This book is about the identification and interpretation of nature’s large-scale patterns of species co-occurrence and what we can deduce from them about how nature works. We present Diamond’s assembly rules. He suggested that similar species avoid each other, choosing different islands or, on large islands, different elevations within an island, for no better explanation than to avoid each other. Diamond concentrated on birds in two island groups off New Guinea—the Solomons and the Bismarcks. Diamond’s ideaswere vigorously challenged by those who suggested the patterns were simply chance occurrences. In a series of papers, some argued that Diamond’s assembly rules were poorly constructed and that, moreover, his observations did not support them. Certainly, critics made an important contribution to the study of ecological patterns by requiring observed distributions to be compared to carefully constructed null hypotheses. Developing appropriate statistical methods to analyze these patterns in nature is difficult, though it is now a solved problem. We confirm patterns of mutual exclusivity in some island groups, though not all. Finally, we extend these ideas to species along elevational gradients and to applications involving food webs.