Vzhledem k aktuálnímu epidemiologickému vývoji je univerzitní eskalační semafor, s platností od pondělí 12. října 2020, přepnut na červený stupeň pohotovosti. Více informací zde.

Ekologická a evoluční biologie

Fascinuje nás rozmanitost života.

Podat přihlášku

International applicants for doctoral study (Czech and Slovak Republics applicants not included)
Termín podání přihlášky do půlnoci 30. 11. 2020

Co se naučíte

Ekologická a evoluční biologie je tematicky obsáhlý program, který je zaměřen zejména na studium biosystematiky, taxonomie, ekologie, paleoekologie, evoluční ekologie, evoluční biologie, etologie a rozmanitosti organizmů na úrovni druhů, populací, společenstev a flór a faun různých území. Důraz je kladen na studium interakcí mezi organizmy a jejich prostředím, a mezi organizmy navzájem, např. vztahy parazit-hostitel nebo predátor-kořist. Odborná šíře programu vede k jeho dělení do pěti specializací: Botanika, Ekologie, Hydrobiologie, Parazitologie a Zoologie. Specializace jsou definovány jak taxonomickým zaměřením, tak metodickými přístupy. Jejich vymezení ovšem není plně diskrétní: v některých tematických okruzích se částečně překrývají, což je odrazem mezioborovosti současné biologie.

Program má dvě základní formy studia, prezenční a kombinovanou, které se liší zejména v požadavcích na pravidelnou přítomnost studentů na pracovišti. Prezenční forma je také spojena se zapojením studentů do pravidelné výuky nebo její přípravy. Studenti prezenční formy pobírají měsíční stipendium dle platných a jednotných pravidel fakulty. Přechod z prezenční na kombinovanou formu je možný na základě žádosti studenta.

Praxe

Žádné informace nejsou k dispozici

Chcete vědět víc?

Další informace o studiu a dění na Ústavu botaniky a zoologie naleznete zde:

http://botzool.sci.muni.cz/

https://www.facebook.com/botzool

Uplatnění absolventů

Absolventi doktorského studijního programu Ekologická a evoluční biologie nacházejí uplatnění zejména v akademických nebo rezortních výzkumných ústavech, na vysokých školách přírodovědeckého, pedagogického, zemědělského, lesnického, veterinárního nebo farmaceutického zaměření, ve státních institucích ochrany přírody a krajiny, v přírodovědeckých odděleních muzeí a v soukromých firmách nebo nevládních organizacích zaměřených na problematiku ochrany přírody a životního prostředí nebo zdraví člověka i živočichů, a to jak v České republice, tak i v zahraničí.

Podmínky přijetí

Přijímací řízení probíhá formou prezentace tématu, uvažovaných metod a očekávaných výsledků uchazečem v angličtině a následného pohovoru, na základě čehož komise ověřuje a boduje úroveň odborných znalostí a předpokladů uchazeče k samostatné vědecké práci (0-200 bodů) a znalostí anglického jazyka (0-100 bodů).

Kritéria hodnocení

Pro přijetí musí uchazeč získat minimálně 120 bodů v odborné a minimálně 60 bodů v jazykové části zkoušky.

Termíny

1. 8. – 30. 11. 2020

Termín pro podání přihlášek

Podat přihlášku

Možnosti studia

Jednooborové studium se specializací

V rámci jednooborového studia se specializací má student možnost prohloubit si vědomosti v konkrétním zaměření daného studijního programu, specializaci si vybírá jednu. Název specializace pak bude uveden i na vysokoškolském diplomu.

Školitelé a výzkumná zaměření dizertačních prací

Školitelé

Součástí přihlášky je jméno předpokládaného školitele. Školitele si vyhledejte podle profilového zaměření ze seznamu školitelů a konzultujte s ním jeho potenciální školitelství a návrh projektu.

Výzkumná zaměření dizertačních prací

Specializace: Botanika

Aplikovaná ekologie rostlin: obnova biologické diversity a funkcí ekosystémů

Školitel: doc. RNDr. Jakub Těšitel, 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.
Biodiverzita městských biotopů

Školitel: doc. RNDr. Zdeňka Lososová, 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.

Diverzita evropské vegetace a biotopů

Školitel: prof. RNDr. Milan Chytrý, 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.

Funkční ekologie rostlin: od populací po společenstva

Školitel: doc. RNDr. Jakub Těšitel, 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.
Holocenní historie západokarpatských biotopů

Školitel: doc. Mgr. Michal Hájek, 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.

Mikrohabitaty lignikolních druhů hub

Školitel: doc. RNDr. Michal Tomšovský, Ph.D.

Hlavním cílem dizertační práce bude zhodnotit funkční vlastnosti jednotlivých druhů i komplexnějších taxonomických, morfologických nebo ekologických skupin hub vázaných na tlející dřevo. Konkrétně budou získávána a zpracovávána data týkající se vegetační pokryvnosti okolního porostu, tloušťky substrátu (kmeny, větev), lokace a historie substrátu (padlý kmen, stojící mrtvý kmen, vývrat), pokryvnosti mechorosty a stupně rozkladu dřeva, které jsou zásadní pro definici těchto mikrohabitatových ekologických nároků. Z hlediska lesních habitatů se bude jednat o především o druhy hub vázané na dominantní druhy dřevin (Fagus sylvatica, Abies alba, Picea abies) zastoupených v přírodních rezervacích s vyšším zastoupením mrtvého dřeva. Bude věnována pozornost i sukcesní řadě kolonizace dřeva druhy hub v reálném čase, kde se bude vycházet z již získaných originálních dat. Jedním z dílčích cílů bude i interpretace variability biodiverzity hub na celých mrtvých kmenech zahrnujících více mikrohabitatů.

Vegetační ekologie rašelinišť a jiných reliktních ekosystémů

Školitel: doc. 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.

Specializace: Ekologie

Aplikovaná ekologie rostlin: obnova biologické diversity a funkcí ekosystémů

Školitel: doc. RNDr. Jakub Těšitel, 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.
Bat movement ecology and pest control

Školitel: doc. Mgr. Tomáš Bartonička, 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.

Biodiverzita městských biotopů

Školitel: doc. RNDr. Zdeňka Lososová, 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.

Biologie a paleoekologie kontinentálních měkkýšů

Školitel: prof. RNDr. Michal Horsák, 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

Diverzita evropské vegetace a biotopů

Školitel: prof. RNDr. Milan Chytrý, 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.

Ekologie a diverzita rašelinišť

Školitel: doc. Mgr. Michal Hájek, 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.

Role ekologických bariér v biologické rozmanitosti, ekologii společenství a makroekologii

Školitel: doc. Jeffrey Clark Nekola, PhD.

Much variability in ecological pattern is driven by the isolation provided by barriers that keep biotas separated. The purpose of this doctoral research topic topic is to investigate the types of barriers present in natural systems and their importance in creating diversification in both ecological pattern and process. Before initiating the formal application process to doctoral studies, all interested candidates are required to contact doc. Jeffrey Nekola (nekola@sci.muni.cz) for an informal discussion. Examples of potential student doctoral theses: * The role of ecological barriers on species diversity at various spatial and temporal scales * The impact of ecological barriers on speciation and phylogeny * Impact of ecological barriers on ecological process at various scales. More information on the supervisor's scientific interests, projects and activities: http://biology.unm.edu/jnekola.

This topic has already been filled by Barbora Winterova.

Specializace: Hydrobiologie

Dlouhodobé odpovědi makrozoobentosu na antropické disturbance: vlivy znečištění, změny habitatů a klimatických změn

Školitel: Mgr. Jindřiška Bojková, Ph.D.

Akvatické biotopy jsou pod dlouhodobým tlakem různých antropických činitelů, které výrazně ovlivňují podmínky pro život bentických bezobratlých. Historická data o společenstvech a prostředí popisující stav před nástupem silného vlivu stresorů a dlouhodobá data jsou klíčová pro vyhodnocení dopadů antropických činitelů. Disertační práce se zaměří na několik případových studií, které jsou založeny na vyhodnocení změny prostředí a společenstev makrozoobentosu v čase.

Cílem disertace je: (i) popis dopadů silného znečištění a modifikace toků v minulosti na současná společenstva za pomoci porovnání s referenčními historickými daty (změny v diverzitě a distribuci jepic v uplynulých padesáti letech budou vyhodnoceny na základě porovnání dat o výskytu druhů ve 150 tocích po celé ČR v letech 1955–1960 a 2007–2010); (ii) vyhodnotit vliv narůstající teploty a hydrologie toků na jepice a testovat, zda dochází k homogenizaci společenstev (využita budou data z tzv. referenčních toků pro monitoring ekologického stavu toků ČR); (iii) popsat další vývoj společenstva litorálního makrozoobentosu ve vztahu ke změnám v chemismu vody jezer a také změnám v potravní nabídce souběžně se zotavujícího zooplanktonu a fytoplanktonu (zotavování šumavských jezer z acidifikace bude vyhodnoceno na základě zpracování dat z let 2015 a 2019, které doplní dosavadní data z let 1999–2010); (iv) popsat vývoj společenstev makrozoobentosu v tocích po revitalizaci a analyzovat trendy v datech z podrobného víceletého monitoringu tří toků na Šumavě bezprostředně po revitalizaci.

Téma je rezervováno pro Selmu de Donnovou.

Ekologické a historické determinanty výskytu velkých lupenonohých korýšů v Panonské oblasti

Školitel: prof. RNDr. Michal Horsák, Ph.D.

Large branchiopods (Anostraca, Notostraca, Laevicaudata and Spinicaudata) belong to the most endangered aquatic invertebrate taxa, which have been put in risk mainly by degradation and excessive loss of their natural habitats, i.e. temporary pools. These habitats are in central and eastern Europe the most frequently developed on arable land, mimicking natural types of these wetland habitats in big river floodplains after the large-scale river regulation. Although isolated and somewhat unstable by nature, temporary field wetlands have become endangered refugia of many wetland organisms. However, any comprehensive information about these communities is still missing from central Europe. Furthermore, no data also exist on environmental factors shaping these communities, current and historical distribution and temporal dynamics.

The aims of this PhD project are:
(i) to describe temporal dynamics of aquatic invertebrate communities inhabiting field wetlands concerning their life strategies and to determine main environmental drivers of successional patterns;
(ii) to elucidate intraspecific interaction by testing the effect of Triops cancriformis kairomones on the growth, maturation and survival of Branchipus schaefferi, and to explore the impact of T. cancriformis pheromones on the hatching success of its cysts in the laboratory;
(iii) to determine contemporaneous (e.g. type of wetland, water chemistry, climate, land-use) and historical (e.g. isolation, continuity, temporal frequency) predictors of large branchiopod occurrence (based on literature review and field sampling) to create a predictive model for their distribution in the northern part of the Pannonian region;
(iv) using the data gained in the aim #3 to evaluate the influence of historical land-use in three regions (SE Czech Republic, SW Slovakia and NE Austria) differing the human-made modification of the large branchiopod habitats, and to assess changes related to possible climate change scenarios.

The project is reserved for Alžběta Devánová.

Společenstva vodních bezobratlých toků vysychajících během klimatické změny

Školitel: doc. RNDr. Jana Schenková, 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.

Specializace: Parazitologie

Biologie a ekologie zoonotické hlístice Angiostrongylus cantonensis, původce meningitid u zvířat a člověka

Školitel: prof. MVDr. David Modrý, 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.

Celogenomové a amplikonové sekvenování jako nástroj studia strongylidních hlístic

Školitel: Mgr. Barbora Pafčo, 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.

Evoluční ekologie kongenerických monogeneí parazitujících sladkovodní ryby

Školitel: prof. RNDr. Andrea Vetešníková Šimková, PhD.

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.

Koexistence hybridních a polyploidních forem kaprovitých ryb: role parazitizmu

Školitel: prof. RNDr. Andrea Vetešníková Šimková, PhD.

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.

Molekulární epidemiologie a genomika GI nematodů přenášených mezi člověkem, primáty a domácími rezervoárovými hostiteli

Školitel: prof. MVDr. David Modrý, Ph.D.

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.

Srovnávací ekologie klíšťat a přenášených patogenů v ekosystémech střední Evropy

Školitel: prof. MVDr. David Modrý, 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.

Strategie parazitismu u bazálních linií Apicomplexa

Školitel: RNDr. Andrea Bardůnek Valigurová, 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.

Specializace: Zoologie

Biotické a abiotické interakce obratlovců

Školitel: doc. Mgr. Natália Martínková, 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.

Genetické koreláty hybridní sterility samců mezi evropskými poddruhy myší domácí

Školitel: Jaroslav Piálek, CSc.

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.

Rozmanitost a evoluční procesy u drobných savců subsaharské Afriky

Školitel: doc. Mgr. et Mgr. Josef Bryja, Ph.D.

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.

Informace o studiu

Zajišťuje Přírodovědecká fakulta
Typ studia doktorský
Forma prezenční ano
kombinovaná ano
Možnosti studia jednooborově ne
jednooborově se specializací ano
v kombinaci s jiným programem ne
Doba studia 4 roky
Vyučovací jazyk čeština
Spolupracující instituce
  • Akademie věd ČR
  • Ústav biologie obratlovců AV ČR
Oborová rada a oborové komise

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