This project will generate a novel genomic dataset to:
- provide evolutionary insights into the incredibly flexible, but yet poorly understood, life history strategy of parasitic plants;
- address species delimitation in critical taxonomic groups to facilitate conservation efforts;
- develop methodology for incorporating polyploid variation and hybridization in species tree inference (cf Bertrand et al., 2015) using Euphrasia species as a study system.
Family Orobanchaceae comprises parasitic plants, showing all known transitions from obligate to facultative forms of parasitism. The obligate parasitic Orobanchaceae have been receiving much attention research-wise due to their adverse effects on crops, particularly in tropical climates. The green parasites are less studied, however there are data suggesting that they benefit co-occurring species by influencing the structure of plant communities and enhancing nutrient cycling.
Particular emphasis will be given to the genus Euphrasia, a poorly studied taxonomically critical group. The genus is represented by green parasitic (hemiparasitic) plants, which are abundant in tundras, coastal, mountainous, alpine and other nutrient-poor habitats. Euphrasia is notorious for its taxonomic complexity with numerous named, but not always well-distinguished taxa, frequent interspecific hybridization, variation in ploidy levels and high levels of morphological polymorphism (Gussarova, 2008; 2012). Geographical and ecological variation in Euphrasia morphology shows similar trends for different species under similar habitat conditions, suggesting convergent similarity. This complex and dynamic diversity requires adoption of “taxonomic” action plans in conservation to protect evolutionary processes generating Euphrasia diversity (French et al, 2008). In Euphrasia there are also medicinal plants and Red-listed species. Three species of Euphrasia are protected in Sweden, (E. rostkoviana, E. salisburgensis, E. suecica) and one in Norway (E. confusa). The threat for all these species has been identified as change in land use. Other species, Euphrasia scottica and E. rostkoviana ssp. montana, are already reported as regionally extinct in Sweden. Clarification of the taxonomic status of Euphrasia species is, therefore, important for appropriate conservation measures to be implemented. Currently recognized morphology-based species will be tested with reduced genome sequence data generated via selective capture of genomic regions prior to NGS, using “in-solution hybrid capture” technology (Mamanova et al., 2010).
These genomic data will be subsequently analyzed with coalescent-based statistical methods to search for optimal species delimitation using software STEM-hy and by means of data partitioning in *BEAST and DISSECT (Jones et al., 2014). Morphological delimitation will be used as an alternative to a species tree partitioning. Comparison of partition schemes will be conducted using new approaches for model selection such as eg path sampling.
These tasks could potentially accommodate two MSc projects and can be tailored to answer research interests and abilities of the candidates, eg include or not include field work collection.
References:
Bertrand, Y.J.K., Scheen, A.-C., Marcussen, T., Pfeil, B. E., De Sousa, F., & Oxelman, B. 2015. Assignment of homoeologs to parental genomes in allopolyploids for species tree inference, with an example from Fumaria (Papaveraceae) Syst. Biol. 64: 448–471.
Gussarova, G., Popp, M., Vitek, E., & Brochmann C. 2008. Molecular phylogenetics and biogeography of the bipolar Euphrasia (Orobanchaceae): recent radiations of an old genus. Mol. Phyl. Evol. 48: 444–460.
Gussarova, G., Alsos, I.G. & Brochmann C. 2012. Annual plants colonizing the Arctic? Phylogeography and genetic variation in the Euphrasia minima complex (Orobanchaceae). Taxon. 61: 146–160.
Jones, G., Aydin, Z., & Oxelman, B. 2014. DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Bioinformatics. doi: 10.1093/bioinformatics/btu770
Mamanova, L., Coffey, A.J., Scott, C.E., Kozarewa, I., Turner, E.H. … & Turner, D.J. 2010. Target-enrichment strategies for next-generation sequencing. Nature Methods. 7: 111–118.
Veiledere:
Galina Gusarova og Anne Krag Brysting