Alternative format protocol for candidates registered in the Faculty of Biological Sciences

• An alternative style of thesis can only be submitted where (i) the Faculty in which the candidate is registered offers this format of submission and has an approved protocol in place; and (ii) the supervisory team supports this format of submission and is satisfied it is appropriate and meets the protocol in place for that Faculty. 
• Any candidate wishing to submit an alternative style of doctoral thesis which includes published material must discuss this with their Supervisory team at an early point in the candidature so that appropriate support and advice can be given. The final decision on the format of submission and whether an alternative style of thesis will be presented is required at the examination entry stage. 
• In the relevant section of the GRAD examination entry workflow the Supervisor(s) must provide support for the submission of a doctoral thesis including published material and indicate that this is appropriate and that the publication status of the papers already meets the minimum requirements set out by the Faculty. The Supervisory team must also ensure that the nominated examiners are happy to examine this style of thesis submission.
• Publication-based thesis format can be an alternative to those students who at an early stage in the candidature seek to report their research as journal articles. It is not intended to be a default format for all PGRs: for many PGRs the standard chapter format thesis will remain the choice.
• The choice of the thesis format should be discussed in the Supervisory team and decided on sufficiently early during the studies so that the reporting of the research can be fully aligned with the chosen thesis format. 
• Where work which has formed part of any jointly authored publications is included in this alternative style thesis, the Examiners will need to be able to identify the work directly attributable to the candidate to determine whether there is a substantially original contribution to the subject concerned and whether the candidate’s own contribution is at the appropriate level to merit the award of the degree.
• To assist the Examiners with this, an outline of the nature and extent of the candidate’s own contribution and the contribution of co-authors and other collaborators to the publications must be provided on the examination entry workflow. Another co-author to the papers must attest to the information provided (normally the Supervisor).
• The information regarding the publications used and the contributions of the other authors should also be included on page 2 of the thesis (intellectual property and publications page) along with a rationale for submitting the thesis in an alternative format and a brief summary of how the thesis has been constructed. 

• Publications may only be included where the student is the sole, lead, first or primary author on a publication and their contribution is significant. The work must be derived from original research undertaken whilst registered for doctoral study at this University. The term “lead” refers to the contribution of the student to the work, rather than the order in which the names of the authors appear on the publication.
• Work must have been published in peer-reviewed outputs appropriate for the field of research. The publication status (published/accepted) and acceptable externally refereed outputs are not prescribed at a University level and may vary according to discipline. The use of joint-first authored papers is not prescribed at a University level and may vary according to discipline.
• An alternative format PhD thesis can include article manuscripts that have been written for submission for publication in peer-reviewed academic journals, recognised to be relevant to the field of the research. The appropriateness of the peer-reviewed output will be determined by the Supervisory team within the context of the field of research.
• A minimum of three manuscripts must be incorporated into the alternative style thesis.
  • At least one of these must have been formally accepted for publication, but it does not need to have been published at the time of submission of the thesis.
  • At least one other should have been submitted and should have received either an invitation to revise and resubmit or a potential editorial indication that the paper will be accepted subject to major revisions.
  • Other papers should be developed and formatted to be close to being ready for submission. 
• The manuscripts to be included in an alternative format thesis should report findings based on original theoretical or empirical work, modelling etc. that forms a part of the research conducted during the candidate’s postgraduate research studies. This means that for example short published contributions such as opinions, comments or commentaries are not eligible, and nor are publications pre-dating the commencement of postgraduate research studies in Leeds or based on work conducted prior to commencement of postgraduate research studies in Leeds.
• Manuscripts to be included in an alternative format thesis are normally co-authored with supervisors with the student being the first/lead author. The lead-authorship expectation means that where two or more postgraduate research students have co-authored an output it can only be used by one student identified as the lead author as part of their thesis. Papers used within the alternative thesis should be attributed to the University of Leeds and this should appear in the main line of the address.
• The quality of manuscripts included into an alternative format thesis will be assessed through the examination process and not on the basis of their publication status or outlet. 
• The number of published outputs/papers required for the alternative style of doctoral thesis may vary according to discipline and is not prescribed at a University level, but should reflect the quantity, quality and originality of research and analysis expected of a candidate submitting a traditional, chapter style of thesis.  
• The number of manuscripts included into an alternative format thesis must be at least 3; the actual number will depend on the nature of these outputs, the discipline, the nature of research problem addressed, and the structure of the thesis
• An alternative format thesis should NOT mix article manuscript and chapter style content beyond what is specified on this page.
• PGRs intending to submit an alternative style thesis must use regular supervisory meetings to update supervisory teams on the likelihood of meeting the requirements of this and the ‘Published material to be included in the alternative style of doctoral thesis’ section. No extensions to submission deadlines can be made waiting for publications to be accepted. An on-going review must ensure that the decision to revert to the standard PhD thesis format can be made in sufficient time. 

• The incorporation of published outputs/papers into the thesis will inevitably lead to some duplication and it is acknowledged that each publication will have self-contained components that may overlap with that in other sections of the thesis. Nevertheless the work must constitute a continuous body of work which is a coherent and continuous thesis, rather than a series of disconnected publications. As such, there must be: 
  •  an appropriate introduction: which describes the context of the research, the rationale of the investigation, the strategy employed during the research and demonstrated in the thesis, locates the research to its context and establishes its novelty and contribution; and 
  • an extensive critical discussion and conclusion: to support the published material and link these together into a coherent body of work and indicating directions for future work.
• An alternative format thesis should contain an Introductory materials section locating the work to its reviewed peer literature and describing the overall research design and data acquisition/material collection and analysis solutions in order to bind the included manuscripts into a single whole.  
• The integrating material preceding the included manuscripts should not exceed 15000 words in length and it should contain its own list of references.
• The thesis will need to be based on a uniform page layout throughout: this includes formatting the text of the included manuscripts so that they use the same font size, line spacing, margins, referencing etc. practices as the rest of the thesis. Each manuscript shall also include its own list of references. 
• If the manuscripts included into an alternative format thesis have already been accepted for publication and have progressed through production in the publication outlet, a pre-proof stage manuscript should be included into the thesis. 
• When publications are or are to be complemented with supplementary material in print or online publication outlets, the material should be presented as appendices of the thesis.

• Candidates must bear in mind that journal articles/publications can be very restrictive in terms of length.  The alternative style of thesis will be assessed according to the same criteria as a traditional, chapter style thesis including the volume and quality of original research. As such, in addition to the published material the thesis will require the same in-depth discussion, critical analysis, and quantity and quality of work that is required for the award of a doctoral degree under the conventional submission route. It is expected that, where appropriate (and with advice from the team of supervisors), the thesis will include a more in depth discussion of the methodology, results etc than appeared in the original publication. This may vary according to discipline.
• An alternative format thesis should contain a Discussion and conclusions section after the included manuscripts to bind them into a single whole.
• The discussion and conclusions section following the included manuscripts should not exceed 10000 words in length and it should contain its own list of references.
•  Where the manuscripts are or are to be complemented with supplementary material in print or online publication outlets, the material should be presented as appendices of the thesis.
• Appendices can also contain other material providing supplementary information related to any preceding part of the thesis.
• In summary, we would expect the complete alternative thesis to include up to 25,000 words of general introduction and discussion alongside the published or prepared manuscripts and the components outlined in the format and presentation guidelines, as follows: 
  • Introductory materials – limited to 15,000 words and incorporating a Literature Review either as a discrete chapter or as part of a larger introduction.
  • Manuscripts: The three or more published/accepted/planned manuscripts should be inserted following the introductory material. Each manuscripts will contain sections on introduction, methods, results and discussion as per peer-reviewed work in the field. However, these manuscripts must be supplemented by the inclusion of additional results and methods, including full experimental details,  so that the work could be repeated.  This will often mean providing more detail than in a standard publication and may be along the lines of supplementary material from any publication.  However it should be integrated into the thesis so that these details are easily found. Examples may include highly detailed methods that were omitted from the published work, or background experiments or experiments where system optimisation is carried out. 
  •  Discussion and conclusions- limited to 10,000 words and including a general discussion that brings together and synthesises the body of work as a whole.
  • Appendices - appendices should be provided as appropriate and many contain supplementary information to the published work where necessary.
• Any thesis submitted for examination, including those which use published material must include the following (as outlined in the format and presentation guidelines): a title page, intellectual property and publications page, acknowledgements page, abstract, contents, list of abbreviations, references/bibliography and any appendices.
• The publications page  must include information covering the publications used and the contributions of the other authors along with a rationale for submitting the thesis in this format and a brief summary of how the thesis has been constructed.

• A thesis submitted under the alternative style of doctoral thesis route is not expected to exceed the normal page/word limits for the degree concerned.
• It is accepted that the thesis will include copies of published outputs/papers (e.g. off prints of journal articles, book chapters etc), which already have page numbers. Wherever possible there should be sequential numbering of the thesis as a whole. The publications will therefore bear two numbers; the original from the publication and that which indicates their place in the thesis (but ideally in a different location to the page number from the publication).  If this approach is not possible, candidates must ensure that the thesis is clear and easy to navigate by the examiners and any sections of the thesis which are published have been clearly identified. 

• As with the conventional doctoral thesis, examiners should satisfy themselves that the learning outcomes have been met and the thesis as submitted meets the requirements of the doctoral degree as prescribed in the Ordinance and Regulations for Research Degrees.
• The thesis should make an original contribution to the field of research regardless of the format of submission. The alternative style of thesis will be assessed according to the same criteria as a conventional doctoral thesis including the volume and quality of original research and, as such, in addition to the published papers the thesis will require the same in-depth discussion of methodology and results, the same detailed critical analysis, and the same quantity and quality of work required for the award of a doctoral degree under the conventional chapterstyle submission route.
• It is recognised that journal articles/publications can be restrictive in terms of length and the examiners may feel that a more in-depth justification or discussion of e.g. methodology, results, detailed critical analysis is required in the thesis. As such, it is open to the examiners to require revision or expansion to the publication parts of the thesis as part of any editorial and presentational corrections or minor deficiencies. For example, an addendum to a published paper could be added into the thesis itself, if this was deemed necessary by the examiners as part of any corrections. The School/Supervisor would then need to judge whether any issues identified by the examiners warranted contact with the publishers and/or an addendum to a paper in press. 
• Candidates should be clear that, the fact that a thesis contains material that has been published or accepted for publication does not guarantee that the examiners will recommend the award of the degree for which the candidate is being examined.

• Candidates are reminded that the final thesis (after successful examination) must be provided to the University in both hard bound and eThesis format.
• Particular attention should be given to the advice on eThesis preparation, copyright and publication regarding the re-use of published material within an eThesis. Candidates will need to ensure that any publication agreements with the journals concerned include permission to reuse the articles in the thesis.
• See the advice on eThesis preparation, copyright and publication.
• After successful examination PGRs must submit to the University for the award of the degree:
  • 1 complete version of the thesis in pdf eThesis format (full text including all publications)
  • 1 edited version of the eThesis with any publications redacted where it has not been possible to obtain permission for re-publication of the work in the eThesis from the journal/publisher. In these cases the eThesis must include some form of place holder to indicate the publication has been removed with a link/reference (preferably DOIs for journal articles and ISBNs for books) to the original publication source. 

Approved by the Examinations Group June 2017

Version 2 – Updated March 2019

Version 3 – Updated August 2020

Approved by Examinations Group December 2020