Mark F. Watson

Tribes and clades within apiaceae subfamily apioideae: The contribution of molecular data

Phylogenetic analyses of chloroplast gene ( rbc L, mat K), intron ( rpl 16, rps 16, rpo C1) and nuclear ribosomal DNA internal transcribed spacer (ITS) sequences and chloroplast DNA restriction sites, with supplementary data from variation in size of the chloroplast genome inverted repeat, have been used to elucidate major clades within Apiaceae ( Umbelliferae ) subfamily Apioideae Drude. This paper summarizes the results of previously published molecular cladistic analyses and presents a provisional classification of the subfamily based on taxonomic congruence among the data sets. Ten tribes ( Aciphylleae M. F. Watson & S. R. Downie, Bupleureae Spreng., Careae Baill., Echinophoreae Benth., Heteromorpheae M. F. Watson & S. R. Downie, Oenantheae Dumort., Pleurospermeae M. F. Watson & S. R. Downie, Pyramidoptereae Boiss., Scandiceae Spreng. and Smyrnieae Spreng.) are erected or confirmed as monophyletic, with Scandiceae comprising subtribes Daucinae Dumort., Scandicinae Tausch and Torilidinae Dumort. Seven additional clades are also recognized but have yet to be treated formally, and at least 23 genera examined to date are of dubious tribal or clade placement. The utility of these different molecular markers for phylogenetic inference in Apioideae is compared based on maximum parsimony analyses of subsets of previously published molecular data sets. Of the six loci sequenced, the ITS region is seen to be evolving most rapidly and rbc L is the most conservative. Intermediate in rate of evolution are mat K and the three chloroplast introns; with rpl 16 and rps 16 evolving slightly faster than mat K or rpo C1. The analysis of restriction sites, however, provided 2–4 times more parsimony informative characters than any single DNA locus sequenced, with estimates of divergence just slightly lower than that of the ITS region. The trees obtained from separate analyses of these reduced data sets are consistent with regard to the major clades inferred and the relationships among them. Similar phylogenies are obtained by combining data or combining trees, representing the supermatrix and supertree approaches to phylogenetic analysis, respectively. The inferred relationship among the tribes and informally recognized major clades within Apioideae is presented.

Phylogenies reveal predictive power of traditional medicine in bioprospecting

There is controversy about whether traditional medicine can guide drug discovery, and investment in bioprospecting informed by ethnobotanical data has fluctuated. One view is that traditionally used medicinal plants are not necessarily efficacious and there are no robust methods for distinguishing those which are most likely to be bioactive when selecting species for further testing. Here, we reconstruct a genus-level molecular phylogenetic tree representing the 20,000 species found in the floras of three disparate biodiversity hotspots: Nepal, New Zealand, and the Cape of South Africa. Borrowing phylogenetic methods from community ecology, we reveal significant clustering of the 1,500 traditionally used species, and provide a direct measure of the relatedness of the three medicinal floras. We demonstrate shared phylogenetic patterns across the floras: related plants from these regions are used to treat medical conditions in the same therapeutic areas. This finding strongly indicates independent discovery of plant efficacy, an interpretation corroborated by the presence of a significantly greater proportion of known bioactive species in these plant groups than in random samples. We conclude that phylogenetic cross-cultural comparisons can focus screening efforts on a subset of traditionally used plants that are richer in bioactive compounds, and could revitalize the use of traditional knowledge in bioprospecting.

The Prometheus Taxonomic Model: a practical approach to representing multiple classifications

A model for representing taxonomic data in a flexible and dynamic system capable of handling and comparing multiple simultaneous classifications is presented. The Prometheus Taxonomic Model takes as its basis the idea that a taxon can be circumscribed by the specimens or taxa of a lower rank which are said to belong to it. In this model alternative taxon concepts are therefore represented in terms of differing circumscriptions. This provides a more objective way of expressing taxonomic concepts than purely descriptive circumscriptions have been published. Using specimens as the fundamental elements of taxon circumscription also allows for the automatic naming of taxa based upon the distribution and priority of types within each circumscription, and by application of the International Code of Botanical Nomenclature. This approach effectively separates the process of naming taxa (nomenclature) from that of classification, and therefore enables the system to store multiple classifications. The derivation of the model, how it compares with other models, and the implications for the construction of global data sets and taxonomic working practice are discussed.

Circumscription of Apiaceae tribe Oenantheae

Previous molecular systematic investigations into the higher-level relationships of Apiaceae subfamily Apioideae have revealed a strongly supported clade recognised as tribe Oenantheae Dumort. These plants may have clusters of fibrous or tuberous-thickened roots, corky-thickened fruits, and other adaptations for existence in wet or aquatic habitats. In some species, the leaves may be finely dissected or linear-septate and much reduced. We have initiated collaborative studies to produce a comprehensive estimate of phylogeny of the tribe, but such investigations are thwarted because information on the composition of the tribe is lacking. Herein, tribe Oenantheae is circumscribed to include the following genera: Afrocarum, Berula, Bifora (pro parte), Cicuta, Cryptotaenia (pro parte), Cynosciadium, Daucosma, Helosciadium, Lilaeopsis, Limnosciadium, Neogoezia, Oenanthe, Oxypolis, Perideridia, Ptilimnium, Sium, and Trepocarpus. Relationships inferred from phylogenetic analyses of nuclear rDNA ITS sequences from 64 accessions representing all 17 genera reveal that four genera are not monophyletic. Bifora and Cryptotaenia have members that fall outside of the tribe; Berula and Sium each comprise two or more lineages within Oenantheae. The St Helena endemics, Sium bracteatum and S. burchellii, ally with African Berula erecta; this clade is sister to the African endemic species Sium repandum and Afrocarum imbricatum, and this entire group is allied closely with north temperate Berula erecta. Nomenclatural changes are in order, but must await further study. Representatives of eight genera native to North America comprise a monophyletic group, and results from relative rate tests suggest that this lineage is evolving much faster than any other major clade recognised within the tribe.

Phylogenetic relationships of species of Aciphylla (Apiaceae, subfamily Apioideae) and related genera using molecular, morphological, and combined data sets

Abstract Evolutionary relationships of the Australasian genus Aciphylla were investigated using cladistic analyses of molecular (internal transcribed spacer regions 18S‐26S nuclear ribosomal DNA), morphological, and combined data sets. Molecular sequence data provide support for infrageneric groups within Aciphylla and show some agreement with species groups suggested by previous authors. Cladistic analysis of morphological characters traditionally used to describe species within Aciphvlla shows virtually no resolution of relationships, indicating considerable homoplasy within the data set. Analysis of combined molecular and morphological data reveals infrageneric groups that concur with those inferred by the molecular analysis, and shows increased resolution at the species level. The phylogeny resulting from the combined analysis provides a good framework for the interpretation of morphological characters in Aciphylla. Monophyly of Aciphylla is unresolved in all analyses. The Tas‐manian endemic Anisotome procumbens is unexpectedly placed in a clade with those New Zealand Aciphylla species (Aciphylla dobsonii and A. simplex) that have retained the most ancestral character states. Other Australasian Apioideae (Gingidia in part, Lignocarpa, and Scandia) are placed within the larger Aciphylla clade with those species that show an accumulation of derived character states for Aciphylla. Anisotome appears paraphyletic with respect to Aciphylla and the majority of Gingidia species, Taxonomic and biogeographical relationships within Aciphylla and related genera are discussed in the light of the inferred phylogeny.

A Universal Character Model and Ontology of Defined Terms for Taxonomic Description

Taxonomists classify biological specimens into groups (taxa) on the basis of similarities between their observed features (‘characters’). The description of these ‘characters’ is therefore central to taxonomy, but there is currently no agreed model, defined terminology nor methodology for composing these descriptions. This lack of a common conceptual model, together with the individualistic working practices of taxonomists, means that descriptions are not composed consistently, and are not easy to interpret and re-use, nor are datasets comparable. The purpose of the Prometheus II project is to improve the interpretation and comparison of plant descriptions. To this end we propose a new conceptual model for unambiguously representing character descriptions, and have developed a controlled vocabulary as an ontology of defined terms, which will be used to describe specimens according to our character model.

In search of a functional flora—towards a greater integration of ecology and taxonomy

Large-scale biodiversity informatics projects will not properly address the needs of one important potential user group. Ecologists do not have ready access to datasets which allow them to assign plant species to functional types. We believe that information technology has developed sufficiently to allow taxonomists and ecologists to work together to address this need and develop specimen databases to combine taxonomic data with ecological and ecophysiological information so that this information will be assigned to the correct taxon in the future. Digital images provide a rapid and economical method of vouchering specimen data, reducing the need to store physical vouchers in herbaria.

Ontology-Driven Automated Generation of Data Entry Interfaces to Databases

This paper discusses an ontology based approach for the automatic generation of data entry interfaces to databases. An existing domain ontology is mapped to a system domain model, which a domain expert can then specialise using their domain expertise, for their data entry needs as required for individual projects. Based on this specialised domain knowledge, the system automatically generates appropriate data entry interfaces with the aid of a presentation model. By constraining the data entered to a term definition ontology and utilising appropriate defined domain terminology the quality of the collected data can be improved. Compared with traditional model-based user automatic interface development environments, this approach also has the potential to reduce the labour requirements for the expert developer.

Notes relating to the Flora of Bhutan: XXXIII. Umbelliferae, I

Ten new species of Umbelliferae are described from Bhutan, Nepal and Sikkim: Cnidium atropurpureum M.F. Watson, Cortiella lamondiana Fullarton & M.F. Watson, Heracleum bhutanicum M.F. Watson, H. woodii M.F. Watson, Keraymonia pinnatifolia M.F. Watson, Schulzia bhutanica M.F. Watson, Sinocarum longii M.F. Watson, S. minus M.F. Watson, S. pulchellum M.F. Watson and S. woodii M.F. Watson. Two new combinations are made: Cortiella cortioides (C. Norman) M.F. Watson and Meeboldia digitata (Kljuykov) M.F. Watson.

Report of the Special Committee on Registration of Algal and Plant Names (including fossils)

The Special Committee on Registration of Algal and Plant Names (including fossils) was established at the XVIII International Botanical Congress (IBC) in Melbourne in 2011, its mandate being to consider what would be involved in registering algal and plant names (including fossils), using a procedure analogous to that for fungal names agreed upon in Melbourne and included as Art. 42 in the International Code of Nomenclature for algae, fungi, and plants. Because experience with voluntary registration was key to persuading mycologists of the advantages of mandatory registration, we began by asking institutions with a history of nomenclatural indexing to develop mechanisms that would permit registration. The task proved more difficult than anticipated, but considerable progress has been made, as is described in this report. It also became evident that the Nomenclature Section needs a structure that will allow ongoing discussion of registration and associated issues. Simultaneously with this report we are submitting four proposals that would provide such a structure.