Pseudomonas aeruginosa exhibits frequent recombination, but only a limited association between genotype and ecological setting

Pseudomonas aeruginosa is an opportunistic pathogen and an important cause of infection, particularly amongst cystic fibrosis (CF) patients. While specific strains capable of patient-to-patient transmission are known, many infections appear to be caused by unique and unrelated strains. There is a need to understand the relationship between strains capable of colonising the CF lung and the broader set of P. aeruginosa isolates found in natural environments. Here we report the results of a multilocus sequence typing (MLST)-based study designed to understand the genetic diversity and population structure of an extensive regional sample of P. aeruginosa isolates from South East Queensland, Australia. The analysis is based on 501 P. aeruginosa isolates obtained from environmental, animal and human (CF and non-CF) sources with particular emphasis on isolates from the Lower Brisbane River and isolates from CF patients obtained from the same geographical region. Overall, MLST identified 274 different sequence types, of which 53 were shared between one or more ecological settings. Our analysis revealed a limited association between genotype and environment and evidence of frequent recombination. We also found that genetic diversity of P. aeruginosa in Queensland, Australia was indistinguishable from that of the global P. aeruginosa population. Several CF strains were encountered frequently in multiple ecological settings; however, the most frequently encountered CF strains were confined to CF patients. Overall, our data confirm a non-clonal epidemic structure and indicate that most CF strains are a random sample of the broader P. aeruginosa population. The increased abundance of some CF strains in different geographical regions is a likely product of chance colonisation events followed by adaptation to the CF lung and horizontal transmission among patients.

Emotional insecurity in the family and community and youth delinquency in Northern Ireland: A person-oriented analysis across five-waves

Background: Over one billion children are exposed worldwide to political violence and armed conflict. Currently, conclusions about bases for adjustment problems are qualified by limited longitudinal research from a process-oriented, social-ecological perspective. In this study, we examined a theoretically-based model for the impact of multiple levels of the social ecology (family, community) on adolescent delinquency. Specifically, this study explored the impact of children’s emotional insecurity about both the family and community on youth delinquency in Northern Ireland. Methods: In the context of a five-wave longitudinal research design, participants included 999 mother-child dyads in Belfast (482 boys, 517 girls), drawn from socially-deprived, ethnically-homogenous areas that had experienced political violence. Youth ranged in age from 10 to 20 and were 12.18 (SD = 1.82) years old on average at Time 1. Findings: The longitudinal analyses were conducted in hierarchical linear modeling (HLM), allowing for the modeling of inter-individual differences in intra-individual change. Intra-individual trajectories of emotional insecurity about the family related to children’s delinquency. Greater insecurity about the community worsened the impact of family conflict on youth’s insecurity about the family, consistent with the notion that youth’s insecurity about the community sensitizes them to exposure to family conflict in the home. Conclusions: The results suggest that ameliorating children’s insecurity about family and community in contexts of political violence is an important goal toward improving adolescents’ well-being, including reduced risk for delinquency.

Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system.

Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h(2) similar to 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers.

Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers.

A multivariate analysis of beta diversity across organisms and environments

We examined variability in hierarchical beta diversity across ecosystems, geographical gradients, and organism groups using multivariate spatial mixed modeling analysis of two independent data sets. The larger data set comprised reported ratios of regional species richness (RSR) to local species richness (LSR) and the second data set consisted of RSR: LSR ratios derived from nested species-area relationships. There was a negative, albeit relatively weak, relationship between beta diversity and latitude. We found only relatively subtle differences in beta diversity among the realms, yet beta diversity was lower in marine systems than in terrestrial or freshwater realms. Beta diversity varied significantly among organisms' major characteristics such as body mass, trophic position, and dispersal type in the larger data set. Organisms that disperse via seeds had highest beta diversity, and passively dispersed organisms showed the lowest beta diversity. Furthermore, autotrophs had lower beta diversity than organisms higher up the food web; omnivores and carnivores had consistently higher beta diversity. This is evidence that beta diversity is simultaneously controlled by extrinsic factors related to geography and environment, and by intrinsic factors related to organism characteristics.

The imprint of the geographical, evolutionary and ecological context on species-area relationships

Species-area relationships (SAR) are fundamental in the understanding of biodiversity patterns and of critical importance for predicting species extinction risk worldwide. Despite the enormous attention given to SAR in the form of many individual analyses, little attempt has been made to synthesize these studies. We conducted a quantitative meta-analysis of 794 SAR, comprising a wide span of organisms, habitats and locations. We identified factors reflecting both pattern-based and dynamic approaches to SAR and tested whether these factors leave significant imprints on the slope and strength of SAR. Our analysis revealed that SAR are significantly affected by variables characterizing the sampling scheme, the spatial scale, and the types of organisms or habitats involved. We found that steeper SAR are generated at lower latitudes and by larger organisms. SAR varied significantly between nested and independent sampling schemes and between major ecosystem types, but not generally between the terrestrial and the aquatic realm. Both the fit and the slope of the SAR were scale-dependent. We conclude that factors dynamically regulating species richness at different spatial scales strongly affect the shape of SAR. We highlight important consequences of this systematic variation in SAR for ecological theory, conservation management and extinction risk predictions.

Comparison of granulometric methods and sampling strategies used in marine habitat classification and Ecological Status assessment

Sediment particle size analysis (PSA) is routinely used to support benthic macrofaunal community distribution data in habitat mapping and Ecological Status (ES) assessment. No optimal PSA Method to explain variability in multivariate macrofaunal distribution has been identified nor have the effects of changing sampling strategy been examined. Here, we use benthic macrofaunal and PSA grabs from two embayments in the south of Ireland. Four frequently used PSA Methods and two common sampling strategies are applied. A combination of laser particle sizing and wet/dry sieving without peroxide pre-treatment to remove organics was identified as the optimal Method for explaining macrofaunal distributions. ES classifications and EUNIS sediment classification were robust to changes in PSA Method. Fauna and PSA samples returned from the same grab sample significantly decreased macrofaunal variance explained by PSA and caused ES to be classified as lower. Employing the optimal PSA Method and sampling strategy will improve benthic monitoring. © 2012 Elsevier Ltd.

Distribution, occurrence and biotoxin composition of the main shellfish toxin producing microalgae within European waters: A comparison of methods of analysis

Harmful algal blooms (HABs) are a natural global phenomena emerging in severity and extent. Incidents have many economic, ecological and human health impacts. Monitoring and providing early warning of toxic HABs are critical for protecting public health. Current monitoring programmes include measuring the number of toxic phytoplankton cells in the water and biotoxin levels in shellfish tissue. As these efforts are demanding and labour intensive, methods which improve the efficiency are essential. This study compares the utilisation of a multitoxin surface plasmon resonance (multitoxin SPR) biosensor with enzyme-linked immunosorbent assay (ELISA) and analytical methods such as high performance liquid chromatography with fluorescence detection (HPLC-FLD) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) for toxic HAB monitoring efforts in Europe. Seawater samples (n = 256) from European waters, collected 2009-2011, were analysed for biotoxins: saxitoxin and analogues, okadaic acid and dinophysistoxins 1/2 (DTX1/DTX2) and domoic acid responsible for paralytic shellfish poisoning (PSP), diarrheic shellfish poisoning (DSP) and amnesic shellfish poisoning (ASP), respectively. Biotoxins were detected mainly in samples from Spain and Ireland. France and Norway appeared to have the lowest number of toxic samples. Both the multitoxin SPR biosensor and the RNA microarray were more sensitive at detecting toxic HABs than standard light microscopy phytoplankton monitoring. Correlations between each of the detection methods were performed with the overall agreement, based on statistical 2 × 2 comparison tables, between each testing platform ranging between 32% and 74% for all three toxin families illustrating that one individual testing method may not be an ideal solution. An efficient early warning monitoring system for the detection of toxic HABs could therefore be achieved by combining both the multitoxin SPR biosensor and RNA microarray.

Measuring the macrosystem in post-accord Northern Ireland: A social-ecological approach

The macrosystem refers to the overarching patterns that influence behavior at each level of the social ecology (Bronfenbrenner, 1977), making it a necessary component for assessing human development in contexts of political violence. This article proposes a method for systematically measuring the macrosystem in Northern Ireland that allows for a subnational analysis, multiple time units, and indicators of both low-level violence and positive relations. Articles were randomly chosen for each weekday in 2006-2011 from two prominent Northern Irish newspapers and coded according to their reflection of positive relations and political tensions between Catholics and Protestants. The newspaper data were then compared to existing macro-level measurements in Northern Ireland. We found that the newspaper data provided a more nuanced understanding of fluctuations in intergroup relations than the corresponding measures. This has practical implications for peacebuilding and advances our methods for assessing the impact of macro-level processes on individual development.

Nucella lapillus: imposex transcriptome analysis and phenotypic plasticity

O conhecimento de mecanismos de genómica funcional tem sido maioritariamente adquirido pela utilização de organismos modelo que são mantidos em condições laboratoriais. Contudo, estes organismos não reflectem as respostas a alterações ambientais. Por outro lado, várias espécies, ecologicamente bem estudadas, reflectem bem as interacções entre genes e ambiente mas que, das quais não existem recursos genéticos disponíveis. O imposex, caracterizado pela superimposição de caracteres sexuais masculinos em fêmeas, é induzido pelo tributilestanho (TBT) e trifenilestanho (TPT) e representa um dos melhores exemplos de disrupção endócrina com causas antropogénicas no ambiente aquático. Com o intuito de elucidar as bases moleculares deste fenómeno, procedeu-se à combinação das metodologias de pirosequenciação (sequenciação 454 da Roche) e microarrays (Agilent 4*180K) de forma a contribuir para um melhor conhecimento desta interacção gene-ambiente no gastrópode Nucella lapillus, uma espécie sentinela para imposex. O trancriptoma de N. lapillus foi sequenciado, reconstruído e anotado e posteriormente utilizado para a produção de um “array” de nucleótidos. Este array foi então utilizado para explorar níveis de expressão génica em resposta à contaminação por TBT. Os resultados obtidos confirmaram as hipóteses anteriormente propostas (esteróidica, neuroendócrina, retinóica) e adicionalmente revelou a existência de potenciais novos mecanismos envolvidos no fenómeno imposex. Evidência para alvos moleculares de disrupção endócrina não relacionados com funções reprodutoras, tais como, sistema imunitário, apoptose e supressores de tumores, foram identificados. Apesar disso, tendo em conta a forte componente reprodutiva do imposex, esta componente funcional foi a mais explorada. Assim, factores de transcrição e receptores nucleares lipofílicos, funções mitocondriais e actividade de transporte celular envolvidos na diferenciação de géneros estão na base de potenciais novos mecanismos associados ao imposex em N. lapillus. Em particular, foi identificado como estando sobre-expresso, um possível homólogo do receptor nuclear “peroxisome proliferator-activated receptor gamma” (PPARγ), cuja função na indução de imposex foi confirmada experimentalmente in vivo após injecção dos animais com Rosiglitazone, um conhecido ligando de PPARγ em vertebrados. De uma forma geral, os resultados obtidos mostram que o fenómeno imposex é um mecanismo complexo, que possivelmente envolve a cascata de sinalização envolvendo o receptor retinoid X (RXR):PPARγ “heterodimer” que, até à data não foi descrito em invertebrados. Adicionalmente, os resultados obtidos apontam para alguma conservação de mecanismos de acção envolvidos na disrupção endócrina em invertebrados e vertebrados. Finalmente, a informação molecular produzida e as ferramentas moleculares desenvolvidas contribuem de forma significativa para um melhor conhecimento do fenómeno imposex e constituem importantes recursos para a continuação da investigação deste fenómeno e, adicionalmente, poderão vir a ser aplicadas no estudo de outras respostas a alterações ambientais usando N. lapillus como organismo modelo. Neste sentido, N. lapillus foi também utilizada para explorar a adaptação na morfologia da concha em resposta a alterações naturais induzidas por acção das ondas e pelo risco de predação por caranguejos. O contributo da componente genética, plástica e da sua interacção para a expressão fenotípica é crucial para compreender a evolução de caracteres adaptativos a ambientes heterogéneos. A contribuição destes factores na morfologia da concha de N. lapillus foi explorada recorrendo a transplantes recíprocos e experiências laboratoriais em ambiente comum (com e sem influência de predação) e complementada com análises genéticas, utilizando juvenis provenientes de locais representativos de costas expostas e abrigadas da acção das ondas. As populações estudadas são diferentes geneticamente mas possuem o mesmo cariótipo. Adicionalmente, análises morfométricas revelaram plasticidade da morfologia da concha em ambas as direcções dos transplantes recíprocos e também a retenção parcial, em ambiente comum, da forma da concha nos indivíduos da F2, indicando uma correlação positiva (co-gradiente) entre heritabilidade e plasticidade. A presença de estímulos de predação por caranguejos estimulou a produção de conchas com labros mais grossos, de forma mais evidente em animais recolhidos de costas expostas e também provocou alterações na forma da concha em animais desta proveniência. Estes dados sugerem contra-gradiente em alterações provocadas por predação na morfologia da concha, na produção de labros mais grossos e em níveis de crescimento. O estudo das interacções gene-ambiente descritas acima demonstram a actual possibilidade de produzir recursos e conhecimento genómico numa espécie bem caracterizada ecologicamente mas com limitada informação genómica. Estes recursos permitem um maior conhecimento biológico desta espécie e abrirão novas oportunidades de investigação, que até aqui seriam impossíveis de abordar.

Ecological assessment of the red deer population in the Lousã Mountain

Durante o último século, as populações de cervídeos têm aumentado substancialmente um pouco por toda a Europa. O veado Cervus elaphus não foi exceção, apresentando atualmente uma ampla distribuição geográfica. Após a quase extinção de todas as populações selvagens desta espécie em Portugal, o número de efetivos de veado e a área de distribuição da espécie têm aumentado significativamente nas últimas décadas. Esta proliferação deveu-se fundamentalmente aos processos de reintrodução implementados em algumas zonas do país, como foi o caso da Serra da Lousã. Dez anos após a reintrodução, a expansão geográfica e demográfica é já uma realidade e a espécie assume um papel relevante tanto do ponto de vista cinegético como turístico. Com o aumento das populações de ungulados, surge a necessidade de aumentar o conhecimento existente sobre estas espécies, particularmente ao nível das estimativas populacionais, do uso e seleção de habitat, do comportamento e da fisiologia das populações. Neste sentido, um dos objetivos foi comparar quatro métodos de contagem de excrementos em termos de estimativa populacional, aplicabilidade e eficiência. Face aos resultados obtidos, o método de transectos lineares com distance sampling revelou-se o mais eficiente, providenciando uma boa precisão num menor tempo. Relativamente ao uso e seleção do habitat, recorrendo a transectos de contagem de excrementos e a observações diretas, verificou-se que o veado seleciona positivamente habitats que lhe proporcionam simultaneamente alimento e refúgio, como é o caso das áreas de ecótono. A preferência por áreas de ecótono evidencia um comportamento adaptativo de maximização de energia, no qual os animais optam por procurar refúgio na proximidade das áreas de alimentação de forma a minimizarem os dispêndios energéticos. Em termos de dinâmica populacional, verificou-se uma relação entre a densidade de veado e o tamanho dos seus grupos, bem como o efeito nos mesmos do coberto vegetal. Contudo, dado o seu alto dimorfismo sexual em termos de tamanho corporal, as preferências de habitat podem também ser em parte responsáveis pela segregação sexual fora da época de reprodução. Face aos resultados obtidos através do método de observação direta de animais, a segregação sexual surge como consequência da interação entre fatores sociais e de habitat, que resultam de diferentes estratégias reprodutivas por parte de ambos os sexos. As diferentes estratégias reprodutivas são também notórias em termos de condição física e imunológica, com os machos a aumentarem a sua condição durante as épocas de primavera e verão de forma a melhorarem a sua performance durante o cio, e as fêmeas a viverem grande parte do ano no limiar da condição física devido ao seu investimento na sobrevivência da sua descendência. Globalmente, o veado apresenta uma boa adaptação à Serra da Lousã e representa um importante recurso natural para esta região. Contudo, para que a proliferação desta população selvagem continue, é necessária a implementação de medidas de gestão adequadas a este ecossistema mediterrâneo.

Ecological niche modeling, cytogenetics and phylogeography of the genera Geomalacus and Letourneuxia (Gastropoda, Pulmonata) from the Iberian-Moroccan region

First described more that 150 years ago, the systematics of the genera Geomalacus and Letourneuxia (Arionidae, Gastropoda, Pulmonata) is still challenging. The taxonomic classification of arionid species is based on extremely labile characters such as body size or color that depends both on diet and environment, as well as age. Moreover, there is little information on the genetic diversity and population structure of the Iberian slugs that could provide extra clues to disentangle their problematic classification. The present work uses different analytical tools such as habitat suitability (Ecological Niche Modeling - ENM), cytogenetic analysis and phylogeography to establish the geographical distribution and evolutionary history of these pulmonate slugs. The potential distribution of the four Geomalacus species was modeled using ENM, which allowed the identification of new locations for G. malagensis, including a first report in Portugal. Also, it was predicted a much wider distribution for G. malagensis and G. oliveirae than previously known. Classical cytogenetic analyses were assayed with reproductive and a novel use of somatic tissues (mouth and tentacles) returning the number of chromosomes for the four Geomalacus species and L. numidica (n = 31, 2n = 62) and the respective karyotypes. G. malagensis and L. numidica present similar chromosome morphologies and karyotypic formulae, being more similar to each other than the Geomalacus among themselves. We further reconstructed the phylogeny of the genera Geomalacus and Letourneuxia using partial sequences of the mitochondrial cytochrome oxidase subunit I (COI) and the nuclear ribosomal small subunit (18S rRNA), and applied an independent evolutionary rate method, the indicator vectors correlation, to evaluate the existence of cryptic diversity within species. The five nominal species of Geomalacus and Letourneuxia comprise 14 well-supported cryptic lineages. Letourneuxia numidica was retrieved as a sister group of G. malagensis. G. oliveirae is paraphyletic with respect to G. anguiformis. According to our dating estimates, the most recent common ancestor of Geomalacus dates back to the Middle Miocene (end of the Serravallian stage). The major lineage splitting events within Geomalacus occurred during the dry periods of the Zanclean stage (5.3-3.6 million years) and some lineages were confined to more humid mountain areas of the Iberian Peninsula, which lead to a highly geographically structured mitochondrial genetic diversity. The major findings of this are the following: (1) provides updated species distribution maps for the Iberian Geomalacus expanding the known geographic distribution of the concerned species, (2) unravels the cryptic diversity within the genera Geomalacus and Letourneuxia, (3) Geomalacus oliveirae is paraphyletic with G. anguiformis and (4) Letourneuxia numidica is sister group of G. malagensis.

How historical and present climat conditions affected the distribution of the mediterranean whter shrew?:a phylogeographical and ecological approach

Tese de doutoramento, Biologia (Biologia Evolutiva), Universidade de Lisboa, Faculdade de Ciências, 2014

An Analysis of Local Wind and Air Mass Directions and Their Impact on Cladosporium Distribution Using HYSPLIT and Circular Statistics

Ecological studies that examine species-environment relationships are often limited to several meteorological parameters, i.e. mean air temperature, relative humidity, precipitation, vapour pressure deficit and solar radiation. The impact of local wind, its speed and direction are less commonly investigated in aerobiological surveys mainly due to difficulties related to the employment of specific analytical tools and interpretation of their outputs. Identification of inoculum sources of economically important plant pathogens, as well as highly allergenic bioaerosols like Cladosporium species, has not been yet explored with remote sensing data and atmospheric models such as Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT). We, therefore, performed an analysis of 24 h intra-diurnal cycle of Cladosporium spp. spores from an urban site in connection with both the local wind direction and overall air mass direction computed by HYSPLIT. The observational method was a volumetric air sampler of the Hirst design with 1 h time resolution and corresponding optical detection of fungal spores with light microscopy. The atmospheric modelling was done using the on-line data set from GDAS with 1° resolution and circular statistical methods. Our results showed stronger, statistically significant correlation (p ≤ 0.05) between high Cladosporium spp. spore concentration and air mass direction compared to the local wind direction. This suggested that a large fraction of the investigated fungal spores had a regional origin and must be located more than a few kilometers away from the sampling point.

A Community-Level, Mesoscale Analysis of Fish Assemblage Structure in Shoreline Habitats of a Large River Using Multivariate Regression Trees.

The mesoscale (100–102 m) of river habitats has been identified as the scale that simultaneously offers insights into ecological structure and falls within the practical bounds of river management. Mesoscale habitat (mesohabitat) classifications for relatively large rivers, however, are underdeveloped compared with those produced for smaller streams. Approaches to habitat modelling have traditionally focused on individual species or proceeded on a species-by-species basis. This is particularly problematic in larger rivers where the effects of biological interactions are more complex and intense. Community-level approaches can rapidly model many species simultaneously, thereby integrating the effects of biological interactions while providing information on the relative importance of environmental variables in structuring the community. One such community-level approach, multivariate regression trees, was applied in order to determine the relative influences of abiotic factors on fish assemblages within shoreline mesohabitats of San Pedro River, Chile, and to define reference communities prior to the planned construction of a hydroelectric power plant. Flow depth, bank materials and the availability of riparian and instream cover, including woody debris, were the main variables driving differences between the assemblages. Species strongly indicative of distinctive mesohabitat types included the endemic Galaxias platei. Among other outcomes, the results provide information on the impact of non-native salmonids on river-dwelling Galaxias platei, suggesting a degree of habitat segregation between these taxa based on flow depth. The results support the use of the mesohabitat concept in large, relatively pristine river systems, and they represent a basis for assessing the impact of any future hydroelectric power plant construction and operation. By combing community classifications with simple sets of environmental rules, the multivariate regression trees produced can be used to predict the community structure of any mesohabitat along the reach.

Analysis of temporal and spatial variations of forest. A case of study in notheastern Armenia

The forest has a crucial ecological role and the continuous forest loss can cause colossal effects on the environment. As Armenia is one of the low forest covered countries in the world, this problem is more critical. Continuous forest disturbances mainly caused by illegal logging started from the early 1990s had a huge damage on the forest ecosystem by decreasing the forest productivity and making more areas vulnerable to erosion. Another aspect of the Armenian forest is the lack of continuous monitoring and absence of accurate estimation of the level of cuts in some years. In order to have insight about the forest and the disturbances in the long period of time we used Landsat TM/ETM + images. Google Earth Engine JavaScript API was used, which is an online tool enabling the access and analysis of a great amount of satellite imagery. To overcome the data availability problem caused by the gap in the Landsat series in 1988- 1998, extensive cloud cover in the study area and the missing scan lines, we used pixel based compositing for the temporal window of leaf on vegetation (June-late September). Subsequently, pixel based linear regression analyses were performed. Vegetation indices derived from the 10 biannual composites for the years 1984-2014 were used for trend analysis. In order to derive the disturbances only in forests, forest cover layer was aggregated and the original composites were masked. It has been found, that around 23% of forests were disturbed during the study period.