Manipulating waterbody hydroperiod affects movement behaviour and occupancy dynamics in an amphibian

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Evaluating interspecific niche overlaps in environmental and geographic spaces to assess the value of umbrella species

The concept of umbrella species assumes that concentrating resources on the protection of a single species contributes to the conservation of a suite of species and ecological processes belonging to the same ecosystem. The environmental requirements and geographical distribution of the umbrella species should thus overlap those of the group of targeted species. In western France, the conservation of several large grassland floodplains relies on agri‐environmental schemes targeting one single bird species, the corncrake Crex crex. It is considered as an umbrella species but no real assessment of its effectiveness has been carried out so far. We used a two‐step methodology to assess the potential of the corncrake to act as an umbrella species by estimating niche overlap in the environmental and geographic space between the main ground‐nesting species of the bird community in these grasslands, including the corncrake and four passerines. The five species showed substantial differences in their ecological niches so that their distributions did not perfectly overlap. Overlaps in predicted distributions between pairs of species depended on the threshold used to convert suitability to binary maps. Moreover, the number of species that could be protected by a candidate umbrella species was affected by the overlap criterion of success. Although the corncrake may be used as an umbrella species, it would be outperformed by several passerine species. Our study highlights the potential of using niche overlap to select umbrella species. It also reveals the importance of analysing the sensitivity of outputs when changing thresholds and overlap criteria.     

Markedly increased susceptibility to natural sheep scrapie of transgenic mice expressing ovine prp

The susceptibility of sheep to scrapie is known to involve, as a major determinant, the nature of the prion protein (PrP) allele, with the VRQ allele conferring the highest susceptibility to the disease. Transgenic mice expressing in their brains three different ovine PrP(VRQ)-encoding transgenes under an endogenous PrP-deficient genetic background were established. Nine transgenic (tgOv) lines were selected and challenged with two scrapie field isolates derived from VRQ-homozygous affected sheep. All inoculated mice developed neurological signs associated with a transmissible spongiform encephalopathy (TSE) disease and accumulated a protease-resistant form of PrP (PrPres) in their brains. The incubation duration appeared to be inversely related to the PrP steady-state level in the brain, irrespective of the transgene construct. The survival time for animals from the line expressing the highest level of PrP was reduced by at least 1 year compared to those of two groups of conventional mice. With one isolate, the duration of incubation was as short as 2 months, which is comparable to that observed for the rodent TSE models with the briefest survival times. No survival time reduction was observed upon subpassaging of either isolate, suggesting no need for adaptation of the agent to its new host. Overexpression of the transgene was found not to be required for transmission to be accelerated compared to that observed with wild-type mice. Conversely, transgenic mice overexpressing murine PrP were found to be less susceptible than tgOv lines expressing ovine PrP at physiological levels. These data argue that ovine PrP(VRQ) provided a better substrate for sheep prion replication than did mouse PrP. Altogether, these tgOv mice could be an improved model for experimental studies on natural sheep scrapie.     

A set of primers for length and nucleotide‐substitution polymorphism in chloroplastic DNA of Olea europaea L. (Oleaceae)

Chloroplastic DNA (cpDNA) variation at five microsatellite motifs, two insertion‐deletion sites, and eight nucleotide substitution sites was investigated in the Olea europaea complex. Primers were designed for flanking regions of these sites to amplify short cpDNA regions. They provided polymorphism when polymerase chain reaction (PCR) products from a representative sample of 128 O. europaea individuals were either resolved by size into polyacrylamide gels (length polymorphism) or digested with restriction enzymes (nucleotide‐substitution polymorphism). These polymorphisms serve to distinguish most of the cytoplasmic haplotypes previously recognized. Potential application of these markers in O. europaea includes phylogeography, conservation and germplasm identification, even when using poorly preserved material from herbarium specimens or forensic and archaeological materials.     

Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90–0.99) vs. 0.58 (CI = 0.50–0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA‐based approach has the potential to become the next‐generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.     

On the origin of the invasive olives (Olea europaea L., Oleaceae)

The olive tree (Olea europaea) has successfully invaded several regions in Australia and Pacific islands. Two olive subspecies (subspp. europaea and cuspidata) were first introduced in these areas during the nineteenth century. In the present study, we determine the origin of invasive olives and investigate the importance of historical effects on the genetic diversity of populations. Four invasive populations from Australia and Hawaii were characterized using eight nuclear DNA microsatellites, plastid DNA markers as well as ITS-1 sequences. Based on these data, their genetic similarity with native populations was investigated, and it was determined that East Australian and Hawaiian populations (subsp. cuspidata) have originated from southern Africa while South Australian populations (subsp. europaea) have mostly derived from western or central Mediterranean cultivars. Invasive populations of subsp. cuspidata showed significant loss of genetic diversity in comparison to a putative source population, and a recent bottleneck was evidenced in Hawaii. Conversely, invasive populations of subsp. europaea did not display significant loss of genetic diversity in comparison to a native Mediterranean population. Different histories of invasion were inferred for these two taxa with multiple cultivars introduced restoring gene diversity for europaea and a single successful founder event and sequential introductions to East Australia and then Hawaii for cuspidata. Furthermore, one hybrid (cuspidata x europaea) was identified in East Australia. The importance of hybridizations in the future evolution of the olive invasiveness remains to be investigated.     

Fast assembly of the mitochondrial genome of a plant parasitic nematode (Meloidogyne graminicola) using next generation sequencing

Little is known about the variations of nematode mitogenomes (mtDNA). Sequencing a complete mtDNA using a PCR approach remains a challenge due to frequent genome reorganizations and low sequence similarities between divergent nematode lineages. Here, a genome skimming approach based on HiSeq sequencing (shotgun) was used to assemble de novo the first complete mtDNA sequence of a root-knot nematode (Meloidogyne graminicola). An AT-rich genome (84.3%) of 20,030 bp was obtained with a mean sequencing depth superior to 300. Thirty-six genes were identified with a semi-automated approach. A comparison with a gene map of the M. javanica mitochondrial genome indicates that the gene order is conserved within this nematode lineage. However, deep genome rearrangements were observed when comparing with other species of the superfamily Hoplolaimoidea. Repeat elements of 111 bp and 94 bp were found in a long non-coding region of 7.5 kb, as similarly reported in M. javanica and M. hapla. This study points out the power of next generation sequencing to produce complete mitochondrial genomes, even without a reference sequence, and possibly opening new avenues for species/race identification, phylogenetics and population genetics of nematodes.     

Research of anin vitro model to study the expression of fatty acid-binding proteins in the small intestine

In order to find anin vitro model for studying the regulation of the biosynthesis of the cytoplasmic Fatty Acid-Binding Proteins (FABPc) expressed in the small intestine, Intestinal- and Liver-(I- and L-) FABPc expressions were tested by Northern blotting in 8 normal or cancerous intestinal cell lines from man, mouse and rat and in organ culture of mouse jejunal explants. Neither I- nor L-FABPc mRNA was detected in any cell strains tested except in the highly differentiated human enterocyte-like intestinal cell line Caco-2. In this line, Northern blot analysis revealed a single messenger of about 0.7 kb corresponding to the L-FABPc. A two-fold increase in mRNA L-FABPc occurred in differentiated Caco-2 cells treated for 7 days with 0.05 mM bezafibrate, a peroxisome-proliferating hypolipidemic drug. The lack of I-FABPc messengers in this strain led us to seek anotherin vitro model. I- and L-FABPc messengers were found using an organ culture of mouse jejunal explants. A clear rise in I- and, especially, L-FABPc mRNA levels occurred 6 and 24 hr after the addition of 0.05 mM bezafibrate in the culture medium. Our results demonstrate, to our knowledge for the first time, that: 1) organ culture of intestinal explants provides a useful model for studyingin vitro the simultaneous regulation of I- and L-FABPc expressions, 2) biosynthesis of L-FABPc may be exploredin vitro using the Caco-2 cell line, 3) fibrate peroxisome-proliferators exert a direct effect on I- and L-FABPc expression in the small intestine, 4) L-FABPc expression seems to be more sensitive to fibrate action than is I-FABPc expression.Abbreviations I-FABPc cytosolic Intestinal Fatty Acid-Binding Protein - L-FABPc cytosolic Liver Fatty Acid-Binding Protein - bp base pair - EDTA Ethylenediamine Tetraacetic Acid - DMSO Dimethyl Sulfoxide - BSA Bovine Serum Albumin - DMEM Dulbecco's Modified Eagle's Medium - HBSS Hanks Balanced Salt Solution