Paul Wilkin

Review: Plant species identification using digital morphometrics: A review

Plants are of fundamental importance to life on Earth. The shapes of leaves, petals and whole plants are of great significance to plant science, as they can help to distinguish between different species, to measure plant health, and even to model climate change. The growing interest in biodiversity and the increasing availability of digital images combine to make this topic timely. The global shortage of expert taxonomists further increases the demand for software tools that can recognize and characterize plants from images. A robust automated species identification system would allow people with only limited botanical training and expertise to carry out valuable field work. We review the main computational, morphometric and image processing methods that have been used in recent years to analyze images of plants, introducing readers to relevant botanical concepts along the way. We discuss the measurement of leaf outlines, flower shape, vein structures and leaf textures, and describe a wide range of analytical methods in use. We also discuss a number of systems that apply this research, including prototypes of hand-held digital field guides and various robotic systems used in agriculture. We conclude with a discussion of ongoing work and outstanding problems in the area.

Yams reclassified: a recircumscription of Dioscoreaceae and Dioscoreales

Analyses of morphological and molecular characters for Dioscoreales Hook, f. (Chase & al., 1995b; Caddick & al., 2000a; Caddick & al., 2002) have redefined the order, which now comprises three families, Burmanniaceae, Dioscoreaceae, and Nartheciaceae. Since recent analyses of morphological and molecular data sets (Caddick & al., 2002) have indicated well-supported relationships within Dioscoreaceae R. Br., a formal reclassification of the family is presented here. Dioscoreaceae now contain four distinct genera, Dioscorea, Stenomeris, Tacca (previously in Taccaceae), and Trichopus. The Malagasy endemic Avetra sempervirens is close sister to Trichopus zeylanicus, and is here reclassified as a second species of this genus. The dioecious Dioscoreaceae genera, Borderea, Epipetrum, Nanarepenta, Rajania, Tamus, and Testudinaria, are nested within Dioscorea in phylogenetic analyses (Caddick & al., 2002), and are therefore sunk into it.

A Plastid Gene Phylogeny of the Yam Genus, Dioscorea: Roots, Fruits and Madagascar

Abstract Following recent phylogenetic studies of the families and genera of Dioscoreales, the identification of monophyletic infrageneric taxa in the pantropical genus Dioscorea is a priority. A phylogenetic analysis based on sequence data from the plastid genes rbcL and matK is presented, using 67 species of Dioscorea and covering all the main Old World and selected New World lineages. The analysis used 14 outgroup taxa, including Trichopus Gaertn., Tacca J.R. & G. Forster, Stenomeris Planch., Burmannia L. and Thismia Griff. The main findings are: a) that a clade of rhizomatous taxa is sister to the rest of Dioscorea; b) the main Old World groups (such as the right-twining D. sect. Enantiophyllum) are monophyletic and c) there are two distinct lineages among the endemic Malagasy taxa. The consequences of the results for infrageneric classification of Dioscorea is considered, in particular the possibility of greatly simplifying the classifications of Knuth and Burkill. The results are also used to present novel hypotheses of character evolution in selected underground storage organ, inflorescence, fruit and seed characters and to discuss the origins of diversity in Dioscorea.

Molecular systematics of Gagea and Lloydia (Liliaceae; Liliales): implications of analyses of nuclear ribosomal and plastid DNA sequences for infrageneric classification

BACKGROUND AND AIMS Gagea is a Eurasian genus of petaloid monocots, with a few species in North Africa, comprising between 70 and approximately 275 species depending on the author. Lloydia (thought to be the closest relative of Gagea) consists of 12-20 species that have a mostly eastern Asian distribution. Delimitation of these genera and their subdivisions are unresolved questions in Liliaceae taxonomy. The objective of this study is to evaluate generic and infrageneric circumscription of Gagea and Lloydia using DNA sequence data. METHODS A phylogenetic study of Gagea and Lloydia (Liliaceae) was conducted using sequences of nuclear ribosomal internal transcribed spacer (ITS) and plastid (rpl16 intron, trnL intron, trnL-F spacer, matK and the psbA-trnH spacer) DNA regions. This included 149 accessions (seven as outgroups), with multiple accessions of some taxa; 552 sequences were included, of which 393 were generated as part of this research. KEY RESULTS A close relationship of Gagea and Lloydia was confirmed in analyses using different datasets, but neither Gagea nor Lloydia forms a monophyletic group as currently circumscribed; however, the ITS and plastid analyses did not produce congruent results for the placement of Lloydia relative to the major groups within Gagea. Gagea accessions formed five moderately to strongly supported clades in all trees, with most Lloydia taxa positioned at the basal nodes; in the strict consensus trees from the combined data a basal polytomy occurs. There is limited congruence between the classical, morphology-derived infrageneric taxonomy in Gagea (including Lloydia) and clades in the present phylogenetic analyses. CONCLUSIONS The analyses support monophyly of Gagea/Lloydia collectively, and they clearly comprise a single lineage, as some previous authors have hypothesized. The results provide the basis for a new classification of Gagea that has support from some morphological features. Incongruence between plastid and nuclear ITS results is interpreted as potentially due to ancient hybridization and/or paralogy of ITS rDNA.

Plant texture classification using gabor co-occurrences

Leaves provide an important source of data for research in comparative plant biology. This paper presents a method for comparing and classifying plants based on leaf texture. Joint distributions for the responses from applying different scales of the Gabor filter are calculated. The difference between leaf textures is calculated by the Jeffreydivergence measure of corresponding distributions. This technique is also applied to the Brodatz texture database, to demonstrate its more general application, and comparison to the results from traditional texture analysis methods is given.

Alpha e-taxonomy: responses from the systematics community to the biodiversity crisis

SummaryThe crisis facing the conservation of biodiversity is reflected in a parallel crisis in alpha taxonomy. On one hand, there is an acute need from government and non-government organisations for large-scale and relatively stable species inventories on which to build major biodiversity information systems. On the other, molecular information will have an increasingly important impact on the evidential basis for delimiting species and is likely to result in greater scientific debate and controversy on their circumscription. This paper argues that alpha-taxonomy built on the Internet (alpha e-taxonomy) can provide a key component of the solution. Two main themes are considered: (1) the potential of e-taxonomic revisions for engaging both the specialist taxonomic community and a wider public in gathering taxonomic knowledge and deepening understanding of it, and (2) why alpha-species will continue to play an essential role in the conventional definition of species and what kinds of methodological development this implies for descriptive species taxonomy. The challenges and requirements for sustaining e-taxonomic revisions in the long-term are discussed, with particular reference to models being developed by five initiatives with botanical exemplar websites: CATE (Creating a Taxonomic E-Science), Solanaceae Source, GrassBase and EDIT (European Distributed Institute of Taxonomy) exemplar groups and scratchpads. These projects give a clear indication of the crucially important role of the national and regional taxonomic organisations and their networks in providing both leadership and a fruitful and beneficial human and technical environment for taxonomists, both amateur and professional, to contribute their expertise towards a collective global enterprise.

Venation pattern analysis of leaf images

The work investigates pattern recognition methods to detect venation patterns on leaves. An automated technique that involves scale space analysis and an automated technique that includes a combination of edge detectors are compared with a manual technique. A small data set of five images is considered in this initial exploratory work and the results are qualitatively evaluated. The results show that the technique involving scale-space analysis is demonstrated to be a promising research direction to pursue.

A Morphological Cladistic Analysis of the Ipomoeeae (Convolvulaceae)

A cladistic analysis of the tribe Ipomoeeae based on 45 morphological and palynological characters is presented; the results obtained suggest that 1) the Ipomoeeae is monophyletic 2) all of the smaller genera of the tribe (Argyreia Lour., Astripomoea A. Meeuse, Blinkworthia Choisy, Lepistemon Blume, Lepistemonopsis Dammer, Paralepistemon Lejoly & Lisowski, Rivea Choisy, Stictocardia Hallier f. and Turbina Raf. are nested within the largest genus, Ipomoea. The characters defining taxa within the tribe are discussed and the limits and relationships of generic and infrageneric taxa re-evaluated. More research is needed in two areas; a) gene sequence data and b) into key taxa.

Evolution of dimery, pentamery and the monocarpellary condition in the monocot family Stemonaceae (Pandanales)

Stemonaceae are a small family of four genera(Table 1) which occur in Asia and Australia, with onegeographically disjunct species (Croomia pauciflora)native to southeastern U.S.A. (Rogers, 1982; Whetstone,1984). They possess petiolate leaves with a broad lami-na, rather than linear sheathing leaves as in most mono-cots, and flowers with dimerous or pentamerous flowers,rather than trimerous flowers as in many other monocots.The Sumatran genus Pentastemona was previouslyplaced in a separate family Pentastemonaceae (Duyfjes,1991, 1992) because it differs from other Stemonaceae inseveral respects, notably in having pentamerous, epigy-nous flowers, as opposed to tetramerous hypogynousflowers, inaperturate (as opposed to monosulcate) pollen(van der Ham, 1991, 1994), and also differences in seedanatomy (Bouman & Devente, 1992). However, Penta-stemona shares similarities with Stemonaceae in leafvenation, a unilocular ovary, and a characteristic aril.Recent multigene molecular analyses (e.g., Caddick &al., 2002) have placed Pentastemona as sister to all otherStemonaceae, prompting APG II (2003) to replace it inits original position within Stemonaceae (Van Steenis,1982).Within the monocots, earlier suggested affinities ofStemonaceae sensu latohave included Dioscoreales,Liliales and Asparagales (for review see Kubitzki, 1998a,b). However, analyses of molecular data have recentlyassigned Stemonaceae to a recircumscribed and wellsupported order Pandanales, together with Cyclantha-ceae, Pandanaceae, Triuridaceae and Velloziaceae (e.g.,Chase & al., 2000). The families of Pandanales are high-ly diverse in both vegetative and reproductive morpholo-gy, and their floral units are often anomalous with respectto more typical monocot flowers. For example, merism isapparently relatively labile in the order: dimery andtetramery are unusual for monocot flowers in general,but occur in Cyclanthaceae, Triuridaceae and Stemona-ceae. Other outstanding questions of floral structure inStemonaceae include whether the gynoecium is mono-

Pollen Evolution in Yams (Dioscorea: Dioscoreaceae)

Abstract Pollen character evolution in yams (Dioscorea: Dioscoreaceae) was investigated in relation to the phylogeny obtained from a recent combined analysis of rbcL and matK gene sequences. The following characters were evaluated: pollen size, aperture number, sexine ornamentation, perforation density, and orbicule presence or absence. Continuous characters were coded using the gap weighting method. Each character was optimized using MacClade onto a tree selected at random from analyses based on molecular data of Wilkin et al. The results indicate that in Dioscorea pollen size decreases in the more derived clades. The latter observation may be related to the evolution of annually replaced tubers. Aperture number increases from one in the monosulcate Stenophora clade (sister to the rest of Dioscorea) to two in other Dioscorea clades. This may be related to the presence of simultaneous microsporogenesis in Dioscorea. A perforate sexine is plesiomorphic in Dioscorea and a striate pattern has evolved more than once and is particularly characteristic in the Malagasy clade. Sexine ornamentation in the Stenophora clade is diverse. The endemic allotetraploid D. pyrenaica is characterized by large, monosulcate, gemmate pollen. The Dioscorea B clade is characterized by pollen with small, dense perforations. Orbicules occur in all Dioscorea species, but are absent in most of the outgroup taxa.