Penguin-related ranking issues. This is due to a change in the way Penguin 4.0 deals with bad links: it now devalues the links themselves rather than demoting the site they link to. Now that seems pretty clear. If you read Illyes' statements in the article linked above, there are a few takeaways: Spam is downgraded, rather than downgraded sites. There is less need to use a disavow file for Penguin-related ranking penalties. Using the disavow file for Penguin-related issues can help Google help you,
but it's especially useful for sites undergoing manual review. Here's the thing, though - just a day earlier, the following tweets had been exchanged: @BruceClayInc fax number list we haven't changed our recommendations for the disavow tool with this launch — Gary Illyes (@method) September 26, 2016 So now we have a "yes, you should use it for Penguin" and a "no, you don't need it for Penguin." But wait, it gets more fun.
On October 4, 2016, Google Webmaster Trends analyst John Mueller said the following in a Hangout during business hours: [If] these are problematic links that are affected [by Penguin], and you're using a disavow file, then this is a good way for us to pick it up and acknowledge, "Okay, that link is something something you don't want to have associated with this site."