doc. RNDr. Jan Štefka, Ph.D.

Job Position: Head of Laboratory - Laboratory of Molecular Ecology and Evolution , Editor - Folia Parasitologica

Contact details

Phone: +420 387775409
Room: nová budova 5. patro



Curriculum vitae

webs: personal 


publication record

Date of birth:   April 25, 1979

Research interests and expertise

Studies of molecular ecology, biogeography and evolutionary processes in vertebrates and parasites. Reconstructions of population genetic and phylogenetic relationships using molecular and computational biology tools, analyses of multilocus and genomic data. Conservation genetics and invasive species. Field sampling of metazoan biological material.

Fieldwork abroad: Argentina, Bolivia, Brazil, Ecuador (Galápagos), several EU countries, Russia.


2008: PhD degree: Parasitology, Faculty of Science, University of South Bohemia (USB). PhD thesis topic: Host specificity, genetic variability and genealogy in populations of model parasite species.
2003: Master degree: Zoology, Faculty of Biological Sciences, USB. Thesis: Ecological aspects of hybridisation between fire-bellied toads Bombina bombina and B. variegata., 27 pp.
2001: Bachelor degree: Introductory Biology Programme, Faculty of Biological Sciences, USB.

Further education in molecular analyses and genomics:

2012: RADseq Workshop (GENECO, University of Lund, Sweden)
2011: Workshop on Genomics, Europe (Český Krumlov, Czech Rep.)
2009: Workshop on Molecular Evolution, Europe (Český Krumlov, Czech Rep.)

Professional appointments

2014-present: Research scientist – Laboratory head, Biology Centre, CAS.
2016-present: Associate professor (part time, full time from Sept. 2022), Faculty of Science, USB.
2014-2016: Research scientist & lecturer (part time), Faculty of Science, USB.
2011-2013: Postdoc researcher, Biology Centre, CAS & Faculty of Science, USB.
2009-2011: Marie Curie Galapagos Fellow, Entomology Department, NHM, London.

Organisation of international scientific meetings

2016 - 2022: Workshop on Population and Speciation Genomics, Europe, Czech Rep., Co-director.
2018: 6th International Conference on Phthiraptera, Brno, Czech Rep., Scientific Committee Member.
2015 & 2013Workshop on Molecular Evolution, Europe, Czech Rep., Co-director.
2012: Workshop on Genomics, Advanced Topic Sessions, Czech Rep., Associate co-director.
2010: Workshop on Molecular Evolution, Europe, Czech Rep., Teaching Assistant.
Five selected publications

Nazarizadeh M, Martinů J, Nováková M, Stanko M, Štefka J (2022) Phylogeography of the parasitic mite Laelaps agilis in Western Palearctic shows lineages lacking host specificity but possessing different demographic histories. BMC Zool., 7: 15.

Martinů J, Štefka J, Poosakkannu A, Hypša V (2020) “Parasite turnover zone” at secondary contact: a new pattern in host-parasite population genetics. Mol. Ecol., 29: 4653–4664.

Martinů J, Hypša V, Štefka J (2018) Host specificity driving genetic structure and diversity in ectoparasite populations: co-evolutionary patterns in Apodemus mice and their lice. Ecol. Evol., 8: 10008–10022.

Vlček J, Hoeck PEA, Keller LF, Wayhart J, Dolinová I, Štefka J (2016) Balancing selection and genetic drift create unusual patterns of MHCIIβ variation in Galápagos mockingbirds. Mol. Ecol., 25: 4757–4572.

Štefka J, Hoeck PEA, Keller LF, Smith VS (2011) A hitchhikers guide to the Galápagos: co-phylogeography of Galápagos mockingbirds and their parasites. BMC Evol. Biol., 11: 284.


Selected awards and fellowships

2018: Fulbright Fellowship. Fulbright Commission, USA.
2014: Otto Wichterle Award, received from the Czech Academy of Sciences.
2009-2011: Marie Curie Fellowship (IEF, FP7).
2008: Dean’s Award, Faculty of Science, USB, Czech Rep. Price awarded annually to two phd students for excellent scientific and study results.

Invited seminars and conference lectures (last 5 years, selected)

Štefka J (2022) Plenary lecture: Co-evolutionary imprints of genomic diversification in parasite populations. ESEB 2022, Prague, CZ.
Štefka J (2019) Seminars: Lousy & wormy tales: Drivers of population genetic divergence in host-parasite co-evolution. (University of Utah and University of Illinois).
Štefka J (2018) Seminar: Genetic diversity in host-parasite co-evolution (University of Basel).
Štefka J (2018) Seminar: Stowaways: tracing parasite introductions using genetics (Ostrava University).
Štefka J (2017) Seminar: Population genetics of parasite invasions (Masaryk University in Brno).

Teaching and Mentoring

Defended theses: 1 PhD., 5 MSc. and 4 BSc. at the Faculty of Science, University of South Bohemia (FS USB).
Currently supervising: 4 PhD., 1 MSc. and 1 BSc. theses at the FS, USB.
Teaching (at FS USB): Conservation Genetics (2012-present), Population and evolutionary genetics (2016-present); practicals in: Molecular Ecology (2011-present), Molecular Phylogenetics (2014-2015), Bioinformatics (2009) and Field Zoology (2006-2008).

Abroad stays

2018-2019 (10 months): Fulbright Visiting Scholar. University of Illinois Urbana-Champaign. Population genomics.
2009-2011: NHM, London, UK. Cophylogeography of ecological replicates: the coevolution and biogeography of Galapagos mockingbirds and their ectoparasites. Marie Curie Fellowship.
2007 (Nov.-Dec.): Argentina, Bolivia, Brasil. Field sampling with focus on the helminth fauna of endemic fishes.
2006-2007 (several short-term stays): Université Paul Sebatier Toulouse, France, Laboratoire Evolution Diversité Biologique, Research theme: Genetic variability in European populations of Ligula intestinalisBarrande fellowship.
2006 (Apr.-Jun.): University of Glasgow, UK, Faculty of Veterinary Medicine. Research theme: Microsatellite characterization in Ligula intestinalis (Cestoda: Pseudophyllidea), Socrates/Erasmus fellowship.

Peer review

Nat. Ecol. Evol., Mol. Ecol., Mol. Biol. Evol., J. Biogeogr., Biol. J. Linn. Soc., Ecol. Evol., Mol. Phylogenet. Evol., PLoS ONE, J. Zool. Syst. Evol. Res., Int. J. Parasitol., Parasitology, J. Parasitol., Folia Zool., Aquat. Invasions, R. Soc. Open Sci., New Zeal. J. Mar. Freshwater Res., BMC Res. Notes Associate editor (for ectoparasites, ecology and co-evolution) in Folia Parasitologica.

Foreign collaborations (selected, last 5 years)

Dr. Julian Catchen (University of Illinois, USA) - computational population genomics.
Dr. Emiliano Trucchi (Marche Polytechnic University, IT) - population genomics.
Prof. Lukas Keller & Dr. Paquita Hoeck (Zurich University, CH) – Galápagos mockingbird evolution.
Dr. Ivica Králová-Hromadová & Dr. Eva Čisovská (Institute of Parasitology, Slovak Academy of Sciences, SK) - helminth evolution and invasive species.

Bioinformatic skills

Unix command line (advanced), bash scripting (intermediate), R scripting (intermediate), Python scripting (intermediate).

Language skills

Czech (native), English (fluent), Spanish (intermediate), German (basic), Russian (basic).


Total found: 47 records
Bílková P., Vlček J., Cvetković T., Štefka J., Sedláček F. (2024) Odour preferred males led to a higher offspring number in the common vole Mammalian Biology 104 : 287-298.
DOI: 10.1007/s42991-024-00406-6
Martinů J., Tarabai H., Štefka J., Hypša V. (2024) Highly resolved genomes as a tool for studying speciation history of two closely related louse lineages with different host specificities Genome Biology and Evolution 16 : evae045.
DOI: 10.1093/gbe/evae045
Nazarizadeh M., Nováková M., Drábková M. , Catchen J., Olson P., Štefka J. (2024) Highly resolved genome assembly and comparative transcriptome profiling reveal genes related to developmental stages of tapeworm Ligula intestinalis Proceedings of the Royal Society B-Biological Sciences 291 : 20232563.
DOI: 10.1098/rspb.2023.2563
Barth J.M.I., Handley S.A., Kintzl D., Leonard G., Malinsky M., Matschiner M., Meyer B.S., Salzburger W., Štefka J., Trucchi E. (2023) The history and organization of the workshop on population and speciation genomics Evolution: Education and Outreach 16 : 2.
DOI: 10.1186/s12052-023-00182-w
Nazarizadeh M., Nováková M., Loot G., Gabagambi N., Fatemizahed F., Osano O., Presswell B., Poulin R., Vitál Z., Scholz T., Halajian A., Trucchi E., Kočová P., Štefka J. (2023) Historical dispersal and host-switching formed the evolutionary history of a globally distributed multi-host parasite – The Ligula intestinalis species complex Molecular Phylogenetics and Evolution 180 : 107677.
DOI: 10.1016/j.ympev.2022.107677
Vlček J., Miláček M., Vinkler M., Štefka J. (2023) Effect of population size and selection on Toll-like receptor diversity in populations of Galapagos mockingbirds Journal of Evolutionary Biology 336 : 109-120.
DOI: 10.1111/jeb.14121
Drábková  M., Kocot K.M., Halanych K.M., Oakley T.H., Moroz L.L., Kuris A., Garcia-Vedrenne A.E., Pankey M.S., Ellis E.A., Varney R., Štefka J., Zrzavý J. (2022) Different phylogenomic methods support monophyly of enigmatic 'Mesozoa' (Dicyemida plus Orthonectida, Lophotrochozoa) Proceedings of the Royal Society B-Biological Sciences 289 : 1978.
DOI: 10.1098/rspb.2022.0683
Nazarizadeh M., Martinů J., Nováková M., Stanko M., Štefka J. (2022) Phylogeography of the parasitic mite Laelaps agilis in Western Palearctic shows lineages lacking host specificity but possessing different demographic histories BMC Zoology 7 : 15.
DOI: 10.1186/s40850-022-00115-y
Nazarizadeh M., Peterka J., Kubečka J., Vašek M., Jůza T., Ribeiro de Moraes K., Čech M., Holubová M., Souza A., Blabolil P., Muška M., Tsering L., Bartoň D., Říha M., Šmejkal M., Tušer M., Vejřík L., Frouzová J., Jarić I., Prchalová M., Vejříková I., Štefka J. (2022) Different hosts in different lakes: occurrence and prevalence of Ligula intestinalis plerocercoids in Czech water bodies. Folia Parasitologica 69 : 18.
DOI: 10.14411/fp.2022.018
Nazarizadeh M., Peterka J., Kubečka J., Vašek M., Jůza T., Ribeiro de Moraes K., Čech M., Holubová M., Souza A., Blabolil P., Muška M., Tsering L., Bartoň D., Říha M., Šmejkal M., Tušer M., Vejřík L., Frouzová J., Jarić I., Prchalová M., Vejříková I., Štefka J. (2022) Different hosts in different lakes: occurrence and prevalence of Ligula intestinalis plerocercoids in Czech water bodies Folia Parasitologica 69 : 18.
DOI: 10.14411/fp.2022.018
Quijano F.R., Debora G.R., Štefka J., Kowalewski M.M. (2022) Lice in Howler Monkeys and the Ancient Americas: Exploring the Potential Cost of Being Past Pets or Hunting Games In: B. Urbani, D. Youlatos, A.T. Antczak (Eds.), World Archaeoprimatology: Interconnections of Humans and Nonhuman Primates in the Past. Cambridge University Press, Cambridge 183–197.
Radačovská A., Čisovská Bazsalovicsová E., Šoltys K., Štefka J., Minárik G., Gustinelli A., Chugunova J.K., Králová-Hromadová I. (2022) Unique genetic structure of the human tapeworm Dibothriocephalus latus from the Alpine lakes region – a successful adaptation? Parasitology 149 : 1106-1118.
DOI: 10.1017/S0031182022000634
Štefka J., Votýpka J., Lukeš J., Balvín O. (2022) Parasite of the month: Cimex lectularius and Cimex hemipterus (Bed bugs) Trends in Parasitology 38 : 919–920.
DOI: 10.1016/

Documents to download:
Stefka_2022_TrendParasitol (pdf)
Balvín O., Bubová T., Sasínková M., Martinů J., Löv J., Raška T., Štefka J. (2021) Tropické štěnice v evropských domácnostech Vesmír 07 : 460-463.
Balvín O., Sasínková M., Martinů J., Nazarizadeh M., Bubová T., Booth W., Vargo E.L., Štefka J. (2021) Early evidence of establishment of the tropical bedbug (Cimex hemipterus) in Central Europe Medical and Veterinary Entomology 35 : 462-467.
DOI: 10.1111/mve.12522
Drábková  M., Flegrová T., Myšková E., Hypša V., Štefka J. (2021) Genetic analysis of dicyemid infrapopulations suggests sexual reproduction and host colonization by multiple individuals is common Organisms Diversity and Evolution 21 : 437–446.
DOI: 10.1007/s13127-021-00493-0
Yousefi S., Sharifi M., Štefka J. (2021) Comparative phylogeography of two bat species and their mites in Iran shows impact of host sociality and vagility on population structure Journal of Zoological Systematics and Evolutionary Research 59 : 1557–1582.
DOI: 10.1111/jzs.12559
Bazsalovicsova E., Kráľová-Hromadová I., Juhásová L., Mikulíček P., Minárik G., Štefka J. (2020) Comparative analysis of monozoic fish tapeworms Caryophyllaeus laticeps (Pallas, 1781) Lühe, 1910 and newly described Caryophyllaeus chondrostomi Barčák, Oros, Hanzelová, Scholz, 2017 using microsatellite markers Parasitology Research 119 : 3995-4004.
DOI: 10.1007/s00436-020-06898-8
Martinů J., Štefka J., Poosakkannu A., Hypša V. (2020) "Parasite turnover zone” at secondary contact: a new pattern in host-parasite population genetics Molecular Ecology 29 : 4653-4664.
DOI: 10.1111/mec.15653
Vlček J., Štefka J. (2020) Association between louse abundance and MHC II supertypes in Galápagos mockingbirds Parasitology Research 119 : 1597–1605.
DOI: 10.1007/s00436-020-06617-3

More publications


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

Staff search