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  • 1
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    Reply to 'Sources of uncertainties in cod distribution models' (2015)
    Springer Nature
    Details
    Publication Date: 2015-08-22
    Description: Nature Climate Change 5 790 doi: 10.1038/nclimate2762
    Print ISSN: 1758-678X
    Electronic ISSN: 1758-6798
    Topics: Geosciences
    Published by Springer Nature
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  • 2
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    Quaternary coral reef refugia preserved fish diversity (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-05-31
    Description: The most prominent pattern in global marine biogeography is the biodiversity peak in the Indo-Australian Archipelago. Yet the processes that underpin this pattern are still actively debated. By reconstructing global marine paleoenvironments over the past 3 million years on the basis of sediment cores, we assessed the extent to which Quaternary climate fluctuations can explain global variation in current reef fish richness. Comparing global historical coral reef habitat availability with the present-day distribution of 6316 reef fish species, we find that distance from stable coral reef habitats during historical periods of habitat loss explains 62% of the variation in fish richness, outweighing present-day environmental factors. Our results highlight the importance of habitat persistence during periods of climate change for preserving marine biodiversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pellissier, Loic -- Leprieur, Fabien -- Parravicini, Valeriano -- Cowman, Peter F -- Kulbicki, Michel -- Litsios, Glenn -- Olsen, Steffen M -- Wisz, Mary S -- Bellwood, David R -- Mouillot, David -- New York, N.Y. -- Science. 2014 May 30;344(6187):1016-9. doi: 10.1126/science.1249853.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Fribourg, Department of Biology, Chemin du Musee 10, CH-1700 Fribourg, Switzerland. Department of Bioscience, Aarhus University, 8000 C Aarhus, Denmark. ; Laboratoire Ecologie des Systemes Marins Cotiers UMR 5119, CNRS, Institut de Recherche pour le Developpement (IRD), Institut Francais de Recherche pour l'Exploitation de la Mer, UM2, UM1, cc 093, Place E. Bataillon, FR-34095 Montpellier Cedex 5, France. ; IRD, UR 227 CoReUs, LABEX (Laboratoire d'Excellence) Corail, Laboratoire Arago, Boite Postale 44, FR-66651 Banyuls/mer, France. CESAB (Centre de Synthese et d'Analyse sur la Biodiversite)-FRB (Fondation pour la Recherche sur la Biodiversite), Immeuble Henri Poincare, Domaine du Petit Arbois, FR-13857 Aix-en-Provence cedex 3, France. ; Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia. ; IRD, UR 227 CoReUs, LABEX (Laboratoire d'Excellence) Corail, Laboratoire Arago, Boite Postale 44, FR-66651 Banyuls/mer, France. ; Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015 Lausanne, Switzerland. Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland. ; Center for Ocean and Ice, Danish Meteorological Institute, Lyngbyvej 100, 2100 Copenhagen, Denmark. ; Department of Bioscience, Aarhus University, 8000 C Aarhus, Denmark. Department of Ecology and Environment, DHI Water and Environment, 2970 Horsholm, Denmark. ; Australian Research Council Centre of Excellence for Coral Reef Studies, and School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811, Australia. ; Laboratoire Ecologie des Systemes Marins Cotiers UMR 5119, CNRS, Institut de Recherche pour le Developpement (IRD), Institut Francais de Recherche pour l'Exploitation de la Mer, UM2, UM1, cc 093, Place E. Bataillon, FR-34095 Montpellier Cedex 5, France. Australian Research Council Centre of Excellence for Coral Reef Studies, and School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811, Australia. david.mouillot@univ-montp2.fr.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24876495" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Australia ; *Biodiversity ; *Climate Change ; *Conservation of Natural Resources ; *Coral Reefs ; *Fishes
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Arctic warming will promote Atlantic–Pacific fish interchange (2015)
    Springer Nature
    Details
    Publication Date: 2015-02-26
    Description: Potential interchange between north Atlantic and north Pacific fish communities is modelled for future Arctic conditions under climate change. Nature Climate Change 5 261 doi: 10.1038/nclimate2500
    Print ISSN: 1758-678X
    Electronic ISSN: 1758-6798
    Topics: Geosciences
    Published by Springer Nature
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  • 4
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    Gene therapy into photoreceptors and Muller glial cells restores retinal structure and function in CRB1 retinitis pigmentosa mouse models (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-09
    Description: Mutations in the Crumbs-homologue-1 ( CRB1 ) gene lead to severe recessive inherited retinal dystrophies. Gene transfer therapy is the most promising cure for retinal dystrophies and has primarily been applied for recessive null conditions via a viral gene expression vector transferring a cDNA encoding an enzyme or channel protein, and targeting expression to one cell type. Therapy for the human CRB1 disease will be more complex, as CRB1 is a structural and signaling transmembrane protein present in three cell classes: Müller glia, cone and rod photoreceptors. In this study, we applied CRB1 and CRB2 gene therapy vectors in Crb1 -retinitis pigmentosa mouse models at mid-stage disease. We tested if CRB expression restricted to Müller glial cells or photoreceptors or co-expression in both is required to recover retinal function. We show that targeting both Müller glial cells and photoreceptors with CRB2 ameliorated retinal function and structure in Crb1 mouse models. Surprisingly, targeting a single cell type or all cell types with CRB1 reduced retinal function. We show here the first pre-clinical studies for CRB1 -related eye disorders using CRB2 vectors and initial elucidation of the cellular mechanisms underlying CRB1 function.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    Generalized food-deceptive orchid species flower earlier and occur at lower altitudes than rewarding ones (2011)
    Oxford University Press
    Details
    Publication Date: 2011-11-24
    Description: Aims Food-deceptive pollination, in which plants do not offer any food reward to their pollinators, is common within the Orchidaceae. As food-deceptive orchids are poorer competitors for pollinator visitation than rewarding orchids, their occurrence in a given habitat may be more constrained than that of rewarding orchids. In particular, the success of deceptive orchids strongly relies on several biotic factors such as interactions with co-flowering rewarding species and pollinators, which may vary with altitude and over time. Our study compares generalized food-deceptive (i.e. excluding sexually deceptive) and rewarding orchids to test whether (i) deceptive orchids flower earlier compared to their rewarding counterparts and whether (ii) the relative occurrence of deceptive orchids decreases with increasing altitude. Methods To compare the flowering phenology of rewarding and deceptive orchids, we analysed data compiled from the literature at the species level over the occidental Palaearctic area. Since flowering phenology can be constrained by the latitudinal distribution of the species and by their phylogenetic relationships, we accounted for these factors in our analysis. To compare the altitudinal distribution of rewarding and deceptive orchids, we used field observations made over the entire Swiss territory and over two Swiss mountain ranges. Important Findings We found that deceptive orchid species start flowering earlier than rewarding orchids do, which is in accordance with the hypotheses of exploitation of naive pollinators and/or avoidance of competition with rewarding co-occurring species. Also, the relative frequency of deceptive orchids decreases with altitude, suggesting that deception may be less profitable at high compared to low altitude.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Very high resolution environmental predictors in species distribution models: Moving beyond topography? (2014)
    Sage
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    Publication Date: 2014-02-20
    Description: Recent advances in remote sensing technologies have facilitated the generation of very high resolution (VHR) environmental data. Exploratory studies suggested that, if used in species distribution models (SDMs), these data should enable modelling species’ micro-habitats and allow improving predictions for fine-scale biodiversity management. In the present study, we tested the influence, in SDMs, of predictors derived from a VHR digital elevation model (DEM) by comparing the predictive power of models for 239 plant species and their assemblages fitted at six different resolutions in the Swiss Alps. We also tested whether changes of the model quality for a species is related to its functional and ecological characteristics. Refining the resolution only contributed to slight improvement of the models for more than half of the examined species, with the best results obtained at 5 m, but no significant improvement was observed, on average, across all species. Contrary to our expectations, we could not consistently correlate the changes in model performance with species characteristics such as vegetation height. Temperature, the most important variable in the SDMs across the different resolutions, did not contribute any substantial improvement. Our results suggest that improving resolution of topographic data only is not sufficient to improve SDM predictions – and therefore local management – compared to previously used resolutions (here 25 and 100 m). More effort should be dedicated now to conduct finer-scale in-situ environmental measurements (e.g. for temperature, moisture, snow) to obtain improved environmental measurements for fine-scale species mapping and management.
    Print ISSN: 0309-1333
    Electronic ISSN: 1477-0296
    Topics: Geography
    Published by Sage
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  • 7
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    CRB2 acts as a modifying factor of CRB1-related retinal dystrophies in mice (2014)
    Oxford University Press
    Details
    Publication Date: 2014-06-21
    Description: Mutations in the CRB1 gene lead to retinal dystrophies ranging from Leber congenital amaurosis (LCA) to early-onset retinitis pigmentosa (RP), due to developmental defects or loss of adhesion between photoreceptors and Müller glia cells, respectively. Whereas over 150 mutations have been found, no clear genotype–phenotype correlation has been established. Mouse Crb1 knockout retinas show a mild phenotype limited to the inferior quadrant, whereas Crb2 knockout retinas display a severe degeneration throughout the retina mimicking the phenotype observed in RP patients associated with CRB1 mutations. Crb1Crb2 double mutant retinas have severe developmental defects similar to the phenotype observed in LCA patients associated with CRB1 mutations. Therefore, CRB2 is a candidate modifying gene of human CRB1 -related retinal dystrophy. In this study, we studied the cellular localization of CRB1 and CRB2 in human retina and tested the influence of the Crb2 gene allele on Crb1 -retinal dystrophies in mice. We found that in contrast to mice, in the human retina CRB1 protein was expressed at the subapical region in photoreceptors and Müller glia cells, and CRB2 only in Müller glia cells. Genetic ablation of one allele of Crb2 in heterozygote Crb1 +/– retinas induced a mild retinal phenotype, but in homozygote Crb1 knockout mice lead to an early and severe phenotype limited to the entire inferior retina. Our data provide mechanistic insight for CRB1 -related LCA and RP.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 8
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    Plant functional and phylogenetic turnover correlate with climate and land use in the Western Swiss Alps (2014)
    Oxford University Press
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    Publication Date: 2014-09-19
    Description: Aims Understanding the relative importance of historical and environmental processes in the structure and composition of communities is one of the longest quests in ecological research. Increasingly, researchers are relying on the functional and phylogenetic β-diversity of natural communities to provide concise explanations on the mechanistic basis of community assembly and the drivers of trait variation among species. The present study investigated how plant functional and phylogenetic β-diversity change along key environmental and spatial gradients in the Western Swiss Alps. Methods Using the quadratic diversity measure based on six functional traits—specific leaf area, leaf dry matter content, plant height, leaf carbon content, leaf nitrogen content and leaf carbon to nitrogen content alongside a species-resolved phylogenetic tree—we relate variations in climate, spatial geographic, land use and soil gradients to plant functional and phylogenetic turnover in mountain communities of the Western Swiss Alps. Important Findings Our study highlights two main points. First, climate and land-use factors play an important role in mountain plant community turnover. Second, the overlap between plant functional and phylogenetic turnover along these gradients correlates with the low phylogenetic signal in traits, suggesting that in mountain landscapes, trait lability is likely an important factor in driving plant community assembly. Overall, we demonstrate the importance of climate and land-use factors in plant functional and phylogenetic community turnover and provide valuable complementary insights into understanding patterns of β-diversity along several ecological gradients.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Density-based hierarchical clustering of pyro-sequences on a large scale--the case of fungal ITS1 (2013)
    Oxford University Press
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    Publication Date: 2013-05-16
    Description: Motivation: Analysis of millions of pyro-sequences is currently playing a crucial role in the advance of environmental microbiology. Taxonomy-independent, i.e. unsupervised, clustering of these sequences is essential for the definition of Operational Taxonomic Units. For this application, reproducibility and robustness should be the most sought after qualities, but have thus far largely been overlooked. Results: More than 1 million hyper-variable internal transcribed spacer 1 (ITS1) sequences of fungal origin have been analyzed. The ITS1 sequences were first properly extracted from 454 reads using generalized profiles. Then, otupipe, cd-hit-454, ESPRIT-Tree and DBC454, a new algorithm presented here, were used to analyze the sequences. A numerical assay was developed to measure the reproducibility and robustness of these algorithms. DBC454 was the most robust, closely followed by ESPRIT-Tree. DBC454 features density-based hierarchical clustering, which complements the other methods by providing insights into the structure of the data. Availability: An executable is freely available for non-commercial users at ftp://ftp.vital-it.ch/tools/dbc454 . It is designed to run under MPI on a cluster of 64-bit Linux machines running Red Hat 4.x, or on a multi-core OSX system. Contact: dbc454@vital-it.ch or nicolas.guex@isb-sib.ch
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 10
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    Targeted ablation of Crb2 in photoreceptor cells induces retinitis pigmentosa (2014)
    Oxford University Press
    Details
    Publication Date: 2014-06-10
    Description: In humans, the Crumbs homolog-1 ( CRB1 ) gene is mutated in autosomal recessive Leber congenital amaurosis and early-onset retinitis pigmentosa. In mammals, the Crumbs family is composed of: CRB1, CRB2, CRB3A and CRB3B. Recently, we showed that removal of mouse Crb2 from retinal progenitor cells, and consequent removal from Müller glial and photoreceptor cells, results in severe and progressive retinal degeneration with concomitant loss of retinal function that mimics retinitis pigmentosa due to mutations in the CRB1 gene. Here, we studied the effects of cell-type-specific loss of CRB2 from the developing mouse retina using targeted conditional deletion of Crb2 in photoreceptors or Müller cells. We analyzed the consequences of targeted loss of CRB2 in the adult mouse retina using adeno-associated viral vectors encoding Cre recombinase and short hairpin RNA against Crb2. In vivo retinal imaging by means of optical coherence tomography on retinas lacking CRB2 in photoreceptors showed progressive thinning of the photoreceptor layer and cellular mislocalization. Electroretinogram recordings under scotopic conditions showed severe attenuation of the a-wave, confirming the degeneration of photoreceptors. Retinas lacking CRB2 in developing photoreceptors showed early onset of abnormal lamination, whereas retinas lacking CRB2 in developing Müller cells showed late onset retinal disorganization. Our data suggest that in the developing retina, CRB2 has redundant functions in Müller glial cells, while CRB2 has essential functions in photoreceptors. Our data suggest that short-term loss of CRB2 in adult mouse photoreceptors, but not in Müller glial cells, causes sporadic loss of adhesion between photoreceptors and Müller cells.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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