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A Bayesian framework to estimate diversification rates and their variation through time and space
(2011)
Background: Patterns of species diversity are the result of speciation and extinction processes, and molecular phylogenetic data can provide valuable information to derive their variability through time and across clades. Bayesian Markov chain Monte Carlo methods offer a promising framework to incorporate phylogenetic uncertainty when estimating rates of diversification.
Results: We introduce a new approach to estimate diversification rates in a Bayesian framework over a distribution of trees under various constant and variable rate birth-death and pure-birth models, and test it on simulated phylogenies. Furthermore, speciation and extinction rates and their posterior credibility intervals can be estimated while accounting for non-random taxon sampling. The framework is particularly suitable for hypothesis testing using Bayes factors, as we demonstrate analyzing dated phylogenies of Chondrostoma (Cyprinids) and Lupinus (Fabaceae). In addition, we develop a model that extends the rate estimation to a meta-analysis framework in which different data sets are combined in a single analysis to detect general temporal and spatial trends in diversification.
Conclusions: Our approach provides a flexible framework for the estimation of diversification parameters and hypothesis testing while simultaneously accounting for uncertainties in the divergence times and incomplete taxon sampling.
Plants, fungi and algae are important components of global biodiversity and are fundamental to all ecosystems. They are the basis for human well-being, providing food, materials and medicines. Specimens of all three groups of organisms are accommodated in herbaria, where they are commonly referred to as botanical specimens.The large number of specimens in herbaria provides an ample, permanent and continuously improving knowledge base on these organisms and an indispensable source for the analysis of the distribution of species in space and time critical for current and future research relating to global biodiversity. In order to make full use of this resource, a research infrastructure has to be built that grants comprehensive and free access to the information in herbaria and botanical collections in general. This can be achieved through digitization of the botanical objects and associated data.The botanical research community can count on a long-standing tradition of collaboration among institutions and individuals. It agreed on data standards and standard services even before the advent of computerization and information networking, an example being the Index Herbariorum as a global registry of herbaria helping towards the unique identification of specimens cited in the literature.In the spirit of this collaborative history, 51 representatives from 30 institutions advocate to start the digitization of botanical collections with the overall wall-to-wall digitization of the flat objects stored in German herbaria. Germany has 70 herbaria holding almost 23 million specimens according to a national survey carried out in 2019. 87% of these specimens are not yet digitized. Experiences from other countries like France, the Netherlands, Finland, the US and Australia show that herbaria can be comprehensively and cost-efficiently digitized in a relatively short time due to established workflows and protocols for the high-throughput digitization of flat objects.Most of the herbaria are part of a university (34), fewer belong to municipal museums (10) or state museums (8), six herbaria belong to institutions also supported by federal funds such as Leibniz institutes, and four belong to non-governmental organizations. A common data infrastructure must therefore integrate different kinds of institutions.Making full use of the data gained by digitization requires the set-up of a digital infrastructure for storage, archiving, content indexing and networking as well as standardized access for the scientific use of digital objects. A standards-based portfolio of technical components has already been developed and successfully tested by the Biodiversity Informatics Community over the last two decades, comprising among others access protocols, collection databases, portals, tools for semantic enrichment and annotation, international networking, storage and archiving in accordance with international standards. This was achieved through the funding by national and international programs and initiatives, which also paved the road for the German contribution to the Global Biodiversity Information Facility (GBIF).Herbaria constitute a large part of the German botanical collections that also comprise living collections in botanical gardens and seed banks, DNA- and tissue samples, specimens preserved in fluids or on microscope slides and more. Once the herbaria are digitized, these resources can be integrated, adding to the value of the overall research infrastructure. The community has agreed on tasks that are shared between the herbaria, as the German GBIF model already successfully demonstrates.We have compiled nine scientific use cases of immediate societal relevance for an integrated infrastructure of botanical collections. They address accelerated biodiversity discovery and research, biomonitoring and conservation planning, biodiversity modelling, the generation of trait information, automated image recognition by artificial intelligence, automated pathogen detection, contextualization by interlinking objects, enabling provenance research, as well as education, outreach and citizen science.We propose to start this initiative now in order to valorize German botanical collections as a vital part of a worldwide biodiversity data pool.
Die Vorkommen der anthropochoren Aster-Arten im Stadtgebiet von Frankfurt am Main (Symphyotrichum lanceolatum, S. novae-angliae, S. novi-belgii, S. parviflorum, S. salignum) wurden kartiert und historische Dokumente zur Rekonstruktion der Einwanderung ausgewertet. Aktuell konnten 39 Fundorte im Stadtgebiet dokumentiert werden, am häufigsten ist S. lanceolatum. 40 Merkmale wurden untersucht und vermessen, um ihre taxonomische Relevanz zu beurteilen. Als hilfreich zur Unterscheidung der Arten erwiesen sich vor allem verschiedene Merkmale der Hüllblätter. Mit Ausnahme von S. novae-angliae sind die Arten aber morphologisch kaum zu unterscheiden und durch viele Übergänge verbunden. Vergleichsweise gut voneinander abgrenzbar sind die beiden Aggregate von S. novi-belgii (S. salignum, S. novi-belgii) und S. lanceo-latum (S. lanceolatum, S. parviflorum).
Termite mounds represent abundant microhabitats of high biodiversity in tropical savanna ecosystems and are an important source of landscape heterogeneity in Sub–Saharan West Africa. Floristic composition as well as density, structure and zonation of plant cover on the mounds were investigated in northern Benin and compared to the adjacent savanna vegetation. A total of 57 abandoned and densely vegetated termite mounds of comparable size and similarly affected by erosion located in different types of savannas inside and outside of the W National Park and in cotton fields were studied. This study revealed that termitaria are special habitats differing in density, composition and structure from surrounding savannas. The plant cover of termite mounds showed a distinctive zonation. Succulents, geophytes, and lianas were much more abundant on mounds, the family Capparaceae was found exclusively on mounds. The floristic composition and vegetation on termitaria proved to be rather homogeneous; although those mounds located in cotton fields differed by higher abundance of Poaceae and lower species richness.
Aim: To provide distribution information and preliminary conservation assessments for all species of the pineapple family (Bromeliaceae), one of the most diverse and ecologically important plant groups of the American tropics—a global biodiversity hotspot. Furthermore, we aim to analyse patterns of diversity, endemism and the conservation status of the Bromeliaceae on the continental level in the light of their evolutionary history.
Location: The Americas.
Methods: We compiled a dataset of occurrence records for 3,272 bromeliad species (93.4% of the family) and modelled their geographic distribution using either climate‐based species distribution models, convex hulls or geographic buffers dependent on the number of occurrences available. We then combined this data with information on taxonomy and used the ConR software for a preliminary assessment of the conservation status of all species following Criterion B of the International Union for the Conservation of Nature (IUCN).
Results: Our results stress the Atlantic Forest in eastern Brazil, the Andean slopes, Central America and the Guiana Highlands as centres of bromeliad diversity and endemism. Phylogenetically ancient subfamilies of bromeliads are centred in the Guiana highlands whereas the large radiations of the group spread across different habitats and large geographic area. A total of 81% of the evaluated bromeliad species are Possibly Threatened with extinction. We provide range polygons for 3,272 species, as well as newly georeferenced point localities for 911 species in the novel “bromeliad” r package, together with functions to generate diversity maps for individual taxonomic or functional groups.
Main conclusions: Diversity centres of the Bromeliaceae agreed with macroecological patterns of other plant and animal groups, but show some particular patterns related to the evolutionary origin of the family, especially ancient dispersal corridors. A staggering 2/3rds of Bromeliaceae species might be threatened with extinction, especially so in tropical rain forests, raising concerns about the conservation of the family and bromeliad‐dependent animal species.
Hexaploides Chenopodium album ist in Frankfurt am Main (Hessen) häufig. Die Pflanzen unterscheiden sich deutlich in Blütezeit, Höhe, Verzweigung, Blattform und Blütenstandsmorphologie, wobei oft morphologisch einheitliche Pflanzen benachbart wachsen. Die Merkmale variieren unabhängig voneinander und es erscheint nicht sinnvoll, morphologische Gruppen taxonomisch zu fassen.
Correction to: The low-copy nuclear gene Agt1 as a novel DNA barcoding marker for Bromeliaceae
(2020)
Correction to: BMC Plant Biol 20, 111 (2020)
https://doi.org/10.1186/s12870-020-2326-5
In the original publication [1] an incorrect version of Additional file 1 was used during typesetting. The incorrect and correct versions of Additional file 1 are available in this correction article. The original article has been updated. The publisher apologizes to the authors and readers for the inconvenience.
An updated inventory of the Bromeliaceae for Costa Rica is presented including citations of representative specimens for each species. The family comprises 18 genera and 198 species in Costa Rica, 32 species being endemic to the country. Additional 36 species are endemic to Costa Rica and Panama. Only 4 of the 8 bromeliad subfamilies occur in Costa Rica, with a strong predominance of Tillandsioideae (7 genera/150 spp.; 75.7% of all bromeliad species in Costa Rica). 124 species (62.6%) grow exclusively epiphytic, additional 59 spp. (29.8%) are facultative epiphytes. The most diverse genus is Werauhia, with 59 species (29.8% of the Costa Rican bromeliad flora), followed by Tillandsia with 40 species (20.2%) and Guzmania with 28 spp. (8.6%).
The subfamily Bromelioideae is one of the most diverse groups among the neotropical Bromeliaceae. Previously, key innovations have been identified which account for the extraordinary radiation and species richness of this subfamily, especially in the so-called core Bromelioideae. However, in order to extend our understanding of the evolutionary mechanisms, the genomic mechanisms (e.g. polyploidy, dysploidy) that potentially underlie this accelerated speciation also need to be tested. Here, using PI and DAPI staining and flow cytometry we estimated genome size and GC content of 231 plants covering 30 genera and 165 species and combined it with published data. The evolutionary and ecological significance of all three genomic characters was tested within a previously generated dated phylogenetic framework using ancestral state reconstructions, comparative phylogenetic methods, and multiple regressions with climatic variables. The absolute genome size (2C) of Bromelioideae varied between 0.59 and 4.11 pg, and the GC content ranged between 36.73 and 41.43%. The monoploid genome sizes (Cx) differed significantly between core and early diverging lineages. The occurrence of dysploidy and polyploidy was, with few exceptions, limited to the phylogenetically isolated early diverging tank-less lineages. For Cx and GC content Ornstein–Uhlenbeck models outperformed the Brownian motion models suggesting adaptive potential linked to the temperature conditions. 2C-values revealed different rates of evolution in core and early diverging lineages also related to climatic conditions. Our results suggest that polyploidy is not associated with higher net diversification and fast radiation in core bromelioids. On the other hand, although coupled with higher extinction rates, dysploidy, polyploidy, and resulting genomic reorganizations might have played a role in the survival of the early diverging bromelioids in hot and arid environments.
Only a small proportion of introduced plant species become invasive and may eventually create ecological or economic problems. In many species it is still not clear which traits cause biological inva-sions. As a case study we focussed on the fast-spreading Epilobium brachycarpum in Central Europe to investigate the potential of this species to become a transformer or agricultural weed. We (1) documented the spread of the species in Central Europe, (2) modelled its range and (3) seed dispersal, (4) described its phytosociological alignment, (5) analysed the traits of invaded vegetation types, (6) described seed production, population densities and life cycle, (7) did competition and germination tests, and (8) drafted a risk assessment. Relevant traits and characteristics of E. brachycarpum are (i) formation of dense stands under ruderal conditions, (ii) high seed production, (iii) effective seed dispersal, (iv) high competitiveness on bare soils against other ruderal plants, and (v) ecological niche shift com-pared to its native range. We expect E. brachycarpum to settle in the Mediterranean, sub-Mediterranean and many parts of temperate Europe within the next decades in habitats strongly altered by human activities, especially open stands of the alliance Sisymbrion. We predict that E. brachycarpum will become a noxious weed in vineyards, and that it will also colonise vegetation of the alliances Bidention and Carici-Epilobion.