Alexandra H. Wortley

Herbaria are a major frontier for species discovery

Despite the importance of species discovery, the processes including collecting, recognizing, and describing new species are poorly understood. Data are presented for flowering plants, measuring quantitatively the lag between the date a specimen of a new species was collected for the first time and when it was subsequently described and published. The data from our sample of new species published between 1970 and 2010 show that only 16% were described within five years of being collected for the first time. The description of the remaining 84% involved much older specimens, with nearly one-quarter of new species descriptions involving specimens >50 y old. Extrapolation of these results suggest that, of the estimated 70,000 species still to be described, more than half already have been collected and are stored in herbaria. Effort, funding, and research focus should, therefore, be directed as much to examining extant herbarium material as collecting new material in the field.

How many species of seed plants are there

Recent estimates of the number of described species of seed plant have varied by as much as 62%. The underlying methodology of these estimates is characterised and discussed. We present a revised figure for the number of seed plants based on estimating rates of synonymy in a sample of recently monographed taxa. We conclude that some recent figures overestimate the number of described seed plant species by more than 200,000. This discrepancy is explained by an over-reliance on checklists and floristic studies that underestimate synonymy rates.

How Much Data are Needed to Resolve a Difficult Phylogeny? Case Study in Lamiales

Reconstructing phylogeny is a crucial target of contemporary biology, now commonly approached through computerized analysis of genetic sequence data. In angiosperms, despite recent progress at the ordinal level, many relationships between families remain unclear. Here we take a case study from Lamiales, an angiosperm order in which interfamilial relationships have so far proved particularly problematic. We examine the effect of changing one factor-the quantity of sequence data analyzed-on phylogeny reconstruction in this group. We use simulation to estimate a priori the sequence data that would be needed to resolve an accurate, supported phylogeny of Lamiales. We investigate the effect of increasing the length of sequence data analyzed, the rate of substitution in the sequences used, and of combining gene partitions. This method could be a valuable technique for planning systematic investigations in other problematic groups. Our results suggest that increasing sequence length is a better way to improve support, resolution, and accuracy than employing sequences with a faster substitution rate. Indeed, the latter may in some cases have detrimental effects on phylogeny reconstruction. Further molecular sequencing-of at least 10,000 bp-should result in a fully resolved and supported phylogeny of Lamiales, but at present the problematic aspects of this tree model remain.

A MOLECULAR SYSTEMATIC APPROACH TO EXPLORE DIVERSITY WITHIN THE SELLAPHORA PUPULA SPECIES COMPLEX (BACILLARIOPHYTA)1

The common and cosmopolitan freshwater benthic diatom Sellaphora pupula (Kütz.) Mereschk. is a model system for studying the nature of species in microalgae; the biological significance of morphological variation in this species complex has been widely demonstrated. The aim of this study was to establish a two‐gene phylogeny (18S rDNA and rbcL) for 23 Sellaphora taxa, including 19 S. pupula aggregate (agg.) demes or species, S. bacillum (Ehrenb.) D. G. Mann, and S. laevissima (Kütz.) D. G. Mann. A range of analyses on separate and combined data sets indicated that Sellaphora is a monophyletic group containing four major clades. Of the traditionally recognized species, S. bacillum and S. laevissima are natural groups, but S. pupula is paraphyletic or polyphyletic because S. bacillum groups with S. pupula“small lanceolate” and S. lanceolata. Thickened bars at the poles of valves within the core “pupula–bacillum” group may be a morphological synapomorphy; the fossil record suggests that this group is at least 12 million years old. Otherwise, there was no clear pattern in the distribution of different morphologies among the major clades; each clade was also heterogeneous with respect to mating system. More intensive and extensive sampling will doubtless uncover even greater diversity; the challenge lies in its interpretation. Our results demonstrate the limitations of paleoecological, ecological, and biogeographical research based on morphospecies.

Developmental origins of structural diversity in pollen walls of Compositae

Compositae exhibit some of the most complex and diverse pollen grains in flowering plants. This paper reviews the evolutionary and developmental origins of this diversity in pollen structure using recent models based on the behaviour of colloids and formation of micelles in the differentiating microspore glycocalyx and primexine. The developmental model is consistent with observations of structures recovered by pollen wall dissolution. Pollen wall diversity in Compositae is inferred to result from small changes in the glycocalyx, for example ionic concentration, which trigger the self-assembly of highly diverse structures. Whilst the fine details of exine substructure are, therefore, not under direct genetic control, it is likely that genes establish differences in the glycocalyx which define the conditions for self-assembly. Because the processes described here for Compositae can account for some of the most complex exine structures known, it is likely that they also operate in pollen walls with much simpler organisation.

The big machine and the much‐maligned taxonomist DNA taxonomy and the web

Every so often taxonomy enters the mainstream of biological discussion (Bisby et al., 2002; Gewin, 2002; Godfray, 2002; Lee, 2002; Lipscomb et al., 2003; Mallet & Willmott, 2003; Seberg et al., 2003; Tautz et al., 2002, 2003). Most recently, in response to a perceived crisis in taxonomy, two proposals to modify taxonomic practice have been put forward. First, Godfray (2002) has proposed that all new taxonomic revisions are placed on the web, available and accessible to all. In addition, he suggests drawing a line under nomenclatural issues, freeing taxonomists to concentrate on more substantial matters. Second, Tautz et al. (2002, 2003), as others before and since (Hebert et al., 2003), have proposed that DNA sequences should be the central scaffold for taxonomy. Both DNA and web-based taxonomy have been touted as providing practical and technological solutions to a range of issues concerned with the global inventory of taxa. Figure 1 illustrates the research programme of taxonomy, which seeks to document encyclopedic knowledge of all taxa on earth (Wilson, 2003). Recent commentary has suggested that this research programme is in crisis for four reasons. First, the huge shortfall in our current knowledge of taxonomic diversity. It is generally estimated that only around 10% of the world’s biota has so far been described (Wilson, 2000). Second, the pace of progress towards completing the encyclopedia is too slow. For example, the Species Plantarum Project dating back to 1995 which aims to complete a taxonomic account of all vascular plants has in seven years completed only six families comprising 1100 species, a mere 0.25%. At this rate, this valiant and ambitious project will reach completion in 2800 years. What this reflects is the paucity of new taxonomic treatments covering whole families. Other measures of the rate of taxonomic progress across all groups of organisms (e.g. numbers of new species being described per year, or the number of monographs being written) show a similar glacial rate of advancement towards completing the inventory. Third, taxonomists spend a significant part of their time sorting out the often complex synonymy and scattered type material associated with 250 years of previous work (Godfray, 2002) rather than delimiting and describing taxa. Finally, and perhaps more cogently, the reason the encyclopedia of life is viewed as being in crisis is the destruction of habitats and extinction of spe-

Determining the Potential Utility of Datasets for Phylogeny Reconstruction

The utility of morphological and molecular data in phylogenetic inference has been widely debated. Potential utility is intrinsically related to size, so the importance of morphological data in phylogenetic inference is becoming increasingly uncertain as molecular datasets grow rapidly larger. To test the continuing relevance of morphological data, we present an empirical investigation of size in a selection of recent data matrices and contrast the possible methods of measuring relative potential utility. Molecular datasets contained significantly more variable and parsimony-informative characters, and implied a greater number of parsimony-informative character-state changes than morphological ones. The latter is suggested to be the most useful measure of potential utility in phylogeny reconstruction, and shows much greater variability and overlap between molecular and morphological datasets. Morphological datasets often have much greater phylogenetic utility than is apparent from their size, and thus molecular datasets are not always more useful simply because they contain a greater number of aligned characters. We recommend these more accurate measures of utility should be more widely reported in phylogenetic research.

Efficiency of DNA barcodes for species delimitation: A case in Pterygiella Oliv. (Orobanchaceae)

Abstract  DNA barcoding is becoming an increasingly popular means to identify species. The obscure discrimination in the genus Pterygiella calls into question the re‐assessment of the criterion for species delimitation. We collected 20 individuals, representing all five described species of this genus in its distributional range. The aim was to use three proposed barcode DNA regions (rbcL, matK, and ITS) to diagnose Pterygiella species, and examine which barcode is more suitable for discerning the congeneric and related species. The results showed that the core barcodes matK and rbcL were comparatively less effective. However, the ITS region, especially ITS‐1 and ITS‐2, successfully identified all species in the genus. Furthermore, the secondary structure of ITS‐2 RNA, especially compensatory base changes, appears complementary to classical primary sequence analysis for DNA barcoding.

Pollen and the Evolution of Arctotideae (Compositae)

Recent molecular studies have elucidated the phylogeny of Compositae tribe Arctotideae, and found it to contain two, well supported, monophyletic subtribes, Arctotidineae and Gorteriinae, as well as some polyphyletic and problematic genera. On the basis of this new information, it may now be possible to identify diagnostic characters and synapomorphies to support the groupings defined within Arctotideae. Pollen characters have been shown to be particularly variable in Compositae. This paper aims to investigate the utility of those characters in the context of recent molecular phylogenies, in order to determine synapomorphic and diagnostic characters in Arctotideae. The pollen of each genus is described, illustrated with scanning electron micrographs, and optimised on a phylogeny of the tribe. Many pollen characters were found to be very informative when considered in the context of the current best estimate of phylogenetic relationships. Pollen morphology provides synapomorphies for clades at a number of hierarchical levels within Arctotideae, including the two subtribes, Arctotidinae and Gorteriinae, the grouping of Eremothamnus and Hoplophyllum, and smaller clades. It also supports the exclusion of Platycarpha from the tribe. The plesiomorphic palynological state for the tribe is discussed. Particular attention is paid to the evolution of different patterns of lophae (surface ridges). A single origin for the lophate condition is proposed as the most parsimonious mode of evolution in Arctotideae.

TAXONOMY AND PHYLOGENY RECONSTRUCTION: TWO DISTINCT RESEARCH AGENDAS IN SYSTEMATICS

The state of systematics, a vital biological discipline investigating fundamental questions about the earths biological diversity, is currently the subject of concern amongst the UK scientific and political communities. The scope of this complex field is redefined in terms of a number of linked agendas. Currently, key areas of research can be divided into the reconstruction of phylogeny and taxonomy, here defined as the description, delimitation and inventory of species. Molecular data have great potential to elucidate the relationships between taxa and, together with recent methodological advances, have instigated a resurgence of interest in phylogeny reconstruction. A literature survey indicates a decline in interest and investment in taxonomy, as defined above, an activity for which morphological data supply most information. We highlight the need to restore the balance in activity and profile between phylogeny reconstruction and morphology-based taxonomy, to redress the plight of systematics and dependent biological research.