A Rosid Is a Rosid Is a Rosid . . . or Not

The current structure of 583 Magnoliopsida (Dicotyledons) and 584 Liliopsida (Monocotyledons) in the Dewey Decimal Classification (DDC) system reflects changes made when the life sciences were thoroughly revised in 1996. Since that time, considerable progress has been made in the phylogenetic classification of angiosperms (flowering plants). In particular, APG III, the 2009 version of the classification developed by the Angiosperm Phylogeny Group, is finding use as a tool to organize both botanical information and botanical collections. The Dewey Editorial Office has received a request to revise 583–584 in light of this taxonomy ―as appropriate‖; relevant revisions would be likely to include both structural and terminological changes. In deciding how to provide accommodation for APG III, the Dewey editorial team must address many issues: Is APG III now stable enough and accepted broadly enough to be adopted as the basis for a major revision of the DDC? Should revisions in 583–584 be coordinated with parallel revisions in other parts of the life sciences? What revision strategies can be considered in revising 583-584 to accommodate APG III? What are their various strengths and weaknesses? How have other major classification schemes (e.g., the UDC) accommodated APG III? Discussion of these issues is guided by the principles (―editorial rules‖) that govern development of the DDC

Third-codon transversion rate-based _Nymphaea_ basal angiosperm phylogeny -- concordance with developmental evidence

Flowering plants (angiosperms) appeared on Earth rather suddenly approximately 130 million years ago and underwent a massive expansion in the subsequent 10-12 million years. Current molecular phylogenies have predominantly identified _Amborella_, followed by _Nymphaea_ (water lilies) or _Amborella_ plus _Nymphaea_, in the ANITA clade (_Amborella_, Nymphaeales, Illiciaceae, Trimeniaceae and Austrobaileyaceae) as the earliest angiosperm. However, developmental studies suggest that the earliest angiosperm had a 4-cell/4-nucleus female gametophyte and a diploid endosperm represented by _Nymphaea_, suggesting that _Amborella_, having an 8-cell/9-nucleus female gametophyte and a triploid endosperm, cannot be representative of the basal angiosperm. This evolution-development discordance is possibly caused by erroneous inference based on phylogenetic signals with low neutrality and/or high saturation. Here we show that the 3rd codon transversion (P3Tv), with high neutrality and low saturation, is a robust high-resolution phylogenetic signal for such divergences and that the P3Tv-based land plant phylogeny cautiously identifies _Nymphaea_, followed by _Amborella_, as the most basal among the angiosperm species examined in this study. This P3Tv-based phylogeny contributes insights to the origin of angiosperms with concordance to fossil and stomata development evidence

Flower heating following anthesis and the evolution of gall midge pollination in Schisandraceae

Premise of the study: Flower heating is known from a few species in 11 of the c. 450 families of flowering plants. Flowers in these families produce heat metabolically and are adapted to beetles or flies as pollinators. Here, we focus on the Schisandraceae, an American/Asian plant family known to exhibit flower heating in some species, but not others, raising the question of the adaptive function of heat production. Methods: We used field observations, experiments, and ancestral trait reconstruction on a molecular phylogeny for Schisandraceae that includes the investigated species. Key results: At least two Chinese species of Illicium are exclusively pollinated by gall midges that use the flowers as brood sites (not for pollen feeding). Continuous monitoring of flower temperatures revealed that the highest temperatures were attained after the flowers’ sexual functions were over, and experiments showed that post-anthetic warming benefited larval development, not fruit development. Midge larvae in flowers with trimmed tepals (and hence a lower temperature) died, but fruit set ratios remained unchanged. Based on the DNA phylogeny, gall midge pollination evolved from general fly/beetle pollination several times in Schisandraceae, with some species adapted to flower-breeding midges, others to pollen-feeding midges. Conclusions: Flower heating may be an ancestral trait in Schisandraceae that became co-opted in species pollinated by flower-breeding midges requiring long-persistent warm chambers for larval development

Leaf cuticular morphology links Platanaceae and Proteaceae

Int. J. Plant Sci. 166(5):843–855. © 2005 by The University of Chicago.The leaf cuticular morphology of extant species of Platanus was investigated using light and scanning electron microscopy. All species are shown to possess trichome bases of the same type as those commonly found in Proteaceae. Of particular significance are compound forms that consist of an annular surface scar associated with more than one underlying epidermal cell. These are found on the adaxial leaf surfaces of all species of Platanus and are also clearly evident on the abaxial surface of Platanus orientalis. This type of trichome base is therefore interpreted as the first detected nonreproductive morphological synapomorphy linking Proteaceae and Platanaceae. Also, the laterocytic, sometimes paracytic, or anomocytic arrangement of subsidiary cells in Platanus is distinct from the general state in Proteaceae, which is brachyparacytic and presumably derived. In Bellendena, possibly the most basal genus of extant Proteaceae, subsidiary cell arrangements resemble those of Platanus. These results are discussed with respect to leaf fossil records of Proteales, where it is concluded that the combination of brachyparacytic stomata and compound trichome bases is strong evidence for Proteaceae.Raymond J. Carpenter, Robert S. Hill, and Gregory J. Jorda

MarkerMiner 1.0: a new application for phylogenetic marker development using angiosperm transcriptomes

Premise of the study: Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited. Methods and Results: We developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. Our new tool identified as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales. Conclusions: MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development

Changing to APG II :

In the summer of 2006, the Science Division at the Royal Botanic Garden Edinburgh made the decision to change the classification system used in their collections of pressed and preserved plants from the modified Bentham and Hooker system to that published by the Angiosperm Phylogeny Group (APG). As a result of that decision the Horticulture Division also decided to change its records and plant labels to the APG system. This paper describes the effect this had on the work of staff in both the Science and Horticulture Divisions as their collections had to be reorganized and relabelled to show the new family orders

Сучасні погляди на філогенію та положення родини Orchidaceae Juss. у системі однодольних рослин

The article provides an overview of recent publications devoted to phylogeny and taxonomy of the family Orchidaceae Juss., with a special reference to molecular phylogenetics. Modern methods of molecular taxonomy and phylogenetics are powerful tools that clarified many long-debated problems in phylogenetic systematics of orchids. In the recent phylogenetic systems (APG, APG II and others) Orchidaceae are placed in or near the extended order Asparagales, most probably at the base of the asparagalean clade. Recent age estimations for major angiosperm groups yielded rather unexpected results indicating that the orchid clade might be among the most ancient clades of extant monocots (molecular clock estimations at ca. 110 millions years). Ancestral orchids were probably terrestrial plants, and the epiphytic habit developed in the family many times and independently in different groups. The currently accepted topology of the phylogenetic tree of Orchidaceae indicates five major clades corresponding to subfamilies Apostasioideae, Vanilloideae, Cypripedioideae, Orchidoideae, Epidendroideae. Many traditionally accepted genera proved to be polyphyletic or paraphyletic, which will result in many taxonomic and nomenclatural changes. Special studies of morphological, biogeographical and other peculiarities of critical taxa are needed to explain the newly discovered molecular phylogenetic patterns in orchids.Наведено короткий огляд сучасних публікацій, присвячених філогенії і систематиці родини Orchidaceae Juss., з урахуванням даних молекулярної філогенетики. Сучасні методи молекулярної систематики і філогенетики є потужними засобами досліджень, які дали змогу з’ясувати багато проблем у філогенетичній систематиці орхідних. У нових філогенетичних системах (APG, APG II та ін.) Orchidaceae включено до розширеного порядку Asparagales (найвірогідніше, при основі цієї клади) або поряд з ним. Останні оцінки віку основних груп покритонасінних рослин виявили досить несподівані результати, які свідчать про те, що філогенетична гілка орхідей може бути однією з найдревніших клад сучасних однодольних (за оцінкою методу “молекулярного годинника” – близько 110 млн років). Предки орхідних, ймовірно, були наземними рослинами, а епіфітизм виникав у родині неодноразово й незалежно в різних групах. Прийнята нині топологія філогенетичного дерева Orchidaceae вказує на існування п’яти основних клад, що відповідають підродинам Apostasioideae, Vanilloideae, Cypripedioideae, Orchidoideae, Epidendroideae. Багато традиційно визнаних родів виявилися поліфілетичними або парафілетичними групами, що зумовило необхідність численних таксономічних та номенклатурних змін. Для пояснення нової молекулярно-філогенетичної концепції в межах Orchidaceae потрібні спеціальні дослідження морфологічних, біо-географічних та інших особливостей критичних таксонів

Phylogenetic structure and formation mechanism of shrub communities in arid and semiarid areas of the Mongolian Plateau

The mechanisms of species coexistence within a community have always been the focus in ecological research. Community phylogenetic structure reflects the relationship of historical processes, regional environments, and interactions between species, and studying it is imperative to understand the formation and maintenance mechanisms of community composition and biodiversity. We studied the phylogenetic structure of the shrub communities in arid and semiarid areas of the Mongolian Plateau. First, the phylogenetic signals of four plant traits (height, canopy, leaf length, and leaf width) of shrubs and subshrubs were measured to determine the phylogenetic conservation of these traits. Then, the net relatedness index (NRI) of shrub communities was calculated to characterize their phylogenetic structure. Finally, the relationship between the NRI and current climate and paleoclimate (since the Last Glacial Maximum, LGM) factors was analyzed to understand the formation and maintenance mechanisms of these plant communities. We found that desert shrub communities showed a trend toward phylogenetic overdispersion; that is, limiting similarity was predominant in arid and semiarid areas of the Mongolian Plateau despite the phylogenetic structure and formation mechanisms differing across habitats. The typical desert and sandy shrub communities showed a significant phylogenetic overdispersion, while the steppified desert shrub communities showed a weak phylogenetic clustering. It was found that mean winter temperature (i.e., in the driest quarter) was the major factor limiting steppified desert shrub phylogeny distribution. Both cold and drought (despite having opposite consequences) differentiated the typical desert to steppified desert shrub communities. The increase in temperature since the LGM is conducive to the invasion of shrub plants into steppe grassland, and this process may be intensified by global warming