This is just my view from the Am Nat journal office of course!
1) The manuscript arrives in the web system. One of us in the journal office gives it what the system calls a technical check--Is the PDF readable? Did the math symbols turn into tiny empty boxes? Is it double spaced? We try to minimize annoyance, but reviewers hate it if isn't formatted right, so we're just trying to save you grief later.
2) The manuscript then waits for one of the three deciding editors to claim it. This depends on people's schedules, but it generally moves along every day. The deciding editor finds the time to look the manuscript over and determine whether it can fit our niche. If it seems like it can or they aren't sure, it goes to the next stage...
3) The manuscript gets assigned to an associate editor. We get manuscripts across a broad spectrum of subjects. Though we have quite a few associate editors, we sometimes struggle to get a manuscript assigned. AEs have busy schedules and not all have the expertise needed for that manuscript. We also avoid loading up an AE all at once.
4) If the manuscript seems like it might fit our niche, the AE then develops a list of six suggested reviewers to send to the journal office. If the manuscript is a bit of a stretch for the AE, then developing that list can take a bit of time and exploration.
5) The journal office takes that list and checks for availability and some basic conflicts of interest. We try to give reviewers at least two months off between assignments. Then two reviewers are invited to review. If we don't get a response to the invitation in a few days, we follow up, wait a day, and then move down the list until we find two reviewers who agree to review. As can be imagined, this process can take some time for some manuscripts especially at some busy times of year. If we run out of names, we ask the AE for more suggestions and start the process over.
6) The standard due date for a review is 21 days after the reviewer agrees to review.
7) When the reviews are completed, the journal office checks them over to make sure the fields are filled out, there aren't any obvious missing bits, and any attachments uploaded correctly. When both reviews are in, the manuscript is returned to the associate editor for a recommendation. The deadline for the recommendation is two weeks since we expect that an AE may have to set aside a considerable block of time to sort out what needs to happen next.
8) The AE writes the recommendation and the manuscript moves back to the deciding editor, who reads over the whole package--manuscript, reviews, and recommendation--before writing the decision letter.
9) Finally, the decision letter is assembled and sent by the journal office.
We try to keep a manuscript moving along, but there are many steps when many busy people might take a little longer. We in the office work regular office hours (and have vacations and weekends and sick days), so if you submit your paper late on Friday, you won't hear from us until Monday.
The problem is always how to balance thorough with timely. When thorough review works well, it works very well indeed. I really appreciated how much it could mean for an author when I read Meghan Duffy's blog post about how review at Am Nat improved her paper:
So when it takes a little longer, we ARE trying to get you the most useful feedback we can in as timely a period as we can, while trying to gauge whether the manuscript fits our niche.