RNDr. Jan Brabec, Ph.D.
Job Position: Associated scientist - Laboratory of Genomics and Diversity of Protists
E-mail:
brabcak@paru.cas.cz
Room:
nová budova 5. patro
Jan Brabec is an evolutionary biologist with over 20 years of experience in molecular phylogenetics of eukaryotic parasites, with a primary focus on parasitic helminths. His research has evolved from gene-based analyses to genome-wide approaches, emphasizing innovative methods for extracting genomic data from microscopic life stages and preserved museum specimens. This shift has enabled deeper insights into organismal history and evolutionary dynamics. Over the past decade, his interests have expanded to understanding the processes that shape the diversity and distribution of parasitic taxa.
Since 2022, Jan has been a member of the Laboratory of Genomics and Diversity of Protists, where he investigates the phylogenomics of metamonads—anaerobic unicellular flagellates with remarkable ecological diversity. His current research centers on amphizoic diplomonads, a rare group of microbial eukaryotes capable of living both freely and within hosts. He aims to uncover the genomic foundations and metabolic capacities that enable this dual lifestyle, identify evolutionary pressures acting on diplomonad genomes in natural environments, and experimentally test their metabolic flexibility and adaptive responses under contrasting ecological conditions.
Research fields
Molecular evolution of anaerobic protists, single cell transcriptomics.
Phylogenomics and evolution of parasitism of parasitic flatworms (Neodermata) and thorny-headed worms (Acanthocephala).
Molecular taxonomy of fish cestodes, differential diagnostics of helminth parasites.
Historical DNA sequencing of museum's wet collection specimens (museomics).
Ongoing research projects
Understanding the evolution of amphizoic organisms: genomic basis and metabolic potential of
organisms capable of living freely and inside hosts
Diplomonads are unicellular eukaryotic flagellates, mostly known as endobionts and parasites of vertebrates, but also include free-living representatives that have secondarily escaped host association by reacquiring lost metabolic traits via lateral gene transfer. Hexamita inflata is unique among free-living diplomonads for its ability to thrive both freely in sediments and as a horse leech endobiont. Such ecologically flexible species, termed amphizoic, are rare in nature. Our project will dissect the genomic basis and metabolic capacities of H. inflata, and examine gene flow between its ecologically distinct populations. Using single cell transcriptomics and pooled genome sequencing from longitudinally sampled leeches, sediments, and experimental evolution cultures, we aim to reveal the genomic flexibility and evolutionary pressures that enable survival in contrasting environments.
Scientific collaborations
I actively collaborate with researchers such as Prof. Tomáš Scholz (Biology Centre CAS), Dr. Isabel Blasco-Costa (Muséum d'histoire naturelle, Geneva), and Dr. Jesús Hernández-Orts (Natural History Museum, London) on various projects under the broad umbrella of molecular evolution, ecology, and taxonomy of parasitic worms. With Tomáš Scholz, I focus primarily on the molecular taxonomy of fish tapeworms. With Isabel Blasco-Costa, we test and implement novel methodologies for phylogenomics using formalin-fixed museum specimens (i.e., museomics). With Jesús Hernández-Orts, we are currently investigating evolutionary processes in thorny-headed worms (Acanthocephala).
Employment history
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
Education
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
Research visits
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
