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Journal: Molecular Ecology Resources

Abbreviation

Mol. Ecol. Resour.

Publisher

Wiley-Blackwell

Journal Volumes

ISSN

1755-098X
1755-0998

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Publications1 - 10 of 29
  • Scanning amplicons with CRISPR-Dx detects endangered amphibians in environmental DNA
    Item type: Journal Article
    Leugger, Flurin; Schmidlin, Michel; Lüthi, Martina; et al. (2024)
    Molecular Ecology Resources
    More efficient methods for extensive biodiversity monitoring are required to support rapid measures to address the biodiversity crisis. While environmental DNA (eDNA) metabarcoding and quantitative PCR (qPCR) methods offer advantages over traditional monitoring approaches, their large-scale application is limited by the time and labour required for developing assays and/or for analysis. CRISPR (clustered regularly interspaced short palindromic repeats) diagnostic technologies (Dx) may overcome some of these limitations, but they have been used solely with species-specific primers, restricting their versatility for biodiversity monitoring. Here, we demonstrate the feasibility of designing species-specific CRISPR-Dx assays in silico within a short metabarcoding fragment using a general primer set, a methodology we term 'ampliscanning', for 18 of the 22 amphibian species in Switzerland. We sub-selected nine species, including three classified as regionally endangered, to test the methodology using eDNA sampled from ponds at nine sites. We compared the ampliscanning detections to data from traditional monitoring at these sites. Ampliscanning was successful at detecting target species with different prevalences across the landscape. With only one visit, we detected more species per site than three traditional monitoring visits (visual and acoustic detections by trained experts), in particular more elusive species and previously undocumented but expected populations. Ampliscanning detected 25 species/site combinations compared to 12 with traditional monitoring. Sensitivity analyses showed that larger numbers of field visits and PCR replicates are more important for reliable detection than many technical replicates at the CRISPR-Dx assay level. Given the reduced sampling and analysis effort, our results highlight the benefits of eDNA and CRISPR-Dx combined with universal primers for large-scale monitoring of multiple endangered species across landscapes to inform conservation measures.
  • Novel microsatellite DNA loci for Bombus terrestris (Linnaeus, 1758)
    Item type: Journal Article
    Stolle, Eckart; Rohde, Mandy; Vautrin, Dominique; et al. (2009)
    Molecular Ecology Resources
    We present details and characteristics of 123 novel polymorphic microsatellite DNA loci for Bombus terrestris. Thirty‐four of these loci have been tested in nine other Bombus species and 25 of them showed polymorphisms in at least one species. These microsatellite DNA loci together with the already established 60 loci will be useful for characterizing wild and managed populations of B. terrestris and other Bombus species as well as for detailed genetic studies in including mapping studies and genome annotations.
  • Development of novel microsatellite markers for the grassland species Lolium multiflorum, L. perenne and Festuca pratensis
    Item type: Journal Article
    Studer, Bruno; Widmer, Franco; Enkerli, Jürg; et al. (2006)
    Molecular Ecology Resources
    Twelve microsatellite markers were isolated from Lolium multiflorum. Allelic variability and cross‐species amplification were assessed on 16 individuals of each of the three grassland species L. multiflorum, Lolium perenne and Festuca pratensis. Cross‐species amplification success was 100% for L. perenne and 83% for F. pratensis. The number of alleles detected ranged from one to 14 with an average of 3.4. While three microsatellite loci were polymorphic in all three species, one marker produced species‐specific alleles in all three species. These microsatellite markers provide a valuable tool for population genetic studies within and among species of the Festuca–Lolium complex.
  • Polymorphic microsatellite loci in the parasitic wasp Cotesia glomerata (Hymenoptera: Braconidae)
    Item type: Other Journal Item
    Zhou, Yihong; Gu, Hainan; Dorn, Silvia (2005)
    Molecular Ecology Resources
    Five polymorphic microsatellite loci were isolated in a gregarious endoparasitoid, Cotesia glomerata, using an enrichment protocol. We detected two to 15 alleles per locus in a sample of 50 female wasps collected from a field population near Zürich, Switzerland. The observed heterozygosities ranged from 0.21 to 0.92. These markers are currently being used in our studies of sex determination in this species.
  • Real-time PCR to quantify composition of arbuscular mycorrhizal fungal communities
    Item type: Journal Article
    Thonar, C.; Erb, A.; Jansa, J. (2012)
    Molecular Ecology Resources
  • Isolation and characterization of six microsatellite loci in the drywood termite Cryptotermes secundus (Kalotermitidae)
    Item type: Journal Article
    Fuchs, A.; Heinze, J.; Reber-Funk, C.; et al. (2003)
    Molecular Ecology Resources
  • Isolation and characterization of EST-derived microsatellite loci from the fungal wheat pathogen Phaeosphaeria nodorum
    Item type: Journal Article
    Stukenbrock, Eva H.; Banke, Søren; Zala, Marcello; et al. (2005)
    Molecular Ecology Resources
    Eleven polymorphic microsatellite loci and one minisatellite locus originating from expressed sequence tag (EST) libraries of Phaeosphaeria (syn. Stagonospora) nodorum were isolated and characterized. The satellite markers were used to genotype isolates from field populations collected in China, North America and South Africa. The number of alleles per locus ranged from two to 15. Genotype diversity ranged from 87.5 to 95.3 and gene diversity from 0.1 to 0.8. The variable levels of polymorphism within and among populations of P. nodorum renders these 12 satellite loci ideal markers for population genetic analysis of P. nodorum.
  • The quest for Y-chromosomal markers
    Item type: Journal Article
    Greminger, Maja P.; Krützen, Michael; Schelling, Claude; et al. (2010)
    Molecular Ecology Resources
    Tracing maternal and paternal lineages independently to explore breeding systems and dispersal strategies in natural populations has been high on the wish‐list of evolutionary biologists. As males are the heterogametic sex in mammals, such sex‐specific patterns can be indirectly observed when Y chromosome polymorphism is combined with mitochondrial sequence information. Over the past decade, Y‐chromosomal markers applied to human populations have revealed remarkable differences in the demographic history and behaviour between the sexes. However, with a few exceptions, genetic data tracing the paternal line are lacking in most other mammalian species. This deficit can be attributed to the difficulty of developing Y‐specific genetic markers in non‐model organisms and the general low levels of polymorphisms observed on the Y chromosome. Here, we present an overview of the currently employed strategies for developing paternal markers in mammals. Moreover, we review the practical feasibility and requirements of various methodological strategies and highlight their future prospects when combined with new molecular techniques such as next generation sequencing.
  • Increased accuracy of species lists developed for alpine lakes using morphology and cytochrome oxidase I for identification of specimens
    Item type: Journal Article
    Deiner, Kristy; Knapp, Roland A.; Boiano, Daniel M.; et al. (2013)
    Molecular Ecology Resources
  • Influence of parameter settings in automated scoring of AFLPs on population genetic analysis
    Item type: Journal Article
    Herrmann, Marc; Holderegger, Rolf; van Strien, Maarten J. (2013)
    Molecular Ecology Resources
Publications1 - 10 of 29