Many full-service airlines have an interline e-ticketing agreement with each other. This is by no means restricted by their Alliance. We tend to find most major international carriers need help from the Canadian domestic carriers to get travellers to a point within Canada or the USA from which they can take over.
For instance, in Eastern Canada, Emirates has an agreement with both Air Canada and WestJet to uplift clients to Toronto where Emirates will take over and fly you to Dubai. From Western Canada, Emirates enlists the help of Alaska Airlines to get travellers to Seattle or Los Angeles amongst other options.
By virtue of an airline forming an interline agreement, this will allow both airlines to see passengers coming from one carrier to the next, or alternatively allow the first carrier to thru-check a passenger from their origin all the way to their destination, including baggage.
When you have one ticket and multiple airlines, they will be able to see the complete itinerary from a review of the e-ticket and check you in accordingly. However, if you are travelling on two separate tickets, the first carrier can still thru-check you once you notify them of your situation and present your onward carriers e-ticket.