Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 53
Filtrar
Mais filtros










Base de dados
Intervalo de ano de publicação
1.
Trends Ecol Evol ; 2021 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-34799145

RESUMO

Despite much criticism, black-or-white null-hypothesis significance testing with an arbitrary P-value cutoff still is the standard way to report scientific findings. One obstacle to progress is likely a lack of knowledge about suitable alternatives. Here, we suggest language of evidence that allows for a more nuanced approach to communicate scientific findings as a simple and intuitive alternative to statistical significance testing. We provide examples for rewriting results sections in research papers accordingly. Language of evidence has previously been suggested in medical statistics, and it is consistent with reporting approaches of international research networks, like the Intergovernmental Panel on Climate Change, for example. Instead of re-inventing the wheel, ecology and evolution might benefit from adopting some of the 'good practices' that exist in other fields.

2.
J Infect ; 83(1): 84-91, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-33892016

RESUMO

OBJECTIVES: SARS-CoV-2 emerged in South Asia in 2019 and has resulted in a global pandemic. Public Health England (PHE) Manchester rapidly escalated testing for SARS-CoV-2 in the highest COVID-19 incidence location in England. The results of the PHE Manchester SARS-CoV-2 surveillance during the first wave are presented. METHODS: Retrospective data were collected for patients fitting the PHE SARS-CoV-2 case definition from 11th February to 31st August 2020. Respiratory tract, tissue, faecal, fluid and cerebrospinal (CSF) samples were tested for SARS-CoV-2 by a semi-quantitative real-time reverse-transcription PCR. RESULTS: Of the 204,083 tests for SARS-CoV-2, 18,011 were positive demonstrating a positivity of 8.90%. Highest positivity was in nasal swabs (20.99%) followed by broncheo-alveolar lavage samples (12.50%). None of the faecal, fluid or CSF samples received were positive for SARS-CoV-2. CONCLUSIONS: There was a high incidence of SARS-CoV-2 patients in the North-West of England during the first UK wave of the Covid-19 pandemic. Highest positivity rate was in nasal specimens suggesting this is the optimum sample type within this dataset for detecting SARS-CoV-2. Further studies are warranted to assess the utility of testing faecal, fluid and CSF samples. Rapid escalation of testing via multiple platforms was required to ensure prompt diagnosis and isolate infected cases to reduce transmission of the virus.


Assuntos
COVID-19 , Vírus da SARS , Ásia , Inglaterra/epidemiologia , Humanos , Pandemias , Estudos Retrospectivos , Vírus da SARS/genética , SARS-CoV-2
3.
Int J Mol Sci ; 22(3)2021 Jan 26.
Artigo em Inglês | MEDLINE | ID: mdl-33530493

RESUMO

The impact of the Gram-negative bacterium Escherichia coli (E. coli) on the microbiomic and pathogenic phenomena occurring in humans and other warm-blooded animals is relatively well-recognized. At the same time, there are scant data concerning the role of E. coli strains in the health and disease of cold-blooded animals. It is presently known that reptiles are common asymptomatic carriers of another human pathogen, Salmonella, which, when transferred to humans, may cause a disease referred to as reptile-associated salmonellosis (RAS). We therefore hypothesized that reptiles may also be carriers of specific E. coli strains (reptilian Escherichia coli, RepEC) which may differ in their genetic composition from the human uropathogenic strain (UPEC) and avian pathogenic E. coli (APEC). Therefore, we isolated RepECs (n = 24) from reptile feces and compared isolated strains' pathogenic potentials and phylogenic relations with the aforementioned UPEC (n = 24) and APEC (n = 24) strains. To this end, we conducted an array of molecular analyses, including determination of the phylogenetic groups of E. coli, virulence genotyping, Pulsed-Field Gel Electrophoresis-Restriction Analysis (RA-PFGE) and genetic population structure analysis using Multi-Locus Sequence Typing (MLST). The majority of the tested RepEC strains belonged to nonpathogenic phylogroups, with an important exception of one strain, which belonged to the pathogenic group B2, typical of extraintestinal pathogenic E. coli. This strain was part of the globally disseminated ST131 lineage. Unlike RepEC strains and in line with previous studies, a high percentage of UPEC strains belonged to the phylogroup B2, and the percentage distribution of phylogroups among the tested APEC strains was relatively homogenous, with most coming from the following nonpathogenic groups: C, A and B1. The RA-PFGE displayed a high genetic diversity among all the tested E. coli groups. In the case of RepEC strains, the frequency of occurrence of virulence genes (VGs) was lower than in the UPEC and APEC strains. The presented study is one of the first attempting to compare the phylogenetic structures of E. coli populations isolated from three groups of vertebrates: reptiles, birds and mammals (humans).


Assuntos
Doenças dos Animais/microbiologia , Infecções por Escherichia coli/veterinária , Filogenia , Répteis/microbiologia , Escherichia coli Uropatogênica/classificação , Escherichia coli Uropatogênica/genética , Animais , Proteínas de Escherichia coli/genética , Especificidade de Hospedeiro , Humanos , Tipagem de Sequências Multilocus , Doenças das Aves Domésticas/microbiologia , Virulência/genética , Fatores de Virulência/genética
4.
Ecol Modell ; 436: 109288, 2020 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-32982015

RESUMO

In this letter we present comments on the article "A global-scale ecological niche model to predict SARS-CoV-2 coronavirus" by Coro published in 2020.

7.
Trends Ecol Evol ; 35(1): 56-67, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31676190

RESUMO

With the expansion in the quantity and types of biodiversity data being collected, there is a need to find ways to combine these different sources to provide cohesive summaries of species' potential and realized distributions in space and time. Recently, model-based data integration has emerged as a means to achieve this by combining datasets in ways that retain the strengths of each. We describe a flexible approach to data integration using point process models, which provide a convenient way to translate across ecological currencies. We highlight recent examples of large-scale ecological models based on data integration and outline the conceptual and technical challenges and opportunities that arise.


Assuntos
Biodiversidade , Ecologia , Modelos Teóricos
8.
Sci Rep ; 9(1): 7766, 2019 05 23.
Artigo em Inglês | MEDLINE | ID: mdl-31123274

RESUMO

Despite its value for conservation decision-making, we lack information on population abundances for most species. Because establishing large-scale monitoring schemes is rarely feasible, statistical methods that combine multiple data sources are promising approaches to maximize use of available information. We built a Bayesian hierarchical model that combined different survey data of the endangered Eld's deer in Shwesettaw Wildlife Sanctuary (SWS) in Myanmar and tested our approach in simulation experiments. We combined spatially-restricted line-transect abundance data with more spatially-extensive camera-trap occupancy data to enable estimation of the total deer abundance. The integrated model comprised an ecological model (common to both survey types, based on the equivalence between cloglog-transformed occurrence probability and log-transformed expected abundance) and separate observation models for each survey type. We estimated that the population size of Eld's deer in SWS is c. 1519 (1061-2114), suggesting it is the world's largest wild population. The simulations indicated that the potential benefits of combining data include increased precision and better sampling of the spatial variation in the environment, compared to separate analysis of each survey. Our analytical approach, which integrates the strengths of different survey methods, has widespread application for estimating species' abundances, especially in information-poor regions of the world.


Assuntos
Conservação dos Recursos Naturais/métodos , Monitoramento Ambiental/métodos , Animais , Teorema de Bayes , Cervos , Espécies em Perigo de Extinção/tendências , Modelos Estatísticos , Mianmar , Densidade Demográfica , Inquéritos e Questionários
9.
Parasit Vectors ; 12(1): 142, 2019 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-30909930

RESUMO

BACKGROUND: The invasive temperate mosquito Aedes japonicus japonicus is a potential vector for various infectious diseases and therefore a target of vector control measures. Even though established in Germany, it is unclear whether the species has already reached its full distribution potential. The possible range of the species, its annual population dynamics, the success of vector control measures and future expansions due to climate change still remain poorly understood. While numerous studies on occurrence have been conducted, they used mainly presence data from relatively few locations. In contrast, we used experimental life history data to model the dynamics of a continuous stage-structured population to infer potential seasonal densities and ask whether stable populations are likely to establish over a period of more than one year. In addition, we used climate change models to infer future ranges. Finally, we evaluated the effectiveness of various stage-specific vector control measures. RESULTS: Aedes j. japonicus has already established stable populations in the southwest and west of Germany. Our models predict a spread of Ae. j. japonicus beyond the currently observed range, but likely not much further eastwards under current climatic conditions. Climate change models, however, will expand this range substantially and higher annual densities can be expected. Applying vector control measures to oviposition, survival of eggs, larvae or adults showed that application of adulticides for 30 days between late spring and early autumn, while ambient temperatures are above 9 °C, can reduce population density by 75%. Continuous application of larvicide showed similar results in population reduction. Most importantly, we showed that with the consequent application of a mixed strategy, it should be possible to significantly reduce or even extinguish existing populations with reasonable effort. CONCLUSION: Our study provides valuable insights into the mechanisms concerning the establishment of stable populations in invasive species. In order to minimise the hazard to public health, we recommend vector control measures to be applied in 'high risk areas' which are predicted to allow establishment of stable populations to establish.


Assuntos
Aedes/fisiologia , Controle de Mosquitos/métodos , Mosquitos Vetores/fisiologia , Estações do Ano , Animais , Mudança Climática , Feminino , Alemanha , Espécies Introduzidas , Modelos Teóricos
10.
Sci Adv ; 5(1): eaat4858, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30746437

RESUMO

Demand for models in biodiversity assessments is rising, but which models are adequate for the task? We propose a set of best-practice standards and detailed guidelines enabling scoring of studies based on species distribution models for use in biodiversity assessments. We reviewed and scored 400 modeling studies over the past 20 years using the proposed standards and guidelines. We detected low model adequacy overall, but with a marked tendency of improvement over time in model building and, to a lesser degree, in biological data and model evaluation. We argue that implementation of agreed-upon standards for models in biodiversity assessments would promote transparency and repeatability, eventually leading to higher quality of the models and the inferences used in assessments. We encourage broad community participation toward the expansion and ongoing development of the proposed standards and guidelines.


Assuntos
Biodiversidade , Modelos Teóricos , Monitoramento Ambiental/normas , Guias como Assunto , Revisão por Pares , Análise Espaço-Temporal
11.
J Med Microbiol ; 68(2): 188-196, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30561295

RESUMO

PURPOSE: Members of the ST127 uropathogenic E. coli (UPEC) clone have a high virulence potential and are also highly virulent in insect infection models. However, strains of this lineage are reported in relatively low numbers in many studies. ST127 strains are also usually widely susceptible to antibiotics and, consequently, their true prevalence may be under-recognized as they will be eradicated during empirical therapy. A genuine concern is the possibility that members of this highly virulent lineage will acquire resistance, leading to a more serious threat. The aim of this study was to design and validate a PCR assay specific to ST127. METHODOLOGY: Genomic sequences obtained from various UPEC isolates from the leading clones were used in comparative genomic analyses to allow identification of highly discriminatory sequences specific to E. coli ST127. The fliC (flagellin) and a homologue of the upaG (autotransporter adhesin) gene were identified as meeting our criteria and were used to develop a multiplex PCR assay. A total of 143 UPEC isolates representing 99 different MLST clones from three locations (North West and South West England and Riyadh, Saudi Arabia) were used to validate the PCR assay. RESULTS: The multiplex PCR readily identified all 29 E. coli ST127 isolates but, equally importantly, produced no false positives with representatives of any of the other 98 STs tested. CONCLUSION: We report the design and validation of a specific multiplex PCR for the rapid and reliable identification of ST127, which can be used for enhanced surveillance for this high-risk clone.


Assuntos
Escherichia coli Extraintestinal Patogênica/isolamento & purificação , Reação em Cadeia da Polimerase Multiplex , Infecções por Escherichia coli/microbiologia , Proteínas de Escherichia coli/genética , Escherichia coli Extraintestinal Patogênica/genética , Escherichia coli Extraintestinal Patogênica/patogenicidade , Flagelina/genética , Genômica , Humanos , Anotação de Sequência Molecular , Reação em Cadeia da Polimerase Multiplex/métodos , Reação em Cadeia da Polimerase Multiplex/normas , Sensibilidade e Especificidade , Fatores de Tempo , Infecções Urinárias/microbiologia , Urina/microbiologia , Virulência , Sequenciamento Completo do Genoma
12.
J Anim Ecol ; 87(5): 1418-1428, 2018 09.
Artigo em Inglês | MEDLINE | ID: mdl-30133819

RESUMO

European rabbits (Oryctolagus cuniculus) have been exposed to rabbit haemorrhagic disease virus (RHDV) and myxoma virus (MYXV) in their native and invasive ranges for decades. Yet, the long-term effects of these viruses on rabbit population dynamics remain poorly understood. In this context, we analysed 17 years of detailed capture-mark-recapture data (2000-2016) from Turretfield, South Australia, using a probabilistic state-space hierarchical modelling framework to estimate rabbit survival and epidemiological dynamics. While RHDV infection and disease-induced death were most prominent during annual epidemics in winter and spring, we found evidence for continuous infection of susceptible individuals with RHDV throughout the year. RHDV-susceptible rabbits had, on average, 25% lower monthly survival rates compared to immune individuals, while the average monthly force of infection in winter and spring was ~38%. These combined to result in an average infection-induced mortality rate of 69% in winter and spring. Individuals susceptible to MYXV and immune to RHDV had similar survival probabilities to those having survived infections from both viruses, whereas individuals susceptible to both RHDV and MYXV had higher survival probabilities than those susceptible to RHDV and immune to MYXV. This suggests that MYXV may reduce the future survival rates of individuals that endure initial MYXV infection. There was no evidence for long-term changes in disease-induced mortality and infection rates for either RHDV or MYXV. We conclude that continuous, year-round virus perpetuation (and perhaps heterogeneity in modes of transmission and infectious doses during and after epidemics) acts to reduce the efficiency of RHDV and MYXV as biocontrol agents of rabbits in their invasive range. However, if virulence can be maintained as relatively constant through time, RHDV and MYXV will likely continue realizing strong benefits as biocontrol agents.


Assuntos
Infecções por Caliciviridae , Vírus da Doença Hemorrágica de Coelhos , Myxoma virus , Animais , Coelhos , Austrália do Sul , Virulência
13.
Mol Ecol ; 27(12): 2714-2724, 2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29761593

RESUMO

In addition to the processes structuring free-living communities, host-associated microbiota are directly or indirectly shaped by the host. Therefore, microbiota data have a hierarchical structure where samples are nested under one or several variables representing host-specific factors, often spanning multiple levels of biological organization. Current statistical methods do not accommodate this hierarchical data structure and therefore cannot explicitly account for the effect of the host in structuring the microbiota. We introduce a novel extension of joint species distribution models (JSDMs) which can straightforwardly accommodate and discern between effects such as host phylogeny and traits, recorded covariates such as diet and collection site, among other ecological processes. Our proposed methodology includes powerful yet familiar outputs seen in community ecology overall, including (a) model-based ordination to visualize and quantify the main patterns in the data; (b) variance partitioning to assess how influential the included host-specific factors are in structuring the microbiota; and (c) co-occurrence networks to visualize microbe-to-microbe associations.


Assuntos
Microbiota/genética , Ecologia , Filogenia
14.
J Anim Ecol ; 87(4): 1034-1045, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-29577274

RESUMO

The effects of different environmental drivers on the changes in species' population abundances can be difficult to disentangle as they often act simultaneously. Researchers have built statistical models that include environmental variables (such as annual temperature) or species attributes (such as a species' temperature preference), which are assumed to detect the impacts of specific drivers (such as climate change). However, these approaches are often applied separately or, if combined, not explicitly compared. We show the complementary insights gained by applying both these approaches to a community dataset on Danish terrestrial birds. We use our analysis to compare the relative importance of climate change and agricultural land-use change for the abundance changes within the community between 1983 and 2013. Population models were fitted to the community data of species' annual abundances with predictors comprising: species attributes (species' temperature and habitat preferences), environmental variables (climatic and agricultural land-use change variables) or both. Relationships between species' abundances and environmental variables were used to identify the drivers associated with average abundance changes of species in the community. Relationships between species' abundances and their attributes were used to understand the drivers causing interspecific variation in abundance changes. Warmer winters were positively associated with community-level abundances, and warm-adapted species had more positive abundance changes than cold-adapted ones. Agricultural land-use area was negatively associated with community-level abundances, and birds using a high proportion of meadow and habitat specialists had more negative abundance changes than birds using other habitats and habitat generalists. Effect sizes of environmental variables were larger for agricultural land-use change while those of species attributes were larger for climate change. The environmental data approach suggested that agricultural land-use change has decreased the average abundances of species in the community, affecting total community size while the species attribute-based approach suggested that climate change has caused variation in abundance among species, affecting community composition. Environmental variables and species attributes that are hypothesized to link to specific drivers can be used together to provide complementary information on the impacts of different drivers on communities.


Assuntos
Agricultura/métodos , Aves/fisiologia , Mudança Climática , Traços de História de Vida , Animais , Dinamarca , Modelos Estatísticos , Densidade Demográfica
15.
Sci Total Environ ; 621: 588-599, 2018 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-29195206

RESUMO

Long-term observations on riverine benthic invertebrate communities enable assessments of the potential impacts of global change on stream ecosystems. Besides increasing average temperatures, many studies predict greater temperature extremes and intense precipitation events as a consequence of climate change. In this study we examined long-term observation data (10-32years) of 26 streams and rivers from four ecoregions in the European Long-Term Ecological Research (LTER) network, to investigate invertebrate community responses to changing climatic conditions. We used functional trait and multi-taxonomic analyses and combined examinations of general long-term changes in communities with detailed analyses of the impact of different climatic drivers (i.e., various temperature and precipitation variables) by focusing on the response of communities to climatic conditions of the previous year. Taxa and ecoregions differed substantially in their response to climate change conditions. We did not observe any trend of changes in total taxonomic richness or overall abundance over time or with increasing temperatures, which reflects a compensatory turnover in the composition of communities; sensitive Plecoptera decreased in response to warmer years and Ephemeroptera increased in northern regions. Invasive species increased with an increasing number of extreme days which also caused an apparent upstream community movement. The observed changes in functional feeding group diversity indicate that climate change may be associated with changes in trophic interactions within aquatic food webs. These findings highlight the vulnerability of riverine ecosystems to climate change and emphasize the need to further explore the interactive effects of climate change variables with other local stressors to develop appropriate conservation measures.


Assuntos
Mudança Climática , Ecossistema , Invertebrados , Rios , Animais , Conservação dos Recursos Naturais , Europa (Continente) , Espécies Introduzidas , Temperatura
16.
Proc Biol Sci ; 284(1863)2017 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-28931734

RESUMO

Identifying patterns in the effects of temperature on species' population abundances could help develop a general framework for predicting the consequences of climate change across different communities and realms. We used long-term population time series data from terrestrial, freshwater, and marine species communities within central Europe to compare the effects of temperature on abundance across a broad range of taxonomic groups. We asked whether there was an average relationship between temperatures in different seasons and annual abundances of species in a community, and whether species attributes (temperature range of distribution, range size, habitat breadth, dispersal ability, body size, and lifespan) explained interspecific variation in the relationship between temperature and abundance. We found that, on average, warmer winter temperatures were associated with greater abundances in terrestrial communities (ground beetles, spiders, and birds) but not always in aquatic communities (freshwater and marine invertebrates and fish). The abundances of species with large geographical ranges, larger body sizes, and longer lifespans tended to be less related to temperature. Our results suggest that climate change may have, in general, positive effects on species' abundances within many terrestrial communities in central Europe while the effects are less predictable in aquatic communities.


Assuntos
Biodiversidade , Mudança Climática , Ecossistema , Temperatura , Distribuição Animal , Animais , Tamanho Corporal , Europa (Continente) , Longevidade , Dinâmica Populacional , Estações do Ano
17.
Nat Ecol Evol ; 1(3): 67, 2017 Feb 17.
Artigo em Inglês | MEDLINE | ID: mdl-28812743

RESUMO

Climate change, land-use change, pollution and exploitation are among the main drivers of species' population trends; however, their relative importance is much debated. We used a unique collection of over 1,000 local population time series in 22 communities across terrestrial, freshwater and marine realms within central Europe to compare the impacts of long-term temperature change and other environmental drivers from 1980 onwards. To disentangle different drivers, we related species' population trends to species- and driver-specific attributes, such as temperature and habitat preference or pollution tolerance. We found a consistent impact of temperature change on the local abundances of terrestrial species. Populations of warm-dwelling species increased more than those of cold-dwelling species. In contrast, impacts of temperature change on aquatic species' abundances were variable. Effects of temperature preference were more consistent in terrestrial communities than effects of habitat preference, suggesting that the impacts of temperature change have become widespread for recent changes in abundance within many terrestrial communities of central Europe.

18.
Nat Commun ; 7: 12793, 2016 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-27597446

RESUMO

Anthropogenic changes in climate and land use are driving changes in migration patterns of birds worldwide. Spatial changes in migration have been related to long-term temperature trends, but the intrinsic mechanisms by which migratory species adapt to environmental change remain largely unexplored. We show that, for a long-lived social species, older birds with more experience are critical for innovating new migration behaviours. Groups containing older, more experienced individuals establish new overwintering sites closer to the breeding grounds, leading to a rapid population-level shift in migration patterns. Furthermore, these new overwintering sites are in areas where changes in climate have increased temperatures and where food availability from agriculture is high, creating favourable conditions for overwintering. Our results reveal that the age structure of populations is critical for the behavioural mechanisms that allow species to adapt to global change, particularly for long-lived animals, where changes in behaviour can occur faster than evolution.


Assuntos
Envelhecimento , Migração Animal/fisiologia , Aves/fisiologia , Mudança Climática , Animais , Meio Ambiente , Estações do Ano , Estados Unidos
20.
FEMS Microbiol Rev ; 40(5): 686-700, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-27358393

RESUMO

With high-throughput sequencing (HTS), we are able to explore the hidden world of microscopic organisms to an unpre-cedented level. The fast development of molecular technology and statistical methods means that microbial ecologists must keep their toolkits updated. Here, we review and evaluate some of the more widely adopted and emerging techniques for analysis of diversity and community composition, and the inference of species interactions from co-occurrence data generated by HTS of marker genes. We emphasize the importance of observational biases and statistical properties of the data and methods. The aim of the review is to critically discuss the advantages and disadvantages of established and emerging statistical methods, and to contribute to the integration of HTS-based marker gene data into community ecology.


Assuntos
Archaea/genética , Bactérias/genética , Fungos/genética , Marcadores Genéticos/genética , Microbiota/genética , Archaea/classificação , Bactérias/classificação , Biodiversidade , Interpretação Estatística de Dados , Fungos/classificação , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Sequência de DNA/métodos
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...