Recognizing the forest for the trees: testing temporal patterns of cladogenesis using a null model of stochastic diversification

Computer simulations are developed and employed to examine the expected temporal distributions of nodes under a null model of stochastic lineage bifurcation and extinction. These Markovian models of phylogenetic process were constructed so as to permit direct comparisons against empirical phylogenetic trees generated from molecular or other information available solely from extant species. For replicate simulated phylads with n extant species, cumulative distribution functions (cdf's) of branching times were calculated, and compared (using the Kolmogorov-Smirnov test statistic D) to those from three published empirical trees. Molecular phylogenies for columbine plants and avian cranes showed statistically significant departures from the null expectations, in directions indicating recent and ancient species' radiations, respectively, whereas a molecular phylogeny for the Drosophila virilis species group showed no apparent historical clustering of branching events. Effects of outgroup choice and phylogenetic frame of reference were investigated for the columbines and found to have a predictable influence on the types of conclusions to be drawn from such analyses. To enable other investigators to statistically test for nonrandomness in temporal cladogenetic pattern in empirical trees generated from data on extant species, we present tables of mean cdf's and associated probabilities under the null model for expected branching times in phylads of varying size. The approaches developed in this report complement and extend those of other recent methods for employing null models to assess the statistical significance of pattern in evolutionary trees.      

Predicting urban outdoor thermal comfort by the Universal Thermal Climate Index UTCI—a case study in Southern Brazil

Recognising that modifications to the physical attributes of urban space are able to promote improved thermal outdoor conditions and thus positively influence the use of open spaces, a survey to define optimal thermal comfort ranges for passers-by in pedestrian streets was conducted in Curitiba, Brazil. We applied general additive models to study the impact of temperature, humidity, and wind, as well as long-wave and short-wave radiant heat fluxes as summarised by the recently developed Universal Thermal Climate Index (UTCI) on the choice of clothing insulation by fitting LOESS smoothers to observations from 944 males and 710 females aged from 13 to 91 years. We further analysed votes of thermal sensation compared to predictions of UTCI. The results showed that females chose less insulating clothing in warm conditions compared to males and that observed values of clothing insulation depended on temperature, but also on season and potentially on solar radiation. The overall pattern of clothing choice was well reflected by UTCI, which also provided for good predictions of thermal sensation votes depending on the meteorological conditions. Analysing subgroups indicated that the goodness-of-fit of the UTCI was independent of gender and age, and with only limited influence of season and body composition as assessed by body mass index. This suggests that UTCI can serve as a suitable planning tool for urban thermal comfort in sub-tropical regions.     

Deriving the operational procedure for the Universal Thermal Climate Index (UTCI)

The Universal Thermal Climate Index (UTCI) aimed for a one-dimensional quantity adequately reflecting the human physiological reaction to the multi-dimensionally defined actual outdoor thermal environment. The human reaction was simulated by the UTCI-Fiala multi-node model of human thermoregulation, which was integrated with an adaptive clothing model. Following the concept of an equivalent temperature, UTCI for a given combination of wind speed, radiation, humidity and air temperature was defined as the air temperature of the reference environment, which according to the model produces an equivalent dynamic physiological response. Operationalising this concept involved (1) the definition of a reference environment with 50% relative humidity (but vapour pressure capped at 20 hPa), with calm air and radiant temperature equalling air temperature and (2) the development of a one-dimensional representation of the multivariate model output at different exposure times. The latter was achieved by principal component analyses showing that the linear combination of 7 parameters of thermophysiological strain (core, mean and facial skin temperatures, sweat production, skin wettedness, skin blood flow, shivering) after 30 and 120 min exposure time accounted for two-thirds of the total variation in the multi-dimensional dynamic physiological response. The operational procedure was completed by a scale categorising UTCI equivalent temperature values in terms of thermal stress, and by providing simplified routines for fast but sufficiently accurate calculation, which included look-up tables of pre-calculated UTCI values for a grid of all relevant combinations of climate parameters and polynomial regression equations predicting UTCI over the same grid. The analyses of the sensitivity of UTCI to humidity, radiation and wind speed showed plausible reactions in the heat as well as in the cold, and indicate that UTCI may in this regard be universally useable in the major areas of research and application in human biometeorology.     

Synopsis of the species of Chloromyxum Mingazinni, 1890 (Myxozoa: Myxosporea: Chloromyxidae)

A synopsis of the species of Chloromyxum Mingazinni, 1890 (Myxozoa: Myxosporea: Chloromyxidae) is presented, including 140 nominal species. For each species the most relevant morphological and morphometric characteristics are indicated. Included are data on the site of infection within the host, the original host and the host locality, plus a full bibliography of the original records for these species. A diagrammatic illustration of a spore of each species is also provided.     

Cytogenetic and immunological changes after dermal exposure to polycyclic aromatic hydrocarbons and UV radiation

Goeckerman's therapy (GT), which combines exposure to coal tar (polycyclic aromatic hydrocarbons - PAHs) and UV radiation (UV) is often used as the first option for treatment of psoriasis. However, PAHs and UV represent mutagenic, carcinogenic and immunotoxic agents. Therefore GT can represent a health risk for the patients. The group under observation consisted of thirty patients undergoing GT. Before and after the treatment, blood samples were collected and chromosomal aberrations and selected immunological markers were determined. The relationships between chromosomal aberrations and immunological markers and the extent (duration) of exposure to GT were evaluated. The Psoriasis Area and Severity Index (PASI) score confirmed the high efficacy of GT. However, significantly elevated levels of chromosomal aberrations of peripheral lymphocytes were also found after the therapy (p<0.001). The levels of chromosomal abnormalities correlated to the extent and the total duration of exposure to PAHs (r = 0.682, p<0.01 and r = 0.605, p<0.05). After the therapy, significantly decreased levels of IgE, IgM isotypes of immunoglobulin, alpha(2)-macroglobulin and transferrin together with beta(2)-microglobulin were found. From the immunological markers listed above only the decreased level of alpha(2)-macroglobulin correlated to the extent of exposure to PAHs (r = -0.568, p<0.05). No correlation was found between chromosomal aberrations, significantly changed immunological markers and the duration of UV exposure. Our study revealed that GT has a significant impact on both genetic and immunological parameters of psoriatic patients. The results indicate that GT could increase genotoxic risk and modulates immunity of treated patients.     

Amino acid size, charge, hydropathy indices and matrices for protein structure analysis

Background  

Prediction of protein folding and specific interactions from only the sequence (ab initio) is a major challenge in bioinformatics. It is believed that such prediction will prove possible if Anfinsen's thermodynamic principle is correct for all kinds of proteins, and all the information necessary to form a concrete 3D structure is indeed present in the sequence.     

Molecular characterisation of Neoparamoeba strains isolated from gills of Scophthalmus maximus

Small subunit ribosomal RNA gene sequences were determined for 5 amoeba strains of the genus Neoparamoeba Page, 1987 that were isolated from gills of Scophthalmus maximus (Linnaeus, 1758). Phylogenetic analyses revealed that 2 of 5 morphologically indistinguishable strains clustered with 6 strains identified previously as N. pemaquidensis (Page, 1970). Three strains branched as a clade separated from N. pemaquidenis and N. aestuarina (Page, 1970) clades. Our analyses suggest that these 3 strains could be representatives of an independent species. In a more comprehensive eukaryotic tree, strains belonging to Neoparamoeba spp. formed a monophyletic group with a sister-group relationship to Vannella anglica Page, 1980. They did not cluster with Gymnamoebae of the families Hartmannellidae, Flabellulidae, Leptomyxidae or Amoebidae presently available in GenBank.     

Molecular phylogeny of Crematogaster subgenus Decacrema ants (Hymenoptera: Formicidae) and the colonization of Macaranga (Euphorbiaceae) trees

To elucidate the evolution of one of the most species-rich ant-plant symbiotic systems, the association between Crematogaster (Myrmicinae) and Macaranga (Euphorbiaceae) in South-East Asia, we conducted a phylogenetic analysis of the ant partners. For the phylogenetic analysis partial mitochondrial cytochrome oxidase I and II were sequenced and Maximum Parsimony analysis was performed. The analyzed Crematogaster of the subgenus Decacrema fell into three distinct clades which are also characterized by specific morphological and ecological traits (queen morphology, host-plants, and colony structure). Our results supported the validity of our currently used morphospecies concept for Peninsula Malaysia. However, on a wider geographic range (including North and North-East Borneo) some morphospecies turned out to be species complexes with genetically quite distinct taxa. Our phylogenetic analysis and host association studies do not indicate strict cocladogenesis between the subgenus Decacrema and their Macaranga host-plants because multiple ant taxa occur on quite distinct host-plants belonging to different clades within in the genus Macaranga. These results support the view that host-shifting or host-expansion is common in the ants colonizing Macaranga. Additionally, the considerable geographic substructuring found in the phylogenetic trees of the ants suggests that allopatric speciation has also played a role in the diversification and the current distribution of the Decacrema ants.