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the establishment, effects, and transitory nature of divergence hitchhiking around key ecologically important genes, and describe a 2-stage model for genetic divergence during ecological speciation with gene flow.

The origin of species is only slightly less mysterious now than it was 150 years ago when Darwin published his famous book (Darwin, 1859). Although Darwin’s idea that natural selection drives speciation has finally been widely accepted (Coyne and Orr, 2004), we still have much to learn about the nature and time course of the genetic changes that cause speciation under natural selection (Schluter, 2001, 2009; Via and West, 2008).


Pivotal ideas developed during the modern synthesis of the 1930s–1940s have largely determined the course of modern speciation research. Ernst Mayr (1942) developed the biological species concept, putting reproductive isolation at the center of speciation and making analysis of the evolution of reproductive isolation a clear target for speciation research. Mayr also stressed that the evolution of reproductive isolation is a fragile process that can only proceed if geographical separation renders gene flow impossible, firmly establishing allopatric speciation as the norm. Theodosius Dobzhansky (1937) identified a wide array of traits that could cause reproductive isolation, but focused much of his own research into speciation on postzygotic genetic incompatibilities (Dobzhansky, 1934), as did H. J. Muller (1942). At the time, hybrid sterility was a particularly problematic aspect of speciation because it had been unclear since Darwin (1859) how such a disadvantageous trait could evolve under natural selection. By providing a clear mechanism by which hybrid sterility could evolve (Coyne and Orr, 2004, pp. 269 and 270), Dobzhansky-Muller genetic incompatibilities (DMIs) took center stage in the genetic analysis of speciation, where they have remained ever since. Collectively, the architects of the synthesis outlined a retrospective approach to speciation that I call “the spyglass,” because it starts late in the process (or after it is complete) and looks back in time to infer the causes of speciation (Fig. 1.1A).

Unquestionably, this approach has been a rich source of information about the kinds of barriers to gene flow that can isolate species [e.g., Otte and Endler (1989); Howard and Berlocher (2003)], but alternative ideas about speciation and how to study it have met with considerable resistance during the past 70 years. Even today, allopatric speciation remains the null model against which all other mechanisms for speciation must be tested (Coyne and Orr, 2004, p. 158), and DMIs are widely regarded as

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