Authors' attitude toward adopting a new workflow to improve the computability of phenotype publications.

Critical to answering large-scale questions in biology is the integration of knowledge from different disciplines into a coherent, computable whole. Controlled vocabularies such as ontologies represent a clear path toward this goal. Using survey questionnaires, we examined the attitudes of biologists toward adopting controlled vocabularies in phenotype publications.

Which methods are the most effective in enabling novice users to participate in ontology creation? A usability study.

Producing findable, accessible, interoperable and reusable (FAIR) data cannot be accomplished solely by data curators in all disciplines. In biology, we have shown that phenotypic data curation is not only costly, but it is burdened with inter-curator variation. We intend to propose a software platform that would enable all data producers, including authors of scientific publications, to produce ontologized data at the time of publication.

Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes.

To use published phenotype information in computational analyses, there have been efforts to convert descriptions of phenotype characters from human languages to ontologized statements. This postpublication curation process is not only slow and costly, it is also burdened with significant intercurator variation (including curator-author variation), due to different interpretations of a character by various individuals. This problem is inherent in any human-based intellectual activity.

RAD sequencing resolves the phylogeny, taxonomy and biogeography of Trichophoreae despite a recent rapid radiation (Cyperaceae).

Trichophoreae is a nearly cosmopolitan Cyperaceae tribe that contains ~17 species displaying striking variation in size, inflorescence complexity, and perianth morphology. Although morphologically distinct, the status of its three genera (Cypringlea, Oreobolopsis and Trichophorum) is controversial because recent phylogenetic studies have suggested they might not be reciprocally monophyletic. However, previous analyses have shown conflicting topologies and consistently poor support due to an initial rapid diversification of the tribe.

The rediscovery of the rare Vietnamese endemic redefines generic limits in the Scirpo-Caricoid Clade (Cyperaceae).

For those familiar with boreal bogs and wet tundra, species of ("the cotton grasses") will undoubtedly represent some of the most striking and memorable taxa they have encountered. This small genus of 20 Holarctic sedge species (Cyperaceae) is remarkable because its inflorescences produce large, brilliantly white to rusty-red cottony masses when its flowers develop a perianth of highly elongated bristles after anthesis. In this study, we document the rediscovery of , a narrow Vietnamese endemic known from only two collections made approximately 7 km apart near Sa Pa in Lào Cai Province over 75 years ago.

Incentivising use of structured language in biological descriptions: Author-driven phenotype data and ontology production.

Phenotypes are used for a multitude of purposes such as defining species, reconstructing phylogenies, diagnosing diseases or improving crop and animal productivity, but most of this phenotypic data is published in free-text narratives that are not computable. This means that the complex relationship between the genome, the environment and phenotypes is largely inaccessible to analysis and important questions related to the evolution of organisms, their diseases or their response to climate change cannot be fully addressed. It takes great effort to manually convert free-text narratives to a computable format before they can be used in large-scale analyses.

Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada.

Premise Of The Study: Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada.

Methods: Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%).

Why are there so many sedges? Sumatroscirpeae, a missing piece in the evolutionary puzzle of the giant genus Carex (Cyperaceae).

For over a century, the origins and mechanisms underlying the diversification of the enormous temperate genus Carex (>2100 species; Cariceae, Cyperaceae) have remained largely speculative. Characteristics such as its diverse ecology, varied biogeography, and intriguing cytology have made Carex a powerful model for studying plant evolution, but its uncertain sister-group relationships hinder its use in studies that depend on accurate ancestral state estimates and biogeographic inferences. To identify the sister to Carex, we estimated the phylogeny of all genera in the Cariceae-Dulichieae-Scirpeae clade (CDS) using three plastid and two nuclear ribosomal markers.

Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics.

Despite the promise that molecular data would provide a seemingly unlimited source of independent characters, many plant phylogenetic studies are still based on only two regions, the plastid genome and nuclear ribosomal DNA (nrDNA). Their popularity can be explained by high-copy numbers and universal polymerase chain reaction (PCR) primers that make their sequences easily amplified and converted into parallel datasets. Unfortunately, their utility is limited by linked loci and limited characters resulting in low confidence in the accuracy of phylogenetic estimates, especially when rapid radiations occur.

Three new, early diverging Carex (Cariceae, Cyperaceae) lineages from East and Southeast Asia with important evolutionary and biogeographic implications.

Traditional Cariceae and Carex (1966 spp.) classifications recognised five genera (Carex, Cymophyllus, Kobresia, Schoenoxiphium, Uncinia) and four subgenera (Carex, Vignea, Vigneastra, Psyllophora). However, molecular studies have shown that only Carex, divided into five major lineages (the Core Carex, Schoenoxiphium, Core Unispicate, Vignea and Siderostictae Clades), is natural.

Design, synthesis, and characterization of heparin-binding peptoids.

A series of N-substituted glycine oligomers (peptoids) of varying length and side chains was synthesized with the aim of producing peptidomimetics that would bind with high affinity to heparin and thereby neutralize its anticoagulant activity. To this end, a library of 29 peptoids was synthesized using solid phase synthesis methodologies. The general design of the peptoids was the repeating trimer sequence N(cationic side chain)-N(alkyl or benzyl side chain)-N(α-chiral side chain), where the monomers are N-substituted glycine residues bearing the indicated side chains.

Comparative population structure and genetic diversity of Arceuthobium americanum (Viscaceae) and its Pinus host species: insight into host-parasite evolution in parasitic angiosperms.

In a recent study we revealed that the parasitic angiosperm Arceuthobium americanum is comprised of three distinct genetic races, each associated with a different host in regions of allopatry. In order to assess the role of host identity and geographical isolation on race formation in A. americanum, we compared the genetic population structure of this parasite with that of its three principal hosts, Pinus banksiana, Pinus contorta var.

The discovery of three genetic races of the dwarf mistletoe Arceuthobium americanum (Viscaceae) provides insight into the evolution of parasitic angiosperms.

A population genetic approach was used to explore the evolutionary biology of the parasitic angiosperm Arceuthobium americanum Nutt. ex Engelm. (Viscaceae).