First, we must remember that it is Humanity, the scientific tendency toward taxonomy, that “defines” a species, or even a “family” of living organisms. Take, for example, Linnaeus’ system for dividing plants into types. While his first divisions are clear and understandable, his division of different species of roses gets pretty arbitrary, especially when we consider human-invented species. To answer your question, the causes of one species dying out while closely related species survive can often be traced to loss of environments. Much of that can be blamed on Humanity’s greed, over-consumption, and disregard for the consequences of selfish choices (orangutans in Madagascar, for example, to say nothing of hunting rare species just for sport). In fairness to Humanity, too, we are the only species that is even aware that efforts can be made to preserve species and encourage diversity, or that sees value in doing do. Another cause is natural selection “weeding out” some species, a kind of accordion-like reduction of genetic choices; for example, the Darwinian Galapagos Island bird species have suffered much loss of diversity, simply because some of the species became unviable with time. Finally, environmental changes (whether man-made or not) can deplete species. Take for example the depletion of the polar bear. In short, species survive or not based on many factors, and when those factors change, some species survive and some do not.