Berit Gehrke

A rapid and inexpensive method for the direct PCR amplification of DNA from plants

UNLABELLED PREMISE OF THE STUDY We present a rapid and inexpensive alternative to DNA isolation for polymerase chain reaction (PCR) amplification from plants. • METHODS AND RESULTS The method involves direct PCR amplification from material macerated in one buffer, followed by dilution and incubation in a second buffer. We describe the procedure and demonstrate its application for nuclear and plastid DNA amplification across a broad range of vascular plants. • CONCLUSIONS The method is fast, easy to perform, cost-effective, and consequently ideal for large sample numbers. It represents a considerable simplification of present approaches requiring DNA isolation prior to PCR amplification and will be useful in plant systematics and biotechnology, including applications such as DNA barcoding.

Species richness, endemism and species composition in the tropical Afroalpine flora

Plant species richness and endemism on oceanic islands is dependent on island age, size, elevation and distance to nearest source of migrants. Mainland ‘island’ systems, such as the cool-adapted tropical-alpine flora of the mountains in Africa, are less well studied. Here we analyse the tropical Afroalpine flora, found on highly isolated mountains straddling the equator. Using the β-sim index in a hierarchical clustering approach combined with ordination methods and mantel tests, we locate four geographical groups: West Africa, northern East Africa, western East Africa and eastern East Africa. We show that these groupings are better explained as the consequence of geographical isolation rather than environmental filtering. We further show that the species richness of the tropical Afroalpine mountain regions—similar to oceanic islands—can be explained by a model including age, area size, elevation and isolation. Levels of endemism are best explained by species richness in combination with area and isolation. Overall we develop a comprehensive model of the species richness, endemism and composition of the tropical Afroalpine flora.

Oligocene niche shift, Miocene diversification – cold tolerance and accelerated speciation rates in the St. John’s Worts (Hypericum, Hypericaceae)

BackgroundOur aim is to understand the evolution of species-rich plant groups that shifted from tropical into cold/temperate biomes. It is well known that climate affects evolutionary processes, such as how fast species diversify, species range shifts, and species distributions. Many plant lineages may have gone extinct in the Northern Hemisphere due to Late Eocene climate cooling, while some tropical lineages may have adapted to temperate conditions and radiated; the hyper-diverse and geographically widespread genus Hypericum is one of these.ResultsTo investigate the effect of macroecological niche shifts on evolutionary success we combine historical biogeography with analyses of diversification dynamics and climatic niche shifts in a phylogenetic framework. Hypericum evolved cold tolerance c. 30 million years ago, and successfully colonized all ice-free continents, where today ~500 species exist. The other members of Hypericaceae stayed in their tropical habitats and evolved into ~120 species. We identified a 15–20 million year lag between the initial change in temperature preference in Hypericum and subsequent diversification rate shifts in the Miocene.ConclusionsContrary to the dramatic niche shift early in the evolution of Hypericum most extant species occur in temperate climates including high elevations in the tropics. These cold/temperate niches are a distinctive characteristic of Hypericum. We conclude that the initial release from an evolutionary constraint (from tropical to temperate climates) is an important novelty in Hypericum. However, the initial shift in the adaptive landscape into colder climates appears to be a precondition, and may not be directly related to increased diversification rates. Instead, subsequent events of mountain formation and further climate cooling may better explain distribution patterns and species-richness in Hypericum. These findings exemplify important macroevolutionary patterns of plant diversification during large-scale global climate change.

Megaphylogenetic Specimen-Level Approaches to the Carex (Cyperaceae) Phylogeny Using ITS, ETS, and matK Sequences: Implications for Classification

Abstract We present the first large-scale phylogenetic hypothesis for the genus Carex based on 996 of the 1983 accepted species (50.23%). We used a supermatrix approach using three DNA regions: ETS, ITS and matK. Every concatenated sequence was derived from a single specimen. The topology of our phylogenetic reconstruction largely agreed with previous studies. We also gained new insights into the early divergence structure of the two largest clades, core Carex and Vignea clades, challenging some previous evolutionary hypotheses about inflorescence structure. Most sections were recovered as non-monophyletic. Homoplasy of characters traditionally selected as relevant for classification, historical misunderstanding of how morphology varies across Carex, and regional rather than global views of Carex diversity seem to be the main reasons for the high levels of polyphyly and paraphyly in the current infrageneric classification.

Which changes are needed to render all genera of the German flora monophyletic

Abstract: The use of DNA sequence data in plant systematics has brought us closer than ever to formulating well-founded hypotheses about phylogenetic relationships, and phylogenetic research keeps on revealing that plant genera as traditionally circumscribed often are not monophyletic. Here, we assess the monophyly of all genera of vascular plants found in Germany. Using a survey of the phylogenetic literature, we discuss which classifications would be consistent with the phylogenetic relationships found and could be followed, provided monophyly is accepted as the primary criterion for circumscribing taxa. We indicate whether and which names are available when changes in generic assignment are made (but do not present a comprehensive review of the nomenclatural aspects of such names). Among the 840 genera examined, we identified c. 140 where data quality is sufficiently high to conclude that they are not monophyletic, and an additional c. 20 where monophyly is questionable but where data quality is not yet sufficient to reach convincing conclusions. While it is still fiercely debated how a phylogenetic tree should be translated into a classification, our results could serve as a guide to the likely consequences of systematic research for the taxonomy of the German flora and the floras of neighbouring countries. Citation: Kadereit J. W., Albach D. C., Ehrendorfer F., Galbany-Casals M., Garcia-Jacas N., Gehrke B., Kadereit G., Kilian N., Klein J. T., Koch M. A., Kropf M., Oberprieler C., Pirie M. D., Ritz C. M., Röser M., Spalik K., Susanna A., Weigend M., Welk E., Wesche K., Zhang L.-B. & Dillenberger M. S. 2016: Which changes are needed to render all genera of the German flora monophyletic? — Willdenowia 46: 39–91. doi: http://dx.doi.org/10.3372/wi.46.46105 Version of record first published online on 24 March 2016 ahead of inclusion in April 2016 issue.

The evolution of dwarf shrubs in alpine environments: a case study of Alchemilla in Africa

BACKGROUND AND AIMS Alpine and arctic environments worldwide, including high mountains, are dominated by short-stature woody plants (dwarf shrubs). This conspicuous life form asserts considerable influence on local environmental conditions above the treeline, creating its own microhabitat. This study reconstructs the evolution of dwarf shrubs in Alchemilla in the African tropical alpine environment, where they represent one of the largest clades and are among the most common and abundant plants. METHODS Different phylogenetic inference methods were used with plastid and nuclear DNA sequence markers, molecular dating (BEAST and RelTime), analyses of diversification rate shifts (MEDUSA and BAMM) and ancestral character and area reconstructions (Mesquite). KEY RESULTS It is inferred that African Alchemilla species originated following long-distance dispersal to tropical East Africa, but that the evolution of dwarf shrubs occurred in Ethiopia and in tropical East Africa independently. Establishing a timeframe is challenging given inconsistencies in age estimates, but it seems likely that they originated in the Pleistocene, or at the earliest in the late Miocene. The adaptation to alpine-like environments in the form of dwarf shrubs has apparently not led to enhanced diversification rates. Ancestral reconstructions indicate reversals in Alchemilla from plants with a woody base to entirely herbaceous forms, a transition that is rarely reported in angiosperms. CONCLUSIONS Alchemilla is a clear example of in situ tropical alpine speciation. The dwarf shrub life form typical of African Alchemilla has evolved twice independently, further indicating its selective advantage in these harsh environments. However, it has not influenced diversification, which, although recent, was not rapid.

Frequent colonization and little in situ speciation in Senecio in the tropical alpine-like islands of eastern Africa

PREMISE OF THE STUDY Floras of continental habitat islands, like those of islands, originate mostly through colonization, which can be followed by in situ speciation. We here address the question of the relative importance of colonization and in situ diversification in the high-altitude areas of the eastern African high mountains, the tropical Afroalpine Region, using the most species-rich genus in the region, Senecio, as an example. METHODS We expanded earlier Senecioneae phylogenies by adding more tropical African species and analyzed our phylogenetic tree biogeographically. KEY RESULTS Senecio contains at least five clades with tropical African species, all of them containing tropical afroalpine species. Between four to 14 independent colonization events into the tropical Afroalpine most likely from montane regions in southern Africa were found. Additionally, relationships of tropical afroalpine species to Palearctic and South American taxa were identified. Although some in situ diversification occurred in Senecio in the tropical Afroalpine, the resulting number of species per clade is never higher than seven. CONCLUSION Like other genera, Senecio colonized the tropical Afroalpine several times independently. Comparison with Mt. Kinabalu, a small tropical alpine-like region in Southeast Asia, and alpine-like regions in the Andes implies that rates of in situ speciation might be linked to area size.

Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-Level Analysis of Public DNA Database Data

Abstract Major public DNA databases — NCBI GenBank, the DNA DataBank of Japan (DDBJ), and the European Molecular Biology Laboratory (EMBL) — are invaluable biodiversity libraries. Systematists and other biodiversity scientists commonly mine these databases for sequence data to use in phylogenetic studies, but such studies generally use only the taxonomic identity of the sequenced tissue, not the specimen identity. Thus studies that use DNA supermatrices to construct phylogenetic trees with species at the tips typically do not take advantage of the fact that for many individuals in the public DNA databases, several DNA regions have been sampled; and for many species, two or more individuals have been sampled. Thus these studies typically do not make full use of the multigene datasets in public DNA databases to test species coherence and select optimal sequences to represent a species. In this study, we introduce a set of tools developed in the R programming language to construct individual-based trees from NCBI GenBank data and present a set of trees for the genus Carex (Cyperaceae) constructed using these methods. For the more than 770 species for which we found sequence data, our approach recovered an average of 1.85 gene regions per specimen, up to seven for some specimens, and more than 450 species represented by two or more specimens. Depending on the subset of genes analyzed, we found up to 42% of species monophyletic. We introduce a simple tree statistic—the Taxonomic Disparity Index (TDI)—to assist in curating specimen-level datasets and provide code for selecting maximally informative (or, conversely, minimally misleading) sequences as species exemplars. While tailored to the Carex dataset, the approach and code presented in this paper can readily be generalized to constructing individual-level trees from large amounts of data for any species group.

Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

The coincidence of long distance dispersal and biome shift is assumed to be the result of a multifaceted interplay between geographical distance and ecological suitability of source and sink areas. Here, we test the influence of these factors on the dispersal history of the flowering plant genus Erica (Ericaceae) across the Afrotemperate. We quantify similarity of Erica climate niches per biogeographic area using direct observations of species, and test various colonisation scenarios while estimating ancestral areas for the Erica clade using parametric biogeographic model testing. We infer that the overall dispersal history of Erica across the Afrotemperate is the result of infrequent colonisation limited by geographic proximity and/or niche similarity. However, the Drakensberg Mountains represent a colonisation sink, rather than acting as a “stepping stone” between more distant and ecologically dissimilar Cape and Tropical African regions; and strikingly, the most dramatic examples of species radiations in Erica were the result of single unique dispersals over longer distances between ecologically dissimilar areas, contradicting the rule of phylogenetic biome conservatism. These results highlight the importance of rare biome shifts, in which a unique dispersal event fuels evolutionary radiations.