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Species are units for understanding the evolution of diversity over large geographical scales and long timescales. This chapter investigates the processes causing proliferation and demise of species diversity within lineages and regions. Phylogenetic approaches have focused on documenting speciation and extinction rates, but mechanistic theory explaining variation in rates is scarce. Diversity patterns are better explained by geographical and ecological opportunity than by correlates of speciation and extinction rates per se. The neutral theory of biodiversity provides a framework that can be adapted to predict diversity patterns in terms of limits due to competition for space and resources, and species turnover (which cannot be detected directly from phylogenetic trees). These theories bring macroevolutionary and microevolutionary theories closer together. In particular, diversity patterns are the outcome of individual selection and dispersal playing out over long timescales. Some of the processes influencing species patterns can also structure diversity at higher taxonomic levels.

A topic extensively debated is whether sciences that focus on historical entities are somehow fundamentally different from those sciences that are not concerned with the history of the entities they study. This duality has been treated when authors have discussed the difference between contingent and nomothetic approaches, between historical and functional approaches, and between pattern and process based approaches The history of thought on these concepts will be considered here, with special emphasis placed on writings in macroevolutionary theory and phylogenetics. A central focus will be documenting how these “dualities” should not be viewed as truly distinct. Furthermore, it is argued that repeated analysis of contingent histories is the key to discovering the nomothetic principles that exist in the history of life. This is in fact a central tenet of the hierarchical view of evolution.

Modern macroevolutionary theory can be viewed as an expansion of the Modern Synthesis involving the interpretation of patterns and processes above the organizational level of organisms packaged in local populations, including modes and processes of speciation and the emergence and development of clades. New interpretations of the fossil record (punctuated equilibria, species selection, regional and global mass extinctions and recoveries) are the empirical and conceptual building blocks in this theoretical expansion. But as in most microevolutionary thinking, macroevolutionary theory has rarely placed ecologic processes on equal footing with evolutionary processes: ecology is seen as the stage, backdrop or product of adaptive evolution; all the important action actually involves evolutionary transformations. Several new movements in macroevolutionary theory (Turnover Pulse Hypothesis, Coordinated Stasis, the Sloshing Bucket Model), however, require attention to be focused on patterns of stability and reorganization/replacement of large ecologic systems in order to understand patterns of evolutionary stasis and turnover (invasion/abandonment, extinction, bouts of adaptive speciation) recorded in the fossil record. Connecting macroevolutionary patterns to macroecologic dynamics (the Theory of Macroevolutionary Consonance) could lead on to discovery of further conceptual connections and a more complete explication of large-scale patterns in the history of life.