47 research outputs found
Freshwater fish biomonitoring in the Alpine area using eDNA metabarcoding
No full textMany freshwater fish are experiencing critical population declines with risk of local or global extinction
because of intense anthropogenic pressure and this can have serious consequences on freshwater
ecosystem functioning and diversity. Current fish monitoring techniques for large rivers and lakes, however,
have known shortcomings. Within the Water Framework Directive (WFD, 2000/60/EC) environmental DNA
(eDNA) based methods are proving to be a promising tool for freshwater fish biodiversity assessment.
Within the EU project Eco-AlpsWater, advanced high throughput sequencing (HTS) techniques are used to
improve the traditional WFD monitoring approaches by using environmental DNA (eDNA) collected in
Alpine waterbodies. An eDNA metabarcoding approach has been evaluated by using mock samples within
an intercalibration test, and has been used to study fish biodiversity of eight lakes and six rivers of the
Alpine region including four EC countries (Austria, France, Italy, Slovenia) and Switzerland. This approach,
based on HTS sequencing of a section of the mitochondrial 12S rRNA, allowed to assess freshwater fish
biodiversity and their distribution in the different habitats. These data represent the first attempt to
provide a comprehensive description of freshwater fish diversity confirming the applicability of eDNA
metabarcoding analyses for fish biomonitoring in Alpine and perialpine lakes and rivers
eDNA metabarcoding biodiversity of freshwater fish in the Alpine area
No full textEnvironmental DNA (eDNA) based methods are proving to be a promising tool for freshwater fish biodiversity
assessment in Europe within the Water Framework Directive (WFD, 2000/60/EC) especially for large rivers
and lakes where current fish monitoring techniques have known shortcomings. Many freshwater fish are
experiencing critical population declines with risk of local or global extinction because of intense
anthropogenic pressure and this can have serious consequences on freshwater ecosystem functioning and
diversity. Within the EU project Eco-AlpsWater, advanced high throughput sequencing (HTS) techniques are
used to improve the traditional WFD monitoring approaches by using environmental DNA (eDNA) collected
in Alpine waterbodies. An eDNA metabarcoding approach specifically designed to measure freshwater fish
biodiversity in Alpine lakes and rivers has been extensively evaluated by using mock samples within an
intercalibration test. This eDNA method was validated and used to study fish biodiversity of eight lakes and
six rivers of the Alpine region including four EC countries (Austria, France, Italy, Slovenia) and Switzerland.
More in detail, this metabarcoding approach, based on HTS sequencing of a section of the 12S rRNA gene,
was used to assess freshwater fish biodiversity and their distribution in the different habitats. These data
represent the first attempt to provide a comprehensive description of freshwater fish diversity in different
ecosystems of the Alpine area confirming the applicability of eDNA metabarcoding analyses for the
biomonitoring of fish inhabiting Alpine and perialpine lakes and rivers
Experimental study on the utilisation of substitute food resources by parasitic wasps and syrphid flies attacking the rosy apple aphid Dysaphis plantaginea (Passerini) (Homoptera :Aphididae)
No full textThe rosy apple aphid Dysaphis plantaginea (Passerini) (Homoptera: Aphididae) is the most serious pest apple aphid in view of the scale of damages inflicted to the fruits by a small number of individuals. Although numerous natural enemies have been associated with D. plantaginea, they are unable to halt infestations soon enough in most commercial apple orchards obliging fruit growers to control it chemically to prevent severe economic losses. In order to reinforce the contribution of indigenous aphidophaga in regulating rosy apple aphids, the use of insectary plants selected to support two groups of specialist aphid antagonists, notably aphid parasitoids and aphidophagous monovoltine syrphids, was investigated. 1. A first step consisted in selecting appropriate plant species. The rowan tree Sorbus aucuparia L. and the common elder Sambucus nigra L. were selected for their ability to support substitute aphids for the rosy apple aphid parasitoid E. persicae Froggatt (Hymenoptera: Braconidae, Aphidiinae) and monovotine syrphids (Diptera: Syrphidae) respectively. 2. Next, trials were conducted to induce substitute aphid infestations on their host plants by introducing eggs of Dysaphis sorbi Kaltenbach on rowan and small colonies of Aphis sambuci L. on elder. The resulting aphid populations which developed on their respective host plants in spring proved to be exploited by the natural enemies expected, i.e. E. persicae and monovoltine syrphids of the genus Epistrophe. Besides, diapause mummies of E. persicae and diapausing last-instar Epistrophe larvac were recorded on rowan and in the elder litter respectively, indicating the successful settlement of the antagonists in the orchard environment. A complementary investigation devoted to syrphid adults indicated that females of all species recorded ovipositing on the eider shrubs, including Epistrophe spp. had consumed a large majority of apple pollen grains as a protein source required for egg maturation. 3. To comfort our choice in the two groups of aphidophaga considered, a study dedicated to their respective phenology versus the one of D. plantaginea showed that they could both potentially halt rosy apple aphid infestations by attacking the aphids while the latter still occupied the primary, fundatrix-induced rosette leaf colonies, i.e. a critical moment in rosy apple aphid control. 4. Finally, marking methods were tested to label E. persicae internally and the egg load of gravid syrphids. These trials were intended to pave the way towards future mark-release-recapture experiments aimed to evaluate the antagonists’ activity range and thus strategically position the insectary plants for optimal aphid biological control in the whole orchard. The first step of new approach in the biological control of D. plantaginea has been set with this study. Its originality lies in the induction of economically indifferent aphid infestations on selected plants introduced in the orchard to encourage well-targeted groups of specialist aphid antagonists. Further trials are still needed to validate the field efficacy of the insectary plant systems developed and evaluate their possible integration within the whole array of pest management tools in both organic and integrated apple production.Doctorat en sciences, Spécialisation biologie animaleinfo:eu-repo/semantics/nonPublishe
Data from: Sex-specific effects of inbreeding in juvenile brown trout
No full text<p>Inbreeding depression, i.e., the reduction of health and vigour in individuals with high inbreeding coefficients, is expected to increase with environmental, social, or physiological stress. It has therefore been predicted that sexual selection and the associated stress usually lead to higher inbreeding depression in males than in females. However, sex-specific differences in life history may reverse that pattern during certain developmental stages. In some salmonids, for example, female juveniles start developing their gonads earlier than males who instead grow faster. We tested whether the sexes are differently affected by inbreeding during that time. To study the effects of inbreeding coefficients that may be typical for natural populations of brown trout (<em>Salmo trutta</em>), and also to control for potentially confounding maternal or paternal effects, we sampled males and females from the wild, used their gametes in a block-wise full-factorial breeding design to produce 60 full-sib families, released the offspring as yolk-sac larvae into the wild, sampled them 6 months later, identified their genetic sex, and used microsatellites to assign them to their parents. We used whole-genome resequencing to calculate the kinship coefficients for each breeding pair and hence the expected average inbreeding coefficient per family. Juvenile growth could be predicted from these expected inbreeding coefficients and the genetic sex: Females reached lower body sizes with increasing inbreeding coefficient, while no such link could be found in males. This sex-specific inbreeding depression led to the overall pattern that females were on average smaller than males by the end of their first summer.</p><p>Funding provided by: Swiss National Science Foundation<br>Crossref Funder Registry ID: https://ror.org/00yjd3n13<br>Award Number: 31003A_159579</p><p>Funding provided by: Swiss National Science Foundation<br>Crossref Funder Registry ID: https://ror.org/00yjd3n13<br>Award Number: 31003A_182265</p><p>See methods in: Bylemans, J., Marques da Cunha, L., Sarmiento Cabello, S., Nusbaumer, D., Uppal, A. and Wedekind, C. (2024) Sex-specific effects of inbreeding in juvenile brown trout. (Molecular Ecology).</p>
Data from: Sex-specific effects of inbreeding in juvenile brown trout
No full text<p>Inbreeding depression, i.e., the reduction of health and vigour in individuals with high inbreeding coefficients, is expected to increase with environmental, social, or physiological stress. It has therefore been predicted that sexual selection and the associated stress usually lead to higher inbreeding depression in males than in females. However, sex-specific differences in life history may reverse that pattern during certain developmental stages. In some salmonids, for example, female juveniles start developing their gonads earlier than males who instead grow faster. We tested whether the sexes are differently affected by inbreeding during that time. To study the effects of inbreeding coefficients that may be typical for natural populations of brown trout (<em>Salmo trutta</em>), and also to control for potentially confounding maternal or paternal effects, we sampled males and females from the wild, used their gametes in a block-wise full-factorial breeding design to produce 60 full-sib families, released the offspring as yolk-sac larvae into the wild, sampled them 6 months later, identified their genetic sex, and used microsatellites to assign them to their parents. We used whole-genome resequencing to calculate the kinship coefficients for each breeding pair and hence the expected average inbreeding coefficient per family. Juvenile growth could be predicted from these expected inbreeding coefficients and the genetic sex: Females reached lower body sizes with increasing inbreeding coefficient, while no such link could be found in males. This sex-specific inbreeding depression led to the overall pattern that females were on average smaller than males by the end of their first summer.</p><p>Funding provided by: Swiss National Science Foundation<br>Crossref Funder Registry ID: https://ror.org/00yjd3n13<br>Award Number: 31003A_159579</p><p>Funding provided by: Swiss National Science Foundation<br>Crossref Funder Registry ID: https://ror.org/00yjd3n13<br>Award Number: 31003A_182265</p><p>See methods in: Bylemans, J., Marques da Cunha, L., Sarmiento Cabello, S., Nusbaumer, D., Uppal, A. and Wedekind, C. (2024) Sex-specific effects of inbreeding in juvenile brown trout. (Molecular Ecology).</p>
rCRUX Generated MarVer3 Marine Mammal Reference Database
No full textrCRUX generated reference database using NCBI nt blast database downloaded in December 2022.
Primer Name: MarVer3 Marine Mammal
Gene: 16S
Length of Target: 232-274
get_seeds_local() minimum length: 160
get_seeds_local() maximum length: 345
blast_seeds() minimum length: 124
blast_seeds() maximum length: 309
max_to_blast: 100
Forward Sequence (5'-3'): AGACGAGAAGACCCTRTG
Reverse Sequence (5'-3'): GGATTGCGCTGTTATCCC
Reference: Valsecchi, E., Bylemans, J., Goodman, S. J., Lombardi, R., Carr, I., Castellano, L., ... & Galli, P. (2020). Novel universal primers for metabarcoding environmental DNA surveys of marine mammals and other marine vertebrates. Environmental DNA, 2(4), 460-476. https://doi.org/10.1002/edn3.72
We chose default rCRUX parameters for get_blast_seeds() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for blast_seeds() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'
Innovative approaches for the evaluation of the ecological conditions and ecosystems functionality of alpine lakes and rivers: the Interreg Alpine Space project Eco-AlpsWater
No full textEco-AlpsWater is a project co-financed by the European Regional Development Fund (ERDF) through the Interreg “Alpine Space” programme. The aim of the project is to improve the traditional water monitoring approaches utilized in the Alpine region (Water Framework Directive-WFD in EU countries and Water Protection Ordinance-WPO in Switzerland) with innovative technologies, providing solid knowledge to support lake and river management plans. The new approach will make use of Next Generation Sequencing (NGS) techniques to analyse environmental DNA (eDNA) extracted from samples collected in lakes and rivers. These new techniques, based on the amplification and analysis of millions of DNA sequences, allow rapid and low cost identification of aquatic organisms. The new generation monitoring will permit to carry out one of the most extensive census of lakes and rivers biodiversity of the Alpine region based on the analysis of hundreds of samples collected in over 50 water bodies. The investigations will focus on the study of bacteria and cyanobacteria, phytoplankton, periphytic communities (including diatoms) and fish. The collected data will allow to identify the areas at risk of toxic cyanobacteria, pathogenic bacteria and alien or potentially invasive organisms. The project, started in 2018 and operational until April 2021, involves 12 partners belonging to 6 countries in the Alpine region (Austria, France, Germany, Italy, Slovenia and Switzerland). The research, started in the first months of 2019, in the Italian context will in particular evaluate the ecological quality of two key environments representative of the great lakes (Garda) and rivers (Adige) south of the Alps.
During the summer months, the survey will be extended to a greater number of lakes and rivers, including other great lakes of the network LTER IT08-Subalpine lakes, small lakes (for example Ledro, Caldaro, Ragogna) and rivers
Data from: Sex-specific life history affected by stocking in juvenile brown trout
No full textSalmonids are a socioeconomically and ecologically important group of fish that are often managed by stocking. Little is known about potential sex-specific effects of stocking, but recent studies found that the sexes differ in their stress tolerances already at late embryonic stage, i.e., before hatchery-born larvae are released into the wild and long before morphological gonad formation. It has also been speculated that sex-specific life histories can affect juvenile growth and mortality, and that a resulting sex-biassed demography can reduce population growth. Here we test whether juvenile brown trout (Salmo trutta) show sex-specific life histories and whether such sex effects differ in hatchery- and wild-born fish. We modified a genetic sexing protocol to reduce false assignment rates and used it to study the timing of sex differentiation in a laboratory setting, and in a large-scale field experiment to study growth and mortality of hatchery and wild-born fish in different environments. We found no sex-specific mortality in any of the environments we studied. However, females started sex differentiation earlier than males, and while growth rates were similar in the laboratory, they differed significantly in the field depending on location and origin of fish. Overall, hatchery-born males grew larger than hatchery-born females while wild-born fish showed the reverse pattern. Whether males or females grew larger was location-specific. We conclude that juvenile brown trout show sex-specific growth that is affected by stocking and by other environmental factors that remain to be identified.Funding provided by: Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen ForschungCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001711Award Number: 31003A_159579Funding provided by: Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen ForschungCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001711Award Number: 31003A_182265Funding provided by: Federal Office for the EnvironmentCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100003338Award Number:See Methods in Palejowski H., Bylemans J., Ammann V., Marques da Cunha L., Nusbaumer D., Castro I., Uppal A., Mobley K.B., Knörr S., Wedekind C. 2022 Sex-specific life history affected by stocking in juvenile brown trout. Front. Ecol. Evol. 10, 869925. (doi:10.3389/fevo.2022.869925)
Evaluating genetic traceability methods for captive-bred marine fish and their applications in fisheries management and wildlife forensics
No full textGrowing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in aquaculture production. Consequently, more captive-bred fish are released into the wild through accidental escape or deliberate releases. The increased mixing of captive-bred and wild fish may affect the ecological and/or genetic integrity of wild fish populations. Unambiguous identification tools for captive-bred fish will be highly valuable to manage risks (fisheries management) and tracing of escapees and seafood products (wildlife forensics). Using single nucleotide polymorphism (SNP) data from captive-bred and wild populations of Atlantic cod Gadus morhua L. and sole Solea solea L., we explored the efficiency of population and parentage assignment techniques for the identification and tracing of captive-bred fish. Simulated and empirical data were used to correct for stochastic genetic effects. Overall, parentage assignment performed well when a large effective population size characterized the broodstock and escapees originated from early generations of captive breeding. Consequently, parentage assignments are particularly useful from a fisheries management perspective to monitor the effects of deliberate releases of captive-bred fish on wild populations. Population assignment proved to be more efficient after several generations of captive breeding, which makes it a useful method in forensic applications for well-established aquaculture species. We suggest the implementation of a case-by-case strategy when choosing the best method
