Google selects a vendor to build hardware for the Nexus each year. They may choose from multiple submissions. The hw vendor is free to submit any device but of course they take one of their existing designs and tweak it slightly. This then becomes the Nexus which is the reference platform for testing and debugging Android, is used for devkits etc for internal builds.
The actual components in the phone, drivers etc can be different from the phone the Nexus is derived from. Google doesn't test devices, they publish the CDD and CTS which allows any oem to test their device to ensure its compatible. This can take a long time due to changes they need to make. What I said is based on things I've heard/read from various people and what is publicly known of Android development.
You still didn't even touch on what things Google implement software wise that was Nexus specific to only the Nexus?