Laboratory of phylogenomics and bioinformatics

In our laboratory, we strive to answer evolutionary questions based on the analysis of genomic data obtained using new sequencing technologies and bioinformatic approaches. The new methods of “massively parallel sequencing” allows to generate up to a hundreds DNA sequence fragments during a single instrument run. This brings previously unsuspected options to zoologists, in terms of phylogenetic and population genetic analysis, detection of speciation mechanisms (e.g., identifying the sections of the genome under selection), or creating genetic maps or metagenomics analysis of composite samples (e.g., stomach contents or bacterial community). In our laboratory, we have also implemented and optimized the Double Digest Restriction Associated DNA (ddRAD) Sequencing method to facilitate the efficient acquisition of large amounts (up to several hundreds) of homologous markers from hundreds of samples per instrument run, including the subsequent sequence data processing.

Head: MSc. Ing. Lubomír Piálek, Ph.D.
e-mail: lubomir.pialek@prf.jcu.cz; lpialek@yahoo.com
tel: +420 387 772 238

Researchers:
RNDr. Radka Piálková, Ph.D.
MSc. Klára Dragová

Collaborating institutions:
The National Grid Infrastructure is operated by MetaCentrum; Department of Ecology, Faculty of Science, Charles University; Institute of Vertebrate Biology, Czech Academy of Sciences; EMBL Genomics Core Facility, Heidelberg, Germany

Selected projects:
– Speciation mechanisms in the evolution of Neotropical cichlids (genus Crenicichla) (Lubomír Piálek, University of South Bohemia)
– Phylogeny and biogeography of Neotropical cichlids (Oldřich Říčan, University of South Bohemia)
– The evolution of reproductive isolation in our two nightingale species (Radka Reifová, Charles University)
– Reproductive modes in lizards (Lukáš Kratochvíl, Charles University)
– Population history of the glacial relic Saxifraga rosacea (Lenka Záveská Drábková, BÚ AV ČR)

Selected publications:
Kratochvíl, L., Vukić, J., Červenka, J., Kubička, L., Johnson Pokorná, M., Kukačková, D., … Piálek, L. (2020). Mixed‐sex offspring produced via cryptic parthenogenesis in a lizard. Molecular Ecology. Early view. https://doi.org/10.1111/mec.15617

Valterová, R., Procházka, P., Požgayová, M., Piálková, R., Piálek, L., Šulc, M., & Honza, M. (2020). Son or daughter, it does not matter: brood parasites do not adjust offspring sex based on their own or host quality. Journal of Ornithology, (161), 977–986. https://doi.org/10.1007/s10336-020-01782-9

Trněný, O., Vlk, D., Macková, E., Matoušková, M., Řepková, J., Nedělník, J., … Knotová, D. (2019). Allelic Variants for Candidate Nitrogen Fixation Genes Revealed by Sequencing in Red Clover (Trifolium pratense). International Journal of Molecular Sciences, 20, 5470. https://doi.org/10.3390/ijms20215470

Piálek, L., Casciotta, J., Almirón, A., & Říčan, O. (2019). A new pelagic predatory pike cichlid (Teleostei: Cichlidae: Crenicichla) from the C. mandelburgeri species complex with parallel and reticulate evolution. Hydrobiologia, doi: 10.1007/s10750-018-3754-1.

Říčan, O., Říčanová, Š., Dragová, K., Piálek, L., Almirón, A., & Casciotta, J. (2019). Species diversity in Gymnogeophagus (Teleostei: Cichlidae) and comparative biogeography of cichlids in the Middle Paraná basin, an emerging hotspot of fish endemism. Hydrobiologia, doi: 10.1007/s10750-018-3691-z.

Albrecht, T., Opletalová, K., Reif, J., Janoušek, V., Piálek, L., Cramer, E. R. A., … Reifová, R. (2018). Sperm divergence in a passerine contact zone: indication of reinforcement at the gametic level. Evolution, doi: 10.1111/evo.13677.

Burress, E. D., Piálek, L., Casciotta, J. R., Almirón, A., Tan, M., Armbruster, J. W., & Říčan, O. (2018). Island- and lake-like parallel adaptive radiations replicated in rivers. Proceedings of the Royal Society B, 285(1870), 20171762.

Pérez-Miranda, F., Mejía, O., Soto-Galera, E., Espinosa-Pérez, H., Piálek, L., & Říčan, O. (2017). Phylogeny and species diversity of the genus Herichthys (Teleostei: Cichlidae). Journal of Zoological Systematics and Evolutionary Research. doi.org/10.1111/jzs.12197

Piálek, L., Burress, E. D., Dragová, K., Almirón, A., Casciotta, J., & Říčan, O. (2018). Phylogenomics of pike cichlids (Cichlidae: Crenicichla) of the C. mandelburgeri species complex: rapid ecological speciation in the Iguazú River and high endemism in the Middle Paraná basin. Hydrobiologia, doi: 10.1007/s10750-018-3733-6.

Aghová, T., Šumbera, R., Piálek, L., Mikula, O., McDonough, M., Lavrenchenko, L. A., Meheretu, Y., Mbau, J. S., & Bryja, J. (2017). Multilocus phylogeny of East African gerbils (Rodentia, Gerbilliscus) reveals the history of the Somali-Masai savannah. Journal of Biogeography, 44(10), 2295-2307.

Awad, M., Piálek, L., Krejčí, Laugier, G., & Nedvěd, O. (2017). Paternity following multiple mating in ladybird Harmonia axyridis. Biocontrol, 62, 297-307.

Říčan, O., Piálek, L., Dragová, K., & Novák, J. (2016). Diversity and evolution of the Middle American cichlid fishes (Teleostei: Cichlidae) with revised classification. Vertebrate Zoology, 66(1), 1–102. (Monograph)

González-Tortuero, E., Rusek, J., Maayan, I., Petrusek, A., Piálek, L., Laurent, S., & Wolinska, J. (2016). Genetic diversity of two Daphnia-infecting microsporidian parasites, based on sequence variation in the internal transcribed spacer region. Parasites and Vectors, 9(1).

González-Tortuero, E., Rusek, J., Turko, P., Petrusek, A., Maayan, I., Piálek, L., … Wolinska, J. (2016). Daphnia parasite dynamics across multiple Caullerya epidemics indicate selection against common parasite genotypes. Zoology, 119(4).