Papers by Alice Valentini
PloS one, 2014
Mate choice is thought to contribute to the maintenance of the spectacularly high polymorphism of... more Mate choice is thought to contribute to the maintenance of the spectacularly high polymorphism of the Major Histocompatibility Complex (MHC) genes, along with balancing selection from parasites, but the relative contribution of the former mechanism is debated. Here, we investigated the association between male MHC genotype and mating success in the brown bear. We analysed fragments of sequences coding for the peptide-binding region of the highly polymorphic MHC class I and class II DRB genes, while controlling for genome-wide effects using a panel of 18 microsatellite markers. Male mating success did not depend on the number of alleles shared with the female or amino-acid distance between potential mates at either locus. Furthermore, we found no indication of female mating preferences for MHC similarity being contingent on the number of alleles the females carried. Finally, we found no significant association between the number of MHC alleles a male carried and his mating success. T...
Trends in Ecology & Evolution, 2009
Nucleic Acids Research, 2007
DNA barcoding should provide rapid, accurate and automatable species identifications by using a s... more DNA barcoding should provide rapid, accurate and automatable species identifications by using a standardized DNA region as a tag. Based on sequences available in GenBank and sequences produced for this study, we evaluated the resolution power of the whole chloroplast trnL (UAA) intron (254-767 bp) and of a shorter fragment of this intron (the P6 loop, 10-143 bp) amplified with highly conserved primers. The main limitation of the whole trnL intron for DNA barcoding remains its relatively low resolution (67.3% of the species from GenBank unambiguously identified). The resolution of the P6 loop is lower (19.5% identified) but remains higher than those of existing alternative systems. The resolution is much higher in specific contexts such as species originating from a single ecosystem, or commonly eaten plants. Despite the relatively low resolution, the whole trnL intron and its P6 loop have many advantages: the primers are highly conserved, and the amplification system is very robust. The P6 loop can even be amplified when using highly degraded DNA from processed food or from permafrost samples, and has the potential to be extensively used in food industry, in forensic science, in diet analyses based on feces and in ancient DNA studies.
Molecular Ecology Resources, 2009
The development of DNA barcoding (species identification using a standardized DNA sequence), and ... more The development of DNA barcoding (species identification using a standardized DNA sequence), and the availability of recent DNA sequencing techniques offer new possibilities in diet analysis. DNA fragments shorter than 100-150 bp remain in a much higher proportion in degraded DNA samples and can be recovered from faeces. As a consequence, by using universal primers that amplify a very short but informative DNA fragment, it is possible to reliably identify the plant taxon that has been eaten. According to our experience and using this identification system, about 50% of the taxa can be identified to species using the trnL approach, that is, using the P6 loop of the chloroplast trnL (UAA) intron. We demonstrated that this new method is fast, simple to implement, and very robust. It can be applied for diet analyses of a wide range of phytophagous species at large scales. We also demonstrated that our approach is efficient for mammals, birds, insects and molluscs. This method opens new perspectives in ecology, not only by allowing large-scale studies on diet, but also by enhancing studies on resource partitioning among competing species, and describing food webs in ecosystems.
Journal of Applied Ecology, 2014
1. The introduction of non-native species is a major threat to biodiversity. While eradication pr... more 1. The introduction of non-native species is a major threat to biodiversity. While eradication programs of well-established invaders are costly and hazardous for non-target species, the early detection of a non-native species at low density is critical for preventing biological invasions in recipient ecosystems. Recent studies reveal that environmental DNA (eDNA) is a powerful tool for detecting target species in aquatic ecosystems, but these studies focus mostly on fish and amphibians. 2. We examine the reliability of using eDNA to detect the presence of an invasive freshwater crustacean species, the red swamp crayfish Procambarus clarkii. Species-specific primers and probes were designed; their specificity was tested using in silico PCR simulations and against tissues of other crayfish species. Limits of detection and quantification were specified for the target DNA sequence by means of quantitative PCR amplifications on dilution series of known amount of P. clarkii DNA. 3. The method was applied to water samples collected in 158 ponds in a French Nature Park, and results were compared to a traditional method using food-baited funnel traps. Environmental DNA had a better detection efficiency but predominantly led to divergent results compared with the trapping method. While habitat features partly explained the failure of crayfish detection by trapping, detection by eDNA was problematic at low crayfish abundances. When P. clarkii was detected, the estimated concentrations of crayfish DNA in water samples were always below the limit of quantification for the target DNA sequence. 4. Synthesis and applications. The combination of environmental DNA (eDNA) and conventional trapping methods is recommended to monitor the invasion by P. clarkii in small waterbodies such as ponds. However, the risk of mortality for non-target species, notably amphibians, has to be carefully evaluated before large-scale deployment of traps. Contrary to fish and amphibians, a low amount of extracellular DNA in water is suspected to be the major limitation for crayfish detection by molecular approaches. Current advancements in PCR technology, together with optimization of the water sampling method, promise upcoming developments of eDNA detection for aquatic invertebrate species.
Frontiers in Zoology, 2009
In order to understand the role of herbivores in trophic webs, it is essential to know what they ... more In order to understand the role of herbivores in trophic webs, it is essential to know what they feed on. Diet analysis is, however, a challenge in many small herbivores with a secretive life style. In this paper, we compare novel (high-throughput pyrosequencing) DNA barcoding technology for plant mixture with traditional microhistological method. We analysed stomach contents of two ecologically important subarctic vole species, Microtus oeconomus and Myodes rufocanus, with the two methods. DNA barcoding was conducted using the P6-loop of the chloroplast trnL (UAA) intron.
Molecular ecology, Jan 19, 2015
Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for a... more 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 into the environment. In this study, we tested if 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) versus 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89% of ...
Uploads
Papers by Alice Valentini