Resolution of deep evolutionary problems, including the origin of the metazoa and the morphologic evolution of higher taxa within the metazoa, have long been sought in the developmental sequence. Haeckel's gastraea theory is perhaps the best example of this endeavor. Since Haeckel's time it has become apparent that the early evolution of animal life cannot be read directly from the developmental sequence. Ontogeny itself evolves making it difficult to even identify homologies in the early development between many phyla and classes. However, all may not be lost; during metazoan development gene expression must be localized in order to differentiate cell types in the body during development. It is this regionalized transcription and translation to protein product that differentiates cell types, organ systems, and the morphologic features that we can identify in the fossil record. The functional importance of the genes in question, and the fact that portions of the protein products of these genes must bind to DNA in order to perform their switching function, leads to extreme sequence conservation. This permits the identification and comparison of homologous genes important in the development of divergent taxa even after the passage of the entire Phanerozoic. If these genes retain a pattern of expression in development as well as conservation of the DNA sequence, then we can identify a homologous process derived from the development of the shared ancestor of the two taxa.

This approach can be used to address the homology of metameric units. Preliminary results indicate that the segmentation gene engrailed is expressed in chiton trochophores in associated with each of the developing plate fields. The engrailed gene is known to control segmentation processes in arthropods and annelids. Evidently the plates in chitons evolved from serial features in a shared ancestor of annelids, arthropods and molluscs. This indicates that the serial features found in molluscs are ancestral (plesiomorphic), and that the evolution of the mollusca has involved the loss or reduction of serial features rather than their de novo evolution in chitons and monoplacophorans as has been suggested by a number of neontologists. The fossil record suggests successive reduction of serial features in molluscs. This paleontological interpretation now finds support in developmental genetics.

Developmental genetics also provides a basis for evolution of body plans. Unusual preoral appendages have evolved in chelicerates, Burgess Shale arthropods such as Yohoia and Leanchoilia, and non arthropod forms such as Opabinia and Tullimonstrum. The differentiation of the vertebral column of vertebrates and the segments of arthropods are controlled by homologous genes that are expressed in a anterior to posterior sequence. Out of place (ectopic) expression of posterior genes in the anterior region produces posterior features in the antennal field of arthropods and in the most anterior vertebrae of the vertebrates. This potential for conversion of anterior features was present in the shared ancestor of vertebrates and arthropods. Thus evolution of novel anterior features resulting from ectopic expression could occur in both deuterostomes and protostomes and may account for a range of novel fossil forms. This suggests that parallel evolution of unusual anterior features could occur, and the presence of these features may not be the best character to use in a phylogenetic analyses.

Study of the stratigraphic ranges of reef coral species in scattered sequences (Dominican Republic, Bahamas, Costa Rica, Jamaica, and Florida) suggests that a major episode of faunal turnover occurred in the Caribbean region between early Pliocene and mid Pleistocene time. In a data set composed of all reef corals except the families Mussidae and Oculinidae and the genera Cladocora and Madracis, approximately 90% of the Mio-Pliocene fauna, composed of as many as 65–70 species, became extinct during this time interval. Ten of 27 genera became extinct. Despite the high numbers of extinctions, the total number of species in the Caribbean reef coral fauna dropped only slightly over the time interval, due to similar numbers of originations and extinctions in the fauna. With one possible exception, new species arose in surviving genera, and no new genera formed.

Although similar numbers of species became extinct within early Pliocene, late Pliocene, and early Pleistocene time units, shallow water communities experienced higher numbers of extinctions during the late Miocene and early Pliocene. Deeper water communities experienced higher numbers of extinctions during the late Pliocene and early Pleistocene. Species surviving the turnover episode occur in deeper water communities and belong predominantly to the family Agariciidae. Nearshore grass flat communities contain the highest number of early extinctions. No difference in extinction patterns could be detected between taxa which reproduce primarily by fragmentation and those that reproduce primarily by larval recruitment. Although originations appear evenly distributed among community types, a large number occur in Florida along the northern margin of faunal distribution.

The increased extinctions in shallow water communities and increased originations in the north suggest that turnover occurred primarily in response to change in abiotic factors such as temperature and siltation, and not in response to species-area effects associated with sea level change.

The Pliocene uplift of the Panamanian isthmus isolated previously contiguous Caribbean and eastern Pacific marine faunas, and initiated the development of different selective regimes on opposing sides of the barrier. Contrasting environmental conditions provided the context for different rates and kinds of evolutionary change on either side of the isthmus. The goal of our study is to characterize the rates and types of these paleoenvironmental changes; we employ stable isotopic profiles of venerid bivalve shells from the Miocene-Recent deposits of Panama and Costa Rica.

We analyzed geographic and depth variation in Recent shells as a means of calibrating the fossil analyses. Results from Recent venerids highlight the differences between the Caribbean and eastern Pacific shallow marine environments. Pacific shells typically exhibit strong annual fluctuations in δ18O, associated with seasonal upwelling and its associated cool waters. In shallow, near-shore habitats, freshwater runoff during the rainy season also contributes significantly to annual δ18O cycles. Caribbean shells exhibit negligible annual cyclicity.

We analyzed fossil shells from the Miocene Gatun Formation, and the Pliocene Cayo Agua, Escudo de Veraguas, and Rio Banano Formations from the Caribbean coast, and the Plio-Pleistocene Charco Azul Group from the Pacific coast. Results from fossil shells indicate that annual cycles are well-preserved, and not obscured by diagenesis or other alteration. A strong annual signal in δ18O (amplitude >1.5‰) is found back at least to the Early Pleistocene along the Pacific coast. Some post-uplift Caribbean samples exhibit stronger seasonality than that observed in similar habitats today.