Spanning the Globe – The Plant Phylogeny Poster (PPP) Project

Historically, wallcharts and posters created by botanical illustrators, often highly skilled artists, have played an important role in teaching botany at the university level. Large-scale panels and posters can visualize complex interrelationships and entire stories in a clear and appealing overview in graphs, tables, and diagrams. Carrying this concept of educational tools into the electronic era, the Plant Phylogeny Poster project uses this approach for displaying evolutionary relationships in systematic botany. The Angiosperm Phylogeny Poster (APP) displays, as phylogenetically arranged clades, the orders and families of flowering plants (with orders hyperlinked to APweb, Stevens, 2001–onwards), the Tracheophyte Phylogeny Poster (TPP) families and genera of ferns and gymnosperms, and the Bryophyte Phylogeny Poster (BPP) orders and families of liverworts, mosses, and hornworts. The portfolio currently also includes about 30 posters on individual orders and families of angiosperms. Each group within these evolutionary trees is matched with essentially relevant morphological features, biogeographic occurrences, and other information in compactly condensed text blocks. All posters are freely available online, some in more than 30 languages, coauthored by a team of more than 130 botanists. The posters are regularly updated, current literature is cited. The project is expanding steadily and rapidly.

Discordant Phylogenomic Placement of Hydnoraceae and Lactoridaceae Within Piperales Using Data From All Three Genomes

Phylogenetic relationships within the magnoliid order Piperales have been studied extensively, yet the relationships of the monotypic family Lactoridaceae and the holoparasitic Hydnoraceae to the remainder of the order remain a matter of debate. Since the first confident molecular phylogenetic placement of Hydnoraceae among Piperales, different studies have recovered various contradictory topologies. Most phylogenetic hypotheses were inferred using only a few loci and have had incomplete taxon sampling at the genus level. Based on these results and an online survey of taxonomic opinion, the Angiosperm Phylogeny Group lumped both Hydnoraceae and Lactoridaceae in Aristolochiaceae; however, the latter family continues to have unclear relationships to the aforementioned taxa. Here we present extensive phylogenomic tree reconstructions based on up to 137 loci from all three subcellular genomes for all genera of Piperales. We infer relationships based on a variety of phylogenetic methods, explore instances of phylogenomic discordance between the subcellular genomes, and test alternative topologies. Consistent with these phylogenomic results and a consideration of the principles of phylogenetic classification, we propose to exclude Hydnoraceae and Lactoridaceae from the broad circumscription of Aristolochiaceae, and instead favor recognition of four monophyletic and morphologically well circumscribed families in the perianth-bearing Piperales: Aristolochiaceae, Asaraceae, Hydnoraceae, and Lactoridaceae, with a total of six families in the order.

Ethnobotany and Indigenous Traditional Knowledge in Brazil: Contributions to Research in Ecopsychology

This paper is the result of an investigation of the flora and traditional knowledge in the conception of Javaé indigenous people from the Txuiri village located on Bananal Island, Brazil. The objective is to investigate the plants used by these indigenous people, their diverse uses and to understand how traditional knowledge is passed on to new generations. This is a quali-quantitative, descriptive and interdisciplinary survey, whose data collection strategies included the application of semi-structured questionnaires and collection of plants for cataloguing according to Angiosperm Phylogeny Group or APG III (2009). We identified 28 plant species, used for various purposes such as medicinal use, food, construction, craft and cultural, which were deposited in the Herbarium of the Federal University of Tocantins. Roots, stem and leaf are the plant parts most used by the community. The plants mentioned were most frequently found on the banks of the Javaés River and in the backyard of the residences. Significant traditional knowledge of these people about the plants are transmitted to new generations, through visual, orality and experimentation. Ethnobotanical studies strengthen research in ecopsychology while allowing research into the interactions between human populations and plants.

Plant Phylogeny Posters – Concise Overviews of Plant Phylogeny now in Czech and Slovak

The Plant Phylogeny Posters (PPP) project is a free and regularly updated portfolio providing details of phylogenetic relationships of extant lineages of plants in a clear and appealing format for academia and general interest groups. The portfolio consists of three main posters: Angiosperm Phylogeny Poster (APP), Tracheophyte Phylogeny Poster (TPP), Bryophyte Phylogeny Poster (BPP), plus 30 posters of selected orders and families of angiosperms. Each poster depicts a tree showing the evolutionary relationships of a particular group on the level of orders, families, or genera also listing important apomorphic, plesiomorphic and diagnostic traits. The electronic format of these posters allows for regular updates based on most recent research results – thus the topology of the trees is largely up-to-date. All posters are freely available on ResearchGate and on the webpages of the authors.

Modern views on phylogeny and systematic position of the genus Muscari (Asparagaceae) Miller

Systematic and phylogenetic status of Muscari – valuable ornamental and melliferous genus of flowering plants, still unclear despite numerous explorations. Therefore, the aim of the work was to carry out a critical analysis of publications devoted to phylogeny and taxonomy of the genus Muscari and to clarify its taxonomic position. The article provides a brief overview of the main publications dedicate to phylogeny and taxonomy of the genus. The systematic position of the genus Muscari in the early phylogenetic systems, taxonomic systems of the XX century and modern molecular phylogenetic systems is observed. Modern phylogenetic systems developed by Angiosperm Phylogeny Group (APG III, APG IV) and based on DNA sequence analysis. They show that Muscari belongs to the subfamily Scilloideae, family Asparagaceae s.l., order Asparagales, clusters Monocots. Phylogenetic relationships within the genus Muscari is difficult and controversial. In general, there are two main concepts of the genus Muscari division into subgenus. The first was developed by F. Speta in 1999 and is based on molecular data. In it, the genus is considered in a broad sense (s.l.), and divided into 4 subgenera: Muscari, Leopoldia, Muscarimia and Pseudomuscari. The second, more modern concept was developed by R. Govaerts and presented in the «World Checklist of selected plant families». According R. Govaerts, Muscari is divided into 3 separate genera: Muscari s.str. (=Muscarimia, Botryanthus), Leopoldia and Pseudomuscari. Paleobotanical data analysis established that the ancestral forms of modern Muscari originated approximately 3,29 million BC in the Mediterranean and spread to other regions of the world. The closest phylogenetic relatives of Muscari are the genera Scilla and Bellevalia. Chouardia and Nectaroscilla are also highly related. Comprehensive studies of morphological, biogeographical, molecular and other peculiarities of critical taxa are needed to clarification of the systematic position and phylogenetic relationships within the genus Muscari.

Endosperm of Angiosperms and Genomic Imprinting

Modern ideas about the role of epigenetic systems in the regulation of gene expression allow us to understand the mechanisms of vital activities in plants, such as genomic imprinting. It is important that genomic imprinting is known first and foremost for the endosperm, which not only provides an embryo with necessary nutrients, but also plays a special biological role in the formation of seeds and fruits. Available data on genomic imprinting in the endosperm have been obtained only for the triploid endosperm in model plants, which develops after double fertilization in a Polygonum-type embryo sac, the most common type among angiosperms. Here we provide a brief overview of a wide diversity of embryo sacs and endosperm types and ploidy levels, as well as their distribution in the angiosperm families, positioned according to the Angiosperm Phylogeny Group IV (APG IV) phylogenetic classification. Addition of the new, non-model taxa to study gene imprinting in seed development will extend our knowledge about the epigenetic mechanisms underlying angiosperm fertility.

Characterizing gene tree conflict in plastome-inferred phylogenies

Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict. Using a broad sampling of angiosperm plastomes, we characterize gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type). We uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find alignment length and tree length are strong predictors of concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK, greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes. Our results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that stochastic and systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given documented cases of heteroplasmic recombination. We suggest that researchers should filter genes for topological concordance when performing downstream comparative analyses on phylogenetic data, even when using chloroplast genomes.

Angiosperm phylogeny poster (APP) – Flowering plant systematics, 2019

The Angiosperm Phylogeny Poster – Flowering Plant Systematics is an educational poster presenting an overview of the evolutionary relationships among flowering plants, based on APG IV/APweb and in this update chiefly following the topology of PPA ("Plastid Phylogenomic Angiosperm" see Li HT et al. 2019). The phylogenetic tree depicts the 64 orders and the majority of the 416 families, listing the main apo- and plesiomorphies as well as diagnostic and nondiagnostic anatomical, morphological, and phytochemical features for orders and higher ranks within the tree along with the number of families, genera, and species for each order. The intuitive color-coding facilitates memorization and teaching. The poster is now available in 25 languages (all downloadable from ResearchGate).

Angiosperm phylogeny poster (APP) – Flowering plant systematics, 2019

The Angiosperm Phylogeny Poster – Flowering Plant Systematics is an educational poster presenting an overview of the evolutionary relationships among flowering plants, based on APG IV/APweb and in this update chiefly following the topology of PPA ("Plastid Phylogenomic Angiosperm" see Li HT et al. 2019). The phylogenetic tree depicts the 64 orders and the majority of the 416 families, listing the main apo- and plesiomorphies as well as diagnostic and nondiagnostic anatomical, morphological, and phytochemical features for orders and higher ranks within the tree along with the number of families, genera, and species for each order. The intuitive color-coding facilitates memorization and teaching. The poster is now available in 25 languages (all downloadable from ResearchGate).