Project description. In biodiversity conservation, protection of species diversity has gained most attention (IUCN Red List) while considerably less attention has been drawn to genetic diversity within species, partly because of methodological constraints. In small isolated populations, genetic variation is lost due to genetic drift. Genetic variation is vital for the potential for adaptation to changes in the abiotic and biotic environment as well as protecting populations from inbreeding depression. Restoration of species in areas where they are currently extinct, may increase the connectivity between populations and increase the total population size resulting in reduced loss of genetic diversity. Conservation genetics is a well-established interdisciplinary science that applies genetic methods to the conservation and restoration of biodiversity. Although many fungal species are sensitive to habitat fragmentation, especially loss of old growth forests, few conservation genetic studies have focused on fungi, partly because of its hidden life style belowground or within substrates. The few studies focusing on the genetic variation in wood decay fungi in Fennoscandia (Kauserud & Schumacher, 2001; 2002;2003; Högberg et al.1999; Högberg and Stenlid 1999; Franzén et al. 2007) have been hampered by methodological limitations, most importantly that only a limited number of DNA loci have been investigated. Restriction-site associated DNA (RAD) sequencing technique takes advantage of new high-throughput sequencing technologies and delivers high-resolution population genomic data with thousands of markers distributed across the genomes (Baird et al. 2008). In this project, using RADseq, the candidate will investigate how loss and fragmentation of habitats at different spatial scales have influenced genetic variation in two congeneric Phellinus species: P. nigrolimitatus and P. viticola. The former has been more negatively affected by forestry in Fennoscandia. The two-main research questions that the candidate will address are (i) Does the level of genetic variation in the two Phellinus species vary throughout Fennoscandia? and (ii) Is genetic variation distributed differently in non-red-listed and red-listed species.
Method. After training in molecular-based techniques such as DNA extraction and library preparation methods for RADsequencing, the candidate will process 150 samples from P. viticola. The sequencing data will first be analyzed using bioinformatics programs (Stacks, Bowtie, SAMtools, VCFtools) to generate SNPs. Using different population genetics software (FineRADStructure, Popgenome) the genome-wide markers will be used to infer the genetic structure, determine gene flow and reveal patterns of dispersal at different spatial scales and statistics analyses mainly in R. Analysed data will be provided for the second species, P. nigrolimitatus. For both species, reference genomes will be available in 2017. Most samples have been collected but depending on the candidates´ interest for field field work, an additional sampling site can be included in the experimental design.
Expectations. The master student must be highly motivated to undertake such a pluri-disciplinary subject. She/He is expected to work independently after training in mycology, molecular techniques and bio-informatics and statistics. The student must be willing to learn new computational/ population genetics tools for handling and analyzing the data. The student will have a desk close to the rest of the group and is expected to be present and participate in daily discussions and weekly meetings in English. Being part of Kauserud´s Group and a larger research project FunGen, (www.mn.uio.no/ibv/english/research/sections/evogene/projects/fungen),the student is expected to collaborate and socialize with other researchers. As most master theses, our goal is to publish the results from the MSc project in an international scientific journal.
Contact information. Jørn Henrik Sønstebø (j.h.sonstebo@ibv.uio.no) and Sundy Maurice
(sundy.maurice@ibv.uio.no)