Evolution of Birds

Part 1. The Evolution of Birds and Biological Diversification. The two chapters of Part 1 will describe the scope of the book. Chapter 1 will lay out the historical development of our current view of avian evolution that has emerged over the last few decades. It will present a brief overview of the advances that have been made in recent years in understanding avian relationships among major clades as well as the spectacular new findings at the species level. Thus, over the course of 2005-2007 we will see the results of three large studies on the higher-level relationships of birds; we will have a generic-level phylogeny for all avian families; and there will be dozens of new studies on speciation within various groups of birds on all continents. Combined with the spectacular new finds that have emerged in recent years on the Mesozoic history of pre-modern birds, these new data will provide the empirical background for a description of avian diversification from the time of the dinosaur-bird transition to the present. These rapid advances in avian evolution also provide a framework to examine major theoretical and empirical questions about how life diversifies. Chapter 2 will introduce the reader to the issues and controversies that characterize contemporary thinking about biological diversification. The chapter compares current theoretical stances within diversification theory and will offer up a precis of a critique of several widely accepted conceptual paradigms that shape much of the current thinking, and thus set the stage for many of the chapters that follow. . Chapter 1. The Evolution of Birds: A Case Study of Biological Diversification. Expected topics:. Birds: the most diverse group of terrestrial vertebrates. Out of dinosaurs: 150 million years of diversification. Evolutionary views about birds: a short history. Understanding how life evolves: the problem of biological diversification. Birds as a case study of diversification. Birds can be shown to exemplify many of the same evolutionary patterns and processes characterizing other groups of organisms (especially vertebrates), therefore they have much to teach us about the general problem of biological diversification. Avian biology is well known. Unprecedented advances in understanding avian relationships at all taxonomic levels have been made in the last decade. The plan of the book: a dialectic on birds and diversification. . Chapter 2. Biological Diversification and the Evolution of Birds. Expected topics:. Biological diversification: what is being explained?. The origin of species and groups of species. Patterns of diversity through space and time. The canonical view of biological diversification. A common thread: Darwin to Simpson to contemporary evolutionary biology. Diversification as a diversity-dependent process: an ecological worldview. Diversification as a diversity-independent process: a taxic worldview. Linking the origin of species to diversification patterns and processes. The plan of the book: a dialectic on diversification and birds. Part 2. The Phylogenetic History of Birds: The Framework. for Understanding Avian Evolution. . Part 2 is comprised of a number of chapters (uncertain at this time), all of which focus on our current understanding of avian phylogenetics. This section will contain much of the empirical findings about the higher-level relationships of birds that will be used in the chapters included in Parts 4-7. The first chapter (Chapter 3) of Part 2 will be devoted to the theory and method of reconstructing avian history. It will not be a long discourse on the details of phylogenetic methodology, although its basics will be described. Instead, the narrative will emphasize the importance of adopting an analytical approach to history, the nature of evidence (molecular, morphological, and others), how phylogenetic hypotheses should be evaluated, the uncertainties of phylogenetic knowledge and how those can be resolved, the role of fossils in interpreting history, and how we make inferences about the temporal dimensions of avian history. Chapter 3 will focus on phylogenetics and historical biogeography. When it is more appropriate, later chapters will examine methods of species delimitation, additional biogeographic analysis, assessing speciation and extinction rates, among other topics. Chapter 3 will end with a general summary of our knowledge about avian history from the perspective of the methodological and evidentiary advances that have influenced the field. . Following this methodological introduction, successive chapters of Part 2 will summarize the phylogenetic history of birds. Chapter 4 will describe the origin of birds, their relationships to other archosaurs, particularly theropod dinosaurs, and will address such compelling subjects such as the origin of feathers and flight, homeothermy, and modern aspects of avian biology. Chapter 5 will present an overview of the Tree of Life for modern birds (Neornithes). It will trace the long-standing controversies over avian higher-level relationships and will present the most current well-supported tree, along with a discussion of the evidence. This tree will represent the organizational framework for all remaining chapters of Part 2. The tree will be partitioned into major clades that will be the subject of detailed discussion in individual chapters. These chapters will not follow traditional taxonomic discussions (orders, families) but their number and content will be determined on a variety of criteria such as size of the clade, its phylogenetic and biological diversity, the amount of information on the history of the group, and so. Several of these chapters can be easily identified at the present time. The base of the neornithine tree is well understood, therefore chapters on the Palaeognathae (tinamous and ratites) and the Galloanserae (galliform and anseriform birds) are obvious. Because of the difficulty of resolving higher relationships within the remainder of modern birds (the Neoaves), there will be an introductory chapter that discusses the nature of this problem and its resolution. Each chapter in this section will have a similarity to its organization and each will have an introduction that explains why the taxa are grouped together (reflecting the tree in Chapter 5), a discussion of their diversity (taxonomic and ecological), distribution, phylogenetic relationships within the group, fossil record, biogeography, tempo of diversification, and evolutionary patterns in morphology, behavior, and so on, as current evidence warrants. Chapter 3. Deciphering Avian History. Expected topics:. The importance of phylogenetics. Narrative history versus analytical (testable) history. Nature of phylogenetic evidence. Taxon/character sampling. Methods of analysis. Understanding time. Growth of phylogenetic knowledge about birds. . Chapter 4. Birds as Archosaurs. Expected topics:. The phylogenetic history of the Archosauria. What is a bird?. The Mesozoic Radiation. Description and discussion of various groups of Mesozoic birds. Patterns of morphological change. Cladistic optimization and narratives of change. Anatomical terminology. Origins of feathers, flight, homeothermy, etc. The evolution of avian biology. Chapter 5. The Major Clades of Modern Birds. Expected topics:. Growth of phylogenetic knowledge about birds. Phylogenetic relationships of the Neornithes: Overview. Classification, rank-free names, problems of ranks. Chapter 6. Palaeognathae. . Expected topics:. Introduction and history. Diversity: species, ecological. Distribution. Phylogenetic relationships. Fossil record. Biogeography. Evolutionary patterns. Chapter 7. Galloanserae. . Expected topics:. Same as Chapter 6. Chapter 8. Neoaves. Expected topics:. Introduction and history. The problem of higher-level relationships within Neoaves. Phylogenetic relationships of Neoaves: what we think we know. The Neoavian wall of death: Real or artifact?. The large-scale temporal and spatial history of birds: overall pattern. . Chapters 9A-Z. Clades of the Neoaves. Expected topics for each chapter:. Same as Chapter 6. Part 3. Species and speciation. Part 3 of the book will cover the problem of the origin of species and the associated topics of phenotypic (sensu lato, including, for example, behavior) and ecological change. It will be stressed that this section of the book is the foundation for understanding patterns of diversity and processes of diversification (Parts 4 and 5) as well as reconstructing the history of continental biotas (Part 6). Chapter 10 will discuss the perennially controversial issue of species concepts. It will make the case theoretically and empirically for the use of the phylogenetic species concept for understanding speciation and diversification. Because of the broad importance of this topic, the chapter will make liberal use of studies beyond birds. Chapter 11, in contrast, will focus on birds and detail the issues of delimiting avian species and understanding variation within and among basal taxonomic units. The chapter will also illustrate in more detail the empirical differences among species concepts as they have been applied to birds. Finally, the chapter will address the problem of how many extant species of birds are there. . A similar logical arrangement will be applied to Chapters 12 and 13. Chapter 12 will examine how species arise and the conceptual and methodological tools we need to understand species' origins. Consequently, it will include a discussion of understanding modes of speciation through phylogenetic and biogeographic analysis as well as through the historical analysis of genetic variation. Finally, the chapter will analyze the theory and methods used to understand the tempo of speciation. Chapter 13 shifts to an empirical review of avian speciation. It will use avian examples to investigate different modes of speciation, and will bring together studies from all parts of the world. One of the key arguments of these two chapters, indeed all of Part 3, is that the more we understand about speciation in the recent biota, the better we will be able to decipher and explain large-scale patterns of diversity through space and time. As such, these chapters provide basic background for the discussions in Parts 4-6. Chapters 14 and 15 will discuss two subjects that are intimately related to the origin of taxonomic diversity, namely the origin of morphogenetic novelty and the evolution of ecological change. Morphogenetic change is here taken in a very broad sense, from change in genetic architecture, developmental pathways, and conventional phenotype. Morphogenetic change in isolated populations that becomes fixed can be used to characterize new taxonomic units. The argument will be that the morphogenetic complexity we see in nature arises as fixed variation in populations and is related to the origin of basal taxa. Thus, understanding the evolution of this change necessarily involves the study of the interface between populations and incipient basal taxonomic units. Chapter 15 will trace some of the same themes, focusing instead on the evolution of ecological change and its relationship to speciation. There is considerable debate about the role of ecological change in promoting speciation versus whether ecological change instead plays a minor role and is generally an epiphenomenon of spatial isolation. The interface of ecology and speciation is complex, theoretically and analytically. The chapter will use speciation patterns in birds and other organisms to examine this problem. Both chapters 14 and 15 will be particularly relevant for the discussions in Parts 4-6. The majority of discussions in the literature about the origin of novelty, key innovations, and the meaning and importance of "macroevolution" ignore the role of speciation. Likewise, many of the predominant theories about speciation and extinction rate controls depend on the mechanisms and importance of ecological change. . Chapter 10. Species and the Ontology of Evolution. . Expected topics:. Theories and Their Entities. What are the Units of Evolution?. The Phylogenetic Species Concept. Phylogenetic Species: Practical Applications. Delimiting basal taxa. Taxic trees versus gene trees. Evidence: morphology, behavior, and molecules. How the Biological Species Concept Confounds Evolutionary Analysis. The Evolutionary Species Concept. Evolutionary Units and Speciation: Advantages of the Phylogenetic Species Concept. . Chapter 11. The Nature of Avian Species. . Expected topics:. Delimiting avian species. Kinds of evidence. The synergy of molecules, morphology, and behavior. Gene trees versus species trees. How many species of birds?. . Chapter 12. The Origin of Species: Theory and Method. . Expected topics:. What is speciation?. The relationship between species concepts and speciation analysis. Models of differentiation: theory. Speciation analysis: methods. Species through time. Species concepts and ancestral-descendant relationships. Tempo of speciation: theory and method. . Chapter 13. The Origin of Avian Species. . Expected topics:. Introduction. Modes of speciation in birds. Avian speciation in continental settings. Avian speciation in insular settings. What avian studies tell us about modes of speciation. . Chapter 14. Speciation and the Origin and Evolution of Morphogenetic Complexity. . Expected topics:. What are evolutionary novelties?. Variation, polymorphism, character modification, and the origin of novelties. Morphological change and ontogenetic change. Processes of differentiation. How characters spread through populations. What is the genetics of speciation?. Is differentiation adaptive?. Historical analysis of adaptation. Speciation and the tempo of morphological change. Evolutionary mode and morphological change. . Chapter 15. Speciation and the Origin and Evolution of Ecological Change. Expected topics:. What is ecological speciation?. The historical analysis of ecological change within the context of speciation. Does ecological change within and among populations promote speciation?. Role of ecological change within context of different modes of speciation. Part 4. The Evolution of Diversity. The six chapters of Part 4 primarily describe a "mechanistic" diversity-independent approach to biological diversification and discuss the observations of avian history for testing the predictions of this theoretical worldview. It will make a "reductionist" argument of sorts: generalizations about speciation and extinction rate-controls must be framed in terms of our knowledge about species-level processes within individual focal groups (such as birds) as well as across other large groups. Chapter 16 summarizes the theoretical structure of, and empirical case for, the diversity-dependent model of diversification. This is followed by an extensive critique. The Chapter then argues that patterns of diversification are better explained by diversity-independent processes of speciation and extinction rate-control. The chapter lays the conceptual foundation for consideration of the rate-controls of speciation (Chapter 17) and extinction (Chapter 19); both chapters not only summarize and evaluate conceptual issues but empirical studies as well. These three chapters will be central for a critical comparison of the D-D and D-I models of diversification in subsequent sections and chapters of the book. Chapters 18 and 20 examine the data from avian history that bear on speciation and extinction rate-controls, respectively. Chapter 21 looks at the particular importance of the Cretaceous-Tertiary mass extinction event and its affect on Earth's biotic history, in general, and avian history, in particular. . Chapter 16. Toward a Mechanistic Theory of Biological Diversification. . Expected topics:. Patterns of diversity: what a theory of biological diversification should explain. The structure of contemporary diversification theory: explication. Speciation and extinction rate controls: diversity dependent (D-D). The ontology of D-D diversification: species, higher taxa, and ecological entities. The underlying causal structure of D-D diversification. D-D diversification theory: critique. Towards a diversity-independent theory of biological diversification. Speciation and extinction rate controls: diversity-independent (D-I). The ontology of D-I diversification: species as entities of diversification. Seeing macroevolution for what it is: changes in patterns of diversity. The importance of conceptual worldviews about diversification. Seeing D-D and D-I explanations as two discrete alternatives is partly didactic. But each entails different ways of explaining patterns and processes of diversification. Each leads to very different expectations of how the biosphere is structured causally. Disentangling the problem of multiple causation. Theory and Method. How can D-D and D-I explanations be tested?. What are the empirical expectations (patterns) of each?. What kinds of methods are required?. Plan for the remainder of Part 4 and links to Parts 5 and 6. . Chapter 17. The Rate-control of Speciation. Expected topics:. Recap from previous chapters. What is speciation?. What are the drivers of speciation?. What is the evidence for speciation mode across diverse clades?. Predictions from speciation theory and empirical studies. Partitioning causation: tests of alternative mechanisms. Tests and evidence. Measuring rates of speciation: general problems. Chapter 18. The Rate-control and Tempo of Avian Speciation. Expected topics:. Recap from previous chapters: speciation in birds. The tempo of avian speciation/diversification. Allopatric speciation and the vicariance of biotas. Historical congruence of differentiation: documentation. Allopatric speciation and areas of endemism. Causes of vicariance. Ages of species. Ecological speciation in birds. Sexual selection the rate of speciation. . Chapter 19. The Rate-control of Extinction. Expected topics:. Nature of extinction. The ontology of extinction and its relation to extinction rates. Extinction of taxa versus loss of individuals. Processes: idiographic description or nomothetic theory?. What is the nature of the generalities we might posit?. Methodological issues. Patterns of extinction. Descriptive patterns: background versus mass. Normal/background extinction". What are the causes?. How general are they?. Mass extinction. What are the causes?. How general are they?. Importance of mass extinction versus background extinction on diversity patterns. The rate-control of extinction. Tests and evidence. The fossil record. Molecular phylogenies and extinction rates. . Chapter 20. Extinction Rates in Birds. Expected topics:. Estimating extinction in birds. Fossil record. Vicariance patterns and missing taxa. Molecular phylogenies and extinction. Chapter 21. Birds and the K/T Mass Extinction. Expected topics:. The controversies. The KT event in general and birds in specific. The scope of the KT extinction event. The spatial and temporal history of birds and the KT boundary: recap. How do we study the effect of the KT extinction on avian diversity and evolution?. What was the effect of the KT extinction event on avian diversity and evolution?. . Part 5. The Evolution of Diversity and Avian Assemblages. What patterns of diversity across space and time need to be explained by a theory of diversification and how well do the D-D and D-I models fare in providing a general explanatory structure for these patterns? Part 5 examines these general questions. The two chapters of this section provide a description of patterns of diversity across different spatial and temporal scales and consider alternative hypotheses of speciation- and extinction rate-control that have been proposed to explain them. Chapter 22 will address large-scale (global) temporal and spatial patterns, whereas Chapter 23 directs attention to patterns of diversity at smaller scales, at the level of ecological assemblages as they are manifested at habitat/ecosystem and biome levels. . Chapter 22. Understanding Large-scale Patterns of Diversity. Expected topics:. Patterns of diversity at different temporal and spatial scales. The Phanerozoic diversity curve. Marine patterns. Terrestrial patterns. Late Cretaceous/Tertiary terrestrial patterns. Spatial diversity patterns: global. Marine patterns. Latitudinal patterns. Continental patterns. Explaining large-scale patterns. D-D diversification explanatory structures. D-I diversification explanatory structures. Integrating speciation and extinction rate-controls. . Chapter 23. Understanding the History of Ecological Assemblages. Expected topics:. Macroecological patterns and historical explanations. Expected patterns at different scales. Reconstructing the history of ecological assemblages: methods. Macroecological theory and history. Phylogenetic and biogeographic methods. Case studies: avian assemblages at the habitat to ecosystem level. Part 6. The assembly of continental avifaunas. In Part 6 the focus returns to birds but at the same time the section addresses the theory and method used to reconstruct the history of continental-sized biotas. The seven chapters of this section will discuss the evolution of the world's continental avifaunas, synthesizing much of the empirical data of Part 2 with a summary of the phylogenetic and biogeographic information currently available for avian taxa on each major continental-scale region. The goal is to describe the taxonomic assembly (origins) and diversification of the contemporary avifaunas. Chapters 24 and 25 will provide, respectively, the necessary paleogeographic and paleoclimatic background for interpreting avian phylogenetic history. Chapter 24 will summarize global-scale intercontinental history over the last 100 million years; Chapter 25 will mirror this treatment with a discussion of the major paleoclimatic patterns. Special attention will be paid to those events that are most critical for interpreting biotic history. Chapters 26-30 will discuss avifaunal evolution for each major continental region. These chapters will also include sections on specific relevant paleogeographic and paleoclimatic events and will discuss differences and similarities between birds and other groups, when relevant. Chapter 24. Global Late Cretaceous-Tertiary Paleogeography. Expected topics:. Late Cretaceous to Recent global paleogeography. The paleogeographic history of Wallacea. The paleographic history of the Caribbean. . Chapter 25. Global Late Cretaceous-Tertiary Paleoclimatology. Expected topics:. Late Cretaceous to Recent continental paleoclimatology. . Chapter 26. The Holarctic Avifauna. Expected topics:. Taxonomic structure and diversity of the avifauna: general patterns. Paleogeographic and paleoclimatic history. The paleontological record. Phylogenetic/biogeographic origins of the biota. Patterns of endemism. Area relationships/patterns of speciation. Case studies. . Chapter 27. The Latin American Avifauna. Expected topics:. Taxonomic structure and diversity of the avifauna: general patterns. Paleogeographic and paleoclimatic history. The paleontological record. Phylogenetic/biogeographic origins of the biota. Patterns of endemism. Area relationships/patterns of speciation. Case studies. . Chapter 28. The African Avifauna. Expected topics:. Taxonomic structure and diversity of the avifauna: general patterns. Paleogeographic and paleoclimatic history. The paleontological record. Phylogenetic/biogeographic origins of the biota. Patterns of endemism. Area relationships/patterns of speciation. Case studies. . Chapter 29. The Asian Avifauna. Expected topics:. Taxonomic structure and diversity of the avifauna: general patterns. Paleogeographic and paleoclimatic history. The paleontological record. Phylogenetic/biogeographic origins of the biota. Patterns of endemism. Area relationships/patterns of speciation. Case studies. . Chapter 30. The Australasian Avifauna. Expected topics:. Taxonomic structure and diversity of the avifauna: general patterns. Paleogeographic and paleoclimatic history. The paleontological record. Phylogenetic/biogeographic origins of the biota. Patterns of endemism. Area relationships/patterns of speciation. Case studies. . Part 7. Avian History and Diversification. Part 7, and its single chapter, is designed to bring together and summarize the themes and conclusions of the book and identify future research needs. . Chapter 31. Avian History and Biological Diversification. Expected topics:. What do we know about avian history?. Tempo of avian diversification. Large-scale patterns of avian biogeography. Neornithine diversification and global paleogeography and paleoclimatology. What does avian history say about alternative models of biological diversification?. To what extent is avian history general?. Unanswered questions