Collections Education: The Extended Specimen and Data Acumen

Biodiversity scientists must be fluent across disciplines; they must possess the quantitative, computational, and data skills necessary for working with large, complex data sets, and they must have foundational skills and content knowledge from ecology, evolution, taxonomy, and systematics. To effectively train the emerging workforce, we must teach science as we conduct science and embrace emerging concepts of data acumen alongside the knowledge, tools, and techniques foundational to organismal biology. We present an open education resource that updates the traditional plant collection exercise to incorporate best practices in twenty-first century collecting and to contextualize the activities that build data acumen. Students exposed to this resource gained skills and content knowledge in plant taxonomy and systematics, as well as a nuanced understanding of collections-based data resources. We discuss the importance of the extended specimen in fostering scientific discovery and reinforcing foundational concepts in biodiversity science, taxonomy, and systematics

Integrative, next-generation, collaborative vascular plant systematics in New Zealand

Systematics is a synthetic science which focuses on species delimitation, taxonomy, classification, and phylogeny, with an additional aim of understanding underlying evolutionary and biogeographic patterns and processes. Systematic research has many downstream benefits including underpinning conservation management, biosecurity and health.  In this short overview article, I will give a brief synopsis of integrative systematics, in which multiple data sets are used to robustly test species limits in a statistical framework, and illustrate why I think we need integrative systematics in New Zealand. I will then discuss examples from my own systematics research, especially on the flowering plant families Plantaginaceae (Ourisia, Plantago, Veronica) and Boraginaceae (Myosotis), as well as from other vascular plant systematics research being done by colleagues in New Zealand and elsewhere. Through these examples, I will show how using an integrative systematics approach to analysing morphological, molecular, cytological and other data sets can aid species delimitation and new species discovery, and allow inferences into questions regarding such diverse themes as diversification, variability and conservation of threatened species, polyploidy (whole genome duplication) and biogeography of New Zealand vascular plants.  I will also argue that the future of systematics should not only be integrative, but also next-generation and collaborative, and that such forward-looking, cooperative research – and the institutional and governmental investment to support it – is essential for New Zealand

Incorporating molecular data in fungal systematics: a guide for aspiring researchers

The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching changes as disciplines in the wake of continual improvement in DNA sequencing technology. A taxonomic study that draws from molecular data involves a long series of steps, ranging from taxon sampling through the various laboratory procedures and data analysis to the publication process. All steps are important and influence the results and the way they are perceived by the scientific community. The present paper provides a reflective overview of all major steps in such a project with the purpose to assist research students about to begin their first study using DNA-based methods. We also take the opportunity to discuss the role of taxonomy in biology and the life sciences in general in the light of molecular data. While the best way to learn molecular methods is to work side by side with someone experienced, we hope that the present paper will serve to lower the learning threshold for the reader.Comment: Submitted to Current Research in Environmental and Applied Mycology - comments most welcom

Fast, linked, and open – the future of taxonomic publishing for plants: launching the journal PhytoKeys

The paper describes the focus, scope and the rationale of PhytoKeys, a newly established, peer-reviewed, open-access journal in plant systematics. PhytoKeys is launched to respond to four main challenges of our time: (1) Appearance of electronic publications as amendments or even alternatives to paper publications; (2) Open Access (OA) as a new publishing model; (3) Linkage of electronic registers, indices and aggregators that summarize information on biological species through taxonomic names or their persistent identifiers (Globally Unique Identifiers or GUIDs; currently Life Science Identifiers or LSIDs); (4) Web 2.0 technologies that permit the semantic markup of, and semantic enhancements to, published biological texts. The journal will pursue cutting-edge technologies in publication and dissemination of biodiversity information while strictly following the requirements of the current International Code of Botanical Nomenclature (ICBN)

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 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

Jumping plant-lice of the Paurocephalinae (Insecta, Hemiptera, Psylloidea): systematics and phylogeny

Much confusion exists with respect to the content and definition of the psyUid subfamily Paurocephalinae. Based on a cladistic analysis of 22 morphological characters (16 adult and 6 larval), the subfamily is redefined to comprise the following five valid genera: Aphorma (3 species), Camarotoscena (12 valid species, with 1 new synonymy), DiC/idophlebia (= Aconopsylla, Haplaphalara, Paraphalaroida, Sinuonemopsylla and Woldaia; 24 species), Paurocephala (52 species) and Syntomoza (= Anomoterga and Homalocephata; 7 species). The tribe Diclidophlebiini is synonymised with the subfamily Paurocephalinae. The seven new generic synonymies produce 25 new species combinations. A key to genera for adults and fifth instar larvae is presented. In their revised definitions the genera exhibit relatively restricted distributions and host ranges: Aphorma: Palaearctic, Oriental - Ranunculaceae; Camarotoscena: Palaearctic - Salicaceae; Diclidophtebia: pantropical - Tiliaceae, Malvaceae, Sterculiaceae, Melastomataceae, Rhamnaceae, Ulmaceae and Euphorbiaceae; Paurocephala: Old World tropics - Moraceae, Urticaceae. Ulmaceae (all Urticales), Malvaceae. Sterculiaceae (all Malvales) and Clusiaceae (rheales); Syntomoza: Oriental, Afrotropical, Palaearctic - Flacourtiaceae, Salicaceae. The following taxa which have been referred to the Paurocephalinae are transferred to other taxa: Atmetocranium to the Calophyidae and Primascena to the Aphalaroidinae; Pseudaphorma is symonymised with Aphatara, and P. astigma with A. polygoni; the position of Strophingia is confirmed in the Strophingiinae.peer-reviewe

Studies on Ranunculus Population: Isozymic Pattern

Species of Ranunculus is small herb grows at quite high altitudes, ranging from several hundreds to more than a thousand meter above sea level. They can occupy a variety of habitats such as moist soils or can even grow sub merged or floating in stream. A few numbers of species from different populations have been recorded to have morphological complexity, which could cause a problem for the work of taxonomists in making decisions. In order to support taxonomists in solving their problem, a new experimental method using SDS-PAGE will be used to explore the isozyme data. The main purpose of this research was to investigate whether or not isozyme data can be used to clarify the morphological complexity of Ranunculus species. In this study, nine species of Ranunculus from different populations were used. Five to twenty plants were sampled for electrophoresis studies. Four enzyme systems: peroxidase, esterase, malate dehydrogenase and acid phosphatase were chosen. The results showed that every enzyme gave its specific pattern in each species and common band always found in nine species tested. This experiment proved that genetic data (isozyme) quite promoting to be applied in higher plant taxonomy in solving the morphological complexity problem. Key words: isozyme, PER, EST, MDH, ACP, Ranunculus