Institute: Institute of Botany
Topic: Phylogenetic reconstruction of Ranunculus sect. Batrachium (Ranunculaceae, Plantae) using DNA hybridization capture techniques
Name of supervisors: dr hab. Joanna Zalewska-Gałosz, prof. UJ; dr Tomasz Suchan (firstname.lastname@example.org)
Section Batrachium (Water Crowfoots) is a monophyletic group of macrophytes classified within cosmopolitan, morphologically, and ecologically diverse genus Ranunculus. In the latest worldwide taxonomic account of the section 30 species, 16 hybrids and 29 hybrid combinations within Batrachium were recognised . Batrachium is regarded as taxonomically the most challenging groups of plants because of extreme phenotypic plasticity, frequent hybridization and introgression, allo- and autopolyploidization, and persistence of genetically independent, sterile lineages. Only recently, thanks to the application of the molecular tools, the modern Batrachium phylogeny starts to clarify. Based on the direct sequencing of selected DNA regions (ITS and cpDNA) some Batrachium taxa were successfully molecularly characterised and general phylogenetic clades were resolved . However, molecular studies revealed also significant intraspecific genetic variation of Ranunculus trichophyllus, not directly related with morphological characters, and genetic split in R. baudotii between populations from coastal regions of the Baltic Sea basin and the populations dispersed though the inland Europe .
The main question to be addressed in the project:
We aim to develop a cost-effective hybridization capture approach allowing sequencing of orthologous loci even from highly degraded DNA samples  and apply it for the Batrachium specimens preserved in different Herbaria. Based on the obtained markers, we will explore genetic information with taxonomic value from the specimens covering large spatial areas and temporal scales, and resolve phylogeny of Batrachium based on acquired data.
Information on the methods/description of work:
We will develop in-house sequence capture protocols for capturing sets of orthologous loci from degraded DNA form the herbarium specimens. The protocols will be based either on the hyRAD technique , allowing the capture of random fraction of the genome, or/and EecSeq, an inexpensive method of exon capture . The student will be in charge of DNA isolation from the vouchers, building genomic libraries and the probes form fresh specimens, testing and performing the hybridization captures. They will characterize the utility of the methods for broader phylogenetic scales and analyse the obtained data to resolve the phylogenetic relationships within the studied group. The training program will equip the student with modern laboratory (the “next-generation sequencing” techniques) as well as bioinformatic skills and taxonomical training.
Additional information (e.g. special requirements from the student):
Working time flexibility and regularity, English fluency. Experience in basic laboratory skills and willingness to learn next generation DNA sequencing techniques and bioinformatic data analysis.
Place/name of potential foreign collaborator:
Gerhard Wiegleb, Department of Ecology, Brandenburg University of Technology Cottbus, Cottbus, Germany [Herbarium collection]
Bobrov, A. Alexander, I.D. Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia [Herbarium collection]
 Wiegleb, G., Bobrov, A. A., Zalewska-Gałosz, J., 2017. A taxonomic account of Ranunculus section Batrachium (Ranunculaceae). Phytotaxa 319: 001–055.
 Bobrov, A.A., Zalewska-Gałosz, J., Jopek, M., Movergoz, E.A., 2015. Ranunculus schmalhausenii (section Batrachium, Ranunculaceae), a neglected water Crowfoot endemic to Fennoscandia - a case of rapid hybrid speciation in postglacial environment of North Europe. Phytotaxa 233: 101–138.
 Suchan, T. et al. 2016. Hybridization capture using RAD Probes (hyRAD), a new tool for performing genomic analyses on collection specimens. PLoS ONE 11: e0151651.
 Puritz, J. B., & Lotterhos, K. E., 2018. Expressed exome capture sequencing: A method for cost‐effective exome sequencing for all organisms. Molecular ecology resources, 18: 1209-1222.