Are we analyzing speciation without prejudice?

Physical isolation has long been the null hypothesis of speciation, with exceptional evidence required to suggest speciation with gene flow. Following recent persuasive theoretical support and strong empirical examples of nonallopatric speciation, one might expect a changed view. However, a review of 73 recent empirical studies shows that when allopatric speciation is suggested, a nonallopatric alternative is rarely considered, whereas the opposite is true in studies suggesting sympatric speciation, indicating a biased treatment of different speciation models. Although increasing support for ecological speciation suggests natural selection as the most critical component of speciation, gene flow remains an issue. Methods for unbiased hypothesis testing are available, and the genetic and phylogeographic data required for appropriate tests can be generated. Focus on phylogenies and functions of individual genes have revealed strong idiosyncratic elements of speciation, such as single genes with possible allopatric origin that make significant contributions during nonallopatric phases of speciation. Hence a more complex picture of speciation is now emerging that will benefit from unbiased evaluation of both allopatric and sympatric mechanisms of speciation.