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.

The tree of life and a new classification of bony fishes.

Charles Darwin appreciated the conceptual difficulty in accepting that an organ as wonderful as the vertebrate eye could have evolved through natural selection. He reasoned that if appropriate gradations could be found that were useful to the animal and were inherited, then the apparent difficulty would be overcome. Here, we review a wide range of findings that capture glimpses of the gradations that appear to have occurred during eye evolution, and provide a scenario for the unseen steps that have led to the emergence of the vertebrate eye.

/pdf/evolution-of-the-vertebrate-eye-opsins-photoreceptors-retina-4p8wvg6ge2.pdf

Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup

As the chronicle of plate motions through time, paleogeography is fundamental to our understanding of plate tectonics and its role in shaping the geology of the present-day. To properly appreciate the history of tectonics—and its influence on the deep Earth and climate—it is imperative to seek an accurate and global model of paleogeography. However, owing to the incessant loss of oceanic lithosphere through subduction, the paleogeographic reconstruction of ‘full-plates’ (including oceanic lithosphere) becomes increasingly challenging with age. Prior to 150 Ma ∼60% of the lithosphere is missing and reconstructions are developed without explicit regard for oceanic lithosphere or plate tectonic principles; in effect, reflecting the earlier mobilistic paradigm of continental drift. Although these ‘continental’ reconstructions have been immensely useful, the next-generation of mantle models requires global plate kinematic descriptions with full-plate reconstructions. Moreover, in disregarding (or only loosely applying) plate tectonic rules, continental reconstructions fail to take advantage of a wealth of additional information in the form of practical constraints. Following a series of new developments, both in geodynamic theory and analytical tools, it is now feasible to construct full-plate models that lend themselves to testing by the wider Earth-science community. Such a model is presented here for the late Paleozoic (410–250 Ma) together with a review of the underlying data. Although we expect this model to be particularly useful for numerical mantle modeling, we hope that it will also serve as a general framework for understanding late Paleozoic tectonics, one on which future improvements can be built and further tested.

Plate Tectonics in the Late Paleozoic

Biology and ecology of fishes in Southern African estuaries

Structure and Evolution of Invertebrate Nervous SystemsDiscovering the BrainThe Structure and Evolution of the SunPolity and Governance: UPSC Prelims 2020 Highly Expected QuestionsThe Structure And Evolution Of StarsThe biology of Latimeria chalumnae and evolution of coelacanthsAn Introduction to the Theory of Stellar Structure and EvolutionSeismic and Numerical Constraints on the Formation and Evolution of Oceanic LithosphereStructure and Evolution of StarsDemocracy and Constitutionalism in IndiaThe Structure of Evolutionary TheoryEvolution of Magmatic and Diamond-Forming Systems of the Earth's Lower MantleComparative Structure and Evolution of Cerebral CortexValue, Competition and ExploitationRecords of the Western Australian MuseumThe Ocean BasinsThe Origin Nature and Evolution of Protoplasmic Individuals and Their AssociationsComparative Structure and Evolution of Cerebral CortexThe Structure and Evolution of StarsAn Introduction to the Evolution of Single and Binary StarsEvolution of the Vertebrate EarThe Evolution of the Primate HandBasic Structure and Evolution of VertebratesMajor Events in Early Vertebrate EvolutionEvolution and Development of FishesStellar InteriorsThe Structure and Evolution of GalaxiesThe Physics of StarsThe Evolution of the Primate HandCosmologyDetermination of Basic Structure-Property Relations for Processing and Modeling in Advanced Nuclear FuelThe Structure and Evolution of the SunPhysics, Formation and Evolution of Rotating StarsStructure and Evolution of Single StarsBuilding the Most Complex Structure on EarthDetermination of Basic Structure-property Relations for Processing and Modeling of Advanced Nuclear FuelsA Program of Ground-Based Astronomy to Complement Einstein ObservationsAn Introduction to the Theory of Stellar Structure and EvolutionRapport Grønlands Geologiske UndersøgelseComparative Genomics and Evolution of Eukaryotic Phospholipidbiosynthesis The Origin, Nature and Evolution of Protoplasmic Individuals and their Associations explores living beings of all levels of complexity in relation to each other and to the various ambient sources that they use to survive: protoplasmic individuals and their associations, cells and their associations, animals, and man. The book considers the concepts of evolution and of living beings; the main stages in biological evolution; the organisms' individuality, nature, way of formation, phylogenetic, and ontogenetic origin; essential property of the organisms of living beings; and creature modeling. The text also discusses the phylogenesis, ontogenesis, and the nature of the soma; the spatial and temporal environment connecting biological and geological evolution; and concepts of feeding and nutrition. Three separate sections describe phylogenetic origin of the first protoplasmic individuals; the protoplasmic individual as defined by its action and experience; and evolution in protoplasmic level.The Physics of Stars, Second Edition, is a concise introduction to the properties of stellar interiors and consequently the structure and evolution of stars. Strongly emphasising the basic physics, simple and uncomplicated theoretical models are used to illustrate clearly the connections between fundamental physics and stellar properties. This text does not intend to be encyclopaedic, rather it tends to focus on the most interesting and important aspects of stellar structure, evolution and nucleosynthesis. In the Second Edition, a new chapter on Helioseismology has been added, along with a list of physical constants and extra student problems. There is also new material on the HertztsprungRussell diagram, as well as a general updating of the entire text. It includes numerous problems at the end of each chapter aimed at both testing and extending student's knowledge.With the development of nuclear physics the theory of the stellar interior entered a new phase. Many new investigations have been conducted and the results published in a variety of specialized media. This book brings these results together in a single volume and summarizes the present status of the theory of stellar evolution. Originally published in 1958. The Princeton Legacy Library uses the latest print-on-demand technology to again make available previously outof-print books from the distinguished backlist of Princeton University Press. These editions preserve the original texts of these important books while presenting them in durable paperback and hardcover editions. The goal of the Princeton Legacy Library is to vastly increase access to the rich scholarly heritage found in the thousands of books published by Princeton University Press since its founding in 1905.Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymes and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.The objective of the funded research is to formulate and carry out a program of groundbased astronomical observations to complement X-ray data accumulated with the Einstein Observatory, and to use the results of these multiwavelength studies in addressing a number of significant astrophysical problems of current interest. The work focuses on three main topics: quasar emission mechanisms and their evolution; the structure and evolution of supernova remnants and the neutron stars which they may contain; and, the processes leading to high energy emission in the outer atmosphere (winds, coronae, etc) of main sequence stars. The physics to be addressed ranges from the generation and energetics of neutron star particle beams and their interaction with the surrounding medium to the details of supernova shock waves and their role in cosmic ray acceleration; from the basic structure of matter at supernuclear densities in neutron star interiors to the basic structure of the Universe as revealed in the evolution of quasars; and, from the study of the radiation processes in distant active galactic nuclei to the identification of the critical parameters which determine the level of coronal activity in nearby late-type stars. A detailed progress report is contained in section C below; sections D and F list the of the research reports and papers.This book equips the reader with a coherent understanding of the structure of the Sun and its evolution and provides all the knowledge required to construct a simplified model of the Sun. The early chapters cover key aspects of basic physics and describe the Sun’s size, mass, luminosity, and

Basic Structure and Evolution of Vertebrates.

Lampreys and hagfish are the only remaining jawless vertebrates and are commonly used as surrogate ancestors for comparative research on living jawed vertebrates. Until recently little was known of the evolutionary history of lampreys as the only known fossils were enigmatic examples from the Carboniferous period, around 300 million years ago. Then earlier this year Nature published a report of a fine specimen from the Cretaceous of China that looked very close to modern forms. This is now joined by a well preserved fossil from the Devonian of South Africa, which at about 360 million years old is the oldest known lamprey. It looks slightly different from modern lampreys, but is the same in essentials and differs from the various now-extinct armoured fishes with which it shared the Devonian world. Lampreys are the most scientifically accessible of the remaining jawless vertebrates, but their evolutionary history is obscure. In contrast to the rich fossil record of armoured jawless fishes, all of which date from the Devonian period and earlier1,2,3, only two Palaeozoic lampreys have been recorded, both from the Carboniferous period1. In addition to these, the recent report of an exquisitely preserved Lower Cretaceous example4 demonstrates that anatomically modern lampreys were present by the late Mesozoic era. Here we report a marine/estuarine fossil lamprey from the Famennian (Late Devonian) of South Africa5,6, the identity of which is established easily because many of the key specializations of modern forms are already in place. These specializations include the first evidence of a large oral disc, the first direct evidence of circumoral teeth and a well preserved branchial basket. This small agnathan, Priscomyzon riniensis gen. et sp. nov., is not only more conventionally lamprey-like than other Palaeozoic examples7,8, but is also some 35 million years older. This finding is evidence that agnathans close to modern lampreys had evolved before the end of the Devonian period. In this light, lampreys as a whole appear all the more remarkable: ancient specialists that have persisted as such and survived a subsequent 360 million years.

http://www-news.uchicago.edu/releases/06/images/061025.lamprey.pdf

A lamprey from the Devonian period of South Africa

A new, third, specimen of Onychoselache traquairi from the Visean (Holkerian) of Scotland allows a significant revision of the anatomy of this stem-group elasmobranch. This first report of material from the Mumbie Quarry exposure of the Glencartholm fish beds presents a new reconstruction of Onychoselache showing broad-based cephalic and nuchal spines, and exceptionally large pectoral fins. Details of the jaws, braincase and postcranial skeleton demonstrate that Onychoselache is a well-characterized member of the Hybodontiformes. Comparisons of the pectoral skeleton with other early chondrichthyan examples, including new material of Tristychius arcuatus and Plesioselachus macracanthus, highlight a range of early chondrichthyan conditions that are incorporated into a revised hybodontiform phylogeny. Close resemblance between Onychoselache and Mesozoic and late Palaeozoic hybodonts implies that these clades diverged within the Carboniferous and Permian. Major differences between Onychoselache and the coeval Tristychius (a modified reconstruction of which is included) indicate that the Neoselachii-Hybodontiformes split is probably Late Devonian, consistent with records of isolated teeth. The pectoral fins of Onychoselache, while unique among Palaeozoic forms, resemble those of Recent bamboo and epaulette sharks (Orectolobiformes). The functional corollary of this convergence is that Onychoselache represents an instance of a non-tetrapod early vertebrate with a near-walking gait.

A new reconstruction of onychoselache traquairi, comments on early chondrichthyan pectoral girdles and hybodontiform phylogeny

The chimaeroids are one of the four principal divisions of the living jawed vertebrates and their evolutionary origins have been hard to discern; here, the study of a skull of the extinct shark Dwykaselachus shows that the chimaeroids nest among the once fairly common and widespread symmoriiforms. The chimaeroids, or Holocephali, are a major group of cartilaginous fishes obscurely related to sharks and rays—obscurely because chimaeroids are very distinctive in their appearance and are difficult to place in evolutionary context. They have eyes so large that the orbits distort the shape of the brain, and they have strange, distinctive teeth. Michael Coates et al. have been studying a skull of the extinct shark Dwykaselachus from the Permian of South Africa. Although the outside of the skull resembles a kind of prehistoric shark known as a symmoriiform, scanning reveals that the braincase is characteristically chimaeroid. That means that the chimaeroids can be placed among the once fairly common and widespread symmoriiforms, and represent the end-stage of a long period of symmoriiform evolution going back to the Devonian. Chimaeroid fishes (Holocephali) are one of the four principal divisions of modern gnathostomes (jawed vertebrates). Despite only 47 described living species1, chimaeroids are the focus of resurgent interest as potential archives of genomic data2 and for the unique perspective they provide on chondrichthyan and gnathostome ancestral conditions. Chimaeroids are also noteworthy for their highly derived body plan1,3,4. However, like other living groups with distinctive anatomies5, fossils have been of limited use in unravelling their evolutionary origin, as the earliest recognized examples already exhibit many of the specializations present in modern forms6,7. Here we report the results of a computed tomography analysis of Dwykaselachus, an enigmatic chondrichthyan braincase from the ~280 million year old Karoo sediments of South Africa8. Externally, the braincase is that of a symmoriid shark9,10,11,12,13 and is by far the most complete uncrushed example yet discovered. Internally, the morphology exhibits otherwise characteristically chimaeroid specializations, including the otic labyrinth arrangement and the brain space configuration relative to exceptionally large orbits. These results have important implications for our view of modern chondrichthyan origins, add robust structure to the phylogeny of early crown group gnathostomes, reveal preconditions that suggest an initial morpho-functional basis for the derived chimaeroid cranium, and shed new light on the chondrichthyan response to the extinction at the end of the Devonian period.

A symmoriiform chondrichthyan braincase and the origin of chimaeroid fishes

New placoderm fishes are described from a black shale lens in the Famennian Witpoort Formation, near Grahamstown, South Africa. Arthrodires include a new species of Groenlandaspis, G. riniensis sp. nov., a new genus of groenlandaspidid, Africanaspis doryssa gen. et sp. nov., and a new species of the antiarch Bothriolepis, B. africana sp. nov. This is the first record of the ubiquitous genera Bothriolepis and Groenlandaspis from the African continent. The South African placoderm fauna has demonstrable links with the eastern Gondwana faunas in the close affinity of the Bothriolepis africana with B. barred of Antarctica, and the high diversity of groenlandaspid species, especially the presence of a very high crested form having affinities to Tiaraspis.

Robert W. Gess

Papers

A lamprey from the Devonian period of South Africa

A new reconstruction of onychoselache traquairi, comments on early chondrichthyan pectoral girdles and hybodontiform phylogeny

A symmoriiform chondrichthyan braincase and the origin of chimaeroid fishes

New placoderm fishes from the Late Devonian of South Africa

Archaeopteris (Progymnospermopsida) from the Devonian of southern Africa