RISSC: a novel database for ribosomal 16S–23S RNA genes spacer regions

A novel database, under the acronym RISSC (Ribosomal Intergenic Spacer Sequence Collection), has been created. It compiles more than 1600 entries of edited DNA sequence data from the 16S–23S ribosomal spacers present in most prokaryotes and organelles (e.g. mitochondria and chloroplasts) and is accessible through the Internet (http://ulises.umh.es/RISSC), where systematic searches for specific words can be conducted, as well as BLAST-type sequence searches. Additionally, a characteristic feature of this region, the presence/absence and nature of tRNA genes within the spacer, is included in all the entries, even when not previously indicated in the original database. All these combined features could provide a useful documen­tation tool for studies on evolution, identification, typing and strain characterization, among others.

Pollen, DNA and Vegetation records from surface sediments of lacustrine lakes along a forest tundra - tundra transect at the Taymyr peninsula, northern Siberia

Reliable information of past vegetation changes are important to project future changes, especially for areas undergoing rapid transitioning such as the boreal treeline. The application of detailed sedDNA records has the potential to enhance our understanding of vegetation changes gained mainly from pollen studies of lake sediments. This study investigates sedDNA and pollen records from 31 lakes along a gradient of increasing larch forest cover in northern Siberia (Taymyr Peninsula) and compares them with vegetation field surveys within the lake's catchment. With respect to vegetation richness, sedDNA recorded 114 taxa, about half of them to species level, while pollen analyses identified 43 pollen taxa. Both approaches exceed the 31 taxa revealed by vegetation field surveys of 400 m**2 plots. From north to south, Larix percentages increase, as is consistently recorded by all three methods. Furthermore, tundra sites are separated from forested sites in the plots of the principal component analyses. Comparison of ordination results by Procrustes and Protest analyses yields a significant fit among all compared pairs of records. Despite the overall comparability of sedDNA and pollen analyses certain idiosyncrasies in the compositional signal are observed, such as high percentages of Alnus and Betula in all pollen spectra and high percentages of Salix in all sedDNA spectra. In conclusion, our results from the treeline show that sedDNA analyses perform better than pollen in recording site-specific richness (i.e. presence/absence of certain vegetation taxa in the direct vicinity of the lake) and perform as good as pollen in tracing regional vegetation composition.

Ensemble prediction distribution maps of macroalgae for current conditions and four climate change scenarios and high resultion bathymetry for Potter Cove, WAP, Antarctica

Species distribution models (SDM) predict species occurrence based on statistical relationships with environmental conditions. The R-package biomod2 which includes 10 different SDM techniques and 10 different evaluation methods was used in this study. Macroalgae are the main biomass producers in Potter Cove, King George Island (Isla 25 de Mayo), Antarctica, and they are sensitive to climate change factors such as suspended particulate matter (SPM). Macroalgae presence and absence data were used to test SDMs suitability and, simultaneously, to assess the environmental response of macroalgae as well as to model four scenarios of distribution shifts by varying SPM conditions due to climate change. According to the averaged evaluation scores of Relative Operating Characteristics (ROC) and True scale statistics (TSS) by models, those methods based on a multitude of decision trees such as Random Forest and Classification Tree Analysis, reached the highest predictive power followed by generalized boosted models (GBM) and maximum-entropy approaches (Maxent). The final ensemble model used 135 of 200 calculated models (TSS > 0.7) and identified hard substrate and SPM as the most influencing parameters followed by distance to glacier, total organic carbon (TOC), bathymetry and slope. The climate change scenarios show an invasive reaction of the macroalgae in case of less SPM and a retreat of the macroalgae in case of higher assumed SPM values.

Six-month outcome for dysphagia following traumatic brain injury: Radiological assessment

The coexistence of a swallowing impairment, or dysphagia, can severely impact upon the medical condition and recovery of a child with traumatic brain injury (TBI; Logemann, Pepe, & Mackay, 1994). Despite this fact, there is limited data that provide evidence of the progression or outcome of dysphagia in the pediatric population post-TBI (Rowe, 1999). The present study aimed to (1) provide a prospective radiologically based profile of swallowing outcome and (2) determine the clinical significance of any persistent physiological swallowing deficits by investigating the presence/absence of any coexistent respiratory complications. Seven children with moderate/severe TBI were evaluated via an initial videofluoroscopic swallowing assessment (VFSS) at an average of 24.1 days postinjury, during the acute phase of management. A follow-up VFSS was conducted at an average of 7 months, 3 weeks postinjury. The physiological impairment, swallowing safety, swallowing efficiency, and functional swallowing outcomes of the acute phase post-TBI were compared with reassessment results at 6 months post-TBI. The presence/absence of lower respiratory tract infection/respiratory complications in the past 6 months postinjury were recorded.VFSS revealed a number of residual physiological oropharyngeal swallowing impairments and reduced swallowing efficiency. However, all participants presented with clinically safe and functional swallowing outcomes at 6 months post-TBI, with no recent history of respiratory complication. This study indicates good functional swallowing and respiratory outcomes for patients at 6-months post-TBI despite the presence of persistent physiological swallowing impairment.

Testing alternative models for the conservation of koalas in fragmented rural-urban landscapes

Predicting the various responses of different species to changes in landscape structure is a formidable challenge to landscape ecology. Based on expert knowledge and landscape ecological theory, we develop five competing a priori models for predicting the presence/absence of the Koala (Phascolarctos cinereus) in Noosa Shire, south-east Queensland (Australia). A priori predictions were nested within three levels of ecological organization: in situ (site level) habitat (< 1 ha), patch level (100 ha) and landscape level (100-1000 ha). To test the models, Koala surveys and habitat surveys (n = 245) were conducted across the habitat mosaic. After taking into account tree species preferences, the patch and landscape context, and the neighbourhood effect of adjacent present sites, we applied logistic regression and hierarchical partitioning analyses to rank the alternative models and the explanatory variables. The strongest support was for a multilevel model, with Koala presence best predicted by the proportion of the landscape occupied by high quality habitat, the neighbourhood effect, the mean nearest neighbour distance between forest patches, the density of forest patches and the density of sealed roads. When tested against independent data (n = 105) using a receiver operator characteristic curve, the multilevel model performed moderately well. The study is consistent with recent assertions that habitat loss is the major driver of population decline, however, landscape configuration and roads have an important effect that needs to be incorporated into Koala conservation strategies.

Ecological studies on:(a) the use of colonisation samplers in relation to biological surveillance of river water quality (b) the requirements of freshwater gastropoda

Some of the factors affecting colonisation of a colonisation sampler, the Standard Aufwuchs Unit (S. Auf. U.) were investigated, namely immersion period, whether anchored on the bottom or suspended, and the influence of riffles. It was concluded that a four-week immersion period was best. S. Auf. U. anchored on the bottom collected both more taxa and individuals than suspended ones. Fewer taxa but more individuals colonised S. Auf. U. in the potamon zone compared to the rhithron zone with a consequent reduction in the values of pollution indexes and diversity. It was concluded that a completely different scoring system was necessary for lowland rivers. Macroinvertebrates colonising S. Auf. U. in simulated streams, lowland rivers and the R. Churnet reflected water quality. A variety of pollution and diversity indexes were applied to results from lowland river sites. Instead of these, it was recommended that an abbreviated species - relative abundance list be used to summarise biological data for use in lowland river surveillance. An intensive study of gastropod populations was made in simulated streams. Lynnaea peregra increased in abundance whereas Potamopyrgas jenkinsi decreased with increasing sewage effluent concentration. No clear-cut differences in reproduction were observed. The presence/absence of eight gastropod taxa was compared with concentrations of various pollutants in lowland rivers. On the basis of all field work it appeared that ammonia, nitrite, copper and zinc were the toxicants most likely to be detrimental to gastropods and that P. jenkinsi and Theodoxus fluviatilis were the least tolerant taxa. 96h acute toxicity tests of P. jenkinsi using ammonia and copper were carried out in a flow-through system after a variety of static range finding tests. P. jenkinsi was intolerant to both toxicants compared to reports on other taxa and the results suggested that these toxicants would affect distribution of this species in the field.

Diversity patterns of amphibians in lowland Amazonian forests in southeastern Peru

Biological diversity is threatened worldwide and it is a priority to generate more information that can be used both for understanding ecological processes and determining conservation strategies. For my dissertation, I focused on amphibian diversity patterns in lowland rainforests of southwestern Amazonia to evaluate the importance of habitat heterogeneity in the region. My main purpose was to test the hypothesis that amphibian communities in different forest types differ in species richness, composition, and abundance. I used standardized visual encounter surveys to quantify the species composition and abundance of amphibians at four sites, each containing four forest types (floodplain, terra firme, bamboo, and palm swamp). I used leaf-litter plots to evaluate the effect of soil and leaf-litter characteristics on species richness and abundance of leaf-litter frogs. I intensively sampled at one site and then sampled three other sites (distance among sites varied 3.5–105 km) to evaluate whether the patterns observed at one site were similar elsewhere. I also updated the information on threatened and potentially threatened amphibians in Peru and my study region. I found that no species appears to have experienced population declines in southeastern Peru, suggesting that the region still contains the original species pool. My results support the hypothesis that amphibian communities differ across forest types and that patterns observed at the local scale (one site) are similar at the regional scale (four sites). My data also indicate that there is no correlation between species composition and geographic distance among sites. Instead, an important proportion of the gamma diversity is represented by habitat-related beta diversity. My leaf-litter plot data showed that part of the variation in the leaf-litter community structure is explained by soil and litter characteristics. I found that soil total phosphorus and, to a lesser extent, humidity, leaf-litter mass, and pH is linked to species presence/absence and abundance. My study provides the first standardized, quantitative comparison of amphibian community structure across four major forest types in southwestern Amazonia and highlights the fact that forest types are complementary and necessary for maintaining high species richness in the region.

Diversity Patterns of Amphibians in Lowland Amazonian Forests in Southeastern Peru

Biological diversity is threatened worldwide and it is a priority to generate more information that can be used both for understanding ecological processes and determining conservation strategies. For my dissertation, I focused on amphibian diversity patterns in lowland rainforests of southwestern Amazonia to evaluate the importance of habitat heterogeneity in the region. My main purpose was to test the hypothesis that amphibian communities in different forest types differ in species richness, composition, and abundance. I used standardized visual encounter surveys to quantify the species composition and abundance of amphibians at four sites, each containing four forest types (floodplain, terra firme, bamboo, and palm swamp). I used leaf-litter plots to evaluate the effect of soil and leaf-litter characteristics on species richness and abundance of leaf-litter frogs. I intensively sampled at one site and then sampled three other sites (distance among sites varied 3.5-105 km) to evaluate whether the patterns observed at one site were similar elsewhere. I also updated the information on threatened and potentially threatened amphibians in Peru and my study region. I found that no species appears to have experienced population declines in southeastern Peru, suggesting that the region still contains the original species pool. My results support the hypothesis that amphibian communities differ across forest types and that patterns observed at the local scale (one site) are similar at the regional scale (four sites). My data also indicate that there is no correlation between species composition and geographic distance among sites. Instead, an important proportion of the gamma diversity is represented by habitat-related beta diversity. My leaf-litter plot data showed that part of the variation in the leaf-litter community structure is explained by soil and litter characteristics. I found that soil total phosphorus and, to a lesser extent, humidity, leaf-litter mass, and pH is linked to species presence/absence and abundance. My study provides the first standardized, quantitative comparison of amphibian community structure across four major forest types in southwestern Amazonia and highlights the fact that forest types are complementary and necessary for maintaining high species richness in the region.

(Table 1) Relative abundance of planktonic foraminifers in ODP Hole 164-997A sediments

Hole 997A was drilled during Leg 164 of the Ocean Drilling Program at a depth of 2770 m on the topographic crest of the Blake Ridge in the western Atlantic Ocean. We report here an analysis of the faunal assemblages of planktonic foraminifers in a total of 91 samples (0.39-91.89 mbsf interval) spanning the last 2.15 m.y., latest Pliocene to Holocene. The abundant species, Globigerinoides ruber, Globigerinoides sacculifer, Neogloboquadrina dutertrei, Globorotalia inflata, and Globigerinita glutinata together exceed over ~70% of the total fauna. Each species exhibits fluctuations with amplitudes of 10%-20% or more. Despite their generally low abundance, the distinct presence/absence behavior of the Globorotalia menardii group is almost synchronous with glacial-interglacial climate cycles during the upper part of Brunhes Chron. The quantitative study and factor analysis of planktonic foraminiferal assemblages shows that the planktonic foraminiferal fauna in Hole 997A consists of four groups: warm water, subtropical gyre (mixed-layer species), gyre margin (thermocline/upwelling species), and subpolar assemblages. The subtropical gyre assemblage dominates throughout the studied section, whereas the abundance of gyre margin taxa strongly control the overall variability in faunal abundance at Site 997. In sediments older than the Olduvai Subchron, the planktonic foraminiferal faunas are characterized by fluctuations in both the subtropical gyre and gyre margin assemblages, similar to those in the Brunhes Chron. The upwelling/gyre margin fauna increased in abundance just before the Jaramillo Subchron and was dominant between 0.7 and 1.07 Ma. The transition from this gyre margin-dominated assemblage to an increase in abundance of the subtropical gyre and gyre margin species occurred around 0.7 Ma, near the Brunhes/Matuyama boundary. The presence of low-oxygen-tolerant benthic foraminifers, pyrite tubes, and abundant diatoms below the Brunhes/Matuyama boundary suggests decreased oxygenation of intermediate waters and more upwelling over the Blake-Bahama Outer Ridge, perhaps because of weaker Upper North Atlantic Deep Water ventilation. The changes in the relative composition of foraminifer assemblages took place at least twice, around 700 and 1000 ka, close to the ~930-ka switch from obliquity-forced climate variation to the 100-k.y. eccentricity cycle. The climate shift at 700 ka suggests a transition from relatively warmer conditions in the early Pleistocene to warm-cool oscillations in the Brunhes Chron.

(Appendix B) Dinoflagellate cysts in Southeast Pacific Ocean surface sediments

orty-eight surface sediment samples from the southeast (SE) Pacific (25-53°S) are investigated for the determination of the spatial distribution of organic-walled dinoflagellate cysts along the western South American continental margin. Fifty-five different taxa are recorded and reflect oceanic or coastal assemblages. The oceanic assemblages are characterised by low cyst concentrations and the dominance of autotrophs, while the coastal assemblages generally contain a higher number of cysts, which are mainly produced by heterotrophic species. Highest cyst concentrations are observed in the active upwelling system offshore Concepción (35-37°S). Brigantedinium spp., Echinidinium aculeatum, Echinidinium granulatum/delicatum and cysts of Protoperidinium americanum dominate assemblages related to upwelling. Echinidinium aculeatum appears to be the best indicator for the presence of all year round active upwelling cells. Other protoperidinioid cysts may also occur in high relative abundances in coastal regions outside active upwelling systems, if the availability of nutrients, co-responsible for the presence/absence of their main food sources such as diatoms and other protists, is sufficient. The importance of nutrient availability as a determining environmental variable influencing cyst signals on a regional scale (SE Pacific) is demonstrated through statistical analyses of the data. Because of the importance of nutrients, uncertainties about the outcomes of quantitative sea-surface temperature (SST) reconstructions (Modern Analogue Technique) based on dinoflagellate cysts may arise, since no interaction between different hydrographical variables is considered in this approach. The combination of the SE Pacific surface sample dataset with other published cyst data from the Southern Hemisphere resulted in a database which includes 350 samples: the 'SH350 database'. This database is used to test the accuracy of the quantitative reconstructions by calculating and comparing the estimated versus observed values for each site. An attempt to perform quantitative SST reconstructions on the last 25 cal ka of site ODP1233 (41°S; 74°27'W) is made and again stresses the importance of other environmental variables such as nutrient availability in determining the dinoflagellate cyst assemblages.

End-to-end modelling for an ecosystem approach to fisheries in the Northern Humboldt Current Ecosystem

This work represents an original contribution to the methodology for ecosystem models' development as well as the rst attempt of an end-to-end (E2E) model of the Northern Humboldt Current Ecosystem (NHCE). The main purpose of the developed model is to build a tool for ecosystem-based management and decision making, reason why the credibility of the model is essential, and this can be assessed through confrontation to data. Additionally, the NHCE exhibits a high climatic and oceanographic variability at several scales, the major source of interannual variability being the interruption of the upwelling seasonality by the El Niño Southern Oscillation, which has direct e ects on larval survival and sh recruitment success. Fishing activity can also be highly variable, depending on the abundance and accessibility of the main shery resources. This context brings the two main methodological questions addressed in this thesis, through the development of an end-to-end model coupling the high trophic level model OSMOSE to the hydrodynamics and biogeochemical model ROMS-PISCES: i) how to calibrate ecosystem models using time series data and ii) how to incorporate the impact of the interannual variability of the environment and shing. First, this thesis highlights some issues related to the confrontation of complex ecosystem models to data and proposes a methodology for a sequential multi-phases calibration of ecosystem models. We propose two criteria to classify the parameters of a model: the model dependency and the time variability of the parameters. Then, these criteria along with the availability of approximate initial estimates are used as decision rules to determine which parameters need to be estimated, and their precedence order in the sequential calibration process. Additionally, a new Evolutionary Algorithm designed for the calibration of stochastic models (e.g Individual Based Model) and optimized for maximum likelihood estimation has been developed and applied to the calibration of the OSMOSE model to time series data. The environmental variability is explicit in the model: the ROMS-PISCES model forces the OSMOSE model and drives potential bottom-up e ects up the foodweb through plankton and sh trophic interactions, as well as through changes in the spatial distribution of sh. The latter e ect was taken into account using presence/ absence species distribution models which are traditionally assessed through a confusion matrix and the statistical metrics associated to it. However, when considering the prediction of the habitat against time, the variability in the spatial distribution of the habitat can be summarized and validated using the emerging patterns from the shape of the spatial distributions. We modeled the potential habitat of the main species of the Humboldt Current Ecosystem using several sources of information ( sheries, scienti c surveys and satellite monitoring of vessels) jointly with environmental data from remote sensing and in situ observations, from 1992 to 2008. The potential habitat was predicted over the study period with monthly resolution, and the model was validated using quantitative and qualitative information of the system using a pattern oriented approach. The nal ROMS-PISCES-OSMOSE E2E ecosystem model for the NHCE was calibrated using our evolutionary algorithm and a likelihood approach to t monthly time series data of landings, abundance indices and catch at length distributions from 1992 to 2008. To conclude, some potential applications of the model for shery management are presented and their limitations and perspectives discussed.

fuzzySim: Fuzzy similarity in species distributions

fuzzySim is an R package for calculating fuzzy similarity in species occurrence patterns. It includes functions for data preparation, such as converting species lists (long format) to presence-absence tables (wide format), obtaining unique abbreviations of species names, or transposing (parts of) complex data frames; and sample data sets for providing practical examples. It can convert binary presence-absence to fuzzy occurrence data, using e.g. trend surface analysis, inverse distance interpolation or prevalence-independent environmental favourability modelling, for multiple species simultaneously. It then calculates fuzzy similarity among (fuzzy) species distributions and/or among (fuzzy) regional species compositions. Currently available similarity indices are Jaccard, Sørensen, Simpson, and Baroni-Urbani & Buser.

As variedades linguísticas do espanhol e os desafios ao seu ensino/aprendizagem

O Espanhol é, cada vez mais, uma língua de destaque no panorama mundial. Daí que surja a necessidade de garantir a qualidade e constante aprimoramento do ensino/aprendizagem desta língua. Um dos nossos propósitos, com o presente estudo, foi aprofundar e refletir sobre os conhecimentos dos alunos acerca da diversidade (intra)linguística do Espanhol, promovendo, deste modo, a sua valorização. Elaborámos, como ponto de partida, um enquadramento teórico que sustenta a investigação onde abordamos a dimensão atual do Espanhol e das suas variedades, bem como a questão dos estereótipos relacionada com o ensino das variedades (intra)linguísticas espanholas. De seguida, procedemos à implementação de um estudo de caso, tendo em conta o Espanhol como língua internacional e pluricêntrica, com variedades distintas. O referido estudo apresenta contornos de investigação-ação e foi desenvolvido num agrupamento de escolas da região de Aveiro, no ano letivo 2014/2015. No decurso do nosso projeto, socorremo-nos de diversas técnicas e instrumentos de recolha de dados, nomeadamente um inquérito por questionário e fichas de atividades para identificar e descrever os estereótipos dos alunos. Neste projeto, analisamos os resultados de uma investigação onde destacamos, por um lado, os estereótipos que alunos portugueses, do 8.º ano de escolaridade, têm sobre a realidade da língua espanhola e das suas variedades, no mundo; por outro lado, a presença/ausência dessa diversidade (intra)linguística nos manuais escolares que acompanharam a turma-alvo do estudo. Com base nos resultados obtidos, foi realizada ainda uma sessão de sensibilização às variedades do Espanhol. Os resultados demonstram que os manuais escolares analisados contêm visões estereotipadas e redutoras sobre a diversidade linguística espanhola, sobrevalorizando, em certa medida, a norma peninsular. Os dados recolhidos através do inquérito por questionário, permitiram-nos concluir que os alunos possuíam visões estereotipadas sobre o Espanhol e as suas variedades. No entanto, mediante a sessão de sensibilização para a valorização da diversidade linguística espanhola, concluímos que foi criado um espaço de reflexão que permitisse quer a reconstrução de estereótipos quer ainda um espaço de diálogo e debate coletivo sobre como as diferenças da língua a podem enriquecer.

Community reintegration and related factors in a Nigerian stroke sample.

Background: The goal of stroke rehabilitation has shifted from mere survival of a victim to how well a survivor can be effectively reintegrated back into the community. Objectives: The present study determined the level of satisfaction with community reintegration (CR) and related factors among Nigerian community-dwelling stroke survivors (CDSS). Methods: This was a cross-sectional survey of 71 volunteering CDSS (35 males, 36 females) from selected South-Eastern Nigerian communities. Reintegration to Normal Living Index was used to assess participants’ CR. Data was analysed using Spearman rank-order correlation, Kruskal-Wallis and Mann-Whitney U tests at p≤0.05. Results: Participants generally had deficits in CR which was either mild/moderate (52.1%) or severe (47.9%). Scores in the CR domains of distance mobility, performance of daily activities, recreational activities and family roles were particularly low (median scores ≤ 4). CR was significantly correlated with and influenced by age (r=-0.35; p=0.00) and presence/absence of diabetes mellitus (u=3.56.50; p=0.01), pre- (k=6.13; p=0.05) and post-stroke employment (k=18.26; p=0.00) status, type of assistive mobility device being used (AMD) (k=25.39; p=0.00) and support from the community (k=7.15; p=0.03) respectively. Conclusion: CR was generally poor for this CDSS sample. Survivors who are older, having diabetes as co-morbidity, using AMD (particularly wheel-chair) and without employment pre- and/or post-stroke may require keener attention. Rehabilitation focus may be targeted at enhancing mobility functions, vocational and social skills.

Biotic and abiotic parameters that distinguish types of temporary ponds in a Portuguese Mediterranean ecosystem

Temporary ponds are seasonal wetland habitats subjected to extreme and unstable ecological conditions. Some are classified as priority habitats for conservation by the European Union Habitats Directive. Our study area was the coastal plain of southwest Portugal, which spans across 100km north to south and hosts a large number of temporary ponds as a consequence of climatic and edaphic characteristics. Field sampling of floristic and edaphic data was carried out in 24 temporary ponds every spring between 2005 and 2008. We recorded a total of 174 plant species identified within visually homogeneous plots. We included the data in a geographic information system and classified ponds according to their floristic composition, using a biotic regionalization analysis based on species presence/absence, which is a practical and unambiguous criterion. We found three significantly different groups of ponds which corresponded to an eco-physiognomic pond typology: Mediterranean temporary ponds, marshlands, and disturbed ponds. For the first two pond types we defined characteristic or indicator plant species. We searched also for relationships between pond type and a series of large-scale climatic, geographic, and geological variables, as well as local-scale physical and chemical properties of the soil. Pond type was distinguished by a complex combination of some of these variables, including environmental energy, soil texture, nitrogen content of the soil and pH. A practical way of discriminating between different