Phylogeny of the Rosidae: A dense taxon sampling analysis

Rosidae, a clade of approximately 90 000 species of angiosperms, exhibits remarkable morphological diversity and extraordinary heterogeneity in habitats and life forms. Resolving phylogenetic relationships within Rosidae has been difficult, in large part due to nested radiations and the enormous size of the clade. Current estimates of phylogeny contain areas of poor resolution and/or support, and there have been few attempts to synthesize the available data into a comprehensive view of Rosidae phylogeny. We aim to improve understanding of the phylogeny of Rosidae with a dense sampling scheme using both newly generated sequences and data from GenBank of the chloroplast rbcL, atpB, and matK genes and the mitochondrial matR gene. We combined sequences from 9300 species, representing 2775 genera, 138 families, and 17 orders into a supermatrix. Although 59.26% of the cells in the supermatrix have no data, our results generally agree with previous estimates of Rosidae phylogeny and provide greater resolution and support in several areas of the topology. Several noteworthy phylogenetic relationships are recovered, including some novel relationships. Two families (Euphorbiaceae and Salvadoraceae) and 467 genera are recovered as non-monophyletic in our sampling, suggesting the need for future systematic studies of these groups. Our study shows the value of a botanically informed bioinformatics approach and dense taxonomic sampling for resolving rosid relationships. The resulting tree provides a starting point for large-scale analyses of the evolutionary patterns within Rosidae.     

A new Erioderma taxon from the Azores

Abstract:The Azorean lichen previously and erroneously referred in the literature toErioderma wrightii , belongs to the complex, widespread species E. leylandii, and is described as subsp.azoricum , possibly representing a relic, ancestral form with a composite chemistry. It is presently only known from Pico where it is under threat owing to the destruction of the forests.     

A numerical approach to the biomechanical analysis of bone fracture healing

Investigations are reported in the literature, by means of experimental, analytical and numerical methods, concerning the biomechanical properties of bone. However, the evolutionary phenomena of bone fracture healing does not have a large reference literature. This work investigates and describes the behaviour of inclined human femur fractures with external fixation up to complete healing. A numerical formulation based on the finite element method has been adopted. Geometric configuration is defined using data from a magnetic resonance process applied to a femur in vivo. A three dimensional model has been developed by adopting an orthotropic material law for cortical bone and an isotropic law for the fracture gap zone. Stress and strain reponses of the bone and fixation device are investigated with reference to the evolutionary behaviour of the healing tissue.     

Triatoma infestans apyrases belong to the 5'-nucleotidase family

Apyrases are nucleoside triphosphate-diphosphohydrolases (EC 3.6.1.5) present in a variety of organisms. The apyrase activity found in the saliva of hematophagous insects is correlated with the prevention of ADP-induced platelet aggregation of the host during blood sucking. Purification of apyrase activity from the saliva of the triatomine bug Triatoma infestans was achieved by affinity chromatography on oligo(dT)-cellulose and gel filtration chromatography. The isolated fraction includes five N-glycosylated polypeptides of 88, 82, 79, 68 and 67 kDa apparent molecular masses. The isolated apyrase mixture completely inhibited aggregation of human blood platelets. Labeling with the ATP substrate analogue 5'-p-fluorosulfonylbenzoyladenosine showed that the five species have ATP-binding characteristic of functional apyrases. Furthermore, tandem mass spectroscopy peptide sequencing showed that the five species share sequence similarities with the apyrase from Aedes aegypti and with 5'-nucleotidases from other species. The complete cDNA of the 79-kDa enzyme was cloned, and its sequence confirmed that it encodes for an apyrase belonging to the 5'-nucleotidase family. The gene multiplication leading to the unusual salivary apyrase diversity in T. infestans could represent an important mechanism amplifying the enzyme expression during the insect evolution to hematophagy, in addition to an escape from the host immune response, thus enhancing acquisition of a meal by this triatomine vector of Chagas' disease.     

Oxymonads are closely related to the excavate taxon Trimastix

Despite intensive study in recent years, large-scale eukaryote phylogeny remains poorly resolved. This is particularly problematic among the groups considered to be potential early branches. In many recent systematic schemes for early eukaryotic evolution, the amitochondriate protists oxymonads and Trimastix have figured prominently, having been suggested as members of many of the putative deep-branching higher taxa. However, they have never before been proposed as close relatives of each other. We amplified, cloned, and sequenced small-subunit ribosomal RNA genes from the oxymonad Pyrsonympha and from several Trimastix isolates. Rigorous phylogenetic analyses indicate that these two protist groups are sister taxa and are not clearly related to any currently established eukaryotic lineages. This surprising result has important implications for our understanding of cellular evolution and high-level eukaryotic phylogeny. Given that Trimastix contains small, electron-dense bodies strongly suspected to be derived mitochondria, this study constitutes the best evidence to date that oxymonads are not primitively amitochondriate. Instead, Trimastix and oxymonads may be useful organisms for investigations into the evolution of the secondary amitochondriate condition. All higher taxa involving either oxymonads or Trimastix may require modification or abandonment. Affected groups include four contemporary taxa given the rank of phylum (Metamonada, Loukozoa, Trichozoa, Percolozoa), and the informal excavate taxa. A new "phylum-level" taxon may be warranted for oxymonads and Trimastix.     

A new taxon in the genusMoehringia (Caryophyllaceae)

The new taxonMoehringia intricata subsp.giennensis, from the calcareous mountains of the south-eastern Iberian Peninsula is described. A comparative morphological study with regard to the most closely related taxa, contributes information of leaf anatomy, seed and pollen morphology, ecology and distribution.     

Enterococcus faecalis hemolysin-bacteriocin plasmids belong to the same incompatibility group

Plasmid pair coexistence was studied both among nine Enterococcus faecalis hemolysin-bacteriocin (Hly-Bcn) plasmids, including pJH2, pAD1, pAM gamma 1, and pIP964, and between pIP964 and five R plasmids. Some of the Hly-Bcn plasmids used were derivatives encoding resistance to erythromycin or tetracycline. The Hly-Bcn plasmids were incompatible with each other; 40 to 100% displacement was observed bilaterally for eight pairs and unilaterally for one pair. In contrast, pIP964 stably coexisted with each of the R plasmids. Entry exclusion was associated with incompatibility for most of the Hly-Bcn plasmids. The nine Hly-Bcn plasmids harbored by E. faecalis form a distinct incompatibility (Inc) group, designated IncHly.     

Phylogenomics with incomplete taxon coverage: the limits to inference

Background  

Phylogenomic studies based on multi-locus sequence data sets are usually characterized by partial taxon coverage, in which sequences for some loci are missing for some taxa. The impact of missing data has been widely studied in phylogenetics, but it has proven difficult to distinguish effects due to error in tree reconstruction from effects due to missing data per se. We approach this problem using a explicitly phylogenomic criterion of success, decisiveness, which refers to whether the pattern of taxon coverage allows for uniquely defining a single tree for all taxa.     

A federated database of taxon pages in the Italian Biodiversity Network

Primary biodiversity data are often organised in federated databases in the framework of big international projects and initiatives. Other data are normally organised into isolated resources: ecological, morphological and morpho-anatomic databases, checklists, archives of digital identification tools, etc. These data, which do not refer specifically to one specimen or observation, but to a taxon, can be addressed to as “taxon-related data”. In the framework of the Italian Biodiversity Network, taxon-related data have been aggregated by using a federated approach, with the creation of a network of data providers, which required the development of a communication protocol, the species-related data (SRD) protocol and of a simple data format (the SRD format). The SRD federated database aggregates currently ca. 70,000 taxon pages for several groups of organisms: vascular plants, lichens, mosses, algae, freshwater fishes and butterflies. All these resources can be queried by using one simple interface in the web portal of the Italian Biodiversity Network (http://www.naturaitalia.it/nnb/).     

A numerical analysis of Tasmanian higher plant endemism

KIRKPATRICK, J. B. & BROWN, M. J., 1984. A numerical analysis of Tasmanian higher plant endemism. Tasmanian endemic plant taxa at the species level or below were placed in geographic elements according to the distribution of their genera. These elements are associated with different environments, the endemic and Antarctic elements being most prominent in rainforest and alpine communities; the cosmopolitan element in alpine communities, and the Australian element in the fire-prone lowland communities. A monothetic divisive classification and minimum spanning tree analysis of a matrix of the occurrence of 242 Tasmanian endemic species from 366 areas resulted in groups of species and lists whose distributions were closely related to precipitation, altitude and vegetation type. The proportions of endemic species in local Tasmanian floras were almost totally explained by altitude and precipitation in a stepwise multiple regression analysis. However, it is possible that many of the endemic species have not been able to occupy their potential range in Tasmania as a result of insufficient time having elapsed for them to fully expand from Glacial refugia.