Modelling the niche for a marine vertebrate: A case study incorporating behavioural plasticity, proximate threats and climate change

[EN] The integration of satellite telemetry, remotely sensed environmental data, and habitat/environmental modelling has provided for a growing understanding of spatial and temporal ecology of species of conservation concern. The Republic of Cape Verde comprises the only substantial rookery for the loggerhead turtle Caretta caretta in the eastern Atlantic. A size related dichotomy in adult foraging patterns has previously been revealed for adult sea turtles from this population with a proportion of adults foraging neritically, whilst the majority forage oceanically. Here we describe observed habitat use and employ ecological niche modelling to identify suitable foraging habitats for animals utilising these two distinct behavioural strategies. We also investigate how these predicted habitat niches may alter under the influence of climate change induced oceanic temperature rises.

Les plasmocytes et leur niche: Étude de la génération de plasmocytes humains in vitro

Chez l’humain, les lymphocytes B mémoires IgG+ et IgA+ sont des cellules clés de l’immunité humorale. Ces cellules mémoires sont maintenues à long-terme dans notre organisme. Elles représentent une défense rapide et efficace contre toutes les infections que nous avons déjà vaincues pendant notre vie. Ces cellules mémoires qui rencontrent à nouveau leur antigène se différencient rapidement en plasmocytes à courte vie, et permettent la sécrétion massive d’immunoglobuline (Ig). La contrepartie mémoire de ces cellules sont les plasmocytes à longue vie qui sont présents dans les niches de la moelle osseuse et y sécrètent en permanence des anticorps protecteurs qui circulent dans le sang. Ces cellules sécrétrices peuvent avoir une durée de vie allant de dizaines d’années à la vie entière de l’individu. Les patients qui reçoivent des traitements de chimiothérapie ou de radiothérapie sont privés de ces cellules mémoires détruites par ces traitements au même titre que les cellules cancéreuses. Ces patients deviennent vulnérables aux infections et leur survie dépend de la régénération rapide de leur système hématopoïétique. Notre équipe a déjà mis au point une méthode pour préparer de grandes quantités des cellules mémoires capables de sécréter des IgG et des IgA. Les présents travaux visent à générer des plasmocytes fonctionnels et capables de survivre à long terme in vitro. La stratégie expérimentale visait à établir des conditions permettant de se rapprocher de l’environnement de la moelle osseuse. Dans un premier temps, nous avons étudié les paramètres permettant la différenciation des lymphocytes B mémoires en plasmocytes. Étant donné l’importance du potentiel redox dans l’environnement de la moelle osseuse, nous avons d’abord tenté d’en contrôler l’impact avec un antioxydant, le N-acétyle cystéine (NAC). Nos résultats ont démontré que le NAC avait un effet significatif et diminuait la phosphorylation de la protéine STAT3 en raison d’une inhibition des kinases JAK2 et JAK3. Étonnamment, cet antioxydant retardait la différenciation de nos lymphocytes B qui étaient stimulés avec une forte interaction CD40-CD154. Par la suite, la comparaison des interactions CD40-CD154 et CD27-CD70 a permis de conclure qu’il était essentiel de réduire à son minimum l’interaction CD40-CD154 et qu’il fallait ajouter les cytokines IL-6 et IL-10. Les cellules CD31+CD38+CD138+ générées présentaient un phénotype similaire à celui des plasmocytes de la moelle osseuse. Malheureusement la fréquence de ces cellules était faible et leur viabilité insuffisante. Afin d’augmenter la survie de ces cellules le dernier volet de nos travaux visait à se rapprocher des niches de la moelle osseuse. Notre but a été atteint en ajoutant des cellules mésenchymateuses issues de la moelle osseuse en présence de 8% de dioxygène (O2). Les cellules CD31+CD38+CD138+ générées ont une excellente viabilité et représentent plus de 50% des cellules totales en culture. De plus, le modèle de culture est maintenant établi dans un milieu exempt de sérum et de protéines animales. Dans l’ensemble, nos résultats permettent de proposer la production ex vivo de plasmocytes autologues avec une perspective thérapeutique pour réduire les risques d’infections des patients devenues immunodéficients, suite à un traitement de radiothérapie ou de chimiothérapie.

Trophic niche overlap of sprat and commercial small pelagic teleosts in the Gulf of Lions (NW Mediterranean Sea)

Increasing abundance of non-commercial sprats and decreasing biomass and landings of commercial anchovies and sardines justify the need to study the feeding ecology and trophic niche overlap of these planktivorous species in the Gulf of Lions. Their diet has been investigated on the basis of stomach content and stable isotope analyses in 2011 and 2012 according to different depths and regions in the study area. The main prey were Corycaeidae copepods, Clauso/Paracalanus, Euterpina acutifrons and Microsetella, for sprats and small copepods, such as Microsetella, Oncaea and Corycaeidae, for anchovies and sardines. This is the first time that the diet of sprats is described in the Gulf of Lions. Sprats fed on a larger size spectrum of prey and seem to be more generalist feeders compared to anchovies and sardines. Ontogenetic changes as well as spatial and temporal variations of the diet occurred in the three species. Stable isotope analysis revealed mobility of sardines and sprats among feeding areas while anchovies exhibited preferred feeding areas. Sprats showed a higher relative condition assessed by C/N ratios than sardines and anchovies. Our results showed an overlap of the trophic niches for the three species, indicating a potential trophic competition in the Gulf of Lions.

Comments on The Origins of Niche Graves In The Złota Culture

This publication constitutes the fruits of National Science Centre research projects (grant no 2011/01/M/HS3/02142 – 6 articles) and the National Programme for the Development of the Humanities (grant no 0108/NPH3/H12/82/2014 – 3 articles). We would like to acknowledge and at the same time express our sincere gratitude for the generosity shown by the following at the Adam Mickiewicz University in making this publication possible: the Dean of the Department of History, Institute of Pre-history and the Eastern Institute.

Using niche modelling of indicator species to predict the distribution of xerophitic shrub dune communities in South-Western Portugal

Inland sand dune systems are amongst the most threatened habitat types of Europe. Affected by severe conditions, these habitats present distinct community compositions, which makes them excellent for studying possible interactions among their integrating species and the environment. We focus on understanding the distribution and cooccurrence of the species from dune plant assemblages as a key step for the adequate protection of these habitats. Using data from an extensive survey we identified the shrub species that could be considered indicators of the different xerophytic scrub dune communities in South West Portugal. Then, we modelled the responses of these species to the environmental conditions using Ecological Niche Factor Analysis. We present some preliminary results elucidating whether using species distribution models of indicator species at a regional scale is a valid approach to predict the distribution of the different types of communities inhabiting these endangered habitats.

Landscape metrics as indicators of coastal morphology and its use in ecological niche modelling of seagrass species

Dependence of some species on landscape structure has been proved in numerous studies. So far, however, little progress has been made in the integration of landscape metrics in the prediction of species associated with coastal features. Specific landscape metrics were tested as predictors of coastal shape using three coastal features of the Iberian Peninsula (beaches, capes and gulfs) at different scales. We used the landscape metrics in combination with environmental variables to model the niche and find suitable habitats for a seagrass species (Cymodocea nodosa) throughout its entire range of distribution. Landscape metrics able to capture variation in the coastline enhanced significantly the accuracy of the models, despite the limitations caused by the scale of the study. We provided the first global model of the factors that can be shaping the environmental niche and distribution of C. nodosa throughout its range. Sea surface temperature and salinity were the most relevant variables. We identified areas that seem unsuitable for C. nodosa as well as those suitable habitats not occupied by the species. We also present some preliminary results of testing historical biogeographical hypotheses derived from distribution predictions under Last Glacial Maximum conditions and genetic diversity data.

Can we use niche models of indicator species to predict the distribution of endangered communities?

European-wide conservation policies are based on the identification of priority habitats. However, research on conservation biogeography often relies on the results and projections of species distribution models to assess species' vulnerability to global change. We assess whether the distribution and structure of threatened communities can be predicted by the suitability of the environmental conditions for their indicator species. We present some preliminary results elucidating if using species distribution models of indicator species at a regional scale is a valid approach to predict these endangered communities. Dune plant assemblages, affected by severe conditions, are excellent models for studying possible interactions among their integrating species and the environment. We use data from an extensive survey of xerophytic inland sand dune scrub communities from Portugal, one of the most threatened habitat types of Europe. We identify indicator shrub species of different types of communities, model their geographical response to the environment, and evaluate whether the output of these niche models are able to predict the distribution of each type of community in a different region.

Using satellite telemetry and environmental niche modelling to inform conservation targets for a long-distance migratory raptor in its wintering grounds

Understanding the ecology of migratory birds during the non-breeding season is necessary for ensuring their conservation. Using satellite telemetry data we describe winter ranging behaviour and movements of pallid harriers Circus macrourus that bred in Kazakhstan. We developed an ecological niche model for the species in Africa, to identify the most suitable wintering areas for pallid harriers and the importance of habitat in determining the location of those areas. We also assessed how well represented suitable areas are in the network of protected areas. Individual harriers showed relatively high fidelity to wintering areas but with potential for interannual changes. The ecological niche model highlighted the importance of open habitats with natural vegetation. Most suitable areas for the species were located in eastern Africa. Suitable areas had a patchy distribution but were relatively well included in the network of protected areas. The preferential use of habitats with natural vegetation by wintering pallid harriers and the patchiness of the most suitable areas highlight the harrier's vulnerability to land-use changes and the associated loss of natural vegetation in Africa. Conservation of harriers could be enhanced by preserving natural grasslands within protected areas and improving habitat management in the human-influenced portions of the species’ core wintering areas.

Niche segregation between immature and adult seabirds: Does progressive maturation play a role?

In long-lived species with slow maturation, prebreeders often represent a large percentage of the individuals alive at any moment, but their ecology is still understudied. Recent studies have found prebreeding seabirds to differ in their isotopic (and trophic) niche from adult breeders attending the same nesting colonies. These differences have been hypothesized to be linked to the less-developed foraging performance of younger and less-experienced immatures or perhaps to their inferior competitive abilities. Such differences from adults would wane as individuals mature (“the progressive ontogenetic shift hypothesis”) and could underpin the prolonged breeding deferral until adulthood displayed by those species. This study documents a marked difference in the nitrogen and carbon isotopic ratios measured in the whole blood of immatures and breeders in 2 pelagic seabird species (Cory’s shearwaters, Calonectris borealis, and black-browed albatrosses, Thalassarche melanophris) nesting in contrasting environments. However, blood isotopic values did not present a relationship with prebreeder age, suggesting no gradual ontogenetic shift from an immature toward an adult isotopic niche. Furthermore, isotopic signatures of sabbatical adults could not be separated from those of immatures attending the same colonies, but were clearly segregated from adult breeders. These results suggest that isotopic differentiation between immatures and breeders is mainly linked to a factor unrelated to previous experience and hence probably unrelated to a hypothetical gradual improvement of foraging competence or competitive abilities. Any ecological differentiation between breeders and nonbreeders is more likely related to the severity of the central-place foraging constraints and to the energetic requirements of reproduction (“the reproductive constraint hypothesis”).

An Integrated Framework To Improve The Concept Of Resource Specialisation.

Resource specialisation, although a fundamental component of ecological theory, is employed in disparate ways. Most definitions derive from simple counts of resource species. We build on recent advances in ecophylogenetics and null model analysis to propose a concept of specialisation that comprises affinities among resources as well as their co-occurrence with consumers. In the distance-based specialisation index (DSI), specialisation is measured as relatedness (phylogenetic or otherwise) of resources, scaled by the null expectation of random use of locally available resources. Thus, specialists use significantly clustered sets of resources, whereas generalists use over-dispersed resources. Intermediate species are classed as indiscriminate consumers. The effectiveness of this approach was assessed with differentially restricted null models, applied to a data set of 168 herbivorous insect species and their hosts. Incorporation of plant relatedness and relative abundance greatly improved specialisation measures compared to taxon counts or simpler null models, which overestimate the fraction of specialists, a problem compounded by insufficient sampling effort. This framework disambiguates the concept of specialisation with an explicit measure applicable to any mode of affinity among resource classes, and is also linked to ecological and evolutionary processes. This will enable a more rigorous deployment of ecological specialisation in empirical and theoretical studies.

Comparative Metagenomic Analysis Of Coral Microbial Communities Using A Reference-independent Approach.

By comparing the SEED and Pfam functional profiles of metagenomes of two Brazilian coral species with 29 datasets that are publicly available, we were able to identify some functions, such as protein secretion systems, that are overrepresented in the metagenomes of corals and may play a role in the establishment and maintenance of bacteria-coral associations. However, only a small percentage of the reads of these metagenomes could be annotated by these reference databases, which may lead to a strong bias in the comparative studies. For this reason, we have searched for identical sequences (99% of nucleotide identity) among these metagenomes in order to perform a reference-independent comparative analysis, and we were able to identify groups of microbial communities that may be under similar selective pressures. The identification of sequences shared among the metagenomes was found to be even better for the identification of groups of communities with similar niche requirements than the traditional analysis of functional profiles. This approach is not only helpful for the investigation of similarities between microbial communities with high proportion of unknown reads, but also enables an indirect overview of gene exchange between communities.

Metacommunity Versus Biogeography: A Case Study Of Two Groups Of Neotropical Vegetation-dwelling Arthropods.

Biogeography and metacommunity ecology provide two different perspectives on species diversity. Both are spatial in nature but their spatial scales do not necessarily match. With recent boom of metacommunity studies, we see an increasing need for clear discrimination of spatial scales relevant for both perspectives. This discrimination is a necessary prerequisite for improved understanding of ecological phenomena across scales. Here we provide a case study to illustrate some spatial scale-dependent concepts in recent metacommunity studies and identify potential pitfalls. We presented here the diversity patterns of Neotropical lepidopterans and spiders viewed both from metacommunity and biogeographical perspectives. Specifically, we investigated how the relative importance of niche- and dispersal-based processes for community assembly change at two spatial scales: metacommunity scale, i.e. within a locality, and biogeographical scale, i.e. among localities widely scattered along a macroclimatic gradient. As expected, niche-based processes dominated the community assembly at metacommunity scale, while dispersal-based processes played a major role at biogeographical scale for both taxonomical groups. However, we also observed small but significant spatial effects at metacommunity scale and environmental effects at biogeographical scale. We also observed differences in diversity patterns between the two taxonomical groups corresponding to differences in their dispersal modes. Our results thus support the idea of continuity of processes interactively shaping diversity patterns across scales and emphasize the necessity of integration of metacommunity and biogeographical perspectives.

Jaguarundi (Puma yagouaroundi) (Geoffroy, 1803) (Carnivora, Felidae) food habits in a mosaic of Atlantic Rainforest and eucalypt plantations of southeastern Brazil

Food habits of jaguarundi (Puma yagouaroundi) (Geoffroy, 1803) (Carnivora, Felidae) were studied between November 2000 and November 2001, in a 24.9 km² area of secondary Atlantic Rainforest and eucalypt plantation, in the Serra de Paranapiacaba, São Paulo State, Brazil. Analyses of 26 fecal and regurgitate samples, obtained over a stretch of 570.1 km, showed the consumption of 19 prey items and 74 prey occurrences. Small mammals were the most frequent food item (42.5%), followed by birds (21%), reptiles (14%) and medium-sized mammals (3%). The percent occurrence (PO) suggests that the diet consisted mainly of small rodents (30%) and birds (21%). We recorded for the first time the predation of Viperidae snakes by P. yagouaroundi. Although having a large list of items and range of dietary niche breadths (Bsta = 0.76), our data show that jaguarundi prey mainly on small vertebrates (mammals, birds or reptiles), and even in tall tropical forests or eucalypt plantations, it preys mostly on animals that come to, or live on, the ground.

Emprego de regras de associação para extração de padrões mercadológicos de touros Nelore com avaliação genética

Objetivou-se com este trabalho utilizar regras de associação para identificar forças de mercado que regem a comercialização de touros com avaliação genética pelo programa Nelore Brasil. Essas regras permitem evidenciar padrões implícitos nas transações de grandes bases de dados, indicando causas e efeitos determinantes da oferta e comercialização de touros. Na análise foram considerados 19.736 registros de touros comercializados, 17 fazendas e 15 atributos referentes às diferenças esperadas nas progênies dos reprodutores, local e época da venda. Utilizou-se um sistema com interface gráfica usuário-dirigido que permite geração e seleção interativa de regras de associação. Análise de Pareto foi aplicada para as três medidas objetivas (suporte, confiança e lift) que acompanham cada uma das regras de associação, para validação das mesmas. Foram geradas 2.667 regras de associação, 164 consideradas úteis pelo usuário e 107 válidas para lift ≥ 1,0505. As fazendas participantes do programa Nelore Brasil apresentam especializações na oferta de touros, segundo características para habilidade materna, ganho de peso, fertilidade, precocidade sexual, longevidade, rendimento e terminação de carcaça. Os perfis genéticos dos touros são diferentes para as variedades padrão e mocho. Algumas regiões brasileiras são nichos de mercado para touros sem registro genealógico. A análise de evolução de mercado sugere que o mérito genético total, índice oficial do programa Nelore Brasil, tornou-se um importante índice para comercialização dos touros. Com o uso das regras de associação, foi possível descobrir forças do mercado e identificar combinações de atributos genéticos, geográficos e temporais que determinam a comercialização de touros no programa Nelore Brasil.

Sub-telomere directed gene expression during initiation of invasive aspergillosis

Aspergillus fumigatus is a common mould whose spores are a component of the normal airborne flora. Immune dysfunction permits developmental growth of inhaled spores in the human lung causing aspergillosis, a significant threat to human health in the form of allergic, and life-threatening invasive infections. The success of A. fumigatus as a pathogen is unique among close phylogenetic relatives and is poorly characterised at the molecular level. Recent genome sequencing of several Aspergillus species provides an exceptional opportunity to analyse fungal virulence attributes within a genomic and evolutionary context. To identify genes preferentially expressed during adaptation to the mammalian host niche, we generated multiple gene expression profiles from minute samplings of A. fumigatus germlings during initiation of murine infection. They reveal a highly co-ordinated A. fumigatus gene expression programme, governing metabolic and physiological adaptation, which allows the organism to prosper within the mammalian niche. As functions of phylogenetic conservation and genetic locus, 28% and 30%, respectively, of the A. fumigatus subtelomeric and lineage-specific gene repertoires are induced relative to laboratory culture, and physically clustered genes including loci directing pseurotin, gliotoxin and siderophore biosyntheses are a prominent feature. Locationally biased A. fumigatus gene expression is not prompted by in vitro iron limitation, acid, alkaline, anaerobic or oxidative stress. However, subtelomeric gene expression is favoured following ex vivo neutrophil exposure and in comparative analyses of richly and poorly nourished laboratory cultured germlings. We found remarkable concordance between the A. fumigatus host-adaptation transcriptome and those resulting from in vitro iron depletion, alkaline shift, nitrogen starvation and loss of the methyltransferase LaeA. This first transcriptional snapshot of a fungal genome during initiation of mammalian infection provides the global perspective required to direct much-needed diagnostic and therapeutic strategies and reveals genome organisation and subtelomeric diversity as potential driving forces in the evolution of pathogenicity in the genus Aspergillus.