They just went smaller - Thunderbolt implements PCIe [1] under the hood. You can connect graphics cards over TB, for example.
[1] It actually implements three protocols that it can switch between based on endpoint negotiation - PCIe, DisplayPort, and in its latest version USB 3.1.
[1] It actually implements three protocols that it can switch between based on endpoint negotiation - PCIe, DisplayPort, and in its latest version USB 3.1.