Speciation is the foundational process ultimately producing the many branches across the Tree of Life. This chapter defines the use of the term “species” so as to provide a practical framework for discussing the process of divergence and the achievement of reproductive isolation. Divergence and speciation in allopatry, with little or no subsequent gene flow, is likely the most common form of speciation. Nonetheless, mathematical models of speciation producing speciation in the face of gene flow are readily constructed, and recent genomic data suggests that such processes are likely widespread in many groups. Three scenarios involving ecological divergence and pre-mating isolation are prevalent: microhabitat specialization can, like geographical isolation, reduce opportunities for mating with alternatively adapted forms; ecological or even neutral divergence in allopatry can yield pleiotropic effects on post-mating compatibility, including intrinsic postzygotic isolation, such as Haldane's Rule; and processes such as reinforcement can select for assortative mating. Sexual selection and genomic barriers such as inversions or polyploidy are additional drivers of speciation. Recent theories of speciation differ from those espoused 50 years ago in placing greater importance on ecological divergence among species and a greater role for gene flow in shaping lineage divergence.
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