As per the author's aritcle it is definitely not a direct connection. FB relies heavily on first-degree connection analysis. If you and I end up in the same phonebook (which the author mentions) or the same photograph and FB connects us, we'll never know why. The not knowing why part makes it uncanny.
Facebook is to people what Google is to websites. It is in the business of enriching its social graph in every way possible and then running profiling algorithms on that graph. Google by contrast crawls and pageranks the crawled graph.
FB has literally hundreds of data sources to enrich their social graph and profile data.
A good start is their list of acquisitions [1] in the space of offline applications, social networking aggregators, contact importers, photo management, private conversations, travel recommendations, check-ins/status updates, etc.
Then consider the FB partnerships with ride hailing services, retail apps, music apps, etc.
Then consider it's own apps and features around events, calendering, photos and instant messaging.
Also consider the state of technology in NLP, AI and image recognition.
Also consider the FB integrations with tens of thousands of apps for social auth, share buttons and advertising.
Writing this post, I have surprised even myself as to how much data they have access to.
[1] https://en.wikipedia.org/wiki/List_of_mergers_and_acquisitio...