Terry Grande

The Tree of Life and a New Classification of Bony Fishes

The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 molecular markers (one mitochondrial and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). Bony fish diversity is represented by 1093 genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.

Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature

Background The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. Methodology/Principal Findings We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. Conclusions/Significance The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.

Evolution of Peripheral Mechanisms for the Enhancement of Sound Reception

The evolutionary history of hearing is a rich and fascinating pageant. The inner ear and the closely related mechanosensory lateral line show a tremendous diversity among living and fossil vertebrates. This chapter documents how these systems have evolved new functions by juxtaposing novel linkages (i.e., transduction mechanisms) between fundamentally conservative hair cell sensors and the outside world. These linkages dictate the ear’s function, and are so diverse that the functions of the ear (and lateral line) have changed repeatedly in vertebrate history. The linkages of the vertebrate ear do indeed bring joy to the comparative biologist, and the evolution of these linkages is the evolution of new sensory functions, many of which may have led to the rapid diversification of individual taxa (e.g., Otophysi) and the expansion of behavioral repertoires. To discuss the evolution of enhanced hearing capabilities, one must understand the primitive functions of the octavolateralis systems, and ask what new functions has evolution wrought, and what are the new stimuli to which the ear responds in derived taxa? To constrain the discussion of the diversity of inner ear linkages, this chapter reviews the evolution of specializations that alter the function of the inner ear in teleost fishes and grant the ability to detect fluctuations in the ambient pressure (i.e., sound). Several instances of lateral line specialization that may provide this system with pressure sensitivity are also described. When the distribution of these specializations is compared to our best estimates of teleost relationships (Fig. 4.1), it appears that the detection of pressure fluctuations (what terrestrially chauvinistic vertebrates call hearing) has evolved dozens of times! This chapter describes some of these novel morphologies in detail and attempts

Phylogenetic Relationships of Extant Esocid Species (Teleostei: Salmoniformes) Based on Morphological and Molecular Characters

Abstract The phylogenetic relationships of extant species of Esox were investigated using both morphological and molecular data. The complete mtDNA cytochrome b gene (cytb) and the second intron of the RAG1 gene were sequenced from multiple specimens of each species and analyzed using maximum parsimony and maximum likelihood. The resulting cladograms were compared with each other and to the morphological cladogram for congruence. Data from all three sources strongly support the monophyly of the genus, and the monophyly of the subgenera Esox (i.e., pikes) and Kenoza (i.e., pickerels). Our data support the sister-group relationship between Esox reicherti and Esox lucius (the Amur and Northern Pike, respectively). Incongruent results between the morphological and RAG1 data and the cytb data, with respect to pickerel interrelationships, suggest hybridization and introgression among pickerel species. Additional research is necessary to explore these results further. This study represents the first study to integrate both morphological and molecular data into a phylogenetic analysis of Esox. It aims to provide a better understanding of esocid evolution and lay the foundation for the interpretation of fossil material assigned to Esox. It also provides preliminary genetic evidence of hybridization among the pickerels.

Ontogeny of the Accessory Neural Arch in Pristigasteroid Clupeomorphs and Its Bearing on the Homology of the Otophysan Claustrum (Teleostei)

Abstract The claustrum, one of the Weberian ossicles of otophysans, is here proposed as homologous to the accessory neural arch (ANA) of lower teleosts. This idea is based on structural and topographical correspondence, as well as on ontogenetic timing of differentiation and ossification. Claustrum and ANA are similar in general shape and occupy the same position relative to other vertebral structures. They are both derived from paired cartilage precursors that differentiate around the anterior part of the neural canal. Also, chondrification and ossification of ANA and claustrum are markedly delayed relative to surrounding elements, such as regular neural arches and supraneurals. The new hypothesis implies that the accessory neural arch is actually present in otophysans (modified as claustrum) and therefore that its loss cannot be considered as an ostariophysan synapomorphy. Loss of a separate accessory neural arch in adults is instead an additional synapomorphy of Gonorynchiformes, a loss homoplastic with various other teleostean subgroups, the largest of which being Ctenosquamata. Despite various developmental differences, ANA may be a basidorsal derivative and therefore homologous to the neural arch series.

A new species of †Notogoneus (Teleostei: Gonorynchidae) from the Upper Cretaceous Two Medicine Formation of Montana, and the poor Cretaceous record of freshwater fishes from North America

ABSTRACT †Notogoneus montanensis, sp. nov. (Teleostei: Ostariophysi: Gonorynchidae) is described from Late Cretaceous freshwater deposits of the Two Medicine Formation of Montana. The species is represented by one articulated skeleton and a partial trunk region of a second individual. Articulated freshwater fish fossils are almost unknown in Early Cretaceous through Middle Paleocene age deposits of North America. Localities such as the Two Medicine fish locality are extremely important to a better understanding of the biodiversity of early North American freshwater teleosts. †Notogoneus montanensis, sp. nov. is the earliest known occurrence of the genus †Notogoneus, and it is the earliest known freshwater gonorynchiform from North America. The distribution of †Notogoneus and other gonorynchid species is briefly reviewed. Additional fragmentary fish fossils found associated with †N. montanensis, sp. nov. include a number of teleost scales, which appear to belong to at least two different taxa other than †N...

Revision of the Genus Gonorynchus Scopoli, 1777 (Teleostei: Ostariophysi)

Five valid species of Gonorynchus (Ostariophysi: Gonorynchiformes: Gonorynchidae) are diagnosed on the basis of internal and external morphology (e.g., vertebrae number, lateral line scale counts, mouth morphology, caudal skeleton morphology). These are Gonorynchus gonorynchus, G. greyi, G. forsteri, G. abbreviatus, and G. moseleyi. A phylogenetic analysis of these species using the outgroups Chanos chanos (a basal gonorynchiform) and tNotogoneus osculus (representing the sister group to Gonorynchus) suggests that G. abbreviatus and G. moseleyi form a monophyletic clade, which is, in turn, the sister group to a clade containing G. greyi, G. gonorynchus, and G. forsteri. Gonorynchus gonorynchus and G. forsteri are sister taxa. This analysis represents the first published phylogenetic analysis of the species of Gonorynchus. A key to the valid species of Gonorynchus is also provided.

Redescription of the Type Species for the Genus ‡Notogoneus (Teleostei: Gonorynchidae) Based on New, Well-Preserved Material

Abstract †Notogoneus osculus Cope, the type species for the geographically widespread Upper Cretaceous to Upper Oligocene genus †Notogoneus (Gonorynchidae), is redescribed in detail based on much new material. This species is known from the Early Eocene Fossil Butte Member of the Green River Formation, southwestern Wyoming. It is geologically the youngest known species of the family Gonorynchidae in North America, although the family is known from Oligocene and Miocene lacustrine deposits of Europe and Australia and is extant today in tropical marine environments of the Pacific (Gonorynchus spp.). In this paper we also correct a number of mistakes in previously published morphological descriptions of †N. osculus (e.g., in skull and caudal skeleton) based on a large, new sample of well-preserved, well-prepared specimens. Accurate description of this species is important because it is the type for the genus and it is also by far the best preserved of all known species of †Notogoneus. In addition, it may shed new light on the interrelationships of Gonorynchidae (work in progress by the authors). †Notogoneus appears to have inhabited a freshwater, subtropical environment. Based on distribution data and species diversity within the Green River Formation, we suspect that †N. osculus may have been a migratory fish, living in the central (off-shore) regions of Fossil Lake during part of its life, and in connecting streams and rivers during other parts of its life. Most or all species of the genus †Notogoneus are known from freshwater deposits and species are known from North America, Europe, Asia and Australia. Species of the extant gonorynchid genus Gonorynchus are all marine and are known from the Indo-Pacific and southern Atlantic.

A cladistic analysis of fossil and living gonorynchiform ostariophysan fishes

Abstract The phylogenetic relationships of the order Gonorynchiformes (Teleostei; Ostariophysi) have been broadly discussed in the last three decades; but no cladistic analysis had been attempted to date. The present paper presents the preliminary results of a cladistic analysis comprising all the available fossil (mostly Mesozoic) and living forms. This preliminary analysis confirms the monophyly of the Gonorynchiformes; this order being the sister-taxon of the Otophysi (monophyletic group comprising all other Ostariophysi). The interrelationships of the Gonorynchiformes differ; however; from hypotheses of previous papers; mainly in the definition and relationships of the Chanidae; the Gonorynchidae; and the Kneriidae.

EVOLUTION OF THE WEBERIAN APPARATUS

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