has acted. By this definition, bindin is considered to be evolving quickly in the genera Echinometra, Strongylocentrotus, and Heliocidaris (Biermann, 1998; Landry et al., 2003; Metz and Palumbi, 1996; Zigler et al., 2003) and slowly in Lytechinus, Arbacia, and Tripneustes (Metz et al., 1998; Zigler and Lessios, 2003a, 2004). Although positive selection could not be statistically demonstrated for any comparison between species of Lytechinus, we consider the bindin of L. williamsi and Lytechinus variegatus variegatus as rapidly evolving, because its divergence is much higher than expected from comparisons of COI between these species. The COI haplotypes of L. williamsi and L. variegatus are intermingled, whereas bindin sequences are reciprocally monophyletic, suggesting the possibility of selection on the latter (Zigler and Lessios, 2004).
Estimation of time since species separation from COI divergence assumes a molecular clock, which is calibrated by the complete closure of the seaway between the eastern Pacific and the Atlantic by the isthmus of Panama at ≈3.1 million years ago (Coates and Obando, 1996). In all comparisons involving tropical genera, Atlantic and Pacific species are included. The divergence between clades presumably split by the isthmus provides a rough calibration of a molecular clock for each genus, allowing us to place a general time frame on species divergence patterns.
Polytypic species and low levels of genetic divergence between allopatric entities within an ocean basin are common in the genera Tripneustes, Lytechinus, and Eucidaris (Fig. 8.1). For example, in the genus Eucidaris, all Atlantic nominal species or subspecies, Eucidaris tribuloides, Eucidaris clavata, and Eucidaris tribuloides variegatus africana form one single genetic cluster with no distinction among them (Lessios et al., 1999). Together, this broad polytypic species is sister to the Eastern Pacific pair Eucidaris galapagensis and Eucidaris thouarsi. Based on a molecular rate estimate provided by the rise of the isthmus of Panama, the latter two sister species diverged ≈2 million years ago. An allopatric neighbor of these species, the widely distributed Pacific–Indian ocean species Eucidaris metularia is not a close relative of the eastern Pacific species. Rather, this species is an ancient offshoot in the genus, having diverged 5–8 million years ago.
The genus Tripneustes shows a pattern of dissimilar geographic distribution of genetic variation in two major oceanic regions (Lessios et al., 2003a). Tripneustes depressus from the eastern Pacific and Tripneustes gratilla from the rest of the Indo-Pacific are genetically indistinguishable, forming a single geographically widespread species complex that occupies most of the world’s tropical oceans. The Atlantic species Tripneustes