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I am writing my PhD thesis within the natural sciences (ecology), following the typical structure of introduction, literature review, material & methods, results, discussion, conclusion.

For some of my analyses I am using a method which was developed about 90 years ago and has become the "standard" method in my field. I'd like to outline the origin and development of that method, along with some downsides that have become obvious in the past decades (and which I am trying to overcome by extending the method).

Is it appropriate to do so within the methods section (instead of just having a plain description of the methods I have applied)? Or would I rather include that in an extra chapter in the literature review (where I am so far rather focussing on describing the existing knowledge rather than methods)? Or even put it in the introduction?

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I'm not in ecology, but my sense is that as a separate section (or entire separate chapter, if the coverage would be substantial enough for that) near the end of your literature review could well be the best place for this. In my field (library and information science) the literature review chapter sometimes includes a review of the research literature followed by a review of theories or practices that are to be used or have strong impact on the research to be done, but are not really about describing the methods to be used (even though theories and practices certainly impact one's choice of method(s)). While in your case this is a method instead of a theory, you say it is an especially common approach and I think you are right to approach a review of it in some form. That review may serve well near the end of your literature review as a bridge between the review of existing research findings and the methods chapter.

FuzzyLeapfrog has a point, though, in that while there may be some general guidance and suggestions that can be offered, your own situation is very context-specific. Your dissertation chair and/or committee should be able to give this more context-specific guidance in where they would most expect to see this material, given your proposed study, department, university, specialty, and field.

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While there's no "right" answer here, I would put this sort of discussion in the introduction/background as its own subsection. In that section, you're providing the motivation for the research, as well as any relevant information that the user needs to understand the paper. This seems to fit that definition nicely.

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There is no general answer to your question.

I added an extra chapter about the historical development of the applied method(s) in my dissertation. It was Chapter 2, right after the introduction (Chapter 1) and before the specific setup of the method (Chapter 3).

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