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Diversity-based security approaches have been studied for several decades since the 1970's. The concept of diversity-by-design emerged in the 1980's and, since then, diversity-based system design research has been explored to build more secure and dependable systems. In this work, we are particularly interested in providing an in-depth, comprehensive survey of existing diversity-based approaches, insights, and future work directions for those who want to conduct research on developing secure and dependable cyber-physical systems (CPSs) using diversity as a system design feature. To be specific, this survey paper provides: (i) The common concept of diversity based on a multidisciplinary study of diversity from nine different fields along with the historical evolution of diversity-by-design for security; (ii) The design principles of diversity-based approaches; (iii) The key benefits and caveats of using diversity-by-design; (iv) The key concerns of CPS environments in introducing diversity-by-design; (v) A variety of existing diversity-based approaches based on five different classifications; (vi) The types of attacks mitigated by existing diversity-based approaches; (vii) The overall trends of evaluation methodologies used in diversity-based approaches, in terms of metrics, datasets, and testbeds; and (viii) The insights, lessons, and gaps identified from this extensive survey.