Zuzana Musilová

CURRICULUM VITAE – ZUZANA MUSILOVÁ

My general research interest is in evolutionary genomics and transcriptomics of fishes.

EDUCATION AND ACADEMIC CAREER:

2015 – pres. – Assistant Professor (since September 2015) Charles University in Prague, Czech Republic.

2011 – 2015 – Post-Doctoral fellow (September 2011 – August 2015) SciEx-NMS foundation; Novartis - Universität Basel Excellence Scholarship for Life Sciences Salzburger Lab, Zoological Institute, University of Basel project: CICHLIDOMICS: next generation sequencing and molecular evolutionary analysis in East African cichlid fishes

2006 – 2011 – Ph.D. (Zoology) Charles University in Prague, Czech Republic thesis: Phylogeny and biogeography of Neotropical and African cichlids: multilocus phylogenetic methods in evolutionary studies

2001 – 2006 – M.Sc. (Zoology) Charles University in Prague, Czech Republic thesis: Molecular phylogeny of Neotropical cichlids of the tribe Cichlasomatini (Perciformes: Cichlidae: Cichlasomatinae) with biogeographic implications

LABORATORY RESEARCH EXPERIENCE:

2011 – 2015 – Salzburger Lab, Zoological Institute, University of Basel, Switzerland. 2004 – 2011 – Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Science, Czech Republic, Europe. 2006 (Jan–May) – research stay in Cytogenetic laboratory in Department of Environmental Biology, University of Lisbon, Portugal, Europe. 2004 – 2006 – Laboratory for Biodiversity Research, Department of Zoology, Charles University in Prague, Czech Republic, Europe.

LIST OF SCIENTIFIC PUBLICATIONS:

Publication record: 16 peer‐reviewed articles: 14 in journals with Impact Factor (incl. 1 Monograph)

Peer‐reviewed articles with Impact Factor:

MUSILOVÁ, Z., RICAN. O., RICANOVA, S., JANSTA P, GAHURA O., NOVAK J. 2015. Phylogeny and historical biogeography of trans-Andean cichlid fishes (Teleostei: Cichlidae). Vertebrate Zoology. 65 (3), 333-350

STAROSTOVÁ, Z., & MUSILOVÁ, Z. (in press). The complete mitochondrial genome of the Madagascar ground gecko Paroedura picta (Squamata: Gekkonidae). Mitochondrial DNA.

CORTESI, F.*, MUSILOVÁ, Z.*, STIEB, S.M., HART, N.S., SIEBECK, U.E., MALMSTRØM, M., TØRRESEN, O.K., JENTOFT, S., CHENEY,K.L., MARSHALL, N.J., CARLETON, K.L., & SALZBURGER, W. 2015. Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes. Proceedings of National Academy of Sciences, 112(5), 1493–1498; * = equal contribution

(highlighted and commented by: Harris, R.M. & Hofmann, H.A. 2015. Seeing is believing: Dynamic evolution of gene families. PNAS 112(5), 1252–1253)

MUSILOVÁ Z., INDERMAUR A., BITJA NYOM A.R., TROPEK R., MARTIN C. & SCHLIEWEN U.K. 2014. Report on persistence of Stomatepia mongo, an endemic cichlid fish of the Barombi Mbo crater lake, SW Cameroon, with notes on its ecology and behaviour. Copeia 3, 556–560.

DORN, A.*, MUSILOVÁ, Z.*, PLATZER, M., REICHWALD, K., & CELLERINO A. 2014. The strange case of East African annual fish: aridification correlates with diversification for a savannah aquatic group. BMC Evolutionary Biology 14 (1), 210; * = equal contribution

TROPEK R., SEDLÁČEK O., BECK J., KEIL P., MUSILOVÁ Z., ŠÍMOVÁ I. & STORCH D. 2014. Comment on “High-‐resolution global maps of 21st-‐century forest cover change”. Science, 344: 981.

HODAŇOVÁ, L., KALOUS, L., MUSILOVÁ, Z. 2014. Comparative cytogenetics of Neotropical cichlid fishes (Nannacara , Ivanacara and Cleithracara) indicates evolutionary reduction of diploid chromosome numbers. Comparative Cytogenetics, 8(3): 1–15 (2014).

CHOLEVA, L., MUSILOVÁ Z., KOHOUTOVA-‐SEDIVA A., PACES J., RAB P., JANKO K. 2014. Distinguishing between incomplete lineage sorting and genomic introgressions: complete fixation of allospecific mitochondrial DNA in a sexually reproducing fish (Cobitis; Teleostei), despite clonal reproduction of hybrids. PLoS ONE. (doi: 10.1371/journal.pone.0080641)

MUSILOVÁ, Z., KALOUS, L., PETRTYL, M., & CHALOUPKOVA, P. 2013. Cichlid fishes in the Angolan headwaters region: molecular evidence of the ichthyofaunal contact between the Cuanza and Okavango-‐Zambezi systems, PLoS ONE 8(5):e65047.

JANKO, K., MARSHALL, C., MUSILOVÁ, Z., HOUDT, J.V., COULOUX, C., CRUAUD, C., & LECOINTRE, G. 2012. Multilocus analyses of an Antarctic fish species flock (Teleostei, Notothenioidei, Trematominae): Phylogenetic approach and test of the early-radiation event. Molecular Phylogenetics and Evolution, 60(3), 305–16. MUSILOVÁ, Z., SCHINDLER, I. & STAECK, W., 2009 -‐ Description of Andinoacara stalsbergi sp. n. (Teleostei: Cichlidae: Cichlasomatini) from Pacific coastal rivers in Peru, and annotation on the phylogeny of the genus. Vertebrate Zoology, 59(2): 131-‐141.

MUSILOVÁ, Z., ŘÍČAN, O. & NOVÁK, J., 2009 -‐ Phylogeny of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae) based on morphological and molecular data, with the description of a new genus, Journal of Zoological Systematics and Evolutionary research, 47: 234-‐ 247.

MUSILOVÁ, Z., ŘÍČAN, O., JANKO, K. & NOVÁK, J., 2008 -‐ Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae), Molecular Phylogenetics and Evolution, 46:2, 659-‐672.

Monographs:

ŘÍČAN, O., MUSILOVÁ, Z., MUŠKA, M. & NOVÁK, J., 2005: Development of Colour Patterns in Neotropical Cichlids (Perciformes: Cichlidae: Cichlasomatinae). Folia Zoologica, 54: Monograph 1. 1-‐ 46.

Peer-reviewed articles without Impact Factor:

KALOUS, L., MUSILOVÁ, Z., PETRTYL, M., & CHALOUPKOVA, P. 2010. First record of African pike Hepsetus odoe (Bloch, 1794) from the river Kukemá (upper Kwanza River Basin). Proceedings of the „Workshop on Animal Biodiversity”, Jevany. p. 61–64. ISBN: 978-‐80-‐213-‐2146-‐5

KRAJÁKOVÁ, L., MUSILOVÁ, Z., KALOUS, L., Karyotype characterizations in two South American Cichlasomatini species (Perciformes, Cichlidae). Proceedings of the „Workshop on animal biodiversity”, Jevany. p.78 – 80. ISBN: 978-‐80-‐213-‐2146-‐5

LIST OF SUBMITTED MANUSCRIPTS OR IN PREPARATION: CORTESI, F., MUSILOVÁ, Z., STIEB, S. M., HART, N. S., SIEBECK, U. E., CHENEY, K., SALZBURGER, W., MARSHALL, N. J. From crypsis to mimicry: changes of skin pigmentation and the configuration of the visual system during ontogenetic habitat transitions in a coral reef fish. (submitted). MUSILOVÁ, Z., CORTESI, F., HANEL., R., STIEB., S., DE BUSEROLLES., F., MATSCHINER., M, MALMSTROEM, M., JENTOFT, S., TORENSEN, U., DAVIES, W., CARLETON, K. MARSHALL., N.J., SALZBURGER, W. Opsin genes duplications and alternative origin of color vision in deep sea fish? (in prep.) MUSILOVÁ, Z. & SALZBURGER, W. Phylogenomics of cichlid fishes from lake Tanganyika: new approach to solve old questions? (in prep.) MUSILOVÁ, Z., STAROSTOVÁ, Z. & SALZBURGER, W. Mitogenomics of neotropical cichlid fishes shows higher substitution rate in dwarf species. (in prep.) MUSILOVÁ, Z., GANTE, H.F., HABLUETZEL, P. Adaptive radiation in South American cichlids? Evolution of the genus Apistogramma. (in prep.)

SELECTED CONFERENCE CONTRIBUTIONS:

2015, September (talk) – Ecological speciation in evolution of cichlids from the Barombi Mbo crater lake. Cichlid Science meeting in Graz, Austria.

2015, August (talk) – Loss and (re)gain of color vision in deep-‐sea fishes: uncovering the secrets of 100 teleost genomes. Congress of European Society for Evolutionary Biology (ESEB) in Lausanne, Switzerland.

2014, September (talk) – Cichlid fishes from crater lakes: model for sympatric speciation research. Workshop: Genomics of the Speciation Continuum in Fribourg, Switzerland.

2014, June (poster) – Life in the dark: evolution of opsin genes in cichlid fishes from the Barombi Mbo crater lake and adaptation to deep waters. Congress of Society for Molecular Biology and Evolution (SMBE) in San Juan (Puerto Rico).

2014, February (talk) – Biogeography of Neotropical dwarf cichlid genus Apistogramma: Amazonia is the species-‐richest but not an ancestral region. Biology 14 in Geneva, Switzerland.

2013, August (poster) – Adaptive evolution of the opsin genes in African crater lake cichlids? Congress of European Society for Evolutionary Biology (ESEB) in Lisbon, Portugal.

INVITED RESEARCH TALKS: 2010 – University of South Bohemia, Ceske Budejovice, Czech Republic 2014, 2015 – Charles University in Prague, Czech Republic (2 x) 2015 – National Museum of Natural History, Madrid, Spain

RELEVANT COURSES AND WORKSHOPS:

2014, September – “Genomics of the Speciation Continuum” – workshop in Fribourg, Switzerland 2014, January – „RNA-seq: from experiment planing to statistical data analysis“ – Swiss Institute of Bioinformatics, Basel, Switzerland 2013, October – „OIST Practical Workshop on High-Throughput Sequencing Data Analysis” – Okinawa Institute of Science and Technology, Japan (selected participant) 2013, January – „Advanced NGS course – de novo assembly“ – Wageningen, Netherlands 2012, January – „Workshop on Genomics“ - Cesky Krumlov, Czech Republic 2012, January – „Advanced topic: Bioconductor“, Cesky Krumlov, Czech Republic 2009, Sept/Oct – „Phylogeographical Analysis“ - Workshop and PhD/Master course, Department of Botany, Prague, Czech Republic 2008, January – „Workshop on Molecular Evolution in Europe“, Cesky Krumlov, Czech Republic 2006, September - „Phylogenetic Analysis: Theory and Practice“ by Willi Hennig Society workshop, Institute of Botany, Pruhonice, Czech Republic

CONFERENCE (CO-)ORGANIZER: 2017 – Main organizer of the scientific meeting “Cichlid Science” in Prague 2021 – Preliminary member of the organization committee for ESEB (European Society for Evolutionary Biology) meeting in Prague

STUDENT SUPERVISION: Krajáková Lucie – Master thesis, 2009. University of Life Sciences, Prague, Czech Rep. Albergati Lia – Master thesis, 2014. University of Basel, Switzerland Hodaňová Lucie – PhD. thesis, 2014. University of Life Sciences, Prague, Czech Rep. (consultant) TEACHING EXPERIENCE:

2010 – Analyzing phylogenetic data (weekend course, main lecturer; University of Life Sciences, Prague); 2007 – 2009 – Phylogenetic Workshop (co‐organizer of the workshop on a monthly basis; Charles University in Prague); 2008 – “Perciformes” – 1 lecture in the framework of Ichthyology lectures (University of Life Sciences, Prague); 2007, 2008 – European fish identification (practical to “Zoology of Vertebrates” lecture; Charles University in Prague); 2007, 2008 – Fish dissection (practical to “Animal Morphology” lecture; Charles University in Prague); 2007 – Genetics Methods is Zoology (practical part, AFLP; Charles University in Prague); 2006, 2007 – “Fish behaviour” (practical ethological observation in the framework of “Ethology” lecture; Charles University in Prague)

2011 – Phylogenetics, 2011 – Biogeography (lectures for Biology Olympiad summer camp “Bestvina”); 2011 – Vertebrate evolution, 2009 – What is a species?, 2009 – Fish Identification (lectures for the high-school Biology summer camp “Arachne”)

REVIEWER SERVICE FOR PEER-REVIEW JOURNALS: BMC Evolutionary Biology, Journal of Biogeography, Environmental Biology of Fishes, Hydrobiologia, BioMed Research International

SELECTED AWARDS & GRANTS:

“Life under dark pressure: adaptive evolution in deepwater cichlid fishes”. Novartis Universität Basel Excellence Scholarship for Life Sciences, 2013. Donor: Novartis & University of Basel. „CICHLIDOMICS: next generation sequencing and molecular evolutionary analysis in East African cichlid fishes“. Post-Doctoral fellow, 2011 - 2013. Donor: SciEx-NMS. „Adaptive evolution of cichlid fishes from volcanic crater lakes: how to adapt vision to live in deepwater and to catch more food?“ Fieldwork grant, 2013. Donor: Basler Stiftung für Biologische Forschung. „Phylogeography of African cichlid genera Serranochromis and Tilapia: white spot on the Angola biogeographic map“. 2010. Donor: Grant Agency of Charles University (GAUK). „Evolution of the Neotropical Cichlids (Perciformes: Cichlidae): multiloci methods in the phylogenetic study“. 2007 – 2009. Donor: Grant Agency of Charles University (GAUK).

FIELD WORK EXPERIENCE:

2014, 2012 – Zambia, 2014, 2013, 2012, 2011 – Cameroon (5 x), 2010 – Panama, Costa Rica, 2009 – Colombia, 2008, 2007 – Angola, 2008 – Bosnia and Herzegovina, 2007 – Peru, 2005 – Venezuela, 2004 – Argentina