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Final Report Summary - FUNDISTRAIT (Fungal conservation genetics: species traits and dispersal)

The funding for the project FunDisTrait (Fungal species dispersal traits) was granted to Sundy Maurice in the call FP7-PEOPLE-2013-IEF, the research was carried out between 4th July 2014 and 3rd July 2016 in the section for genetics and evolutionary biology at the University of Oslo, under the supervision of Pr. Håvard Kauserud.

The main objective of this project was to reveal microorganisms’ dispersal capacities and correlate the population genetic structures across North Europe of multiple co-occurring fungal species (polypore) with a variety of life-history characteristics. In order to accomplish this overall project objective, the research was sub-stratified into different deliverables throughout the whole duration of the project. The first task of this study was to implement a reduced representation sequencing technique (RAD sequencing) for high-throughput application in population genetics of fungi. Consequently, a pilot study has been conducted and the deliverables provided are an optimized protocol and a procedure for the bio-informatics data analysis. Optimising the RAD technology and implementing the protocol on fungi, has resulted in scientific collaborations with other research groups interested in the technique. Both mentoring and guidance have been provided to two research groups (University of Copenhagen, Denmark and Flødevigen Marine Research Station, Norway), this action fulfills the scope of the Marie Curie Fellowship that is the transfer of knowledge acquired and the integration of networks. A second task was to address a broad scale population genetics over Fenno-scandia (Norway, Finland and Sweden), this very challenging research question was sub-divided to different scales (forest-level, small-scale and broad–scale). The deliverables for the sampling resulted into more than 1200 fungal samples, geo-localised, identified and deposited in the UiO fungarium.

In terms of training activities, FunDisTrait aimed to broaden scientific competence of the researcher in the mastering next-generation sequencing technologies and to reach a good level in bio-informatics. The training in bio-informatics analysis of data generated from RADseq was enriched by courses and workshop attended at the University of Lund, Sweden and at University of Edinburgh, Scotland. The researcher also followed two weeks workshops of high level, held by prominent experts in genomics (2015) and in population genetics and speciation (2016) in Cesky Krumlov, Czech Republic. The training objectives have therefore been fully attained during the project.

Two scientific papers presenting the results of the project are currently under preparation and will be submitted soon (2016) to high-impact journals. The first manuscript is a methodological study based on the application of RAD sequencing technology to reveal, first the feasibility on fungal samples and second its implementation in a high-throughput manner, necessary for population genetics. Technical limits have been identified and methodological improvements have been implemented to the existing protocol (Baird et al. 2008). A comparative data analysis with and without reference genomes has been performed and different biological hypothesis have been tested. From the results, we can conclude that (i) the expected number of RADtags obtained from the in silico analysis, with PstI as restriction enzyme on reference genomes, is in concordance with the observed number of RAD markers generated by the technique (ii) there is no significant difference between the proportion of aligned sequences to a reference genome when comparing data from environmental samples to axenic cultures, suggesting that contamination of fruit body by other species is very low. For further analysis, DNA has been extracted directly from the fruit bodies of polypore species, thus skipping the laborious part of isolating cultures. Finally (iii), the high-density of functional and neutral markers (SNPs) sampling with RADseq technique markedly outperformed other technical approaches (for example based on our experience with microsatellites from Serpula lacrymans), enabling the inference of population genetic structure on different geographic scales. A manuscript is under preparation and a submission to the journal of Molecular Ecology Resources is aimed for the end of this year. Based on these results, the RAD technique has been applied to detect the genetic diversity within species (20-25 individuals) and among species (11 species) on a small geographic scale in a boreal forest in Finland (Issakka, Kuhmo). This old-growth spruce-dominated forest presents the particularity of hosting a high diversity of polypore species, ranging from the least concerned to the threatened ones (IUCN Red list of threatened species). Recent habitat loss and fragmentation at the landscape level has not yet been reflected in the population sizes in the northern part of Finland. The aim of this second study is to reveal the genetic diversity within species and among species at a small geographic scale, without physical barriers and within an ecosystem that has undergone the same history of forestry. The genetic-based data has been linked to the species traits and interpreted in the timeline of the landscape evolution in the Kuhmo region. Based on the species´ historical demography, we conclude that polypore species have responded differently to habitat loss and fragmentation. Differences in allelic frequencies and populations sizes exhibited among species suggest that the abilities to persist as an isolated population could be threatened while species presenting larger population size may present higher fitness. This study brings insights about genetic variation of fungi at a finer geographic scale. A manuscript is under preparation and will be submitted to the journal Trends in Ecology and Evolution by the end of 2016. In the meanwhile, the results have been presented at the 3rd European Conference on Fungal Genetics, Paris (April 3rd- 6th 2016).

FunDisTrait has been conducted in a way that the researcher has gain savoir-faire in project management along the progress of the different work packages. In order to pursue research in this field of conservation biology, the researcher has seized the opportunity granted by FP7-PEOPLE to set up long lasting collaborations and applied for grants during the last two years (2014-2016). As a thematic continuity to FunDisTrait, the researcher has received funding from the Research Council of Norway for a new project FunGen (Co-PI, RCN project number 254746, 2016-2019, 1M€). FunGen is a collaborative project involving 4 international scientific partners (NINA, NIBIO, SLU Uppsala, SLU Umeå), stakeholders in forestry and conservation of biodiversity, as well as national agricultural and environmental agencies. In several ways, the Marie Curie project has fully contributed in promoting the researcher´s carrier.

Contact information:

Sundy Maurice
Section for Genetics and Evolutionary Biology
Department of Biology - University of Oslo
Postboks 1066 Blindern, 0316 Oslo

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