Population disjunctions have been proposed to play an important role in speciation processes. In this study, we have examined the possible role of the Pacific Ocean-Sea of Cortez disjunction as a contributing factor to cryptic speciation in a reef fish, the opaleye, Girella nigricans. Mitochondrial control region (D-loop) sequences (380 bp) of 117 individuals completely separated opaleye populations from the Pacific Ocean and the Sea of Cortez. Although opaleye exhibit pelagic larval stages that remain in the water column for several months, gene flow between the Pacific Ocean and the Sea of Cortez was found to be extremely limited (FST = 0.84, Nm = 0.10). Whereas limited gene flow and reciprocal monophyly suggest that the observed physical and genetic disjunction are potentially contributing to the incipient speciation of Pacific and Sea of Cortez opaleye, moderate levels of D-loop sequence divergence (3.3%) and the absence of fixed allozyme markers challenge this idea. Pacific Coast populations also exhibited restricted gene flow levels (FST = 0.25, Nm = 1.49) across Punta Eugenia, a recognized oceanographic boundary along the Baja California coast. Thus, opaleye individuals grouped into three clades: one clade in the Sea of Cortez, one Pacific clade south of Punta Eugenia, and one Pacific clade north of Punta Eugenia. Future work in this region will determine if our results can be generalized to other disjunct populations.
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