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Guidelines for PhD study in botany

These principles are set by the PhD. Study Board (further Board) primarily as a recommendation and a guide for PhD students. The principles are based on the Higher Education Act, the Study and Examination Regulations of the Charles University, the Scholarship Regulations of the Charles University and the Rules for the Organisation of Studies at the Faculty of Science.




• Doctoral study is primarily an independent study of the candidate under the guidance of a supervisor, in which the primary role is played by the one's own research culminating in a doctoral thesis and its presentation to the scientific community.

• The study includes participation in specialised lectures and presentations at seminars.

• Part of the full-time form of study is participation in scientific events at the department (seminars, post-seminars, defences, etc.).

• The Doctoral Board assesses the course of doctoral studies at least once a year.

• The supervisor is usually an employee of the Faculty of Science of the Charles University or the Botanical Institute of the CAS. If the supervisor is not an employee of either of these institutions, the PhD student must also have a consultant, either from the Faculty of Science or the Botanical Institute.


Requirements in the admission procedure

• The prerequisites for study, for independent scientific work and the level of professional knowledge are demonstrated by an oral interview with members of the admissions committee.

• The admissions committee is usually 3-5 members; all members of the PhD. Study board may participate in the admissions examination.

• Other admission requirements and further conditions of the admission procedure are set annually by the Dean of the Faculty and can be found on the web page of the doctoral studies at the Faculty of Science.

• For the admission exam, the applicant submits to the committee a proposal of the topic and content of the thesis in written and electronic form and a potential supervisor. The proposal for the topic and content of the thesis shall address the scientific merit of the topic, its feasibility, funding opportunities, and connections to existing teams in the field; typically 1-3 pages of text. (The proposal may be structured according to the Doctoral Thesis Plan Outline.)

• For the entrance exam, they will prepare a presentation of this topic of the thesis lasting about 10 minutes. In addition to the candidate's professional skills, the admissions committee evaluates this presentation, the scientific interest and relevance of the topic, and the clarity of the presentation.

• During the admission exam, the participation of a potential supervisor is possible, whose interest and opinion is an important guide in the decision of the admission committee. If the supervisor is not an employee of the Faculty of Science or the Institute of Botany, the participation of a consultant is also appropriate. The participation of the potential supervisor and the consultant in the admission exam is the responsibility of the applicant.

• The reason for the low score of the applicant in the admission procedure is mainly:

• the applicant has not demonstrated the necessary prerequisites for study and independent scientific work

• the applicant has not submitted a proposal for the topic and content of the thesis and a potential supervisor.

• the applicant has not convinced the admissions committee that the proposed topic is sufficiently relevant and that it can be used as the basis for a defensible doctoral thesis


Doctoral student's study plan

• The study plan is drawn up by the doctoral student together with the supervisor and, if necessary, with the head of the department where the dissertation will be carried out. The doctoral student's study plan shall be submitted to the Doctoral Board via SIS by the deadline. It is reviewed and approved by the Board according to the timetable set by the Dean.

• This plan includes:

• Planned course of research activities including study visits and internships and recommended literature. This should be prepared in accordance with the Principles for the Doctoral Thesis Plan.

• The names of the specialised lectures/courses that the PhD student will attend and the deadlines for their completion set so that the majority of them are completed during the first half of the study (in the first 3 semesters). The Board may require the supplementation of the draft study plan with additional specialised lectures or courses so that the level of knowledge at the end of the study corresponds to the required standard of the Faculty of Science of Charles University. It is desirable that the chosen courses are related to the topic of the dissertation. Courses organised for PhD students (not Master's lectures) should be included in priority.

• Participation in the departmental seminar and post-seminar of the relevant department throughout the study period is a mandatory part of the study plan.

• state doctoral examination in the (3rd-)4th semester of study.


• The student may build on his/her previous qualifying work in the doctoral thesis, but there must be a significant qualitative shift in the exploration of the topic. The results of previous qualifying work may become part of the publications in the doctoral thesis, but only as an additional element. Publications resulting solely or mainly from data submitted in the master degree thesis may not be part of the doctoral dissertation.

• The curriculum may be amended and refined with the approval of the Board.

• Changes to the topic of the doctoral thesis are subject to approval by the Board. The proposal to change the topic must include a statement from the supervisor. In this case, the Board will consider whether a new curriculum will be required.



Requirements for PhD students during their studies

• Dissertation work. This is evaluated by the supervisor and the supervisor's evaluation is part of the doctoral student's report submitted once a year to the Board.

• By the end of the second semester of study at the latest, the doctoral student must present his/her topic at a departmental seminar where a public discussion of the topic of the doctoral thesis will take place. This presentation typically takes the form of a poster.

• Defense of the thesis report for the first year of study before a committee appointed by the Board. Successful defence of the topic and the first year's thesis is a prerequisite for continuation of studies.

• Passing the examinations prescribed by the study plan.

• The state doctoral examination, usually in the (3rd-)4th semester of study.

• No later than the end of the sixth semester of study, the doctoral student will present the results of his/her project and the outlook for the rest of the doctoral studies at a seminar of the department. Prior to this presentation, the doctoral student will present the tangible outputs of his/her project (articles, manuscripts, posters, etc.) to the Board.

• By the end of the third year at the latest, the PhD student will have spent at least one month in a research internship. A scientific internship is a study or work placement at a scientific workplace with a topic close to the topic of the doctoral thesis, usually abroad. It must not be a stay at the supervisor's workplace.

• Beyond this obligation, the Board recommends that each student spend a minimum of three months at such a workplace (again, preferably abroad). 

• It is highly advisable that the PhD student (i) submits a first-authored article to the review process by the end of the second year of his/her studies, (ii) submits a second article (which does not have to be first-authored) to the review process by the end of the third year of his/her studies, and (iii) submits a rough draft of the introduction of his/her PhD thesis to the Board by the mid-term of the fourth year of studies.

• Presentation of the results of the PhD project to the professional public. The Board recommends that during the first three years of study (4 years for the combined form of study) the PhD student present his/her results at least once (in the form of a poster or lecture) at a renowned international conference (usually foreign) and publish in reputable professional journals during the same period.

• Students are expected to actively participate in the scientific activities of the department, especially in regular departmental seminars and in doctoral seminars and post-seminars.

• The date of the doctoral examination and the seminar presentation are usually postponed by one year for students of the combined form of study (doctoral examination in the 5th-6th semester, seminar presentation after the 7th semester).

• Teaching activities at the department are not part of the doctoral student's study obligations. However, it is desirable that doctoral students participate in teaching activities to a reasonable extent during their studies.

• Changes to the duties outlined herein may only be made with the approval of the Board.


Evaluation of PhD students during their studies

• The Branch Council evaluates the students' activities regularly, at least once a year. In doing so, it evaluates whether the student is fulfilling all points of his/her study plan.

• The student's success during his/her studies is evaluated primarily by his/her professional publications related to the topic of the doctoral thesis and by presentations of the results of his/her work to the scientific community. Successful students are expected to be able to conduct independent research and communicate scientifically in English, including publications in international journals.

• The doctoral student prepares the evaluation documents in the form of an annual activity report. The report with the supervisor's opinion is submitted to the Board by the deadline set by the Dean (usually at the end of September) via SIS. The obligation to submit the report applies to all doctoral students, both presessional and combined, throughout the duration of their studies. If a doctoral student fails to submit the report by the deadline, the student is deemed not to have fulfilled the obligations of the study plan. In this case, the Board will propose termination of the study.

• The doctoral student's performances at seminars (especially presentations of the doctoral topic in the first year of study and performances in the third year of study) and other activities at the workplace also serve to evaluate the doctoral student.

• At the end of the first year, a committee appointed by the departmental board evaluates the doctoral student's progress report for the first year of study. On the basis of this committee's assessment, the subject board will make a statement as to whether the student has fulfilled the requirements of the first year of study.

• For the continuous evaluation of a doctoral student's studies, the Board appoints a three-member committee that is permanent throughout the entire period of study. One of its members is the student's supervisor. This committee proposes the approval of the study plan at the beginning of the study, evaluates the doctoral student's performance in the first year, carries out an attendance evaluation after the first year of study, evaluation after subsequent years, forms part of the examination committee for the state doctoral examination, evaluates the rough draft of the introduction of the thesis in the fourth year and acts as part of the reading committee for the doctoral thesis.

• The results of the evaluation of doctoral students' studies are used by the Board in its other activities, in particular to influence the course of the doctoral student's studies.


State Doctoral Examination

• The State Doctoral Examination must be taken according to the specifications given in the study plan, usually in the (3rd-)4th semester for the regular form of study. The application for the State Doctoral Examination shall be submitted by the student in writing to the Department of Doctoral Studies.

• The examination is held before an examination committee, and is adapted to the specific topic of the student. The PhD examination demonstrates (i) a general overview of the entire discipline of botany (to be listed as the subject Botany in the application form) and (ii) detailed knowledge in the field of the PhD thesis (to be listed in the application form as "Topics of the PhD thesis", or directly list the short title).

• In addition to these two core subjects, the applicant specifies in the application form another field of interest, usually from the following list: Algology, Mycology, Lichenology, Bryology, Phytopathology, Algal Ecology, Fungal Ecology, Lichen and bryophyte ecology, Systematics and evolution of higher plants, Biosystematics, Reproductive biology, Molecular markers, Numerical methods in taxonomy, Vegetation of Central Europe, Plant ecology, Biomes of the earth, Community ecology, Paleoecology, Population biology of plants, Phytogeography.

• The application for the doctoral examination must be accompanied by a report on up-to-date work on the doctoral thesis, which must include a clarification of the objectives of the thesis, a statement on the current progress towards their solution, planned changes in the solution, etc. (in an expected length of approx. 10 pages). This report may include already published or forthcoming articles to which the initial analytical part will refer. This paper must be submitted to the chair of the committee at least 14 days before the actual examination.

• The examination proper typically begins by a very short (less than 3 mins) outline of the student's Ph.D. project, highlighting main ideas, hypotheses to be tested, and approaches taken to test these hypotheses. In the first part of the examination, the committee primarily discusses the submitted report; the second part of the examination they will typically ask broader questions to permit the candidate to show his/her familiarity with the discipline.

• If a student fails the examination, the examination board will usually recommend areas of study and literature to be addressed. The student takes the same subjects in the re-examination as in the original examination. A new version of the report must also be submitted. It is necessary to apply for the re-examination within one year of the failed attempt. Otherwise, the student cannot be evaluated in category A (fulfilling the study plan).


Form of dissertation

• The form of the dissertation is regulated by the Rules for the Organisation of Studies of the Faculty of Science of the Charles University ("Pravidla pro organizaci studia").

• The expected form of the dissertation is a collection of at least three thematically related texts written in English in the format of scientific articles and accompanied by a broader unifying introduction to the subject. As a rule, at least two of these articles are first-authored. At least one of these articles must have been published or accepted for publication in an internationally recognised scientific journal (this normally means a journal with an impact factor as defined by ISI; journals with an IF in the lower quarter of the relevant ISI-defined category are only appropriate in well-justified cases). Acceptance for publication must be credibly documented. All articles must be related to the dissertation topic. The introduction must be a substantial part of the thesis (the length of an average article) and must thoroughly introduce the framework and context of the topic, the aims of the thesis and place the individual articles in their overall context. The thesis must also include a broader summary of the significance of the results of each article to the discipline, either as the final part of the introduction or in a separate conclusion. All of the above sections (introduction, published/accepted articles, unpublished texts in article format, conclusion) must be part of the actual dissertation text (not an appendix). In justified cases, the dissertation may take the form of a complete scientific monograph, which must be first-authored and accepted for publication.

• All parts of the dissertation must be formatted in the same way. The use of PDF files with journal copyright is not allowed for published or accepted articles.

• If the dissertation includes publications in which other authors have contributed, the thesis must be accompanied by a statement from the supervisor (or the corresponding author of each publication) specifying the student's contribution to the results. The student's contribution to the collective work included in the dissertation must be substantial, both in the collection and processing of data and in the interpretation and preparation of the manuscript.

• a separately published thesis summary ("autoreferat") is not required.

• The defended theses are published on the university server. When submitting a thesis for defence, it is advisable to request an extension of the deadline for publication of the full thesis in cooperation with the supervisor.


Defence of the dissertation

• The entire process between the submission of the thesis and the actual defence is managed by the chair of the defence committee, who is appointed by the dean together with the entire committee on the proposal of the Board.

• After the submission of the thesis, the chair of the defense committee will submit the thesis to a three-member group ("reading committee") to review the thesis. If it finds that the thesis does not meet the requirements or contains serious deficiencies, it will return the thesis for revision. In doing so, it shall indicate the modifications to the thesis which are necessary for it to be accepted for defence. With the agreement of the Chair of the Board, the thesis may be submitted to the reading committee before the actual formal submission. 

• The thesis is reviewed by two referees, at least one of whom is from abroad (usually an expert in the applicant's narrower field). The referees are proposed by the chair of the committee, usually in consultation with the supervisor and the candidate, and approved by the defence committee.

• The defence is conducted in English and is open to the public. At the defence, the candidate presents the thesis in a 25-30 minute presentation. In the subsequent part, the candidate answers questions from the referees (not all of which have to be in the referee's report; referees are encouraged not to include part of their questions in the report) and questions from the audience.

• The outcome of the defence is decided by a vote of the defence committee.

• For exceptional work, the committee may propose a "cum laude" evaluation. Theses that have been defended no later than the fifth year of study and are based on at least three good articles published (or accepted for publication) in good journals may be proposed for this evaluation. Good journals are generally defined as journals with an IF in the first quartile of the relevant category.


Completion of studies

• The maximum duration of study in a doctoral programme is set by the relevant regulations.

• The date of the proper completion of the doctoral studies is the date on which the dissertation is defended. It follows from the provisions of the Study and Examination Regulations that both the state doctoral examination and the dissertation must be passed within a given number of years of enrolment (i.e. it is not sufficient to submit the dissertation).

• Failure to meet this requirement will result in termination of studies for failure to meet the requirements of the program of study. The OR requires that the dissertation be submitted for defence at least eighteen weeks before the maximum period of study expires.

• If a doctoral student decides to abandon his/her studies for any reason, he/she must notify the PhD Studies Department of the Faculty of Arts of Charles University in writing (to be addressed to the relevant Vice-Dean with a copy to the Departmental Board).


These rules come into force on 1.5.2022


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