Wednesday, February 10, 2016

Two openings (PhD and PostDoc)

Announcements from the Metabarcoding website:

Deciphering genome skimming data over a broad taxonomic scale (the PhyloAlps data) to study the dynamic of the organelle genome evolution.

**A PhD position is open at LECA - Grenoble - France.**

Candidates will have to apply for a PhD Fellowship competitive exam organized by the "Ecole Doctorale Chimie et Sciences du Vivant" PhD school of the Grenoble Alpes University.

The competitive exam is open to students holding a master degree in science.

Candidates must have broad interests and training in evolution and by the development of new data analysis methods able to deal with high-throughput genomic data. This PhD project has to be considered as a true bioinformatic project covering biological topics but also requiring computer science developments. Therefore, to allow big-data analysis, candidates must have very strong abilities in bioinformatics including programming.

This PhD project proposes to use an unprecedented data set of several thousands of data of low coverage shotgun genome sequencing to study the evolutionary dynamics of organelle genome in plants. Interesting avenues for research could be explored by the candidate. Among them, the genetic transfers between the nuclear, the mitochondrial and the chloroplastic genomes and the impact of the repeated sequences on the dynamic of evolution are particularly promising. A third important topic that could be explored by the candidate is conducting a formal test of whether circular topology classically considered for plants’ chloroplast genomes can be considered true for all plant clades. The results will be put in relation with the phylogeny and the ecological characteristics of plant species considered in order to test whether some of the observed genomic properties can be associated to specific clades and to particular environments and species life-history traits.

Data sources :
The PhD project will be mainly based on the PhyloAlps sequencing initiative, which is currently producing a large dataset of genomic data constituted by a low coverage genome sequencing for each species of plant belonging the european Alpine Flora. This initiative will yield about 6,000 sequenced specimens, which can used to obtain the complete sequence of the organelle genome for each species sequenced. This project will also be within a framework of international collaborations including the Nowegian Barcode of Life (NorBOL) initiative that will provide similar data for about 2,000 additional specimens belonging the arctic flora.

Contact :

ECOGEN - Ecosystem change and species persistence over time: a genome-based approach


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

Sub goals:

  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.

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.... [for the remainder of the text and the citations follow this linked text].
Contact : Prof. Inger Greve Alsos
Tromsø University Museum
NO-9037 Tromsø

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