Search

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.

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, theFagus crenata – F. sylvaticas.l. lineage, and its distant relativeF. japonica.The observed 4,963 unique 5S-IGS variants reflect a complex history of hybrid origins, lineage sorting, mixing via secondary gene flow, and intra-genomic competition between two or more paralogous-homoeologous 5S rDNA lineages. We show that modern species are genetic mosaics and represent a striking case of ongoing reticulate evolution during the past 55 million years.Significance statementThe evolution of extra-tropical wind-pollinated tree genera involves dynamic speciation processes. High-throughput sequencing of the multi-copy, potentially multi-locus 5S rDNA reveals a complex history of hybrid origins, lineage sorting and mixing, and intra-genomic competition between paralogous-homeologous loci in the core group of Eurasian beech trees (genusFagus) and their distant relative,F. japonica. The modern species are genetic mosaics and represent a striking case of at least 55 million years of ongoing reticulate evolution.

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.

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. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification due to climatic transitions or ecological opportunity.The support we find 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.

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 biome with increasingly arid conditions, with modern African savannahs the surviving remnant. Here, we test this reconstruction using plant fossils spanning 14-4 million years ago from sites in Greece, Bulgaria, Turkey, the Tian Shan Mountains and Baode County in China, and East Africa. The western Eurasian sites had a continuous forest cover of deciduous or evergreen angiosperms and gymnosperms, with 15% of 1,602 fossil occurrences representing conifers, which were present at all but one of the sites. Raup-Crick analyses reveal high floristic similarity between coeval eastern Mediterranean and Chinese sites, and low similarity between Eurasian and African sites. The disagreement between plant-based reconstructions, which imply that late Miocene western Eurasia was covered by evergreen needleleaf forests and mixed forests, and mammal-based reconstructions, which imply a savannah biome, throws into doubt the approach of inferring Miocene precipitation and open savannah habitats solely from mammalian dental traits. Organismal communities are constantly changing in their species composition, and neither animal nor plant traits by themselves are sufficient to infer entire ancient biomes. The plant fossil record, however, unambiguously rejects the existence of a cohesive savannah biome from eastern Asia to northeast Africa.

Aim: Winteraceae comprise c.130 species in seven genera, with the greatest species diversity in the Pacific (Pseudowintera, Zygogynum), Australia (Bubbia, Tasmannia), New Guinea (Belliolum, Bubbia, Zygogynum, Tasmannia) and Madagascar (Takhtajania). Only Drimys occurs in South America. Because of their Cretaceous leaves, wood and pollen fossils, and their lack of xylem vessels, Winteraceae throw light on early angiosperm evolution. We describe a Winteraceae pollen tetrad from the Paleocene of Greenland, review the family's fossil record and palaeogeography and document its current climate preferences. Location: Worldwide. Methods: Extant and fossil pollen were studied with light and scanning electron microscopy. Molecular phylogenetic and character mapping approaches were used to infer the evolution of pollen characters, and 37,842 collections from the Global Biodiversity Information Facility were used to infer the climate and vegetation types occupied by today's Winteraceae and to compare them to the Paleocene climate and vegetation of Greenland as inferred from the fossil record of other families. Results: Winteraceae are the only flowering plants with persistent, acalymmate tetrads composed of ulcerate grains with a distinct reticulate sculpturing. The tetrad described here as Pseudowinterapollis agatdalensis Grimsson & Zetter spec. nov. comes from Agatdalen valley in western Greenland and dates to the Early Paleocene, Danian, 64-62Ma. It shows the complete character suite of modern Winteraceae and overlaps the LM characters of the three previously known Pseudowinterapollis species from Australia, New Zealand and South Africa. The palaeoflora of the Agatdal Formation consisted of a mixed deciduous-evergreen forest resembling habitats where Winteraceae occur today. Main conclusions: Macro- and microfossil records of Winteraceae extend back to the Upper Cretaceous in both Laurasia and Gondwana, and the family's biogeography, like that of its sister family, Canellaceae, cannot be understood by focusing only on southern Gondwana. Winteraceae instead were part of broadleaved forests in Paleocene and Eocene North American and Greenland and may have reached Europe via the North Atlantic Land Bridge, explaining Eocene Winteraceae wood in northern Germany.

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 deposits suggests that morphotypes of the Quercus drymeja complex are very similar to a number of extant Himalayan, East Asian, and Southeast Asian species of Quercus Group Ilex and may indicate subtropical, relatively humid conditions. Quercus mediterranea comprises leaf morphotypes that are encountered in modern Mediterranean species of Quercus Group Ilex, but also in Himalayan and East Asian members of this group indicating fully humid or summer-wet conditions. The fossil taxa Quercus drymeja and Q. mediterranea should be treated as morphotype complexes, which possibly comprised different biological species at different times. Quercus mediterranea, although readily recognizable as a distinct morphotype in early to late Miocene plant assemblages, may in fact represent small leaves of the same plants that constitute the Quercus drymeja complex. Based on the available evidence, the taxa [GG1] forming the Q. drymeja complex and Q. mediterranea thrived in fully humid or summer-wet climates. The onset of the modern vegetational context of Mediterranean sclerophyllous oaks is difficult to trace, but may have been during the latest Pliocene/early Pleistocene. 440886

Background Drosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum, together with the highly succulent and species-rich tribe Ruschieae, constitute the ‘core ruschioids’ in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution. Methods Using chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species of Drosanthemum with multiple accessions for widespread species. A well-curated, geo-referenced occurrence dataset comprising the 134 genetically analysed and 863 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole. Results Phylogenetic inference supports nine clades within Drosanthemum, seven of which group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as cryptic species. In-depth analyses of sequence patterns in each gene region were used to reveal phylogenetic affinities inside the retrieved clades in more detail. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are genetically and morphologically diverse. In contrast, less species-rich, genetically less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest that the main lineages arose from an initial rapid radiation, with subsequent diversification in some clades.

BackgroundDrosanthemum,the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species,Drosanthemumtogether with the highly succulent and species-rich tribe Ruschieae constitute the ‘core ruschioids’ in Aizoaceae. WithinDrosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution.MethodsUsing chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species represented by multiple accessions ofDrosanthemum. A well-curated, geo-referenced occurrence data set comprising the phylogenetically studied and 867 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole.ResultsPhylogenetic inference supports nine clades withinDrosanthemum, seven of them group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera withinDrosanthemum, with exceptions such as (pseudo-) cryptic species. In-depth analyses of sequence patterns in each gene region revealed phylogenetic affinities not obvious in the phylogenetic tree. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgeneraDrosanthemump.p., Vespertina, Xamera) that are molecular and morphologically diverse. In contrast, less species-rich, molecularly less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua,Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest initial rapid radiation generating the main lineages, with some clades showing subsequent diversification.

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).

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, we assess species diversity and reconstruct a first comprehensive taxonomic 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 geographic patterns of species coevolution within Sect. Cerris and its sister section Ilex. We identified two widespread and ancestral haplotypes, and less common, locally restricted, derived variants. Signatures shared with Mediterranean species of Sect. Ilex, but not with the East Asian Cerris siblings, 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 efficient for establishing a molecular-taxonomic framework and to reveal hybridization and reticulation processes. Four main evolutionary lineages were identified. The first lineage comprises 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 the most derived and comprises Q. suber, the cork oak, and Q. crenata. Quercus cerris and Q. trojana displayed exceptional levels of variation; Q. macrolepis and Q. euboica, previously treated as subspecies of Q. ithaburensis and Q. trojana, likely deserve an 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. Phylogeographic inferences on the origin and diversification of Quercus Sect. Cerris are provided to fill an important gap in the knowledge of oak diversity and evolution.

The impact of historical and present drivers on forest biodiversity is poorly understood. A better understanding is mandatory to ensure conservation and appropriate management of biodiversity and ecosystem functions in the face of climate warming and increasing demand for wood products. Here, we assess forest management strategies for maintaining plant biodiversity in Central European beech forests, with a focus on Germany. We show that (1) diversity of the German vascular plant flora increased exponentially during the Holocene reaching 3874 species mainly through apomictic and hybrid speciation. Vascular plant species confined to forests comprise about 10 % of this flora. No loss in vascular plants restricted to forests occured over the past 250 years despite of forest management; (2) the indigenous arboreal flora has a low diversity (64 tree species) compared with other continents due to environmental changes in the last 2 million years; (3) forest management has maintained a high plant diversity in the past. It should be an aim of silviculture to ensure this in the future; and (4) only 22 of the indigenous tree species are commercially used; nine of these commercially used species are threatened by diseases. We introduce the concept of palaeo-neophytes to address genera that existed in Central Europe during the latest Cenozoic. The introduction of species of palaeo-neophytic genera and sub-Mediterranean species is discussed as a measure to buffer negative effects on native species caused by climate change and spread of novel diseases.

A major concern in molecular clock dating is how to use information from the fossil record to calibrate genetic distances from DNA sequences. Here we apply three Bayesian dating methods that differ in how calibration is achieved— "node dating" (ND) in BEAST, "total evidence" (TE) dating in MrBayes, and the "fossilized birth-death" (FBD) in FDPPDiv— to infer divergence times in the royal ferns. Osmundaceae have 16-17 species in four genera, two mainly in the Northern Hemisphere and two in South Africa and Australasia; they are the sister clade to the remaining leptosporangiate ferns. Their fossil record consists of at least 150 species in ∼17 genera. For ND, we used the five oldest fossils, whereas for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils, we included up to 36 rhizomes and frond compression/impression fossils, which for TE dating were scored for 33 morphological characters. We also subsampled 10%, 25%, and 50% of the 36 fossils to assess model sensitivity. FBD-derived divergence ages were generally greater than those inferred from ND; two of seven TE-derived ages agreed with FBD-obtained ages, the others were much younger or much older than ND or FBD ages. We prefer the FBD-derived ages because they best fit the Osmundales fossil record (including Triassic fossils not used in our study). Under the preferred model, the clade encompassing extant Osmundaceae (and many fossils) dates to the latest Paleozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, the FBD approach yielded speciation and extinction rates that overlapped those obtained from just neontological data. However, FBD estimates of speciation and extinction are sensitive to violations in the assumption of continuous fossil sampling; therefore, these estimates should be treated with caution. (Bayesian inference; fossilized birth-death dating; molecular clock calibration; node dating; total evidence dating; royal ferns.)

A new fossil flower, Kajanthus lusitanicus gen. et sp. nov, is described from the Early Cretaceous (late Aptian–early Albian) Chicalhao site near the village of Juncal, western Portugal, based on a single coalified specimen. The flower is small, actinomorphic, trimerous and bisexual, slightly compressed and with floral organs tightly adhering. The perianth is organised in more than two whorls. The inner two whorls consist of six bulky, apparently fleshy parts. The outer perianth whorls consist of narrow parts. There are six stamens, arranged in two whorls. The filaments are thick and anthers tetrasporangiate. The pollen sacs are protruding with extrorse dehiscence. Pollen observed in situ is tricolpate, tectate, finely punctate-perforate, compressed and more or less spherical in polar view with a diameter of about 15 µm. The gynoecium is superior and composed of three free carpels. Non-destructive virtual sectioning of the single flower using synchrotron radiation X-ray tomographic microscopy reve...

The phylogenetic structure of Asclepiadoideae (Apocynaceae) has been elucidated at the tribal and subtribal levels in the last two decades. However, to date, the systematic positions of seven Asian genera, Cosmostigma, Graphistemma, Holostemma, Pentasachme, Raphistemma, Seshagiria and Treutlera, have not been investigated. In this study, we examine the evolutionary relationships among these seven small enigmatic Asian genera and clarify their positions in Asclepiadoideae, using a combination of plastid sequences of rbcL, rps16, trnL and trnL- F regions. Cosmostigma and Treutlera are resolved as members of the non-Hoya clade of Marsdenieae with strong support (maximum parsimony bootstrap support value BSMP = 96, maximum likelihood bootstrap support value BSML = 98, Bayesian-inferred posterior probability PP = 1.0). Pentasachme is resolved as sister of Stapeliinae to Ceropegieae with moderate support (BSMP = 64, BSML = 66, PP = 0.94). Graphistemma, Holostemma, Raphistemma and Seshagiria are all nested in the Asclepiadeae-Cynanchinae clade (BSMP = 97, BSML = 100, PP = 1.0). The study confirms the generally accepted tribal and subtribal structure of the subfamily. One exception is Eustegia minuta, which is placed here as sister to all Asclepiadeae (BSMP = 58, BSML = 76, PP = 0.99) and not as sister to the Marsdenieae + Ceropegieae clade. The weak support and conflicting position indicate the need for a placement of Eustegia as an independent tribe. In Asclepiadeae, a sister group position of Cynanchinae to the Asclepiadinae + Tylophorinae clade is favoured (BSMP = 84, BSML = 88, PP = 1.0), whereas Schizostephanus is retrieved as unresolved. Oxystelma appears as an early-branching member of Asclepiadinae with weak support (BSMP = 52, BSML = 74, PP = 0.69). Calciphila and Solenostemma are also associated with Asclepiadinae with weak support (BSMP = 37, BSML = 45, PP = 0.79), but all alternative positions are essentially without support. The position of Indian Asclepiadoideae in the family phylogeny is discussed. (c) 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 601-619.

Following molecular and morphological study, four new species in Drosanthemum, belonging to the subgenera Drosanthemum, Necopina, and Speciosa, are described: D. nollothense, D. obibense, D. ecclesianum and D. brakfonteinense. In subgenus Quastea, a cryptic species imitating D. cymiferum is identified and discussed, but not formally described.

From mesic to arid: Leaf epidermal features suggest preadaptation in Miocene dragon trees (Dracaena)

Betulaceae, with 120–150 species in six genera, are a family of Fagales that occurs mainly in the Northern Hemisphere. Previous studies of the evolution of Alnus, Betula, Carpinus, Corylus, Ostrya and Ostryopsis have relied on a relatively small number of sequence data and molecular clocks with fixed-point calibrations. We exploited GenBank to construct Betulaceae matrices of up to 900 sequence accessions and 9300 nucleotides of nuclear and plastid DNA; we also computed species consensus sequences to build 46- and 29-species matrices that strike a balance between species sampling and nucleotide sampling. Trees were rooted on Ticodendraceae and Casuarinaceae, and divergence times were inferred under relaxed and strict molecular clocks, using alternative fossil constraints. The data support the traditional two subfamilies, Betuloideae (Alnus, Betula) and Coryloideae, and show that Ostryopsis is sister to Ostrya/Carpinus. The fossil record and molecular clocks calibrated with alternating fossils indicate that the stem lineage of Betulaceae dates back to the Upper Cretaceous, the two subfamilies to the Palaeocene and the most recent common ancestors of each of the living genera to the mid- to late Miocene. A substitution rate shift in Coryloideae between 25 and 15 Mya preceded the mid-Miocene climatic optimum and may be linked to temperate niches that became available following the mid-Miocene. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172, 465–477.

In this chapter, we review major classification schemes proposed for oaks by John Claudius Loudon, Anders Sandoe Orsted, William Trelease, Otto Karl Anton Schwarz, Aimee Antoinette Camus, Yuri Leonardovich Menitsky, and Kevin C. Nixon. Classifications of oaks (Fig. 2.1) have thus far been based entirely on morphological characters. They differed profoundly from each other because each taxonomist gave a different weight to distinguishing characters; often characters that are homoplastic in oaks. With the advent of molecular phylogenetics our view has considerably changed. One of the most profound changes has been the realisation that the traditional split between the East Asian subtropical to tropical subgenus Cyclobalanopsis and the subgenus Quercus that includes all other oaks is artificial. The traditional concept has been replaced by that of two major clades, each comprising three infrageneric groups: a Palearctic-Indomalayan clade including Group Ilex (Ilex oaks), Group Cerris (Cerris oaks) and Group Cyclobalanopsis (cycle-cup oaks), and a predominantly Nearctic clade including Group Protobalanus (intermediate or golden cup oaks), Group Lobatae (red oaks) and Group Quercus (white oaks, with most species in America and some 30 species in Eurasia). In addition, recent phylogenetic studies identified two distinct clades within a wider group of white oaks: the Virentes oaks of North America and a clade with two disjunct endemic species in western Eurasia and western North America, Quercus pontica and Q. sadleriana. The main morphological feature characterising these phylogenetic lineages is pollen morphology, a character overlooked in traditional classifications. This realisation, along with the now available (molecular-)phylogenetic framework, opens new avenues for biogeographic, ecological and evolutionary studies and a re-appraisal of the fossil record. We provide an overview about recent advances in these fields and outline how the results of these studies contribute to the establishment of a unifying systematic scheme of oaks. Ultimately, we propose an updated classification of Quercus recognising two subgenera with eight sections. This classification considers morphological traits, molecular-phylogenetic relationships, and the evolutionary history of one of the most important temperate woody plant genera.

BackgroundWe revisit the palaeopalynological record of Loranthaceae, using pollen ornamentation to discriminate lineages and to test molecular dating estimates for the diversification of major lineages.MethodsFossil Loranthaceae pollen from the Eocene and Oligocene are analysed and documented using scanning-electron microscopy. These fossils were associated with molecular-defined clades and used as minimum age constraints for Bayesian node dating using different topological scenarios.ResultsThe fossil Loranthaceae pollen document the presence of at least one extant root-parasitic lineage (Nuytsieae) and two currently aerial parasitic lineages (Psittacanthinae and Loranthinae) by the end of the Eocene in the Northern Hemisphere. Phases of increased lineage diversification (late Eocene, middle Miocene) coincide with global warm phases.DiscussionWith the generation of molecular data becoming easier and less expensive every day, neontological research should re-focus on conserved morphologies that can be traced through the fossil record. The pollen, representing the male gametophytic generation of plants and often a taxonomic indicator, can be such a tracer. Analogously, palaeontological research should put more effort into diagnosing Cenozoic fossils with the aim of including them into modern systematic frameworks.

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.

Summary The fields of phylogenetic tree and network inference have dramatically advanced in the past decade, but independently with few attempts to bridge them. Here we provide a framework, implemented in the phangorn library in R, to transfer information between trees and networks. This includes: (i) identifying and labelling equivalent tree branches and network edges, (ii) transferring tree branch support to network edges, and (iii) mapping bipartition support from a sample of trees (e.g. from bootstrapping or Bayesian inference) onto network edges. The ability to readily combine tree and network information should lead to more comprehensive evolutionary comparisons and inferences.

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 genusQuercus(oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilexL.,Q. cocciferaL.,Q. aucheriJaub. & Spach.,Q. alnifoliaPoech.) was explored at three chloroplast markers (rbcL, trnK/matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing allQuercussubgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. High plastid divergence in members ofQuercusGroup Ilex, including haplotypes shared with related, but long isolated oak lineages, point towards multiple geographic origins of this group of oaks. The results suggest that incomplete lineage sorting and repeated phases of asymmetrical introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split withinQuercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.

Denk T., Grimm G. W. & Roseler A.-K.: When field botany meets history: taxonomy of Platanus mexicana in Mexico. — Willdenowia 42: 99-115. June 2012. — Online ISSN 1868-6397; © 2012 BGBM Berlin-Dahlem. Stable URL: http://dx.doi.org/10.3372/wi.42.42113 The recently described Platanus mexicana var. interior of Nixon & J. M. Poole is critically evaluated. We show that the type of the name P. mexicana, collected by Berlandier in 1827, is virtually identical to morphotypes typically found within the range of P. mexicana var. interior. The reason for the taxonomic confusion is twofold: the variability of the abaxial leaf tomentum across the distribution range of P. mexicana and uncertainties concerning the type locality of P. mexicana. Field observations at the type locality of P. mexicana var. interior and throughout the range of P. mexicana show that the morphotype represented by the holotype is rarely found in the main distribution range of P. mexicana in Veracruz, Puebla, Oaxaca and Chiapas. Our fin...

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 releves (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 releves 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.

The endangered European relict species complex Lathyrus pannonicus shows distinct morphological variation, reflected by the number of subspecies recognized, and complicated patterns of genetic variation. The traditionally recognized subspecies appear to possess different ecological preferences and disjunct distributions, particularly in the western range of the species. In this study, L. pannonicus was investigated by the correlation of distance matrices based on phytosociological, ecological, molecular and morphological data. Ecological characteristics of selected stands of L. pannonicus throughout Europe were assessed using ‘Ellenberg values’ of all the constituent taxa in phytosociological releves. Genetic distances were calculated using recently developed methods to analyse high degrees of intra-individual nuclear-encoded internal transcribed spacer variability. We found that the remarkable genetic (and morphological) diversity in L. pannonicus could not be explained solely by the fragmentation of the distributional range. Instead, patterns of morphological and genetic differentiation were a reflection of the moisture regime in the sampled stands. Two major lineages could be identified: (1) a lineage adapted to dry conditions (Ellenberg indicator F-value ≤ 3.5) and (2) a lineage preferring moist conditions (F-value ≥ 4.5). Although both lineages occurred in close proximity in the Pannonian area, they appeared to be reproductively isolated in general. Further data are needed to determine whether these genetically and ecologically defined lineages, or ecospecies, within the L. pannonicus species complex can be formalized as (Linnaean) species or subspecies. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165, 402–421.

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.

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 northwestern 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.

Monetianthus mirus gen. et sp. nov. is described based on a single coalified flower from the Early Cretaceous (Late Aptian‐Early Albian) Vale de Agua locality, western Portugal. The flower is actinomorphic and probably bisexual, with a perianth of nine or 10 tepals, an androecium of 20 stamens, and a syncarpous gynoecium with a partly inferior ovary of 12 carpels arranged radially around a central column. Phyllotaxis of tepals and stamens is uncertain. Nondestructive synchrotron radiation x‐ray tomographic microscopy of internal structures documents laminar placentation with around six anatropous and ascending ovules in each locule. Comparison of Monetianthus with living plants indicates a clear relationship to extant Nymphaeales in particular with the Barclaya and Nymphaeoideae clade. Monetianthus thus provides evidence of crown group Nymphaeales, and probably crown group Nymphaeaceae, at a very early stage in the initial diversification of flowering plants.

Patterns of tectum ornamentation in pollen of Quercus (oak trees, Fagaceae) are investigated using high‐resolution scanning electron microscopy. Tectum ornamentation 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, and Formanodendron. Such a simple type of tectum ornamentation is also known to represent an early developmental stage in infrageneric groups of Quercus that have otherwise complex ornamentation (Quercus and Lobatae). Ornamentation of the tectum in the infrageneric Cyclobalanopsis group can be derived from the plesiomorphic Ile...

We present SSU rDNA data resolving the seasonal and geographical distribution of 'cryptic' genetic types of the planktonic foraminifer morphospecies Globigerinoides ruber in the eastern Atlantic Ocean and the Mediterranean Sea. Analysis of 262 sequences revealed the presence of five genetic types belonging to two distinct lineages. Although the morphospecies G. ruber occurs throughout the investigated region, its constituent 'cryptic' genetic types show a pattern of widespread exclusion, which is difficult to reconcile with the concept of ubiquitous dispersal. One of the newly discovered genetic types was exclusively found at stations in the Mediterranean Sea, possibly representing the smallest-scale example of endemism known in planktonic foraminifera. In general, our results suggest that the geographical scale of mutual exclusion between the genotypes is negatively correlated with their phylogenetic relatedness: the most similar and most recently diverged pair of siblings showed the strongest evidence for small-scale competitive exclusion. This pattern is consistent with the concept of niche partitioning, implying decreasing level of competition between genetic types with increasing degree of genetic divergence.

Virgulinella fragilis can be mainly observed in different, separated, oxygen-depleted and sulfide-enriched environments around the world and seems to be well adapted to such extreme habitats. Dispersal mechanisms behind this geographical distribution pattern are not yet understood. To analyze the genetic differentiation of geographically isolated populations, we conducted molecular phylogenetic analyses of the small subunit (SSU) ribosomal DNA (rDNA) and internal transcribed spacers (ITS) of rDNA nucleotide sequences in populations of V. fragilis collected in the South Atlantic (upwelling area off Namibia) and in the Pacific (Wellington Harbor, New Zealand, and Namako-ike, Japan). Our molecular analyses revealed SSU rDNA and ITS sequences strikingly similar or identical among these three disjunct populations. Such a low molecular genetic differentiation, a fixation rate converging to zero, could either arise from rapid dispersal, ultraslow mutation rates due to a strictly asexual mode of reproduction, unlimited genetic exchange between populations or the existence of a resting stage for survival under unfavorable conditions. We discuss each explanation and conclude that V. fragilis might possibly represent a protozoan trapped in evolutionary stasis.

To clarify the taxonomic status of tomatoes (“Lycopersicon”) and their relationship to the members of sect. Petota of genus Solanum L., organization of the rDNA external transcribed spacer (5′ ETS) was studied in 33 Solanum and “Lycopersicon” species. Phylogenetic reconstruction revealed that three major groups can be distinguished. Non-tuber-bearing species of ser. Etuberosa as well as tuber-bearing Central American diploids appeared as a paraphyletic group. The first of two well-defined clades embraced all tuber-bearing South American species and Central American polyploids. The other clade (named “tomato clade”) contains non-tuber-bearing species of ser. Juglandifolia and tomato species of ser. Neolycopersicon, which appears to be imbedded in sect. Petota. The new 5′ ETS variant D characterized by a cluster of downstream subrepeats is characteristic for the tomato clade. The variant D originated directly from the most ancestral variant A found in ser. Etuberosa and the Central American diploids, whereas variants B and C specific for the tuber-bearing South American species and Central American polyploids represent a parallel lineage of molecular evolution. The sequence analysis demonstrates the existence of an evolutionary trend of parallel multiplication of specific motifs in 5′ ETS in different groups of sect. Petota.

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 converging to subtropical, per-humid or monsoonal conditions. Studies based on the Coexistence Approach have had a marked impact in literature, generating over 10,000 citations thus far. However, recent studies have pointed out inherent theoretical and practical problems entangled in the application of this widely used method. But so far little is known how results generated by the Coexistence Approach are affected by subjective errors, data errors, and violations of the basic assumptions. The majority of Coexistence Approach studies make use of the Palaeoflora database (the combination of which will be abbreviated to CA + PF). Testing results produced by CA + PF studies has been hindered by the general unavailability of the contents in the underlying Palaeoflora database; two exceptions are the mean-annual temperature tolerances and lists of assigned associations between fossils and nearest-living relatives. Using a recently published study on the Eocene of China, which provides the first and only insight into the data structure of the Palaeoflora database, we compare the theory and practice of Coexistence Approach using the Palaeoflora database (CA + PF). We show that CA + PF is riddled by association and climate data error. We reveal flaws in the application of the Coexistence Approach, which is often in stark contrast to the theory of the method. We show that CA + PF is highly vulnerable against numerous sources of errors, mainly because it lacks safeguards that could identify unreliable data. We demonstrate that the CA + PF produces coherent, pseudo-precise results even for artificially generated, random plant assemblages. Alternative MCR-NLR methods can surpass the most imminent deficits of the Coexistence Approach, and may be used as a stop-gap until more accurate bioclimatic and distribution data on potential Eurasian NLRs, and theoretically and statistically robust methods will become available. Finally, general guidelines are provided for the future application of methods using the mutual climatic range with nearest living relatives approach when reconstructing climate from plant fossil assemblages.

The Cretaceous and Palaeogene floras of western Greenland that were initially described as part of the classical work “Flora fossilis arctica” by Oswald Heer in the 19th century are currently under revision. The Nuussuaq Basin has repeatedly been investigated by geologists and marine invertebrate palaeontologists. These studies provide a modern stratigraphic framework and a basis for revisions of various Cretaceous to Eocene floras from this region, and the correlation of fossil material to stratigraphic units and formal formations. This paper is the first in a series of papers that (i) correlate macrofossil (museum) material and fossil-rich localities with the modern lithostratigraphic framework, (ii) describe new pollen, spores, and other marine/freshwater palynomorphs, and (iii) revise the macrofossil remains from the Agatdalen area (particularly the Danian Agatdal Formation). Since the work of B. Eske Koch in the 1960s and 70s, questions emerged about the correlation of plant fossiliferous outcrops and whether the so-called Agatdalen flora, referred to the Agatdal Formation, originates from a single sedimentary unit or not. In this paper, we summarise the stratigraphy of the Agatdalen area and correlate the fossil plant-bearing outcrops described by Koch to the current lithostratigraphy. We establish which plant fossils belong to the Agatdal Formation and re-assign a great number of other plant fossils to their correct formations. New palynological material is briefly described and correlated to the macrofossil localities and the Agatdal Formation. Previous accounts on the macrofossils (leaves, fruits, seeds) are briefly discussed and directions for future revisions are outlined.