Gonad morphology at the gross anatomical or histological levels has long been studied by fisheries biologists to identify annual reproductive cycles and length of breeding season, among other goals. Comparative surveys across vertebrate taxa have not been detailed enough, however, to describe fully the differences and similarities among gonads of bony fishes and other vertebrates, and to use gonad morphology in phylogenetic systematic analyses. An emerging constant among vertebrates is the presence of a germinal epithelium composed of somatic and germ cells in both males and females. In females, the germinal epithelium lines the ovarian lamellae. In males, arrangement of the germinal epithelium into compartments varies among osteichthyans: basal taxa have an anastomosing tubular testis, whereas derived taxa have a lobular testis. The lobular testis is proposed as a synapomorphy of the Neoteleostei. The annual reproductive cycle is hypothesized to be the source of morphological variation among testis types. Elongation of germinal compartments during early maturation may result in a transition from anastomosing tubular to lobular testes. In all male atherinomorphs surveyed, spermatogonia are restricted to the distal termini of lobules rather than being distributed along the lobule; there is an epithelioid arrangement of Sertoli and germ cells rather than a germinal epithelium. Arrest of the maturation-regression phases is hypothesized to lead to formation of the atherinomorph testis. Atherinomorphs also have a distinctive egg with fluid, rather than granular, yolk. Variation among germinal epithelia is interpreted in a developing phylogenetic framework to understand evolution of gonad morphology and to propose gonad characters for phylogenetic analyses.

The use of fossils in the phylogenetics of extant clades traditionally has been a contentious issue. Fossils usually are relatively incomplete, and their use commonly leads to an increase in the number of equally most parsimonious trees and a decrease in the resolution of phylogenies. Fossils alone, however, provide certain kinds of information about the biological history of a clade, and computer simulations have shown that even highly incomplete material can, under certain circumstances, increase the accuracy of a phylogeny, rather than decrease it.

Because empirical data are still scarce on the effects of the inclusion of fossils on phylogenetic reconstructions, we attempted to investigate this problem by using a relatively well-known group of acanthomorph fishes, the Tetraodontiformes (triggerfishes, pufferfishes, and ocean sunfishes), for which robust phylogenies using extant taxa already exist and that has a well-studied fossil record. Adding incomplete fossil taxa of tetraodontiforms usually increases the number of equally most parsimonious trees and often decreases the resolution of consensus trees. However, adding fossil taxa may help to correctly establish relationships among lineages that have experienced high degrees of morphological diversification by allowing for a reinterpretation of homologous and homoplastic features, increasing the resolution rather than decreasing it. Furthermore, taxa that were scored for 25% or more of their characters did not cause a significant loss of resolution, while providing unique biological information.

Fishes represent an extremely diverse group of vertebrates with a deeply rooted evolutionary history. An understanding of their biology is being enriched by advancements in phylogenetic analysis and genomics, which are providing the framework for deciphering their evolutionary relationships and the molecular details that govern their evolution. Recent discoveries about the structure and function of fish genomes suggest the occurrence of large-scale genome level duplications within the stem lineage of the Actinopterygii (ray-finned fishes). However, little is understood about the effects, if any, of this event in relation to organismal complexity or species diversity. In this manuscript, I propose a hypothesis to test whether there is a likely relationship linking vertebrate genomes, organisms and species diversity. In so doing, I discuss the problems inherent in defining the complexity of genomes and organisms and provide simplifying assumptions that enable a preliminary test of the hypothesis. Results of this test suggest the likelihood of linkage between large-scale genome changes and organismal complexity early in vertebrate evolution but not in the evolution of the ray-finned fishes. A particularly interesting implication of the results is that there may be a limit to the effects of genome level duplications on organismal complexity and species diversity.

To investigate jaw evolution in beloniform fishes, we reconstructed the phylogeny of 54 species using fragments of two nuclear (RAG2 and Tmo-4C4) and two mitochondrial (cytochrome b and 16S rRNA) genes. Our total molecular evidence topology refutes the monophyly of needlefishes (Belonidae) and halfbeaks (Hemiramphidae), but supports the monophyly of flyingfishes (Exocoetidae) and sauries (Scomberesocidae). Flyingfishes are nested within halfbeaks, and sauries are nested within needlefishes. Optimization of jaw characters on the tree reveals a diverse array of evolutionary changes in ontogeny. During their development, needlefishes pass through a “halfbeak” stage that closely resembles the adult condition in the hemiramphid halfbeaks. The reconstruction of jaw transitions falsifies the hypothesis that halfbeaks are paedomorphic derivatives of needlefishes. Instead, halfbeaks make up a basal paraphyletic grade within beloniforms, and the needlefish jaw morphology is relatively derived. The parallel between needlefish ontogeny and beloniform phylogeny is discussed, and clades amenable to future morphological analysis are proposed.

The evolution of feeding mechanisms in the ray-finned fishes (Actinopterygii) is a compelling example of transformation in a musculoskeletal complex involving multiple skeletal elements and numerous muscles that power skull motion. Biomechanical models of jaw force and skull kinetics aid our understanding of these complex systems and enable broad comparison of feeding mechanics across taxa. Mechanical models characterize how muscles move skeletal elements by pulling bones around points of rotation in lever mechanisms, or by transmitting force through skeletal elements connected in a linkage. Previous work has focused on the feeding biomechanics of several lineages of fishes, but a broader survey of skull function in the context of quantitative models has not been attempted. This study begins such a survey by examining the diversity of mechanical design of the oral jaws in 35 species of ray-finned fishes with three main objectives: (1) analyze lower jaw lever models in a broad phylogenetic range of taxa, (2) identify the origin and evolutionary patterns of change in the linkage systems that power maxillary rotation and upper jaw protrusion, and (3) analyze patterns of change in feeding design in the context of actinopterygian phylogeny. The mandibular lever is present in virtually all actinopterygians, and the diversity in lower jaw closing force transmission capacity, with mechanical advantage ranging from 0.04 to 0.68, has important functional consequences. A four-bar linkage for maxillary rotation arose in the Amiiformes and persists in various forms in many teleost species. Novel mechanisms for upper jaw protrusion based on this linkage for maxillary rotation have evolved independently at least five times in teleosts. The widespread anterior jaws linkage for jaw protrusion in percomorph fishes arose initially in Zeiformes and subsequently radiated into a wide range of premaxillary protrusion capabilities.

Coral reefs contain the most speciose communities of fishes on this planet, so it is appropriate to use these to explore how fish species are organized into communities. While descriptive data suggest that the diverse communities of fish on coral reefs are equilibrial assemblages of species, all finely adapted to specific and unique ecological roles, these are highly dynamic, non-equilibrial assemblages with structure driven more by patterns of recruitment and loss of individual fishes, than by patterns of resource allocation among differently adapted phenotypes. As a consequence, local assemblages differ in structure, and structure wanders through time. Individual fish are confronted by different mixes of species in different times and places. The recruitment process that drives these dynamics is complex, being governed by several mechanisms, and local populations receive some portion of their recruitment from distant sources. Information on this connectivity among local populations is critically important for management which is based increasingly on use of marine protected areas (no-take zones) both to conserve, and to provide sustainable fisheries. At present, however, we do not know the spatial scale or the extent of this connectivity, and this critical knowledge gap impedes both management, and fundamental understanding.