The influence of non-climate predictors at local and landscape resolutions depends on the autecology of the species

Species distribution models have come under criticism for being too simplistic for making robust future forecasts, partly because they assume that climate is the main determinant of geographical range at large spatial extents and coarse resolutions, with non-climate predictors being important only at finer scales. We suggest that this paradigm might be obscured by species movement patterns. To explore this we used contrasting kangaroo (family Macropodidae) case studies: two species with relatively small, stable home ranges (Macropus giganteus and M.robustus) and three species with more extensive, adaptive ranging behaviour (M.antilopinus, M.fuliginosus and M.rufus). We predicted that non-climate predictors will be most influential to model fit and predictive performance at local spatial resolution for the former species and at landscape resolution for the latter species. We compared residuals autocovariate - boosted regression tree (RAC-BRT) model statistics with and without species-specific non-climate predictors (habitat, soil, fire, water and topography), at local- and landscape-level spatial resolutions (5 and 50km). As predicted, the influence of non-climate predictors on model fit and predictive performance (compared with climate-only models) was greater at 50 compared with 5km resolution for M.rufus and M.fuliginosus and the opposite trend was observed for M.giganteus. The results for M.robustus and M.antilopinus were inconclusive. Also notable was the difference in inter-scale importance of climate predictors in the presence of non-climate predictors. In conclusion, differences in autecology, particularly relating to space use, may contribute to the importance of non-climate predictors at a given scale, not model scale per se. Further exploration of this concept across a range of species is encouraged and findings may contribute to more effective conservation and management of species at ecologically meaningful scales. © 2014 Ecological Society of Australia.

Dysglycaemia and other predictors for progression or regression from impaired fasting glucose to diabetes or normoglycaemia

Aims. Diabetes mellitus is a growing health problem worldwide. This study aimed to describe dysglycaemia and determine the impact of body composition and clinical and lifestyle factors on the risk of progression or regression from impaired fasting glucose (IFG) to diabetes or normoglycaemia in Australian women. Methods. This study included 1167 women, aged 20-94 years, enrolled in the Geelong Osteoporosis Study. Multivariable logistic regression was used to identify predictors for progression to diabetes or regression to normoglycaemia (from IFG), over 10 years of follow-up. Results. At baseline the proportion of women with IFG was 33.8% and 6.5% had diabetes. Those with fasting dysglycaemia had higher obesity-related factors, lower serum HDL cholesterol, and lower physical activity. Over a decade, the incidence of progression from IFG to diabetes was 18.1 per 1,000 person-years (95% CI, 10.7-28.2). Fasting plasma glucose and serum triglycerides were important factors in both progression to diabetes and regression to normoglycaemia. Conclusions. Our results show a transitional process; those with IFG had risk factors intermediate to normoglycaemics and those with diabetes. This investigation may help target interventions to those with IFG at high risk of progression to diabetes and thereby prevent cases of diabetes.

Nest site selection and flying capacity of neotropical wasp Angiopolybia pallens (Hymenoptera: Vespidae) in the Atlantic Rain Forest, Bahia State, Brazil

In order to evaluate the flying capacity and nest site selection of Angiopolybia pallens (Lepeletier, 1836), we made 17 incursions (136 hours of sample efforts) in Atlantic Rain Forest environments in Bahia state. Our data show this wasp prefers to nest on wide leaves of bushes and short trees (nests between 0.30 and 3m from the ground) placed in half-shady environments (clearings and shadowed cultivations). The logistic regression model using Quasi-Newton method provided a good description of the flying capacity observed in A. pallens (x 2 = 91.52; p≪0.001). According to the logistic regression model, the A. pallens flight autonomy is low, flying for short distances and with an effective radius of action of about 24m measured from their nests, which means a foraging area of nearly 1,800 m 2.

The use of the carbon-13 in the partitioning of photosynthate in vegetative and reproductive twigs of 'Sweet' passion fruit

This study's objective is to evaluate the photosynthates partitioning and source-sink relationships, in vegetative and reproductive twigs of sweet passion fruit, using the carbon-13, stable isotope of carbon. The leaves of vegetative and reproductive twigs were placed in a sealed chamber and 13CO 2 were injected for 30 minutes. After six hours, the different organs of the twig were collected and immersed in liquid nitrogen (-196°C). All plant samples were oven-dried, powdered and combusted in an elemental analyzer. The results showed that the methodology was efficient to evaluate the partitioning of photosynthates. In the vegetative twigs, the new open leaves, the closed leaves and growth meristem were the principal sink for the source leaves enriched with 13CO 2. In the reproductive twigs with only flowers buds, the source-sink relationship was changed and the flowers buds turn to be the principal sink and the growing leaves were secondary sinks. The presence of young fruits changed again the source-sink relationship of the twig, and they were the principal sinks. The apical leaves, with 60% of final leaf area were also a sink for photosynthates.

Wood and leaf anatomy of Copaifera langsdorffii dwarf trees

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Biodiversidade dos parasitas de peixes provenientes do rio Sapucaí-Mirim, Estado de São Paulo, Brasil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A molecular phylogeny of bivalve mollusks: ancient radiations and divergences as revealed by mitochondrial genes

The main scope of my PhD is the reconstruction of the large-scale bivalve phylogeny on the basis of four mitochondrial genes, with samples taken from all major groups of the class. To my knowledge, it is the first attempt of such a breadth in Bivalvia. I decided to focus on both ribosomal and protein coding DNA sequences (two ribosomal encoding genes -12s and 16s -, and two protein coding ones - cytochrome c oxidase I and cytochrome b), since either bibliography and my preliminary results confirmed the importance of combined gene signals in improving evolutionary pathways of the group. Moreover, I wanted to propose a methodological pipeline that proved to be useful to obtain robust results in bivalves phylogeny. Actually, best-performing taxon sampling and alignment strategies were tested, and several data partitioning and molecular evolution models were analyzed, thus demonstrating the importance of molding and implementing non-trivial evolutionary models. In the line of a more rigorous approach to data analysis, I also proposed a new method to assess taxon sampling, by developing Clarke and Warwick statistics: taxon sampling is a major concern in phylogenetic studies, and incomplete, biased, or improper taxon assemblies can lead to misleading results in reconstructing evolutionary trees. Theoretical methods are already available to optimize taxon choice in phylogenetic analyses, but most involve some knowledge about genetic relationships of the group of interest, or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications. The method I proposed measures the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, it also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed to implement all analyses.

Comparative Ultrastructure and Molecular Phylogeny of Selenidium melongena n. sp and S. terebellae Ray 1930 Demonstrate Niche Partitioning in Marine Gregarine Parasites (Apicomplexa)

Gregarine apicomplexans are a diverse group of single-celled parasites that have feeding stages (trophozoites) and gamonts that generally inhabit the extracellular spaces of invertebrate hosts living in marine, freshwater, and terrestrial environments. Inferences about the evolutionary morphology of gregarine apicomplexans are being incrementally refined by molecular phylogenetic data, which suggest that several traits associated with the feeding cells of gregarines arose by convergent evolution. The study reported here supports these inferences by showing how molecular data reveals traits that are phylogenetically misleading within the context of comparative morphology alone. We examined the ultrastructure and molecular phylogenetic positions of two gregarine species isolated from the spaghetti worm Thelepus japonicus: Selenidium terebellae Ray 1930 and S. melongena n. sp. The ultrastructural traits of S. terebellae were very similar to other species of Selenidium sensu stricto, such as having vermiform trophozoites with an apical complex, few epicytic folds, and a dense array of microtubules underlying the trilayered pellicle. By contrast, S. melongena n. sp. lacked a comparably discrete assembly of subpellicular microtubules, instead employing a system of fibrils beneath the cell surface that supported a relatively dense array of helically arranged epicytic folds. Molecular phylogenetic analyses of small subunit rDNA sequences derived from single-cell PCR unexpectedly demonstrated that these two gregarines are close sister species. The ultrastructural differences between these two species were consistent with the fact that S. terebellae infects the inner lining of the host intestines, and S. melongena n. sp. primarily inhabits the coelom, infecting the outside wall of the host intestine. Altogether, these data demonstrate a compelling case of niche partitioning and associated morphological divergence in marine gregarine apicomplexans. (C) 2014 Elsevier GmbH. All rights reserved.

Towards greater accuracy in individual-tree mortality regression

Background mortality is an essential component of any forest growth and yield model. Forecasts of mortality contribute largely to the variability and accuracy of model predictions at the tree, stand and forest level. In the present study, I implement and evaluate state-of-the-art techniques to increase the accuracy of individual tree mortality models, similar to those used in many of the current variants of the Forest Vegetation Simulator, using data from North Idaho and Montana. The first technique addresses methods to correct for bias induced by measurement error typically present in competition variables. The second implements survival regression and evaluates its performance against the traditional logistic regression approach. I selected the regression calibration (RC) algorithm as a good candidate for addressing the measurement error problem. Two logistic regression models for each species were fitted, one ignoring the measurement error, which is the “naïve” approach, and the other applying RC. The models fitted with RC outperformed the naïve models in terms of discrimination when the competition variable was found to be statistically significant. The effect of RC was more obvious where measurement error variance was large and for more shade-intolerant species. The process of model fitting and variable selection revealed that past emphasis on DBH as a predictor variable for mortality, while producing models with strong metrics of fit, may make models less generalizable. The evaluation of the error variance estimator developed by Stage and Wykoff (1998), and core to the implementation of RC, in different spatial patterns and diameter distributions, revealed that the Stage and Wykoff estimate notably overestimated the true variance in all simulated stands, but those that are clustered. Results show a systematic bias even when all the assumptions made by the authors are guaranteed. I argue that this is the result of the Poisson-based estimate ignoring the overlapping area of potential plots around a tree. Effects, especially in the application phase, of the variance estimate justify suggested future efforts of improving the accuracy of the variance estimate. The second technique implemented and evaluated is a survival regression model that accounts for the time dependent nature of variables, such as diameter and competition variables, and the interval-censored nature of data collected from remeasured plots. The performance of the model is compared with the traditional logistic regression model as a tool to predict individual tree mortality. Validation of both approaches shows that the survival regression approach discriminates better between dead and alive trees for all species. In conclusion, I showed that the proposed techniques do increase the accuracy of individual tree mortality models, and are a promising first step towards the next generation of background mortality models. I have also identified the next steps to undertake in order to advance mortality models further.

Lateglacial and Holocene vegetation belts in the Pirin Mountains (southwestern Bulgaria)

Pollen stratigraphy of a core 270 cm long from Lake Dalgoto at 2310 m in the Northern Pirin Mountains, southern Bulgaria, was treated by optimal partitioning and compared to a broken-stick model to reveal statistically significant pollen zones. The vegetational reconstructions presented here are based on pollen percentages and pollen influx, on comparisons of modern and fossil pollen spectra, and on macrofossil dates from other sites in the mountains. During the Younger Dryas (11000–10200 14C yr BP), an open xerophytic herb vegetation with Artemisia and Chenopodiaceae was widely developed around the lake. Deciduous trees growing at lower elevations contributed to the pollen rain deposited at the higher-elevation sampling sites. Specifically, from 10200 to 8500 yr BP, Quercus, Ulmus, Tilia and Betula expanded rapidly at low and intermediate elevations, and between 8500 and 6500 yr BP they extended to higher elevations close to the upper forest limit, which was formed by Betula pendula at about 1900 m. Coniferous species were limited in the region at this time. After 6500 yr BP, the expansion of conifers (Pinus peuce, P. sylvestris, P. mugo, Abies alba) at high elevations forced the deciduous trees downward. Between 6500 and 3000 yr BP, the forest limit at 2200 m was formed by P. peuce, and A. alba had its maximum vertical range up to 1900 m. Later the abundance and vertical range of P. peuce and A. alba were reduced. After 3000 yr BP, Picea expanded.

Factors associated with HPV16 status and survival among patients with squamous cell carcinoma of the oropharynx

Background: Squamous cell carcinoma of the oropharynx (SCCOP) is characterized by local tumor aggressiveness, high recurrence rates, a high incidence of second primary tumors, and medical comorbidities. Significant trends in demographic and clinical characteristics as well as survival among SCCOP patients have been observed over time, likely owing to the changing etiology of the disease. Human papillomavirus type 16 (HPV16) infection is associated with a significant proportion of these cancers. Biomarkers that may aid in identifying patients that are at higher risk of recurrence and death are important so that these patients may be followed more closely to improve their quality of life. ^ Study population and methods: The retrospective review (Specific Aim 2) included 3891 newly diagnosed, previously untreated patients presenting to our institution between 1955 and 2004. A total of 2299 patients treated at our institution were included in survival and recursive partitioning analysis. The prospective cohort study (Specific Aim 3) included 266 patients presenting to our institution between January 2006 and September 2009. ^ Results: The results from the retrospective review showed that over time, patients presented at younger ages and were more likely to have base of tongue/tonsil tumors and to be never/former smokers and moreover survival improved significantly over time. In survival and recursive partitioning analyses, the TNM staging system was efficient in prognosticating patients prior to 1995. However, in the recent decade, the TNM staging system was completely inadequate. The factors having the greatest positive effect on overall survival since 1995 were those common to HPV-associated SCCOP. The results from the prospective cohort study indicate that patients with high nodal stage and those with late stage disease have increased levels of pretreatment serum HPV DNA. ^ Conclusions: We saw a distinct improvement in survival among SCCOP patients over the past 50 years at our institution. The main factors contributing to this were changes in clinical characteristics, in particular surrogates for HPV status. The current TNM staging system for SCCOP is inadequate and incorporation of HPV status (and perhaps smoking status) is encouraged. Furthermore, although pretreatment circulating levels of HPV DNA was associated with higher N category and overall disease stage, it has limited utility as a marker for recurrence among SCCOP patients.^

Comparing the effectiveness of equivalence partitioning, branch testing and code reading by stepwise abstraction applied by subjects

Some verification and validation techniques have been evaluated both theoretically and empirically. Most empirical studies have been conducted without subjects, passing over any effect testers have when they apply the techniques. We have run an experiment with students to evaluate the effectiveness of three verification and validation techniques (equivalence partitioning, branch testing and code reading by stepwise abstraction). We have studied how well able the techniques are to reveal defects in three programs. We have replicated the experiment eight times at different sites. Our results show that equivalence partitioning and branch testing are equally effective and better than code reading by stepwise abstraction. The effectiveness of code reading by stepwise abstraction varies significantly from program to program. Finally, we have identified project contextual variables that should be considered when applying any verification and validation technique or to choose one particular technique.

Arboretum et fruticetum britannicum; or, The trees and shrubs of Britain, native and foreign, hardy and half-hardy, pictorially and botanically delineated, and scientifically and popularly described; with their propagation, culture, management, and uses in the arts, in useful and ornamental plantations, and in landscape-gardening; preceded by a historical and geographical outline of the trees and shrubs of temperate climates throughout the world,

"List of books referred to..." v. 1, p. cxc-ccxxvi.

Nursery practice for trees and shrubs suitable for planting on the prairie-plains /

Caption title.

Regional patterns of agricultural land use and deforestation in Colombia

An expanding human population and associated demands for goods and services continues to exert an increasing pressure on ecological systems. Although the rate of expansion of agricultural lands has slowed since 1960, rapid deforestation still occurs in many tropical countries, including Colombia. However, the location and extent of deforestation and associated ecological impacts within tropical countries is often not well known. The primary aim of this study was to obtain an understanding of the spatial patterns of forest conversion for agricultural land uses in Colombia. We modeled native forest conversion in Colombia at regional and national-levels using logistic regression and classification trees. We investigated the impact of ignoring the regional variability of model parameters, and identified biophysical and socioeconomic factors that best explain the current spatial pattern and inter-regional variation in forest cover. We validated our predictions for the Amazon region using MODIS satellite imagery. The regional-level classification tree that accounted for regional heterogeneity had the greatest discrimination ability. Factors related to accessibility (distance to roads and towns) were related to the presence of forest cover, although this relationship varied regionally. In order to identify areas with a high risk of deforestation, we used predictions from the best model, refined by areas with rural population growth rates of > 2%. We ranked forest ecosystem types in terms of levels of threat of conversion. Our results provide useful inputs to planning for biodiversity conservation in Colombia, by identifying areas and ecosystem types that are vulnerable to deforestation. Several of the predicted deforestation hotspots coincide with areas that are outstanding in terms of biodiversity value.