RNDr. Jan Brabec, Ph.D.

Job Position: Associated scientist - Laboratory of Genomics and Diversity of Protists

Contact details

E-mail: brabcak@paru.cas.cz
Room: nová budova 5. patro


Research focus

Phylogenomics and genomic adaptations to parasitism of parabasalid protists.

Phylogenomics and evolution of parasitism of parasitic flatworms (Neodermata) and thorny-headed worms (Acanthocephala).

Molecular taxonomy of fish cestodes. 

Molecular ecology and population genomics of metazoan parasites of fish. 

Historical DNA sequencing of museum's wet collection specimens (museomics).

Molecular identification and differential diagnostics of helminth parasites. 


Ongoing research projects

Origin of parasitism in Neodermata

One of the research lines of a multi-lab project granted to Tomáš Scholz to which I contribute transcriptomic 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. 


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.

Curriculum vitae

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



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


Total found: 41 records
Brabec J., Rochat E.C., Knudsen R., Scholz T., Blasco-Costa I. (2023) Mining various genomic resources to resolve old alpha-taxonomy questions: a test of the species hypothesis of the Proteocephalus longicollis species complex (Cestoda: Platyhelminthes) from salmonid fishes (Cestoda: Platyhelminthes). International Journal for Parasitology 53 : 197–205.
DOI: 10.1016/j.ijpara.2022.12.005
Marick J., Brabec J., Choudhury A., Scholz T., Ash A. (2023) The evolution of an ancient tapeworm lineage in its catfish hosts: vicariance, dispersal and diversification in Gangesiinae (Cestoda: Proteocephalidae) Zoological Journal of the Linnean Society 198 : 509–533.
DOI: 10.1093/zoolinnean/zlac098
Uribe M., Brabec J., Chaparro-Gutiérrez J.J., Hermosilla C. (2023) Neglected zoonotic helminthiases in wild canids: new insights from South America Frontiers in Veterinary Science 10 : 1235182.
DOI: 10.3389/fvets.2023.1235182
Kuchta R., Kołodziej-Sobocińska M., Brabec J., Młocicki D., Salamatin R., Scholz T. (2021) Sparganosis (Spirometra) in Europe in the molecular era Clinical Infectious Diseases 72 : 882–890.
DOI: 10.1093/cid/ciaa1036
Scholz T., Brabec J., Hrubá K., Jirků M. (2021) High species diversity of fish tapeworms in congeneric hosts in Africa: revision of Monobothrioides (Cestoda: Caryophyllidea), including description of two new species and molecular phylogeny Organisms Diversity and Evolution 21 : 447–466.
DOI: 10.1007/s13127-021-00492-1
Scholz T., Waeschenbach A., Oros M., Brabec J., Littlewood D. (2021) Phylogenetic reconstruction of early diverging tapeworms (Cestoda: Caryophyllidea) reveals ancient radiations in vertebrate hosts and biogeographic regions International Journal for Parasitology 51 : 263-277.
DOI: 10.1016/j.ijpara.2020.09.009
Uribe M., Payán E., Brabec J., Vélez J., Taubert A., Chaparro-Gutiérrez J.J., Hermosilla C. (2021) Intestinal Parasites of Neotropical Wild Jaguars, Pumas, Ocelots, and Jaguarundis in Colombia: Old Friends Brought Back from Oblivion and New Insights Pathogens 10 : 822.
DOI: 10.3390/pathogens10070822
de Chambrier A., Brabec J., Scholz T. (2020) Molecular data reveal unexpected species diversity of tapeworms of Australasian reptiles: revision of Kapsulotaenia (Cestoda: Proteocephalidae) Zootaxa 4869 : 529–561.
DOI: 10.11646/zootaxa.4869.4.4
Ebmer D., Navarrete M.J., Muñoz P., Flores L.M., Gärtner U., Brabec J., Poppert S., Taubert A., Hermosilla C. (2020) Anthropozoonotic parasites circulating in synanthropic and pacific colonies of South American sea lions (Otaria flavescens): non-invasive techniques data and a review of the literature Frontiers in Marine Science 7 : 543829.
DOI: 10.3389/fmars.2020.543829
de Chambrier A., Brabec J., Tran B.T., Scholz T. (2019) Revision of Acanthotaenia von Linstow, 1903 (Cestoda: Proteocephalidae), parasites of monitors (Varanus spp.), based on morphological and molecular data. Parasitology Research 118 : 1761–1783.
DOI: 10.1007/s00436-019-06326-6
Řežábková L., Brabec J., Jirků M., Dellerba M., Kuchta R., Modrý D., Parker W., Jirků-Pomajbíková K. (2019) Genetic diversity of the potentially therapeutic tapeworm Hymenolepis diminuta (Cestoda: Cyclophyllidea). Parasitology International 71 : 121–125.
DOI: 10.1016/j.parint.2019.04.009
Scholz T., Choudhury A., Uhrová L., Brabec J. (2019) The Proteocephalus species-aggregate in freshwater centrarchid and percid fishes of the Nearctic region (North America) Journal of Parasitology 105 : 798–812.
DOI: 10.1645/19-89
Scholz T., Kuchta R., Brabec J. (2019) Broad tapeworms (Diphyllobothriidae), parasites of wildlife and humans: Recent progress and future challenges International Journal for Parasitology: Parasites and Wildlife 9 : 359–369.
DOI: 10.1016/j.ijppaw.2019.02.001
Brabec J., Scholz T., Štefka J. (2018) Development of polymorphic microsatellites for the invasive Asian fish tapeworm Schyzocotyle acheilognathi Parasitology International 67 : 341-343.
DOI: 10.1016/j.parint.2018.01.007
Hernandez Orts J., Scholz T., Brabec J., Kuzmina T., Kuchta R. (2018) Does the number of genital organs matter? Case of the seal tapeworm Diphyllobothrium (syn. Diplogonoporus) tetrapterus (Cestoda: Diphyllobothriidea) Canadian Journal of Zoology 96 : 193-204.
DOI: 10.1139/cjz-2017-0013
Scholz T., Tavakol S., Uhrová L., Brabec J., Přikrylová I., Mašová Š., Šimková A., Halajian A., Luus-Powell W. (2018) An annotated list and molecular data on larvae of gryporhynchid tapeworms (Cestoda: Cyclophyllidea) from freshwater fishes in Africa Systematic parasitology 95 : 567–590.
DOI: 10.1007/s11230-018-9796-y
Waeschenbach A., Brabec J., Scholz T., Littlewood D., Kuchta R. (2017) The catholic taste of broad tapeworms – multiple routes to human infection International Journal for Parasitology 47 : 831-843.
DOI: 10.1016/j.ijpara.2017.06.004
Young C., Miller M.A., Kuchta R., Brabec J., Newsome S.D., Dailey M. (2017) First Report of an Adult Tapeworm (Cestoda: Diphyllobothriidea) in a Southern Sea Otter (Enhydra lutris nereis) Journal of Wildlife Diseases 53 : 934-937.
DOI: 10.7589/2017-01-020
Brabec J., Kuchta R., Scholz T., Littlewood D. (2016) Paralogues of nuclear ribosomal genes conceal phylogenetic signal within the invasive Asian fish tapeworm lineage: evidence from next generation sequencing data International Journal for Parasitology 46 : 555-562.
DOI: 10.1016/j.ijpara.2016.03.009
Briscoe A., Bray R., Brabec J., Littlewood D. (2016) The mitochondrial genome and ribosomal operon of Brachycladium goliath (Digenea: Brachycladiidae) recovered from a stranded minke whale Parasitology International 65 : 271-275.
DOI: 10.1016/j.parint.2016.02.004

More publications


Biology Centre CAS
Institute of Parasitology
Branišovská 1160/31
370 05 České Budějovice

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