Another group posts a preprint on a similar work to my own. I decide that I do not want to submit a preprint but rather go straight for a journal publication. Will the chances of my publication be jeopardized by the appearance of this earlier preprint?

We have discussed this scenario with several journals and the response received so far is that editors consider only peer-reviewed work in applying criterion of originality. They do not use preprints as a basis of deciding whether to send work out for review and ultimately accept it. For example, Nature Research’s preprint policy states that “Manuscripts posted on preprint servers will not be taken into account when determining the advance provided by a study under consideration at a Nature Research journal.” 

We note that intentionally ignoring and failing to cite the earlier preprint in an appropriate way in one’s own journal article (or preprint) would be deceitful, as it would be intentionally ignoring work from a scientific colleague in order to advance one’s own work. Such behavior is not tolerated in the physics community (see comments by Paul Ginsparg). It should not be tolerated in biology as well.