Unisexual flowers as a robust synapomorphy in Cariceae (Cyperaceae)? Evidence for bisexual flowers in Schoenoxiphium

Abstract Cariceae, the largest tribe within Cyperaceae, comprises about 2000 species in five genera. Cariceae is usually considered to be distinct from other Cyperaceae by the presence of exclusively unisexual flowers and by the arrangement of the pistillate flowers in single-flowered spikelets that are enclosed by the flask-like spikelet prophyll (utricle or perigynium). The nature of several morphological features of the Cariceae inflorescence remains controversial. The staminate reproductive units, as well as earlier reported bisexual reproductive units in Schoenoxiphium have been considered to be reduced partial inflorescences, or flowers. Aims of this study are to test both interpretat…

Dual colonization of the Palaearctic from different regions in the Afrotropics bySenecio

Aim Investigation of the geographical origin of Senecio and the colonization of the Palaearctic including the relationship of life-history strategy and elevational distribution in the source area and the colonized area. Location Worldwide with a focus on the Afrotropic and the Palaearctic. Methods Sampling focused on adding species from the Afrotropic to existing datasets of Senecio. Two nuclear markers and three chloroplast markers were amplified and sequenced. Maximum likelihood and Bayesian inference were used to infer phylogeny, divergence times, biogeographical history and life-history strategy evolution. Results Senecio originated most likely during the Mid to Late Miocene in western …

MOESM13 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 13. Results: Ancestral area reconstructions inferred using BioGeoBEARS given the best tree under the best fitting model given A: DEC + J; B: DEC; and without range or dispersal constraint: C: DEC + J; D: DEC. For each model the single most probable state is shown first (boxes with areas at nodes) followed by the relative probability of each state represented with pie charts at nodes. Areas are represented by colours: Dark blue for Europe (E); green for Tropical Africa (T); yellow for Madagascar (M); light blue for Drakensberg (D); red for Cape (C); and further colours for widespread distributions as indicated in the legends.

MOESM4 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 4. Methods: Selected bootstrap trees used to represent phylogenetic uncertainty between geographically restricted major clades.

Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-level analysis of Public DNA database data

Pham, Kasey K. [et al.]

A framework infrageneric classification of Carex (Cyperaceae) and its organizing principles

MOESM3 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 3. Methods: Biogeographic models; example files for BioGeoBEARS analyses

New Insights into the Systematics of the Schoenoxiphium Clade (Carex, Cyperaceae)

The Spanish Ministry of Science and Technology supported this research through the project CGL2012-38744 and CGL2016- 77401-P to M. Luceño (Principal Investigator), E. Maguilla, M. Escudero, S. Martín-Bravo, and T. Villaverde and an FPU fellowship (AP2012-2189) from the Spanish Government (Ministry of Education, Culture, and Sport) and a Synthesys grant (GB-TAF-2523) by the European Community Research Infrastructure Program to E.Maguilla.

Carex sect. Rhynchocystis (Cyperaceae): a Miocene subtropical relict in the Western Palaearctic showing a dispersal‐derived Rand Flora pattern

Aim To evaluate how Cenozoic climate changes shaped the evolution and distribution of Carex section Rhynchocystis. Location Western Palaearctic and Afrotropical regions (Rand Flora pattern). Methods DNA regions ITS, ETS (nuclear), matK and rpl32-trnLUAG (plastid) were amplified for 86 samples of species from section Rhynchocystis. Phylogenetic and phylogeographical relationships were inferred using maximum parsimony, Bayesian inference and coalescent-based species tree approaches. Divergence times and ancestral areas were also inferred. Results Carex section Rhynchocystis is a clade that diversified during the middle Miocene in Europe. Most cladogenesis events date to the middle and late Mi…

Synopsis of Carex (Cyperaceae) from sub-Saharan Africa and Madagascar

This synopsis provides a key, synonymy, lectotypification, habitat descriptions and distributions for the 81 species and six additional infraspecific taxa of Carex known from tropical and southern Africa and Madagascar. It is the first treatment of Carex including all tropical and southern temperate areas in Africa since Kukenthal's monograph of subfamily Caricoideae in 1909. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 166, 51–99.

Megaphylogenetic Specimen-level Approaches to the <I>Carex</I> (Cyperaceae) Phylogeny Using ITS, ETS, and <I>matK</I> 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, histo…

MOESM6 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 6 Results: pairwise climate similarity (Schoener’s D) between biogeographic areas per PC axis.

MOESM7 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 7 Results: Pairwise climate similarity (Schoener’s D) between biogeographic areas for combined PC axes.

Staying cool: preadaptation to temperate climates required for colonising tropical alpine-like environments.

Plant species tend to retain their ancestral ecology, responding to temporal, geographic and climatic changes by tracking suitable habitats rather than adapting to novel conditions. Nevertheless, transitions into different environments or biomes still seem to be common. Especially intriguing are the tropical alpine-like areas found on only the highest mountainous regions surrounded by tropical environments. Tropical mountains are hotspots of biodiversity, often with striking degrees of endemism at higher elevations. On these mountains, steep environmental gradients and high habitat heterogeneity within small spaces coincide with astounding species diversity of great conservation value. The …

MOESM12 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 12. Results: Number of all dispersal events (mean and standard deviation of all observed anagenetic ‘a’, ‘d’ dispersals, PLUS cladogenetic founder/jump dispersal) averaged from 50 biogeographical stochastic mappings under the best inferred model using the best tree.

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

53 p., gráf.

MOESM9 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 9. Results: Summary of event counts from 50 biogeographical stochastic mappings under the best inferred model using the best tree.

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

Abstract Background The coincidence of long distance dispersal (LDD) 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. Results We infer that the overall dispersal history of Erica across the Afrotemperate…

MOESM8 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 8. Results of the different models under DEC + J and DEC (generally the better models compared to DIVA-like and BAYAREA-like-models).

MakingCarexmonophyletic (Cyperaceae, tribe Cariceae): a new broader circumscription

We are grateful to the John D. and Catherine T. MacArthur Foundation for funding of the Biodiversity Synthesis Group of the Encyclopedia of Life (EOL) project, which funded our BioSynC Synthesis meeting at the Field Museum in Chicago in September 2011, when the Global Carex Group was formed. We also thank the US National Science Foundation (NSF) for funding our continuing international collaborative work on the phylogeny and classification of Carex under grants DEB 1255901 to ALH and MJW, and DEB 1256033 to EHR. We also acknowledge with thanks funding for nomenclatural research and for attendance at our second meeting during the Monocots V conference in New York in July, 2013, from the Natu…

MOESM10 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 10. Results: Number of range-expansion dispersal events (mean and standard deviation of all observed “d” dispersals) averaged across 50 biogeographical stochastic mappings under the best inferred model using the best tree.

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 af…

The evolution of dwarf shrubs in alpine environments: a case study ofAlchemillain 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 BA…

MOESM11 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 11. Results: Number of cladogenetic dispersal events (mean and standard deviation of all observed jump ‘j’ dispersals) averaged from 50 biogeographical stochastic mappings under the best inferred model using the best tree.

Underestimated regional species diversity in the Cape Floristic Region revealed by phylogenetic analysis of the Erica abietina/E. viscaria clade (Ericaceae)

MOESM2 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 2. Methods: Global environmental space, area ranges, and climate similarity analysis.

Supplementary material 1 from: Gehrke B (2018) Staying cool: preadaptation to temperate climates required for colonising tropical alpine-like environments. PhytoKeys 96: 111-125. https://doi.org/10.3897/phytokeys.96.13353

Detailed examples on how the coding was done :

Supplementary material 3 from: Gehrke B (2018) Staying cool: preadaptation to temperate climates required for colonising tropical alpine-like environments. PhytoKeys 96: 111-125. https://doi.org/10.3897/phytokeys.96.13353

Location of the tropical alpine-like climate regions in the Tropics :

Data from: Megaphylogenetic specimen-level approaches to the Carex (Cyperaceae) phylogeny using ITS, ETS, and matK sequences: implications for classification

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 mis…

MOESM5 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 5. Methods: Mesquite file used for parsimony ancestral state reconstruction including RAXML bootstrap trees.

Data from: Specimens at the center: an informatics workflow and toolkit for specimen-level analysis of public DNA database data

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…

Supplementary material 2 from: Gehrke B (2018) Staying cool: preadaptation to temperate climates required for colonising tropical alpine-like environments. PhytoKeys 96: 111-125. https://doi.org/10.3897/phytokeys.96.13353

List of genera investigated for the analysis including information on generic distribution, coding and references to the literature used :

MOESM1 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 1. Methods: occurrence data.