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Tuesday 9 February 2016
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ECOGEN - Ecosystem change and species persistence over time: a genome-based approach

Marie Curie fellowship at the Tromsø University Museum


Main goal

Develop high taxonomic resolution ancient environmental DNA methods in order to evaluate how drivers of change (human, climate, biota) affect species persistence and ecosystem tipping points in arctic-alpine biomes


1 - Improve methods for full genome analyses of environmental DNA
2 - Compile palaeo data to plan a balanced design of climatic and human impacts
3 - Do full genome analyses of lake cores to obtain information on past presence and abundance of vascular plant species and key herbivores
4 - Identify biotic drivers and disentangle their effects from human land use and climate change on ecosystem resilience and ecosystem services
5 - Estimate species persistence across periods of changes and identify factors causing extinction
6 - Provide methods and knowledge to inform species conservation and ecosystem management

Project tasks

We are seeking a research fellow that will join a cross-disciplinary team (ecology, palaeoecology, genetics, archaeology, geology, niche modelling) working in two geographical regions (Norway and the Alps). We will expand our knowledge on past vascular plant and animal diversity and abundance at a taxonomic depth that has not been possible until now due to methodological limitations. We expect to disentangle the effects of past human land-use (hunting, husbandry, burning, agriculture), climate change, and biota on species and ecosystem changes and thereby be able to answer questions central to our understanding of our biological resources, such as the level of persistence of species and resilience of ecosystems to environmental drivers, the extinction risk of species, and the capacity of mountain landscape to buffer against these changes. By identifying drivers of shifts in ecosystem services through time, we may inform future management.
The successful candidate will work on development of improved technology. The most recent applications of ancient plant DNA analyses are largely developed by our team (Taberlet et al. 2007, Sønstebø et al. 2010, Yoccoz et al. 2012, Willerslev et al. 2014). For vascular plants, the 50-100 base pair long P6 loop region of the chloroplast trnL (UAA) intron is used in a PCR based method (Taberlet et al. 2007), which allows identification of all plant families, most genera (>75%), and one third of the species (Sønstebø et al. 2010). When applied to modern lake sediments, half of the species present within 2 m of lakes were detected (Alsos et al. In prep.). Our recent study of an 8500 year old core from Svalbard show that the method detect all except two genera identified in a macrofossil study from the same lake (Alsos et al. 2015). Overall, 1.2 times more taxa of vascular plants were identified with ancient DNA than macrofossils, and the number of taxa identified per sample was 2.7 times higher for the former. Thus, DNA analyses of Holocene lake sediment can reveal the presence of rare taxa and thereby allow for a better estimation of species persistence. Further, the method is now resource-efficient and repeatable, and it can be extended to any group of organisms, given that a DNA reference library and adequate primers are developed . It also allows for semi-quantitative interpretations based on the number of PCR repeats where taxa are identified (Pansu et al. 2015). We will do minor optimization of these applications and analyse all samples for vascular plants and key herbivores.

Contact : Prof. Inger Greve Alsos
Tromsø University Museum
NO-9037 Tromsø
Email: inger.g.alsos at uit.no

Attached documents

Twitter : @Metabarcoding
Editorial board
  • BRANDNER Melissa
    • University of Nordland
    • Bodø (Norway)
  • BROCHMANN Christian
    • National Centre for Biosystematics
    • Oslo (Norway)
  • CHARITON Anthony
    • CSIRO Land and Water
    • Lucas Heights NA (Australia)
  • DEAGLE Bruce
    • University of Victoria
    • Victoria (Canada)
  • Eric Coissac
    • LECA
    • Grenoble (France)
  • KASAPIDIS Panagiotis
    • Hellenic Center for Marine Research
    • Irakleion, Crete (Greece)
    • Université de Genève
    • Genève 4 (Switzerland)
  • TABERLET Pierre
    • LECA,
    • Grenoble (France)
    • Centre for GeoGenetics
    • Copenhagen (Denmark)
  • ZINGER Lucie
    • IBENS
    • Paris (France)
  • Vodka, Bison and Metabarcoding

    31 July 2015, by BRANDNER Melissa

    The start of last month saw the occurrence of the Fifth Metabarcoding Spring School held in Białowieża National Park , Poland. A variety of scientists attended from all over the globe to learn, share and inspire with unique stories of metabarcoding.
    The scientists at the Mammal Research Institute PAS in Białowieża National Park hosted this year’s workshop. And our hats go off to them for the organizational skills, warmth and hospitality. During the week, experienced metabarcoders gave lectures on their trials and tribulations in the field of metabarcoding, sparking conversations between the attendees. The end of the first day saw flash talks from all participants of the event, creating an icebreaker and showing the wide variety of applications for metabarcoding, including, dietary studies, environmental health, fundamental ecology and exploration of rare and ancient habitats.
    Pierre Taberlet (who is rumoured to run 8000 PCR a day!) taught technical aspects such as DNA extraction in (...)

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