RNDr. Jan Brabec, Ph.D.
Job Position: Postdoc - Laboratory of Helminthology
Molecular phylogenetics and evolution of parasitic flatworms, molecular taxonomy of fish cestodes.
Molecular ecology and population genomics of metazoan parasites of fish.
Development of phylogenomic and population genomic markers for evolutionary studies including historical DNA sequencing (museomics)
Molecular differential diagnostics of helminth parasites.
Ongoing research projects
Origin of parasitism in the Neodermata
One of the research lines of a multi-lab project granted to Tomáš Scholz to which I contribute genomic data and analyses of parasitic flatworms, in collaboration with Roman Kuchta. The early phylogeny of parasitic flatworms (including the widely known cestodes and trematodes) remains to be resolved satisfactorily and we address this issue through de novo characterisation of genomes and transcriptomes of selected representatives of the basal neodermatan lineages, bioinformatic analyses of the genomic data and interpreting individual morphological/ultrastructural traits in the light of this data.
Parasite radiations: Domino effect of host radiations?
A project from my previous postdoctoral position at the Muséum d'histoire naturelle de Genève (supervised by Dr Isabel Blasco-Costa) where I was responsible for carrying out the entire workflow of data generation and participate on data analyses. We are currently busy analyzing the rich dataset, testing various evolutionary ecology hypotheses concerning metazoan fish parasites with complex life cycles. While scientists still known very little about how adaptive radiations of host species affect the associated parasite communities, we try to understand if parasite taxa tend to diversify as a consequence of rapid host speciation, which traits predispose parasites to diversification and what processes generating variability underpin novel adaptations among distinct parasite population leading to speciation. These questions are key to our understanding of the speciation process in parasites and the evolution towards host specificity.
Diversity and phylogenetic relationships of North American tapeworms
A project supervised by Tomáš Scholz for which I provide my expertise in molecular taxonomy and supervise the molecular data generation and phylogenetic analysis part. Representatives of several cestode lineages infect a range of North American freshwater fish groups, including the most primitive lineages of ray-finned fishes. We are interested in describing the diversity of their cestode parasites as well as understanding the mutual interrelationships of the cestodes using combination of classical morphology and electron microscopy techniques as well as molecular phylogenetic approaches including both Sanger- and high-throughput sequencing techniques.
Phylogenomics of formalin-fixed museum flatworms
A joint project of Dr Isabel Blasco-Costa (Muséum d'histoire naturelle de Genève) and myself that strives to test the utility of exome-capture methodologies for capturing highly damaged DNA of formalin-fixed museum specimens. Museum specimens are often the only available representatives for a given group of organisms ever collected, challenging to be recollected from nature again, and whose molecular records are often missing from current phylogenetic or systematic treatments. The aim of this project is to establish an efficient protocol and assess the power of the phylogenomic markers obtained in resolving the interrelationships of these organisms.
If you are a prospective parasitology student (undergraduate or graduate) who finds the field of either molecular phylogenetics and taxonomy of cestodes or evolutionary genomics of flatworm parasites interesting, don’t hesitate to contact me through email or visit me directly at the second floor of the Institute of Parasitology. We can develop an interesting topic for your thesis that will suit your university degree and can be submitted in either Czech or English. You can expect to learn and use modern DNA sequencing techniques and bioinformatics, i.e. skills that are also sought-after out of the academic environment.
2020–now Research assistant, Institute of Parasitology, Biology Centre of the Czech Academy of Sciences
2019–2020 Postdoctoral fellow, Institute of Parasitology, Biology Centre of the Czech Academy of Sciences. Project: AQUAPARA-OMICS: Aquatic parasitism meets biomics – addressing key biological questions using novel datasets and modern analytical tools (Grant Agency of the Czech Republic)
2017–2019 Postdoctoral fellow, Natural History Museum of Geneva, Switzerland.
Project: Parasite radiations: Domino effect of host radiations? (Swiss National Science Foundation)
2012–2017 Postdoctoral fellow, Institute of Parasitology, Biology Centre of the Czech Academy of Sciences. Project: Molecular diagnostics, historical biogeography and genetic structuring of the populations of model platyhelminth parasites
2006–2012 PhD, Parasitology, Faculty of Science, University of South Bohemia in České Budějovice, Czech Republic. Thesis: Molecular systematics and evolution of basal cestode lineages
2004–2006 MSc, Parasitology, Faculty of Biological Sciences, University of South Bohemia in České Budějovice, Czech Republic. Thesis: Paraphyly of pseudophyllidean tapeworms: testing a phylogenetic hypothesis using sequence data (18S & 28S rDNA)
2001–2004 BSc, Biomedical Laboratory Techniques, Faculty of Biological Sciences, University of South Bohemia in České Budějovice, Czech Republic. Thesis: Molecular phylogeny of tapeworms of the order Pseudophyllidea
Dr Tim Littlewood, Life Sciences Department, The Natural History Museum, London, UK, 2013, 2014
Dr Peter Olson, Department of Zoology, The Natural History Museum, London, UK, 2005, 2010
Prof Klaus Brehm, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany, 2006, 2008