That's right. Github tracks you by email. Each Github notification email contains in the HTML part a beacon. Beacons are usually one pixel images with a unique URL to know who did view the email or not - triggered by the HTML rendered downloading the image to display.

Two safeguards against that tracking:

1. don't automatically download images in emails - lot of clients allow or default to this.
2. view email only in plain text: impossible with some email system or client. Like K9-Android or just GMail. (by far this is what I do in Thunderbird)

Now I complain over twitter and according to Github Zach Holman:

"It’s a pretty rad feature for a ton of our users; reading a notification in one should mark the web UI as read too. We dig it."*.

Sorry, but there is no optout to tracking. Holman also said:

"you can just disable images. It’s the same functionality in the email as on the web, though. We’re not spying on anything."*

and

"[...] It’s just in this case there’s zero additional information trading hands."*.

Note that recent events showed me I couldn't trust Github ethics anyway, so I'd rather have them not have the info that them claiming it never change hands.

This wouldn't be important if Mozilla didn't mostly require Github to contribute to certain projects including. I filed bug 1031899. While I can understand the feature, I believe user privacy should be paramount, therefor not being able to disable tracking is a serious ethics issue.

http://www.figuiere.net/hub/blog/?2014/07/11/850-github-tracks-you-by-email