestions for future volumes are welcomed.
The Topics in Geobiology series covers the broad discipline of geobiology that is devoted to docu... more The Topics in Geobiology series covers the broad discipline of geobiology that is devoted to documenting life history of the Earth. A critical theme inherent in addressing this issue and one that is at the heart of the series is the interplay between the history of life and the changing environment. The series aims for high quality, scholarly volumes of original research as well as broad reviews. Geobiology remains a vibrant as well as a rapidly advancing and dynamic field. Given this field's multidiscipline nature, it treats a broad spectrum of geologic, biologic, and geochemical themes all focused on documenting and understanding the fossil record and what it reveals about the evolutionary history of life. The Topics in Geobiology series was initiated to delve into how these numerous facets have influenced and controlled life on Earth. Recent volumes have showcased specific taxonomic groups, major themes in the discipline, as well as approaches to improving our understanding of how life has evolved. Taxonomic volumes focus on the biology and paleobiology of organisms-their ecology and mode of life-and, in addition, the fossil record-their phylogeny and evolutionary patterns-as well as their distribution in time and space. Theme-based volumes, such as predator-prey relationships, biomineralization, paleobiogeography, and approaches to high-resolution stratigraphy, cover specific topics and how important elements are manifested in a wide range of organisms and how those dynamics have changed through the evolutionary history of life. Comments or suggestions for future volumes are welcomed.
SUMMARYStandard models of plant speciation assume strictly dichotomous genealogies in which a spe... more SUMMARYStandard 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 rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi‐copy, potentially multi‐locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra‐genomic recombination. Therefore, it can provide unique insights into the dynamic speciation processes of lineages that diversified tens of millions of years ago. Here, we provide the first high‐throughput sequencing (HTS) of the 5S intergenic spacers (5S‐IGS) for a lineage of wind‐pollinated subtropical to temperate trees, the Fagus crenata – F. sylvatica s.l. lineage, and its distant re...
The internal transcribed spacers ITS1 and ITS2 of the nuclear ribosomal DNA (rDNA) have recently ... more The internal transcribed spacers ITS1 and ITS2 of the nuclear ribosomal DNA (rDNA) have recently been found to display remarkable intraspecific polymorphism, a feature suggested as limiting their value for phylogenetic reconstructions. A comparative study of oligonucleotide motives and intraindividual nucleotide variability across all species of the tree genus Fagus (beech) shows, however, that this intraspecific ITS polymorphism follows a particular pattern, which can be used to detect reticulation and ancient polymorphism within the genus. Coding ITS polymorphisms as phylogenetically informative characters, moreover, resulted in better-resolved phylogenies than traditional 'base-per-base' maximum parsimony and maximum likelihood analyses.
The coexistence approach (CA) is widely used to reconstruct palaeoclimates for the Cenozoic. Most... more The coexistence approach (CA) is widely used to reconstruct palaeoclimates for the Cenozoic. Most published CA analyses relied on climate data for nearest living relatives (NLRs) stored in the Palaeoflora database (PFDB). Here, we used more than two-hundred modern relevés (taxon lists of forest stands) from North American, Caucasian and East Asian forest regions in order to test the ability of CA/PFDB to estimate palaeoclimate. Since only data for mean annual temperature (MAT) are publicly available from the PFDB, we concentrated on this climate parameter. Two criteria were tested: ‘resolution’ and ‘reliability’ of CA/PFDB analyses. The CA assumes that for a given climate parameter (e.g. MAT; mean annual precipitation; coldest month mean temperature etc.) the interval shared by all or nearly all NLRs for a fossil assemblage is best describing the past climatic conditions. Narrow, i.e. well-resolved, intervals are desirable, since they describe most precisely the climate. Our results show that CA/PFDB is unable to reliably reconstruct the actual climates of most of the relevés analysed. CA/PFDB performed best for lowland and mid-altitude stands with MAT of ca 13–16 °C, while producing remarkably incorrect results for warmer lowland stands and cooler stands at higher elevations. This is mainly due to generally incorrect entries of MAT ranges of NLRs in the PFDB. Using corrected MAT tolerances, the reconstructed, low-resolved intervals (3 °C in exceptional cases, typically 5–10 °C) fall within the actual climates. Hence, only dramatic climate changes are likely to be captured in a CA analysis. This renders the coexistence approach useless for the quantitative reconstruction of palaeoclimate and calls for alternative approaches of investigating past climates by means of fossil plants.
Review of Palaeobotany and Palynology, Jan 1, 2009
Biogeographic histories cannot solely rely on cladistic reconstructions. First, a cladogram may b... more Biogeographic histories cannot solely rely on cladistic reconstructions. First, a cladogram may be an insufficient representation of evolution, in particular at low taxonomic levels (here: intrageneric evolution). Diversification and speciation in plants is complex, rarely resulting in a single unambiguous tree-like genealogy. Second, the modern distribution of a monophyletic group (here: genus Fagus) may be highly incomplete. For instance, important areas such as Central Asia and Iceland no longer include the taxon. Third, incorporating fossil taxa, including potential ancestors of modern taxa, into a cladistic phylogeny may be intrinsically difficult. All three issues apply to the Northern Hemispheric genus Fagus, the beech trees. In this study, we use the exceptionally complete fossil record of Fagus to trace its spatiotemporal unfolding throughout the Cainozoic. Fossil taxa are placed in a phylogenetic framework following Darwinian classification by identifying common ancestries and overall patterns of similarity. These lines of evidence are then combined to put up a holistic biogeographic history of Fagus in the Cainozoic, which is discussed in the light of general patterns of morphological and molecular differentiation and diversification. Based on the fossil record, Fagus evolved in the Northern Pacific region. Earliest fossils are known both from Northeast Asia and north-western North America (possibly extending to Axel Heiberg Island) in the Middle Eocene. The range expansion of Fagus into Central Asia and Europe during the Oligocene was accompanied by a first differentiation into a continental Eurasian and northern Pacific lineage. In the Miocene, Fagus is found throughout the Northern Hemisphere up to very high latitudes (e.g., Iceland). By the end of the Miocene several lineages had been established, including putative ancestors of modern taxa (e.g. F. evenensis, the ancestor of subgenus Engleriana). Overall, the Miocene taxa are characterized by conspicuous morphological plasticity reflecting potentially unhindered gene flow. In post-Miocene times, Fagus underwent range reduction and extinction in high latitudes, Central Asia and western North America. The disruption of a former homogeneous area led to the shaping of modern species. The methodological approaches used here for Fagus take into account the particular nature of data sets palaeobotanists are usually confronted with.
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Papers by Thomas Denk