Alastair Culham

How global is the global biodiversity information facility

There is a concerted global effort to digitize biodiversity occurrence data from herbarium and museum collections that together offer an unparalleled archive of life on Earth over the past few centuries. The Global Biodiversity Information Facility provides the largest single gateway to these data. Since 2004 it has provided a single point of access to specimen data from databases of biological surveys and collections. Biologists now have rapid access to more than 120 million observations, for use in many biological analyses. We investigate the quality and coverage of data digitally available, from the perspective of a biologist seeking distribution data for spatial analysis on a global scale. We present an example of automatic verification of geographic data using distributions from the International Legume Database and Information Service to test empirically, issues of geographic coverage and accuracy. There are over 1/2 million records covering 31% of all Legume species, and 84% of these records pass geographic validation. These data are not yet a global biodiversity resource for all species, or all countries. A user will encounter many biases and gaps in these data which should be understood before data are used or analyzed. The data are notably deficient in many of the worlds biodiversity hotspots. The deficiencies in data coverage can be resolved by an increased application of resources to digitize and publish data throughout these most diverse regions. But in the push to provide ever more data online, we should not forget that consistent data quality is of paramount importance if the data are to be useful in capturing a meaningful picture of life on Earth.

An assessment of suprageneric phylogeny inCyperaceae usingrbcL DNA sequences

The phylogeny of suprageneric groups inCyperaceae has been examined by cladistic analysis ofrbcL sequence data of 80 species in 40 genera. The results support the family as monophyletic and derived from a juncaceous grade.Oxychloe (Juncaceae) has moderate support as the sister taxon toCyperaceae. Several monophyletic groups correspond to previously recognised tribes, and some similarities are noted between this analysis and previous cladistic analyses of primarily morphological data. Support is also given for the removal ofHellmuthia from tribeHypolytreae, the transfer ofIsolepis nodosa toFicinia, and the inclusion ofOxycaryum andKyllingiella in tribeCypereae. A polytomy comprisingCyperus, Juncellus, Kyllinga andPycreus indicates a broader circumscription ofCyperus. The greatest uncertainty lies with the generic and tribal status of theScirpeae.

RECLASSIFICATION OF ACTAEA TO INCLUDE CIMICIFUGA AND SOULIEA (RANUNCULACEAE) : PHYLOGENY INFERRED FROM MORPHOLOGY, NRDNA ITS, AND CPDNA TRNL-F SEQUENC E VARIATION

Phylogenetic analyses using parsimony were performed on three independent data sets to test generic relationships between Actaea, Cimicifuga, and Souliea. Analyses of morphology and nuclear ribosomal DNA ITS were performed on 23 species of Cimicifuga, 4 species of Actaea, and the single species of Souliea. Analysis of chloroplast DNA trnL-F was applied to the same species, less two of Cimicifuga. The outgroup taxa Eranthis and Anemonopsis both resolved outside the ingroup in all parsimony analyses, whereas Souliea resolved within it. Jukes-Cantor pairwise sequence distances confirm Eranthis and Anemonopsis to be most distant. Souliea distances are comparable with those of taxa within the Actaea-Cimicifuga assemblage. A strongly supported monophyletic clade including all studied species of Actaea, Cimicifuga, and Souliea was found in all analyses. Evidence presented here allows a broader concept of Actaea to be adopted, reverting to the circumscription of Linnaeus in 1753. Seven sections, based on clades found in the total analysis, could be defined by morphological characters: A. sect. Actaea, sect. Podocarpae, sect. Cimicifuga, sect. Dichanthera, sect. Oligocarpae, sect. Pityrosperma, and sect. Souliea. One species, A. taiwanensis, is newly described and 23 new combinations are made in the ranks of section, species, and variety. Keys are provided to identify taxa at all ranks within the revised circumscription of Actaea. Maps showing the distributions of all seven sections and their constituent species are presented. Phytogeographic patterns suggest a Tertiary origin for the newly redefined genus, with species surviving in refugia during the glacial periods of the Pleistocene.

A phyloclimatic study of Cyclamen

BackgroundThe impact of global climate change on plant distribution, speciation and extinction is of current concern. Examining species climatic preferences via bioclimatic niche modelling is a key tool to study this impact. There is an established link between bioclimatic niche models and phylogenetic diversification. A next step is to examine future distribution predictions from a phylogenetic perspective. We present such a study using Cyclamen (Myrsinaceae), a group which demonstrates morphological and phenological adaptations to its seasonal Mediterranean-type climate. How will the predicted climate change affect future distribution of this popular genus of garden plants?ResultsWe demonstrate phylogenetic structure for some climatic characteristics, and show that most Cyclamen have distinct climatic niches, with the exception of several wide-ranging, geographically expansive, species. We reconstruct climate preferences for hypothetical ancestral Cyclamen. The ancestral Cyclamen lineage has a preference for the seasonal Mediterranean climate characteristic of dry summers and wet winters.Future bioclimatic niches, based on BIOCLIM and Maxent models, are examined with reference to a future climate scenario for the 2050s. Over the next 50 years we predict a northward shift in the area of climatic suitability, with many areas of current distribution becoming climatically unsuitable. The area of climatic suitability for every Cyclamen species is predicted to decrease. For many species, there may be no areas with a suitable climate regardless of dispersal ability, these species are considered to be at high risk of extinction. This risk is examined from a phylogenetic perspective.ConclusionExamining bioclimatic niches from a phylogenetic perspective permits novel interpretations of these models. In particular, reconstruction of ancestral niches can provide testable hypothesis about the historical development of lineages. In the future we can expect a northwards shift in climatic suitability for the genus Cyclamen. If this proves to be the case then dispersal is the best chance of survival, which seems highly unlikely for ant-dispersed Cyclamen. Human-assisted establishment of Cyclamen species well outside their native ranges offers hope and could provide the only means of dispersal to potentially suitable future environments. Even without human intervention the phylogenetic perspective demonstrates that major lineages could survive climate change even if many species are lost.

Phylogenetic relationships withinPelargonium sect.Peristera (Geraniaceae) inferred from nrDNA and cpDNA sequence comparisons

Phylogenetic analysis of nrDNA ITS and trnL (UAA) 5′ exon-trnF (GAA) chloroplast DNA sequences from 17 species ofPelargonium sect.Peristera, together with nine putative outgroups, suggests paraphyly for the section and a close relationship between the highly disjunct South African and Australian species of sect.Peristera. Representatives fromPelargonium sectt.Reniformia, Ligularia s. l. andIsopetalum (the St. Helena endemicP. cotyledonis) appear to be nested within thePeristera clade. The close relationship between the South African and AustralianPeristera is interpreted as being caused by long-range dispersal to Australia, probably as recent as the late Pliocene.

Cylindrocladium buxicola, a new species affecting Buxus spp., and its phylogenetic status

A leaf and twig blight disease of Buxus spp. was found to be associated with a new species of Cylindrocladium. The novel species status was confirmed using morphological characters, sequencing of the ribosomal 5.8S RNA gene and the flanking internal transcribed spacers (ITS), the β-tubulin gene, and the high mobility group (HMG) of the MAT2 mating type gene. Cylindrocladium buxicola is proposed as a new name. Fifteen isolates from the UK and one isolate from New Zealand were paired in all combinations but no fertile perithecia were obtained suggesting that C. buxicola is heterothallic and all isolates belonged to one mating type. AFLP analysis showed that the isolates collected in the UK and New Zealand are genetically homogenous. Phylogenetic analyses indicated that this species falls within a new lineage.

Phylogeny of Actaea including Cimicifuga (Ranunculaceae) inferred from nrDNA ITS sequence variation

Abstract Phylogenetic analysis of the rapidly changing nuclear ribosomal DNA ITS region in all 23 taxa of Cimicifuga and in all five taxa of Actaea was performed. The phylogenetic affinities of Souliea were investigated. Eranthis and Anemonopsis were shown to be separated from the ingroup by a similar number of steps. A monophyletic clade including all studied species of Actaea, Cimicifuga and Souliea is strongly supported and within it a group consisting of all Actaea species and Cimicifuga racemosa is identified. A large but weakly supported clade consisting of only Eurasian species is divided into two subclades; one with taxa possessing yellow staminodia, the other with taxa possessing white staminodia. Three other well supported groups are indicated: one clade consisting of two North American species with long carpel stipes: C. americana and C. laciniata , another with three North American species with short carpel stipes: C. arizonica, C. elata and C. rubifolia , and a third with three eastern Asian species with caducous bracts: C. biternata, C. japonica and C. purpurea . Cimicifuga is paraphyletic at least with respect to Actaea and possibly also with respect to Souliea .

A trnL-F based phylogeny for species of Pelargonium (Geraniaceaea) with small chromosomes

Phylogenetic analysis was performed of 921 positions of trnL (UAA) 5′ exon — trnF (GAA) exon chloroplast DNA regions from 68 representatives ofPelargonium sectt.Campylia, Cortusina, Glaucophyllum, Hoarea, Isopetalum, Ligularia, Otidia, Pelargonium, Peristera, Polyactium, andReniformia, together with five putative outgroup species from sectionsCiconium, Chorisma andJenkinsonia. The total data set therefore comprised 67.2 kb of DNA sequence. Two main ingroup clades were identified: one clade contains sectionsPeristera, Reniformia, andIsopetalum, the other contains sectionsCampylia, Cortusina, Glaucophyllum, Hoarea, Ligularia, Otidia, Pelargonium, Polyactium and two species currently grouped in sect.Peristera. Branching order among five main clades within the latter clade was not resolved. The trnL-F sequence data support monophyly only for sectionsReniformia andHoarea, the remainder of the currently recognized sections ofPelargonium being either paraphyletic or polyphyletic. The data further suggest that sect.Polyactium is diphyletic and that sect.Glaucophyllum is nested within sect.Pelargonium. One relatively derived clade, which represents half of the genus, contains predominantly geophytic and succulent species, occurring in the geographically restricted winter rainfall region of the South African Cape. This pattern is interpreted as reflecting explosive radiation, possibly as an adaptive response to recent aridification in the western Cape.

A Phylogeny of Isolepis (Cyperaceae) Inferred Using Plastid rbcL and trnL-F Sequence Data

Abstract The phylogeny of Isolepis was investigated by cladistic analysis of rbcL and trnL-F sequence data from 69 species in 26 genera of Cyperaceae. The genus Isolepis, as currently circumscribed, is not monophyletic. Three species, I. nodosa, I. Marginata, and I. trolli, are more closely related to Ficinia, whereas the position of I. humillima is uncertain. The remainder of Isolepis is sister to Ficinia and Desmoschoenus and together with Hellmuthia and Scirpoides form a clade sister to Cyperus s.l.; this clade shares the Cyperus-type embryo. Scirpus s.l. is not monophyletic. Scirpus s.s. and other genera with a Fimbristylis-type embryo form a monophyletic clade, whereas Schoenoplectus and other genera with a Schoenoplectus-type embryo form a grade. Communicating Editor: James R. Manhart

The taxonomic significance of naphthoquinones in the Droseraceae

Abstract The distribution of the naphthoquinones 7-methyljuglone and plumbagin was studied among 63 species of the Droseraceae . Both compounds occur in Drosophyllum and Drosera ; only plumbagin was found in Dionaea and Aldrovanda . Within Drosera , naphthoquinones support the classifications of De Candolle and Diels to some extent, with subgenus Drosera containing sections having 7-methyljuglone, often with plumbagin and subgenus Ergaleium containing sections where plumbagin is predominant and 7-methyljuglone rare or absent. Within subgenus Drosera , however, no naphthoquinones were found in three Australasian sections.