Comment Numbering

I know that WP by default uses an OL for the comments. However, I have seen some sites (Matt’s for instance – https://www.photomatt.net) where the list style it set to none, and the number of the comment is being written out to a <span> element.
Is this done by modifying the php in wp-comments.php, or is there a plugin that allows for this?
I can’t seem to find where to edit to get this sort of effect.