Ecological and Evolutionary Biology

Are you worried about biodiversity decline and loss of ecosystem functions? If so, it may be worth devoting your career to the field of ecological restoration. The research focuses mainly on biodiversity restoration of anthropogenic habitats and development of sustainable practices for agro-ecosystems. While dealing mostly with plants, the abiotic context and ecological interactions, e.g. with insect herbivores and pollinators, will also be investigated. Methodology involves a number of different approaches including field observations and experiments, cultivation experiments and analyses of vegetation data. These approaches may be selected or combined to suit individual research questions and preferences of the candidates. Accordingly, individual topics may be studied under the specialization Botany or Ecology. Specific topics include but are not limited to:

• Development of regional seed mixtures
• Testing management measures to enhance biodiversity restoration on re-created grasslands
• Enhancing biodiversity of synanthropic habitats
• Promoting biodiversity and ecosystem functioning using ecosystem engineering abilities of hemiparasitic plants

Please note: Before submitting an official application, the candidates are requested to contact Jakub Těšitel (tesitel@sci.muni.cz) to discuss the specification of the topic.

Školitel

doc. RNDr. Jakub Těšitel, Ph.D.

This research topic aims to explore the diversity of plant communities in urbanized areas and factors, which shape their structure and function. The results of the study will contribute to deeper understanding of biodiversity changes in the face of increasing urbanization. The work either combine field work with analyses of vegetation data or is focused on data analyses only.

Specific topics for individual PhD projects can include:

• Diversity and ecology of urban biota
• Phylogenetic and functional diversity of urban biota
• Potential changes in diversity under increasing urbanization
• Impact of urban areas on biotic invasion
• Human made habitats as potential secondary refugia of native species

Please note: Before submitting an official application, the candidates are requested to contact Zdeňka Lososová (lososova@sci.muni.cz) to discuss the specification of the topic. Candidates from any country are welcome.

Školitel

doc. RNDr. Zdeňka Lososová, Ph.D.

This broad research topic includes various analyses of diversity of European vegetation and habitat types. It includes work with large data on species composition in vegetation plots stored in the European Vegetation Archive (http://euroveg.org/eva-database) and also fieldwork in selected regions of Europe where gaps in vegetation data coverage have been identified.

The basic requirements include knowledge of plants in the field and skills with vegetation data analysis. If your focus is on data analysis rather than on field botany, refer to the same topic in the specialization Ecology

Specific topics for individual PhD projects can include:

• classification of selected vegetation type across Europe or a European region
• analyses and mapping of species alpha, beta and gamma diversity across Europe or European region for specific vegetation or habitat types
• analyses of phylogenetic diversity of plant communities across Europe
• analyses of functional diversity (plant trait patterns) of plant communities across Europe
• relationships between plant community diversity and environmental factors and regional environmental history
• comparative analyses of European vegetation with analogous vegetation on other continents
• patterns of plant invasions in European vegetation and habitat types
• recent changes in species composition and diversity of plant communities and their relationships to environmental change (e.g. land-use change, climate change, eutrophication)
• development of habitat classification systems for applications in nature conservation, forestry or land management

Please note: Before submitting an official application, the candidates are requested to contact Milan Chytrý (chytry@sci.muni.cz) to discuss the specification of the topic. Candidates from any country are welcome, especially if they have previous skills from botanical fieldwork in Europe.

Školitel

prof. RNDr. Milan Chytrý, Ph.D.

The PhD candidate interested in determinants of phylogenetic (PD) and functional (FD) diversity of plant communities will combine field-work with analyses of large datasets of vegetation plots on the European scale obtained from European vegetation Archive. The aims of the study are, for target vegetation type: (1) To detect PD and/or FD of studied plant communities; (2) To detect main factors driving these changes; and (3) to predict how these characteristics of plant communities will be affected by the ongoing climatic change.

Školitel

doc. RNDr. Zdeňka Lososová, Ph.D.

This research topic aims at exploring functional traits of plants; specifically, how they affect plant population dynamics, species interactions and coexistence, ecological niches and geographical distribution. Methodology involves a number of different approaches including field observations and experiments, cultivation experiments and analyses of vegetation data. These approaches may be selected or combined to suit individual research questions and preferences of the candidates. Specific topics include but are not limited to:

• Seasonal niche differentiation as a mechanism of species coexistence in steppe-grasslands
• Large-scale patterns of functional diversity on the European continent
• Ecological interactions of hemiparasitic plants

Please note: Before submitting an official application, the candidates are requested to contact Jakub Těšitel (tesitel@sci.muni.cz) to discuss the specification of the topic. Candidates from any country are welcome.

Školitel

doc. RNDr. Jakub Těšitel, Ph.D.

The research aims to explore the Holocene history of the Western Carpathian habitats using palaeoecological sequences obtained from peat, carbonates or lake sediments. The proxies are those that are relevant for botany, i.e. pollen, macrofossils of bryophytes and vascular plants or diatoms. Other proxies (macrofossils of animals, geochemical proxies) are covered by the topic „Mire ecology and diversity“ offered within the Ecology package. The local multi-proxy studies as well as synthetic large-scale studies could be conducted.

Examples of potential student doctoral projects:

• Holocene development of summit grasslands in the Western Carpathians
• Holocene history of recently endangered ecosystems in the Western Carpathians
• Dynamics of major tree taxa during the Holocene in the Western Carpathians and the surroundings (synthesis)
• Coincidences between prehistoric settlement and agriculture and vegetation development in the Western Carpathians (synthesis)

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Michal Hájek (hajek@sci.muni.cz) for informal discussion and topic specification.

Školitel

prof. Mgr. Michal Hájek, Ph.D.

The research aims to explore the diversity and vegetation ecology of European mires in terms of vascular plants, bryophytes and diatoms. The outcomes contribute to protection of these fascinating but currently vanishing ecosystems and to general ecological and biogeographical knowledge. Other relict ecosystems that have experienced wider distribution in the past (at the Quaternary scale) and now are endangered could be studied as well. Target habitats include also partially anthropogenic ones that recently act as refugium for the relict flora, such as fen and steppe-like grasslands.

Examples of potential student doctoral projects:

• Vegetation diversity and ecology of European mires (specific regions or mire types could be selected)
• Recent changes in fen or grassland ecosystems (explored e.g. using permanent plots)
• Distribution, phylogeography, genetics or ecology of specialised and endagered mire plants (vascular plants. bryophytes)
• Distribution, phylogeography, genetics or ecology of glacial and Early Holocene relicts
• Ecology of extremelly species-rich steppe grasslands of White Carpathians
• Testing appropriate active management measures to protect species-rich relict ecosystems

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Michal Hájek (hajek@sci.muni.cz) for informal discussion and topic specification.

Školitel

prof. Mgr. Michal Hájek, Ph.D.

Are you worried about biodiversity decline and loss of ecosystem functions? If so, it may be worth devoting your career to the field of ecological restoration. The research focuses mainly on biodiversity restoration of anthropogenic habitats and development of sustainable practices for agro-ecosystems. While dealing mostly with plants, the abiotic context and ecological interactions, e.g. with insect herbivores and pollinators, will also be investigated. Methodology involves a number of different approaches including field observations and experiments, cultivation experiments and analyses of vegetation data. These approaches may be selected or combined to suit individual research questions and preferences of the candidates. Accordingly, individual topics may be studied under the specialization Botany or Ecology. Specific topics include but are not limited to:

• Development of regional seed mixtures
• Testing management measures to enhance biodiversity restoration on re-created grasslands
• Enhancing biodiversity of synanthropic habitats
• Promoting biodiversity and ecosystem functioning using ecosystem engineering abilities of hemiparasitic plants

Please note: Before submitting an official application, the candidates are requested to contact Jakub Těšitel (tesitel@sci.muni.cz) to discuss the specification of the topic. Candidates from any country are welcome.

Školitel

doc. RNDr. Jakub Těšitel, Ph.D.

This broad research topic includes various aspects of the ecology of bats. (1) basic research, the central motive of which is to determine the importance of bats for the predation of selected pests and pest control of agricultural stands. The diet composition and supply will be studied at disaster sites and on sites without significant pest influence. The outcomes contribute to to understanding the importance of bats in environmental services. (2) applied research focused on the permeability of the landscape for bats, where the main barriers are line structures (e.g. roads). There are insufficient mitigation measures to enable bats to safely overcome such a barrier. At the same time, areas, corridors through which bats move in the landscape are not well defined.

Specific topics for individual PhD projects can include:

• bat aggregate response with regard to the species foraging strategy. Whether and how often bats forage agricultural pests? Bat as intelligent predator – study of functional response, distribution of food niches. Analysis of the predation pressure - comparison of bats and birds.
• evaluation of the effectiveness of road permeability measures, mitigation measure recommendation
• research and categorisation of migration corridors, migration activity of bats

MORE INFORMATION: www.sci.muni.cz/zoolecol/verteb

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Assoc. Prof. Tomáš Bartonička (bartonic@sci.muni.cz) for informal discussion.

Školitel

doc. Mgr. Tomáš Bartonička, Ph.D.

This research topic aims to explore the diversity of plant communities in urbanized areas and factors, which shape their structure and function. The results of the study will contribute to deeper understanding of biodiversity changes in the face of increasing urbanization. The work either combine field work with analyses of vegetation data or is focused on data analyses only.

Specific topics for individual PhD projects can include:

Diversity and ecology of urban biota
Phylogenetic and functional diversity of urban biota
Potential changes in diversity under increasing urbanization
Impact of urban areas on biotic invasion
Human made habitats as potential secondary refugia of native species

Please note: Before submitting an official application, the candidates are requested to contact Zdeňka Lososová (lososova@sci.muni.cz) to discuss the specification of the topic. Candidates from any country are welcome.

Školitel

doc. RNDr. Zdeňka Lososová, Ph.D.

This doctoral research project focuses on various aspects of diversity patterns, ecology, paleoecology, phylogeny and systematics of terrestrial and freshwater molluscs.

Before initiating the formal application process to doctoral studies, all interested candidates are required to contact Prof. Michal Horsák (horsak@sci.muni.cz) for an informal discussion.

Examples of potential student doctoral theses:

• Drivers of land snail diversity on various spatial and temporal scales
• Phylogeny of land snails and cryptic species complexes
• Biotic interactions affecting mollusc communities
• Development and diet of land snail
• Molluscs in palaeoecological reconstructions
• Molluscs as indicators of past changes since the Last Glacial Maximum

More information on the supervisor's scientific interests, projects and activities: https://www.researchgate.net/profile/Michal_Horsak

Školitel

prof. RNDr. Michal Horsák, Ph.D.

This broad research topic includes various analyses of diversity of European vegetation and habitat types. It includes work with large data on species composition in vegetation plots stored in the European Vegetation Archive (http://euroveg.org/eva-database).

The basic requirements include skills with statistical data analysis (especially in R) or in geoinformatics geographics (geographic information systems or remote sensing). The candidates whose focus is on botanical fieldwork rather than on data analysis should apply for the same topic in the specialization Botany.

Specific topics for individual PhD projects can include:

• analyses and mapping of species alpha, beta and gamma diversity across Europe or European region for specific vegetation or habitat types
• analyses of phylogenetic diversity of plant communities across Europe
• analyses of functional diversity (plant trait patterns) of plant communities across Europe
• relationships between plant community diversity and environmental factors and regional environmental history
• comparative analyses of European vegetation with analogous vegetation on other continents
• patterns of plant invasions in European vegetation and habitat types
• recent changes in species composition and diversity of plant communities and their relationships to environmental change (e.g. land-use change, climate change, eutrophication)
• development of habitat classification systems for applications in nature conservation, forestry or land management

Please note: Before submitting an official application, the candidates are requested to contact Milan Chytrý (chytry@sci.muni.cz) to discuss the specification of the topic. Candidates from any country are welcome.

Školitel

prof. RNDr. Milan Chytrý, Ph.D.

The research aims to explore the diversity and ecology of European mires, especially calcium-rich fens. The outcomes contribute to protection of these fascinating but currently vanishing ecosystems and to general ecological and biogeographical knowledge. The study organisms are especially bryophytes and vascular plants (i.e., vegetation), but also important groups of other organisms such as invertebrates or protists. Recent as well as fossil assemblages are studied.

Examples of potential student doctoral projects:

• Understanding the recent anthropogenic changes in fen ecosystems and testing the appropriate conservation management
• Biondication potential of mire organisms, congruence among mire organisms
• Ecology and ecosystem role of endangered mire bryophytes
• The role of water chemistry, hydrology and climate on species composition and interspecific interactions in mires
• Quaternary history of mire ecosystems and its mirroring in the current distribution and diversity patterns

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Michal Hájek (hajek@sci.muni.cz) for informal discussion and topic specification.

Školitel

prof. Mgr. Michal Hájek, Ph.D.

Research on brood parasitism has enabled considerable advances in our understanding of evolutionary dynamics in general, but it has been largely restricted to avian and insect model systems, limiting its general inferences to evolutionary theory. This project will study the origin, evolutionary trajectories, ecological setting and behavioural adaptations in the brood parasitic system of the cuckoo catfish (Synodontis multipunctatus) and their cichlid fish hosts in Lake Tanganyika and in captivity. It will employ a set of behavioural, genetic, morphological and ecological methods, and utilize the access to field sites in Zambia and Tanzania, as well as large experimental populations of catfish and their hosts in accredited fish facility at the Institute of Vertebrate Biology, Czech Academy of Sciences. The project will characterize interactions between cuckoo catfish and their hosts, as well as contrast between parasitic and non-parasitic closely related catfish species. Overall, this will provide novel insight into conditions for the origin and maintenance of brood parasitism.

Školitel

prof. RNDr. Martin Reichard, Ph.D.

The concept of ecosystem health integrates environmental conditions with the impacts of anthropogenic activities to provide information that can support the sustainable use and management of natural resources. As ecosystem health cannot be measured or observed directly, suitable indicators must be developed and implemented to assess it. Monitoring the diversity and composition of gastrointestinal endosymbionts of sentinel species offers valuable perspectives and tools for investigating and monitoring ecosystem health and improving conservation efforts. Non-human primates, have been proposed as sentinels for the surveillance of emerging pathogens and as ideal models for basic research of natural transmission dynamics, with special emphasis on great apes. Sentinel species can also reflect overall ecosystem and assist in increasing monitoring efficiency at the ecosystem level.
The student will test a hypothesis that anthropogenic disturbance of tropical ecosystems have an impact on the taxonomic/structural and functional patterns of gastrointestinal symbiotic communities of African great apes, sentinels of tropical ecosystem health. The student will use the HTS based metagenomic approaches to study bacterial and selected eukaryotic (e.g. strongylid) communities within gut ecosystem of gorillas and chimpanzees inhabiting model sites in the Albertine Rift and/or Congo Basin. The student will seek indicator taxa for anthropogenic disturbance using a complex approach focusing on both bacterial and eukaryotic assemblages inhabiting the gastrointestinal ecosystem.
The ambition is to develop an approach, which could be used not only to screen great apes’ health, but also to evaluate the health of the whole ecosystem via these sentinel species including predicting risks of emerging infectious disease outbreaks. Ultimately, we aim to implement the monitoring of complex gut communities of great apes as a useful tool in wildlife conservation strategies.
Supervisor: Mgr. Klára Petrželková, Ph.D., email: petrzelkova@ivb.cz
Co-supervisor: Mgr. Barbora Pafčo, Ph.D.

Školitel

Mgr. Klára Petrželková, Ph.D.

Fishes are largely constrained to aquatic environment, but otherwise evolved a vast array of adaptations and life history strategies. With solid understanding of their evolutionary relationships, phylogenetically controlled comparative methods can provide insights into evolutionary trajectories, adaptations and constraints. This project will address life history traits in several clades of freshwater fishes, including killifish, cyprinids and cichlids, for which well-resolved phylogenetic hypotheses are available. It will compare evolution of characters related to reproductive biology, including sexual selection, and to life in challenging environmental conditions. Small part of the project will include experimental work that will provide small dataset of life history traits in bitterling fishes, which will be later used for comparative analyses. The study will be conducted in close collaboration with the Institute of Vertebrate Biology, Czech Academy of Sciences and its accredited fish facility. Overall, this project should provide novel insight into how life history traits evolve and the role of phylogenetic constraints on the evolution of novel adaptations.

Školitel

prof. RNDr. Martin Reichard, Ph.D.

This PhD project aims to improve our understanding of diversification mechanisms in evolutionary and palaeobiogeographic perspectives. Although at ecological time scales highest richness is often seen in systems subjected to moderate rates of environmental fluctuation, at deeper scales it has often been assumed that higher diversity will occur in more stable regions. This study examines whether climatic stability and the existence of multiple Pleistocene refugia promote higher genetic diversity. This question is investigated using molecular genetic methods, phylogenetic analyses, and climate models. Three genera of micro land snails (Euconulus, Pyramidula and Columella) are studied as model systems and their populations in the Holarctic will be analysed.

Školitel

prof. RNDr. Michal Horsák, Ph.D.

The research aims to explore join impact of climatic changes and human alterations on aquatic communities, especially on small occasionally drying river networks. The research is a part of broad international project developing predictions for future biodiversity responses to scenarios of climate change. The study organisms for student doctoral project are aquatic and semiaquatic invertebrates of group Clitellata. They represent the model group of contrasting answers to environmental stressors, having high tolerance to anthropogenic stress (pollution, habitat modification etc.), possessing adaptations for survival during drying period, however, however, with low dispersal abilities. For obtaining different geographic and climatic setting, Czech drying river network will be compared with European ecoregion in different climatic zone to derive current and future community responses to drying.
Examples of potential student doctoral projects: * Spatial and temporal changes of clitellate communities in drying river network,* A comparison of clitellate communities in drying river networks of two different European ecoregions, * The role of dispersal modes for recovery of aquatic assemblies in disturbed (i.e. artificially) and undisturbed (i.e. close to pristine conditions) river parts of drying river network
Please note: Before submitting an official application, the candidates are requested to contact Jana Schenková (schenk@sci.muni.cz) to discuss the specification of the topic.

Školitel

doc. RNDr. Jana Schenková, Ph.D.

The genus Angiostrongylus includes range of parasitic metastrongylid nematodes occurring mostly in rodents and carnivores. A.cantonensis, with rats as its definitive hosts, can infect humans and other mammals (incl. domestic animals) and birds as accidental hosts, causing severe neurological problems. Resulting disease is considered emerging problem worldwide, with impact on wildlife, domestic animas and human health. Being associated with invasive rat species, A. cantonensis represents a prominent example of biological invasion, especially in remote island ecosystems, that lack native, terrestrial mammals and in which the introduced rodents can assume highly novel ecological roles following colonization, including the pathogen spread.

Project revolves around arising questions on ecology of A.cantonensis and risks of its invasion into temperate ecosystems. Topic combines field research on ecology of A.cantonensis in its natural hosts (rodents, mollusks, reptiles) in Macaronesian and Mediterranean islands, with parasite genomics (used as a tool for identification and phylogeography) and with experimental work on invertebrate (mollusks, planarians, insects) and vertebrate hosts (rodents, poikilotherms). If funding and situation allows, part of the research is to be carried out in collaboration with foreign partners in Spain, Italy, Australia and SE Asia.

Školitel

prof. MVDr. David Modrý, Ph.D.

Supervisor: Mgr. Barbora Pafčo, PhD (Institute of Vertebrate Biology, Czech
Academy of Sciences – IVB CAS)

Co-supervisor: Prof. MVDr. David Modrý, PhD (Department of Botany and Zoology
Masaryk University)

Strongylid nematodes are common intestinal parasites, infecting a wide range of
mammalian taxa including humans and closely related non-human primates (NHPs).
They are important human pathogens causing serious health problems and they
constitute a serious health threat to domestic animals, but information about their
impact on health of wild NHPs is limited. Repeated and extensive use of anthelmintic
treatment especially in livestock results in drug resistance and treatment failures. On
contrary, strongylid nematodes can be used in an experimental type of
immunotherapy in humans, so called helminth therapy. Until recently, there were no
high-quality genome sequences for hookworms, making DNA-based diagnosis
difficult. Between 2014 and 2019, four complete human hookworm genomes were
published. However, the genome sequences originate from laboratory-cultivated
individuals in hamsters, which had likely undergone extensive genetic adaptations to
their hamster hosts before genome sequencing.

The main goal of the PhD project is to understand molecular biology of strongylid
nematodes using whole genome sequencing of hookworms naturally infecting humans
and NHPs. Student will assemble third-generation genomes from long-read (Oxford
Nanopore, PacBio) and short-read (Illumina) sequencing data for the strongylid
nematodes. The long-term collaboration between multidisciplinary research group
(Pafco, Modry, Petrzelkova, et al.) and lab of Dr. Erich Schwarz, in particular
strengthened by the Fulbright internship of B. Pafco, contributes to the selection of
suitable methodologies, which will be used during the proposed project. Firstly, the
student will focus on genome sequencing of hookworms naturally infecting humans
and NHPs inhabiting Dzanga-Sangha Protected Areas in Central African Republic,
our long-term field site, where people and free-ranging NHPs live in close proximity.
This is the only locality, where other non-americanus Necator species were described
in humans. Sequencing the genomes of non-laboratory-adapted hookworms from the
wild populations of NHPs and sympatrically living humans will provide a substantially more accurate insight into hookworm genes that enable human infection.
Further, the student will use bioinformatic approaches for the discovery of
immunogens and characterization and prioritization of anthelmintic targets, necessary
for development of better anti-hookworm drugs and vaccines as well as for better use
of strongylids during the helminth therapies. Secondly, student will analyze whole
genomes of worldwide-distributed Necator americanus obtained from geographically
different human populations. Using demographic models together with population
genomics he will reconstruct the probable route and timing of migration of N.
americanus from Africa to other parts of the world.

Specific aims: (i) to assemble complete genome sequences for the human hookworms
from NHPs and humans, (ii) to compare the genomes of human Necator americanus
with originally “primate” Necator species with the aim to find human/primate
adaptations, (iii) to describe proteins and protein coding genes in strongylid
nematodes, in order to search for functional and medically/clinically important traits,
(iv) to apply state-of-the-art genomics and bioinformatics tools, in order to obtain
comprehensive genomic data, which may help to understand epidemiology of
hookworms and (v) to reconstruct the probable route and timing of N. americanus
migration from Africa.

Školitel

Mgr. Barbora Pafčo, Ph.D.

Současná taxonomie parazitických klanonožců (Copepoda) sladkovodních ryb je založena převážně na morfometrických popisech, jelikož pro většinu druhů je k dispozici jen minimum molekulárních dat. Mnoho popisů aktuálně platných druhů klanonožců je tak vzhledem k současnému preferovanému integrativnímu taxonomickému přístupu nedostatečných. Rovněž chybí fylogenetické studie zabývající se vztahy mezi hlavními evolučními parazitickými liniemi korýšů a jejich postavením v rámci celé třídy Copepoda, tak jako i kofylogenetické studie. Z těchto důvodů může aplikace molekulárních analýz při charakterizaci parazitických klanonožců vést k objasnění systematických otázek a testování fylogenetických a biogeografických predikcí.

Cíle práce:
i) analyzovat diverzitu ektoparazitických klanonožců sladkovodních ryb z vybraných zoogeografických oblastí pomocí morfologicko-molekulárních analýz;
ii) rekonstruovat fylogenetické vztahy mezi parazitickými korýši a zároveň objasnit původ parazitických linií v rámci celé skupiny Copedoda a analyzovat potenciální biogeografické asociace v rámci jednotlivých linií parazitických korýšů;
iii) studovat hostitelsko-parazitické vztahy s ohledem na geografickou distribuci, stanoviště a životní strategii hostitelů.

Školitel

Mgr. Mária Seifertová, Ph.D.

One of the research topic of the group of evolutionary ecology of host-parasite interactions represents the studies of host-parasite coevolution using the systems of monogenean parasites and their associated fish hosts. Phylogenetic and cophylogenetic approaches have been applied to infer the patterns of parasite speciation and diversification and to reveal historical routes of dispersion of freshwater fish with current fragmented dispersion. The actual project of A. Vetešníková Šimková focused on the investigation of diversity and phylogeny of host-specific congeneric monogeneans parasitizing cyprinid fish in Middle East representing the important place of historical contacts of fauna among three continents. Actually there is the open position for PhD student within the above mentioned project. The main objective of the PhD thesis will be to analyze the diversity and phylogeny of monogeneans exhibiting different level of host specificity (Dactylogyrus, Gyrodactylus and Diplozooidae). These parasites will be used as supplementary tool to infer the historical contacts of cypriniform fish between Middle East and Mediterranean areas.
Please note: Before submitting an official application, the candidates are requested to contact Andrea Vetešníková Šimková (simkova@sci.muni.cz) to discuss the specification of the topic.

Školitel

prof. RNDr. Andrea Vetešníková Šimková, PhD.

Biologické invaze představují nedílnou součást globálních změn a jako takové mají mimořádný dopad na biodiverzitu. Invazní druhy rostli a živočichů sebou do nových ekosystémů přináší spektrum nepůvodních symbiotických organizmů, které zahrnuje i řadu patogenů. Invazní a nepůvodní druhy a jimi přenášené patogeny jsou tak jednou z významných příčin "nových" onemocnění, která označujeme jako emerging diseases. Tyto patogeny pak mohou mít dopad na původní druhy a stát se i příčinou zoonotických infekcí člověka. Projekt se zaměřuje na nepůvodní druhy savců v evropské fauně (výhledově v Africe) a jimi přenášené patogeny, především ze skupiny helmintů. Jeho cílem je kombinovat široké spektrum metod od přímého průkazu parazitů ve studovaných druzích hostitelů, přes experimentální práci s modelovými druhy savců až po pokročilé laboratorní metody založené na fylogenetických analýzách diverzity, genomice a metagenomických analýzách společenstev studovaných parazitů. V prvních dvou letech projektu se předpokládá práce se dvěma modelovými helminty: hlístice Angiostrongylus cantonensis (Nematoda: Metastrongyloidea) v hlodavcích a hmyzožravcích ostrovních ekosystémů mediteránu a (2) Ashworthius sidemi (Trichostrongyloidea) v evropských kopytnících.

Školitel

prof. MVDr. David Modrý, Ph.D.

One of the research topic of the group of evolutionary ecology of host-parasite interactions represents the studies of genetic disruption in hybrid and polyploid fish hosts. Even natural hybridization in cyprinids is common phenomenon, the frequency of hybrids are relatively low. In contrast, the coexistence of the forms with different ploidy level is extraordinary evolutionary phenomenon in fish. Basically, research group of A. Vetešníková Šimková focused on genetic disruption in fish hybrids hypothesizing the potential broken host-parasite co-adaptation especially for host specific parasites missing their closely associated hosts. However, the genes involved in metabolism and reproduction are in obvious interest as their pattern of expression may explain the mechanisms of current coexistence of hybrid and polyploid forms in cyprinids.
Actually there is the open position for PhD student within the above mentioned research topic. More specifically, the aim of the PhD thesis will be to analyze the transcriptome profile of diploid-polyploid complex of cyprinid fish and to search for the overexpression and underexpression of genes involved in growth, metabolism, reproduction and immunity. The PhD project will also include the experimental parasite infection; the quantification of the differentially expressed genes associated with parasites will be analyzed in diploid, triploid and tetraploid forms of hosts.
Please note: Before submitting an official application, the candidates are requested to contact Andrea Vetešníková Šimková (simkova@sci.muni.cz) to discuss the specification of the topic.

Školitel

prof. RNDr. Andrea Vetešníková Šimková, PhD.

Pathogens shared across humans-wildlife-livestock interface not only affect human and livestock health and global economy, but represents also serious threat for biodiversity. Up to 75% of emerging human disease is considered to have animal origin (being zoonotic), many of them involving wildlife. Vice-versa, increased anthropogenic pressure leads to spillover of parasites from humans and domestic animals into communities of free-ranging mammalian hosts, especially in close-contact situation (captive animals, ecotourism, urban wildlife). Uncovering the molecular diversity in model parasite-multihost systems is a key for understanding the transmission ecology are resulting disease. Strongyloides nematodes are selected as a model study organism as they are widely distributed and transmitted in a vast diversity of mammalian hosts and include important human and animal pathogens. Thanks to phylogenetic proximity of their hosts, Strongyloides spp./genotypes are commonly shared between humans and other primates, with some species of domestic/feral animals involved in local transmission cycles. Project expands ongoing research on zoonotic pathogens involving great apes and cercopithecine primates living in free ranging populations (Africa, Asia), as well as in captive and semi-captive settings. Project combines methodologies of parasite detection and alfa/beta-taxonomy (microscopy and basic NAATs) with sophisticated molecular tools (HTS). In later stage of the project, parasitological data will be combined with parasite and host ecology in order to perform ecological niche modelling through component-based approaches to identify key reservoir species and prioritizing areas for surveillance and control.

Školitel

prof. MVDr. David Modrý, Ph.D.

Struktura parazitických populací, zejména parazitů, u kterých do vývojového cyklu vstupuje rybí hostitel, je velice málo studována vzhledem k nedostatku populačně-genetických markrerů nebo jejích nízké informativnosti. Cílem dizertační práce bude proto studium populační struktury parazitických druhů dvou vybraných taxonů Platyhelminthes a testování relevantních hypotéz (role geografické izolace a vliv toku genů na strukturování parazitických populací, fenotypová populační diferenciace jako potenciální adaptace nebo probíhající speciace, role hostitelské specifity ve strukturování parazitických populací, vliv komplexity vývojového cyklu na populační strukturu parazitů v rybím mezihostiteli/hostiteli). Monogenea a Digenea jsou taxony s odlišnou parazitickou strategií, tj. vykazují odlišnosti z pohledů hostitelské specifity a komplexity vývojového cyklu. Monogena jsou obecně považována za hostitelsky specifická a jejich vývojový cyklus je jednohostitelský. Naopak Digenea vykazují nižší hostitelskou specifitu a jejich vývojový cyklus zahrnuje jednoho nebo více mezihostitelů. Ryby představují definitivní hostitele pro většinu monogeneí, zatímco v případě digeneí vstupují do role mezihostitele nebo definitivního hostitele. Jako modelové druhy studia budou použity dva fylogeneticky příbuzné druhy monogeneí, jeden striktní specialista, druhý generalista, a tři druhy digeneí: první zástupce s dvouhostitelským vývojovým cyklem, kde ryba stojí v pozici definitivního hostitele, parazit s úzkou hostitelskou specifitou na úrovni definitivního hostitele, druhý zástupce rovněž s dvouhostitelským vývojovým cyklem, kde ryba stojí v pozici definitivního hostitele, parazit s širokou hostitelskou specifitou, a třetí zástupce s tříhostitelským vývojovým cyklem, kde ryba stojí v pozici mezihostitele, parazit má strategie generalisty.

Školitel

prof. RNDr. Andrea Vetešníková Šimková, PhD.

The project will first focus on the taxonomic and genetic characterization of the helminth communities of rodent individuals to then explore their potential role in the radiation processes of the Old and New endemic rodents in NG and in the invasion process of the most recent murine colonizers. The parasites selected for this study are helminths of the digestive tract and lungs but blood parasites may also be investigated as complementary models.
iv) Time schedule:
2023 and 2024: Taxonomic and genetic characterization of the helminth communities of rodents in New Guinea
Digestive tracts and lungs from rodents and sympatric marsupial species preserved in ethanol will be dissected. Helminth parasites will be first determined based on parasitological keys and available literature. If some new species are discovered and sufficient material is available, the candidate will perform a taxonomic description of the new species. Finally, the candidate will describe the diversity and community structure of the helminth parasites in Hydromyini and Rattini rodents. We hypothesized that the structure of the helminth communities of Hydromyini rodents will be more diverse due to the older time of colonization and radiation of this group compared to those in the Rattini. By comparing the helminth communities between invasive and endemic rodent species, the candidate will investigate which of the following biological mechanisms: enemy release, immunocompetence advantage or novel weapon may have played a role in the invasion process of the recent colonizers.

2025 Co-evolutionary study of helminths and their rodent hosts
Previous studies have shown that nematodes from the superfamily Trichostrongyloidea and the family Oxyuridae are likely to be the most relevant models for co-phylogenetic studies because they are prevalent, have a direct life cycle and are quite specific to their hosts.
In this task, the candidate will compare patterns of parasites co-diversification between Old and New endemics. The candidate will genotype the nematodes using mt-COX-1 and nuclear ITS-5.8S-ITS2 markers. The genotyping and phylogeny of the rodent hosts have been or are currently investigated either by genomics or Sanger sequencing of several mitochondrial and nuclear markers (mt-CYTB, BRCA1, IRBP, RAG1) by F. Vejmelka for his PhD thesis and will be available to the candidate for co-phylogenetic analyses.

2026. Role of parasitism in the radiation of both rodent groups
By integrating data from parasite ecology and genetics along with data on rodent ecology and geography, we will examine the mechanisms driving the diversification of NG rodents and compare their relative impacts on the two radiations under study.

Školitel

Joëlle,Marie,Chantal Goüy de Bellocq Feuquieres, Ph.D.

Ixodid ticks are vectors of range of tick-borne pathogens, many of which are important for human health. As the reservoirs of infections are almost exclusively free-ranging vertebrates, the transmission cycles of all important tick-borne pathogens tightly depend of the tick ecology in context of given ecosystems. In temperate Palearctic area, the tick genus Ixodes transmits range of pathogens among vertebrates and man. Even though the dominant tick vector in this complex is Ixodes ricinus and I. persulcatus, recently described Ixodes inopinatus attracts lot of attention, as its ecology and vectorial capacity remains unknown. Main goal of the topic is to uncover major aspects of ecology of this new tick species, provide comparison with largely sympatric I. ricinus and evaluate its importance as disease vector, targeting mainly bacterial and protozoan pathogens. The topic combines methods of field ecology, molecular and classical taxonomy of ticks and molecular detection and phylogenetics of pathogens.

Školitel

prof. MVDr. David Modrý, Ph.D.

Apicomplexans are well known as significant pathogens of humans and animals that cause serious diseases such as malaria, toxoplasmosis or cryptosporidiosis. Recent knowledge of Apicomplexa is mainly based on studies of practically important and evolutionary advanced representatives, mostly belonging to intracellular coccidians. However, data on parasites of invertebrates (especially from marine environment) will help to establish a more realistic phylogenetic framework of Apicomplexa and to identify primitive and advanced strategies of parasitism, their emergence and evolution. It is assumed that ancestral apicomplexans parasitised marine annelids and then they spread to other marine invertebrates, freshwater and terrestrial invertebrates, and finally to vertebrates. Our research is dedicated to the reconstruction of the divergence of parasitism strategies in poorly studied Apicomplexa basal groups, which in various ways realise the intracellular, epicellular, and extracellular parasitism in different host organs and cavities. Data on general morphology, ultrastructure (attachment site, cell cortex, cytoskeleton) and biology (feeding and motility modes, life cycle features) of invertebrate parasites - blastogregarines, gregarines, coccidians and alveolates closely related to Apicomplexa - will reveal the main features of their parasitism. Comprehensive analysis of morphological and molecular phylogenetic data will allow to reconstruct the pathways of the origin and evolution of various parasitism strategies in Apicomplexa.

For research purposes we use a combination of parasitological methods including field sampling of host organisms, experimental in vitro assays, microscopic analyses (light, electron and confocal laser scanning microscopy), (immuno)cyto/histochemical, biochemical, and molecular biological approaches.

The student will benefit from teamwork, but at the same time will be fully supported by his/her personal scientific development, independent scientific thinking and initiative.

Examples of potential student doctoral projects:
1. Evolution of host-parasite interactions in early branching Apicomplexa
2. The original motor in gregarine motility: Which came first, subpellicular microtubules or actin filaments?

PLEASE NOTE: Before initiating the formal application process to doctoral studies, interested candidates are requested to contact Andrea Bardůnek Valigurová (andreav@sci.muni.cz) for informal discussion and topic specification.

Školitel

doc. RNDr. Andrea Bardůnek Valigurová, Ph.D.

The main aim of this proposed PhD study is the isolation, identification and quantification of bioactive plant compounds extracted from selected plants consumed by Indonesian Orang-utans for presumed selfmedication purposes, with potential antiparasitic effects on important waterborne protozoal diseases (WBD) namely amoebosis. The potential effect of selected plant food components of orang-utan will be tested in in vitro model.

Školitel

Assoc. Prof. MVDr. Ivona Foitová, Ph.D.

Ongoing climate change is among the the most important stressors affecting biological communities worldwide, increasing average temperatures, the magnitude of seasonal and daily temperature fluctuations, and the severity of extreme weather events. Freshwater habitats are particularly vulnerable as they are often fragmented across the terrestrial landscape and inhabited by organisms that have limited escape ability. Therefore, the stability of these communities depends largely on the individual ability to adapt or acclimate to new conditions. This work will enable more realistic predictions of organismal responses to climate change and their impacts on populations and communities. The student will work to evaluate the complex strategies that amphibians (or other ectotherms) use to cope with a warming climate. This means that the student will combine laboratory and mesocosm experiments to evaluate ectotherm responses to predictable and stochastic variations in temperature and precipitation. The model organisms in this study are newts or alternatively other species that interact with them. The student will gain practical skills in conducting laboratory and mesocosm experiments, maintaining a laboratory newt colony, using advanced technologies to measure behaviour (automated tracking systems) and energy metabolism (aquatic and aerial respirometry), and statistical modelling (univariate and multivariate generalised mixed models). Before submitting an official application, all interested candidates are invited to contact Assoc. Prof. Lumír Gvoždík (gvozdik@ivb.cz) to discuss the details of this topic. Candidates from all countries are welcome.

Školitel

doc. Mgr. Lumír Gvoždík, Ph.D.

Some spider species are expanding their range. For example, Zodarion rubidum has spread from northern Spain to Scandinavia and Ukraine during last 100 years. So the goal of this project would be to investigate how do the spread affects phenotype of the species. Specifically, it includes the following aims (1) to record type of microhabitat and ant prey Zodarion rubidum captures across Europe, (2) to perform morphometric measurements on selected traits (such as body size, colouration), (3) to reconstruct the spread by means of molecular methods to test a hypothesis of human-mediated transportation, (4) to compare hunting efficiancy of populations from south, central and northern Europe, (5) to investigate the role of endosymbionts on the dispersal.

Školitel

prof. Mgr. Stanislav Pekár, Ph.D.

Overview: Organisms respond to their environment by searching for and exploiting a suitable set of resources, wherein they encounter and interact with other organisms. The interactions with the environment and other biota form a complex network of influences that determines survival, fitness and reproduction.

Objectives: The student will combine laboratory experiments, field observations and publicly available data to develop computational models that address the mechanisms governing outcome of vertebrate interactions. The potential tools range from molecular genetic techniques, to spectral imaging or high-resolution microscopy. The student will benefit from working in a diverse research group, where pursuit of their own research interests and opportunities will be encouraged.

Example Ph.D. projects:

• Escaping predator pressure by migration and camouflage
• Three-way interactions leading to diseases - the host, the pathogen and their environment

Examples on past student project can be found at https://www.ivb.cz/en/person/natalia-martinkova/

Before initiating the formal application process to doctoral studies, interested candidates should contact Assoc. Prof. Natália Martínková (martinkova@ivb.cz) for an informal discussion.

Školitel

doc. Mgr. Natália Martínková, Ph.D.

Hematological and biochemical parameters belong among the basic data studied when assessing the health status of wild animals and their populations. Temperate bats, as small hibernating mammals, are subject to the immunosuppressive effect of hibernation, which is mainly manifested by a reduction in the number of available phagocytic cells. This decrease can be explained by a decrease in the production of neutrophils, their increased apoptosis, the adhesion of cells to the vein endothelium or their temporary accumulation in some organs such as the lungs, liver or spleen. In bats, however, high phenotypic plasticity of hibernation strategies has been recorded similarly as in various factors of specific and non-specific immunity. The demands of the individual sexes are also different, thanks to the different timing of reproduction investments. There is a lack of resources on the topic of blood parameters in bats, however, with the increased interest in bats due to their epidemiological potential for zoonotic diseases, there is also a growing interest in research into their immune system. As part of the research, the student will solve the problems of the influence of ecological factors on hematological and biochemical parameters in bats with an overlap into practical application in the differential diagnosis of various diseases and pathogens.

Školitel

doc. Mgr. Jan Zukal, Dr., MBA

1. Collect data on the morphological, ecological and behavioural traits of ant-mimicking arthropods;
2. conduct a meta-analysis of these traits in order to test hypotheses on mimetic accuracy;
3. evaluate the hypothesis of myrmecomorphy in selected arthropod species;
4. analyse the defence chemicals of selected myrmecomorphic arthropods (flies, true bugs, beetles, etc.) to test the hypothesis of quasi-Batesian to Müllerian mimicry;
5. model the selection for myrmecomorphy using an analytical model.

Školitel

prof. Mgr. Stanislav Pekár, Ph.D.

Relevance of the topic
Our Herpetological Diversity research group has been focusing on the diversification of Central African amphibians and reptiles for several years. The topic of this PhD study will build on our team’s previous results and add new insights to the existing knowledge. Previous studies have mostly lacked material from the central Congolian lowland forests. The central objective of this project is to assess the level of distinctiveness of populations of various frog species from the central Congolian forests from those north and west of the Congo River. The specific objectives of this PhD study will be threefold and will focus on selected relevant taxa. (1) Phylogeography; (2) Evolutionary history; (3) Taxonomy. Phylogeography will apply conventional DNA sequencing and comparative approaches to frogs with different ecologies (terrestrial, semiaquatic, scansorial) and high-throughput sequencing (ddRADseq) to one or two selected, geographically well-sampled taxa (probably Ptychadena). Reconstruction of evolutionary history will target one of the diverse but not well-systematically resolved taxa distributed in the Congo Basin, probably the Arthroleptis sylvaticus complex. Methodologically, it will combine molecular and morphological (including osteological; micro-CT scanning) data. Taxonomical implications will be natural outputs of some previous sub-projects.

Aims (in points)
1) Phylogeography of selected frog taxa representing different ecological groups: terrestrial, semiaquatic, scansorial.
2) Evolutionary history of a morphologically seemingly uniform but genetically diverse taxon, probably the Arthroleptis sylvaticus complex.
3) Taxonomy of selected frog taxa: revisions, new species descriptions.

Timeline
Year 1: Compiling samples for laboratory work; performing ddRADseq laboratory work (selected taxa); possible fieldwork; involvement in analyses on a team project; co-authorship on a team project: manuscript 1 (terrestrial frogs).
Year 2: Fieldwork; ddRADseq-data analyses; foreign internship (probably California Academy of Sciences, demographic model-based analyses, collaboration with Dr. Rayna Bell) preparation of manuscript 2 (first-author 1; phylogeography of semiaquatic and scansorial frogs); doctoral examination.
Year 3: Foreign internship (probably University of Florida, micro-CT analyses, collaboration with Dr. David Blackburn); analysis of morphological/osteological data in the evolutionary framework; preparation of manuscript 3 (first-author 2; evolutionary history of a selected taxon).
Year 4: Final analyses necessary for taxonomic outputs; preparation of manuscripts 4 & 5 (selected taxonomic implications); dissertation preparation.

Requirements and support
The material is mostly already available, some of it will be acquired during planned field research, through international cooperation and by borrowing museum material or during museum visits. Laboratory and experimental work will be carried out in the laboratories of the Institute of Vertebrate Biology of the CAS, research facility Studenec, and the project will be financially supported by the Czech Science Foundation (GAČR #23-07331S).

Školitel

RNDr. Václav Gvoždík, Ph.D.

Two house mouse subspecies, Mus m. musculus and M. m. domesticus, that diverged between 0.5 MYR, undergo ancient speciation. Experimental crosses between two laboratory domesticus and one musculus strains produce F1 sterile males controlled by epistatic interaction between 2 loci, the Prdm9 gene on chromosome 17 and X-linked gene(s) Hstx. However, no laboratory borne F1 sterility was reported from a natural hybrid zone between the subspecies. The aim of the PhD study will be assessing and linking allelic variation in Prdm9 gene and Hstx2 region and their interactions to phenotypic variation in hybrid males that will originate from two resources (1) F1 intra- and intersubspecific hybrids and BC males from sterile F1 combinations among 43x43 pairwise intersubspecific crosses of wild-derived strains across the Western Palearctic (https://housemice.cz/en) and (2) hybrid males sampled directly in a hybrid zone between house mice. Analysis of allelic variation in Hstx2 region will be focused on Fmr1nb gene and miR465 miRNA cluster, based on previous studies. In BC males, genome-wide scans of hybrid progeny will be used to map quantitative trait loci (QTL) and infer genotype-phenotype associations to test the validity of laboratory based model of F1 sterility in natural mouse populations. In males from hybrid zone genetic variation in PRDM9/Hstx and Y-linked loci will be detected and linkage and introgression will be analysed to infer their effect on gene flow between the parental genomes.
Molecular analyses and breeding experiments will be realized in a research facility of the Institute of Vertebrate Biology of the Czech Academy of Sciences in Studenec. The student is expected to authorize four papers within 2021-2024 (review on sterility; epistasis in the house mouse hybrid zone; linkage of genetic variation at Prdm9/Hstx loci to fitness in F1 hybrids; QTL mapping of hybrid male sterility). The study is supported by the Czech Science Foundation (grant 19-12774S) in 2019–2021. The project provides also salary for half-time employment.

Time table
2020-2021
Molecular analysis of sex linked and mtDNA diagnostic markers of mice sampled in allopatric populations and hybrid zone;
Selection of 5000 SNP from a STUWMDA 620k Illumina platform array in a way to optimize sets of strain diagnostic markers within musculus strains and genome diagnostic markers between musculus and domesticus genomes; submission of selected SNP and 700 mouse samples to a third party for SeqSNPs;
Sequencing Prdm9 gene in inbred strains; derivation of musculus Prdm9sterile/fertile congenic strains;
Designing of methods of qPCR and expression analysis of genes within the Hstx locus;
Mastering techniques of spermatocytes cells isolation at various stages of spermatogenesis.
2021-2022
Molecular analysis of sex linked and mtDNA diagnostic markers of mice sampled in allopatric populations and hybrid zone;
Genome-wide analysis of QTL associated with sterility from backcross males using data obtained from 5000 SNP array;
Sequencing Prdm9 gene in wild mice, qPCR and expression analysis of genes within the Hstx locus in sperm from different stages of spermatogenesis;
derivation of Prdm9sterile/fertile congenic strains;
Analysis of splice variants in the Fmrnb1 gene and expression analysis of a miR gene cluster in the Hstx region.
2022-2023
Molecular analysis of sex linked and mtDNA diagnostic markers of mice sampled in allopatric populations and hybrid zone; design and experimental crosses of domesticus WDS x musculusFertilebackground.Prdm9sterile and musculusSterilebackground.Prdm9fertile congenic strains;
Genome wide analysis of QTL associated with sterility from backcross males and genotype data obtained from 5000 SNP array;
Data completion, finalization of manuscripts;
Doctoral examination.
2023-2024
Finalization of manuscripts;
Writing up and defence of PhD.

Školitel

Jaroslav Piálek, CSc.

Overview: Diversity of sub-Saharan Africa is still poorly known compared to other tropical regions. Together with the fact that human population is most intensively increasing in this region, knowledge of spatial and temporal patterns of African diversity is highly required for its efficient protection. In the last decade, we performed comprehensive sampling of small mammals (mainly rodents and shrews) in various ecosystems of sub-Saharan Africa, allowing deep understanding of evolutionary processes affecting intra- and interspecific biodiversity. The application of up-to-date approaches of genomics, morphometry, physiology, etc., allows to test the mechanisms causing disproportionate accumulation of diversity in various parts of the continent.

Objectives: The student will work in an international group of young scientists performing interdisciplinary research aiming to understand the evolutionary processes modulating biodiversity in sub-Saharan Africa. The special focus is on the role of environmental (including climatic) changes in Quaternary in processes of speciation and adaptation. Main model groups are rodents, shrews and their various parasites. The outputs of the research are used in biogeographic regionalization, taxonomy, and identification of priority areas for nature conservation.

Examples of Ph.D. projects:
(1)Evolution of rodent biodiversity in Eastern Afromontane biodiversity hot-spot
(2) Biogeographic partitioning of Eastern Africa using comparative phylogenomics of small mammals
(3) Role of elevation on speciation processes in the Ethiopian center of endemism

Ongoing and past student projects can be found at https://www.ivb.cz/en/person/josef-bryja/

Before initiating the formal application process to doctoral studies, interested candidates should contact Assoc. Prof. Josef Bryja (bryja@ivb.cz or bryja@brno.cas.cz) for an informal discussion.

Školitel

prof. Mgr. et Mgr. Josef Bryja, Ph.D.