Climate change, anthropogenic disturbance and the northward range expansion of Lactuca serriola (Asteraceae)

The distribution range of Lactuca serriola, a species native to the summer-dry mediterranean climate, has expanded northwards during the last 250 years. This paper assesses the influence of climate on the range expansion of this species and highlights the importance of anthropogenic disturbance to its spread. Location Central and Northern Europe. Methods Data on the geographic distribution of L. serriola were assembled through a literature search as well as through floristic and herbarium surveys. Maps of the spread of L. serriola in Central and Northern Europe were prepared based on herbarium data. The spread was assessed more precisely in Germany, Austria and Great Britain by pooling herbarium and literature data. We modelled the bioclimatic niche of the species using occurrence and climatic data covering the last century to generate projections of suitable habitats under the climatic conditions of five time periods. We tested whether the observed distribution of L. serriola could be explained for each time period, assuming that the climatic niche of the species was conserved across time. Results The species has spread northwards since the beginning of the 19th century. We show that climate warming in Europe increased the number of sites suitable for the species at northern latitudes. Until the late 1970s, the distribution of the species corresponded to the climatically suitable sites available. For the last two decades, however, we could not show any significant relationship between the increase in suitable sites and the distributional range change of L. serriola. However, we highlight potential areas the species could spread to in the future (Great Britain, southern Scandinavia and the Swedish coast). It is predominantly non-climatic influences of global change that have contributed to its rapid spread. Main conclusions The observation that colonizing species are not filling their climatically suitable range might imply that, potentially, other ruderal species could expand far beyond their current range. Our work highlights the importance of historical floristic and herbarium data for understanding the expansion of a species. Such historical distributional data can provide valuable information for those planning the management of contemporary environmental problems, such as species responses to environmental change.

A new spin on a compositionalist predictive modelling framework for conservation planning: a tropical case study in Ecuador

Knowledge about spatial biodiversity patterns is a basic criterion for reserve network design. Although herbarium collections hold large quantities of information, the data are often scattered and cannot supply complete spatial coverage. Alternatively, herbarium data can be used to fit species distribution models and their predictions can be used to provide complete spatial coverage and derive species richness maps. Here, we build on previous effort to propose an improved compositionalist framework for using species distribution models to better inform conservation management. We illustrate the approach with models fitted with six different methods and combined using an ensemble approach for 408 plant species in a tropical and megadiverse country (Ecuador). As a complementary view to the traditional richness hotspots methodology, consisting of a simple stacking of species distribution maps, the compositionalist modelling approach used here combines separate predictions for different pools of species to identify areas of alternative suitability for conservation. Our results show that the compositionalist approach better captures the established protected areas than the traditional richness hotspots strategies and allows the identification of areas in Ecuador that would optimally complement the current protection network. Further studies should aim at refining the approach with more groups and additional species information.

Hybridization between Brassica napus and B. rapa on a national scale in the United Kingdom

Measures blocking hybridization would prevent or reduce biotic or environmental change caused by gene flow from genetically modified (GM) crops to wild relatives. The efficacy of any such measure depends on hybrid numbers within the legislative region over the life-span of the GM cultivar. We present a national assessment of hybridization between rapeseed (Brassica napus) and B. rapa from a combination of sources, including population surveys, remote sensing, pollen dispersal profiles, herbarium data, local Floras, and other floristic databases. Across the United Kingdom, we estimate that 32,000 hybrids form annually in waterside B. rapa populations, whereas the less abundant weedy populations contain 17,000 hybrids. These findings set targets for strategies to eliminate hybridization and represent the first step toward quantitative risk assessment on a national scale.

Effects of detectability on estimates of geographic range size in bignonieae

Extinction risk has not been evaluated for 96% of all described plant species. Given that the Global Strategy for Plant Conservation proposes preliminary conservation assessments of all described plant species by 2010, herbarium specimens (i.e., primary occurrence data) are increasingly being used to infer threat components from estimates of geographic range size. Nevertheless, estimates of range size based on herbarium data may be inaccurate due to collection bias associated with interspecific variation in detectability. We used data on 377 species of Bignonieae to test the hypothesis that there is a positive relationship between detectability and estimates of geographic range size derived from herbarium specimens. This relationship is expected if the proportion of the true geographic range size of a species that is documented by herbarium specimens is given by the product of the true geographic range size and the detectability of the species, assuming no relationship between true geographic range size and detectability. We developed 4 measures of detectability that can be estimated from herbarium data and examined the relationship between detectability and 2 types of estimates of geographic range size: area of occupancy and extent of occurrence. Our results from regressing estimates of extent of occurrence and area of occupancy on detectability across genera provided no support for this hypothesis. The same was true for regressions of estimated extent of occurrence on detectability across species within genera. Nevertheless, regressions of estimated area of occupancy on detectability across species within genera provided partial support for our hypothesis. We considered 3 possible explanations for this mixed outcome: violation of the assumption of no relationship between true geographic range size and detectability; the relationships between estimated geographic range size and detectability may be an artifact of a negative relationship between estimated area of occupancy and the sampling variance of detectability; detectability may have had 2 opposite effects on estimated species range sizes: one determines the proportion of the true range of a species documented by herbarium specimens and the other determines the distribution of true range size for the species actually observed with herbarium data. Our findings should help improve understanding of the potential biases incurred with the use of herbarium data.

PODOCARPUS SP.PL. REFUGIA IN BRAZIL`S ATLANTIC FOREST: ANALYSING THE PAST TO IMPROVE FUTURE PROTECTION

The Atlantic rainforest has the second highest biodiversity in Brazil. It has been shrinking rapidly in area as a result of intensive deforestation, and only 7% of the original cover now remains, as isolated patches or in ecological reserves. In order to obtain new information on the distribution of the Atlantic rainforest during the Quaternary, we examined herbarium data to locate relevant populations and extracted DNA from fresh leaves from 26 populations. The present-day distribution of endemic Podocarpus populations shows that they are widely dispersed across eastern Brazil, and that the expansion of Podocarpus recorded in single Amazonian pollen records may have originated from either western or eastern populations. Genetic analysis enabled us to determine the boundaries of their regional expansion: northern and central populations of P. sellowii appeared between 5 degrees and 15 degrees S some 16,000 years ago; populations of P lambertii or sellowii have appeared between 15 degrees and 23 degrees S at different times since the last glaciation at least; and P lambertii appeared between 23 degrees and 30 degrees S during the recent expansion of Araucaria forests. The combination of botanical, pollen, and molecular analyses proved to be a rapid means of inferring distribution boundaries for sparse populations and their regional evolution within tropical ecosystems. Today the rainforest refugia we identified have become hotspots that are crucial to the survival of the Atlantic forest under unfavourable climatic conditions and, as such, offer the only possible opportunity for this type of forest to expand in the event of future climate change.

Understanding bias in geographic range size estimates

Aim Estimates of geographic range size derived from natural history museum specimens are probably biased for many species. We aim to determine how bias in these estimates relates to range size. Location We conducted computer simulations based on herbarium specimen records from localities ranging from the southern United States to northern Argentina. Methods We used theory on the sampling distribution of the mean and variance to develop working hypotheses about how range size, defined as area of occupancy (AOO), was related to the inter-specific distribution of: (1) mean collection effort per area across the range of a species (MC); (2) variance in collection effort per area across the range of a species (VC); and (3) proportional bias in AOO estimates (PBias: the difference between the expected value of the estimate of AOO and true AOO, divided by true AOO). We tested predictions from these hypotheses using computer simulations based on a dataset of more than 29,000 herbarium specimen records documenting occurrences of 377 plant species in the tribe Bignonieae (Bignoniaceae). Results The working hypotheses predicted that the mean of the inter-specific distribution of MC, VC and PBias were independent of AOO, but that the respective variance and skewness decreased with increasing AOO. Computer simulations supported all but one prediction: the variance of the inter-specific distribution of VC did not decrease with increasing AOO. Main conclusions Our results suggest that, despite an invariant mean, the dispersion and symmetry of the inter-specific distribution of PBias decreases as AOO increases. As AOO increased, range size was less severely underestimated for a large proportion of simulated species. However, as AOO increased, range size estimates having extremely low bias were less common.

A Digital Repository for the Herbarium Collection of Brasília Botanical Garden

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Establishment of Regional Herbarium Leads to More Than 200 New Flora Atlas Records for New York State

Loss of small herbaria is an unfortunate global trend, and initiation of new collections at small academic institutions is an increasingly rare occurrence. In 2006, a new herbarium was established at the State University of New York College at Plattsburgh. The PLAT herbarium has since grown to more than 7,000 specimens, many of them representative of the flora of northeastern New York (especially Clinton County). Previous to 2006, this region was without a recognized herbarium, the nearest in-state collections being more than 150 miles away. Although botanists have previously worked in the region, relatively few plant species were recorded for Clinton County by the New York Flora Atlas – a resource providing species distribution records based on specimens accessioned in herbarium collections. Given the dearth of available distribution data for Clinton County (including the eastern Adirondack Mountains and the western Lake Champlain valley), this project sought to provide records of previously unreported species by comparing NY Flora Atlas maps with current holdings. 203 species will now be added to the NY Flora Atlas for Clinton County, roughly half of those considered exotic. This exercise has amplified the importance of supporting and maintaining small regional herbaria as repositories of valuable biodiversity information. Likewise, this project also highlights the enduring value of training in floristics and taxonomy.

(Supporting Information) Collection date and location of the analysed herbarium Corallina officinalis samples of the Natural History Museum (BM)

Suporting Information 1; Herbarium Corallina officinalis samples of the Natural History Museum (BM) analysed for the present study. Where the same NHM barcodes are provided for more than one sample, multiple samples were present under the same barcode in the herbarium. (-) indicates samples were not barcoded in the NHM (BM) system.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

[gait Speed, Grip Strength And Self-rated Health Among The Elderly: Data From The Fibra Campinas Network, São Paulo, Brazil].

The article seeks to investigate patterns of performance and relationships between grip strength, gait speed and self-rated health, and investigate the relationships between them, considering the variables of gender, age and family income. This was conducted in a probabilistic sample of community-dwelling elderly aged 65 and over, members of a population study on frailty. A total of 689 elderly people without cognitive deficit suggestive of dementia underwent tests of gait speed and grip strength. Comparisons between groups were based on low, medium and high speed and strength. Self-related health was assessed using a 5-point scale. The males and the younger elderly individuals scored significantly higher on grip strength and gait speed than the female and oldest did; the richest scored higher than the poorest on grip strength and gait speed; females and men aged over 80 had weaker grip strength and lower gait speed; slow gait speed and low income arose as risk factors for a worse health evaluation. Lower muscular strength affects the self-rated assessment of health because it results in a reduction in functional capacity, especially in the presence of poverty and a lack of compensatory factors.

Correlation Between Cephalometric Data And Severity Of Sleep Apnea.

Obstructive sleep apnea syndrome has a high prevalence among adults. Cephalometric variables can be a valuable method for evaluating patients with this syndrome. To correlate cephalometric data with the apnea-hypopnea sleep index. We performed a retrospective and cross-sectional study that analyzed the cephalometric data of patients followed in the Sleep Disorders Outpatient Clinic of the Discipline of Otorhinolaryngology of a university hospital, from June 2007 to May 2012. Ninety-six patients were included, 45 men, and 51 women, with a mean age of 50.3 years. A total of 11 patients had snoring, 20 had mild apnea, 26 had moderate apnea, and 39 had severe apnea. The distance from the hyoid bone to the mandibular plane was the only variable that showed a statistically significant correlation with the apnea-hypopnea index. Cephalometric variables are useful tools for the understanding of obstructive sleep apnea syndrome. The distance from the hyoid bone to the mandibular plane showed a statistically significant correlation with the apnea-hypopnea index.

Censored Linear Regression Models For Irregularly Observed Longitudinal Data Using The Multivariate-t Distribution.

In acquired immunodeficiency syndrome (AIDS) studies it is quite common to observe viral load measurements collected irregularly over time. Moreover, these measurements can be subjected to some upper and/or lower detection limits depending on the quantification assays. A complication arises when these continuous repeated measures have a heavy-tailed behavior. For such data structures, we propose a robust structure for a censored linear model based on the multivariate Student's t-distribution. To compensate for the autocorrelation existing among irregularly observed measures, a damped exponential correlation structure is employed. An efficient expectation maximization type algorithm is developed for computing the maximum likelihood estimates, obtaining as a by-product the standard errors of the fixed effects and the log-likelihood function. The proposed algorithm uses closed-form expressions at the E-step that rely on formulas for the mean and variance of a truncated multivariate Student's t-distribution. The methodology is illustrated through an application to an Human Immunodeficiency Virus-AIDS (HIV-AIDS) study and several simulation studies.

[evaluation Of Data On Live Birth Certificates From The Information System On Live Births (sinasc) In Campinas, São Paulo, 2009].

To assess the completeness and reliability of the Information System on Live Births (Sinasc) data. A cross-sectional analysis of the reliability and completeness of Sinasc's data was performed using a sample of Live Birth Certificate (LBC) from 2009, related to births from Campinas, Southeast Brazil. For data analysis, hospitals were grouped according to category of service (Unified National Health System, private or both), 600 LBCs were randomly selected and the data were collected in LBC-copies through mothers and newborns' hospital records and by telephone interviews. The completeness of LBCs was evaluated, calculating the percentage of blank fields, and the LBCs agreement comparing the originals with the copies was evaluated by Kappa and intraclass correlation coefficients. The percentage of completeness of LBCs ranged from 99.8%-100%. For the most items, the agreement was excellent. However, the agreement was acceptable for marital status, maternal education and newborn infants' race/color, low for prenatal visits and presence of birth defects, and very low for the number of deceased children. The results showed that the municipality Sinasc is reliable for most of the studied variables. Investments in training of the professionals are suggested in an attempt to improve system capacity to support planning and implementation of health activities for the benefit of maternal and child population.

Augmented Mixed Models For Clustered Proportion Data.

Often in biomedical research, we deal with continuous (clustered) proportion responses ranging between zero and one quantifying the disease status of the cluster units. Interestingly, the study population might also consist of relatively disease-free as well as highly diseased subjects, contributing to proportion values in the interval [0, 1]. Regression on a variety of parametric densities with support lying in (0, 1), such as beta regression, can assess important covariate effects. However, they are deemed inappropriate due to the presence of zeros and/or ones. To evade this, we introduce a class of general proportion density, and further augment the probabilities of zero and one to this general proportion density, controlling for the clustering. Our approach is Bayesian and presents a computationally convenient framework amenable to available freeware. Bayesian case-deletion influence diagnostics based on q-divergence measures are automatic from the Markov chain Monte Carlo output. The methodology is illustrated using both simulation studies and application to a real dataset from a clinical periodontology study.