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This chapter examines the way in which evolutionary biologists accomplish the goal of uncovering evolutionary history through the comparative method. This method is contrasted with that of the creationists, who claim that supernatural intervention was required to produce the complexly adaptive attributes of orchids and other organisms. Darwin’s views on this matter are discussed.

Flower development operates through the activities of a set of transcription factors regulating the structural genes necessary for correct organ development in the correct position. The majority of these ABC genes encode MADS box transcription factors, a very ancient family of DNA binding proteins. By tracing the evolutionary history of this gene family, the molecular processes which lie behind the evolution of flowers can be investigated. Since flowers are one of the key distinguishing features of the angiosperms, and have been argued to be responsible for their astonishing radiation into the most species rich plant division by far, the evolution of the MADS box family is of particular interest in reconstructing plant evolutionary history.

The Tree of Life depicts phylogenetic relationships of species lineages. Together with theories of phylogeny and natural selection, it explains common ancestry, descent with modification, and change within lineages. It had a profound influence on comparative biology, which continues to grow as species relationships and the history of biodiversity’s organization are increasingly recognized as critical to hypothesis-testing. Recent major expansion of genomic data has contributed to resolving phylogenetic relationships. With new knowledge of genetic diversity and non-divergent genetic evolutionary processes, the Tree of Life has been challenged as an inaccurate portrayal of the history of life. The debate about its reality stems from different ways of seeing organisms. Should organismal lineages be conceptualized as equivalent to their genomes, or as complex historical and biological systems that retain identity in spite of genetic exchange and other changes? Do organisms have any emergent reality beyond the sum of their genomes? The debate exemplifies the incomplete integration between major subdisciplines of evolutionary biology. Resolution will require further cross-disciplinary research and synthesis across systematics, ecology, genetics, paleontology, and organismal biology. Theory on the nature of organisms, species, and phylogeny must also be re-examined to assess the validity of a universal theory of phylogeny.

This chapter discusses the evolution of the laboratory rat from the origins of rodents in general to the speciation of the genus Rattus. It provides a summary of the evolutionary events leading to R. norvegicus. Because palaeontology, taxonomy, and phylogenetics are intimately related to one another, the chapter is organized in terms of the taxonomy of R. norvegicus. Evolutionary relationships and palaeontological history are discussed with reference to other groups of the same taxonomic rank. For example, the order Rodentia is placed in the context of other mammalian orders. Summarizing the evolutionary history of R. norvegicus provides a basic understanding of how the species has evolved that may be instructive in interpreting the results of behavioral experimentation and/or comparative analyses.

This lecture presents the text of the speech about humans and apes delivered by the author at the 2007 Joint British Academy/British Psychological Society Annual Lecture held at the British Academy. It comments on the claim that an evolutionary perspective is not a competing paradigm for conventional explanations in the social sciences, and explains the why humans are so different from other apes and monkeys, despite the fact that we share so much of our evolutionary history with them.

As the most species‐rich and biologically eclectic of all social insects, ants present considerable challenges to the process of cataloguing and understanding their remarkable diversity. Substantial progress has been made in recent years, however, in identifying the major clades of ants and in clarifying their evolutionary history. We now have a higher classification of ants in which most of the subfamilies and tribes appear to be monophyletic and well diagnosed, with a few notable exceptions. Uncertainty persists regarding the phylogenetic relationships among old lineages at the base of the ant tree and concerning the time frame of ant evolution. The species‐level taxonomy of ants has advanced more fitfully, and ant ecologists have an extensive but far‐from‐complete set of resources for identifying ant species. Ongoing and sustained effort is needed in the area of species discovery and delimitation, and in the delivery of this information to potential users.

This chapter discusses the evolution of oxygen-producing organisms by considering the evolution and assembly of its basic constituent parts. It focuses on the following key questions: (1) What is the evolutionary history of chlorophyll? (2) What are the evolutionary histories of photosystem I and photosystem II (PSII)? (3) What is the origin of the oxygen-evolving complex in PSII? And finally, (4) what is the evolutionary history of Rubisco? In addressing these, the chapter seeks to understand the complex path leading to the evolution of oxygenic photosynthesis on Earth. This event was one of the major transforming events in the history of life. With no oxygenic photosynthesis, there would be no oxygen in the atmosphere; there would also be no plants, no animals, and nobody to tell this story.

The extraordinary power of explanation of evolutionary theory is considered; so too is the rise of genetics and the near death of Darwinism; then the revival of Darwinian theory in the form of the "synthesis" is considered, as are post-synthesis advances, especially the rise in the understanding that individual development needs to be included in any theory of evolution, as well as so-called selfish gene theory; selection theory is examined in greater detail, especially through the work of Darden and Cain and Lewontin; finally the extension of selection theory to how science works is considered as well as to brain development.

Six C-inductive arguments for and against the existence of God are critically discussed in this chapter: the Argument from Consciousness, the Argument from Moral Truth, the Argument from Moral Awareness, the Argument from Providence, the Argument from Evil, and the Argument from Hiddenness. The first four are either not correct C-inductive arguments for the existence of God because the relevance condition is not satisfied, or not good C-inductive arguments for the existence of God because the evidence has not been established. However, both the many prima facie pointless evils in the world, and the fact of God’s hiddenness, provide strong C-inductive arguments against God’s existence, in spite of the various defences put forward by Richard Swinburne.

This chapter reviews studies of rotation, both planar and rotation in depth, in animals. Although the current research has yielded many interesting findings, a complete picture of how animals, both human and nonhuman, recognize rotated objects is not yet clear. In particular, what is lacking is a concise theoretical account that considers both the differences and similarities in the recognition abilities of different organisms. One interesting direction for this research is to take into consideration the unique evolutionary histories of the organisms under study, while continuing to collect new data.

This chapter attempts to reconstruct evolutionary history. Inferring phylogenetic relationships between taxa and character evolution requires relatively sophisticated methods. The chapter describes several techniques and concepts widely used in modern evolutionary biology, first discussing the principles of nomenclature and then looking at modern phylogenetics and the use of cladistics to infer character history and phylogeny. Cladistics can be used to infer character history based on parsimony, a principle that requires as few character transformations as possible. The chapter also discusses the construction of evolutionary trees, paleontological dating of taxa, and molecular dating.

This chapter focuses on the characteristics, evolutionary history, and historical distribution of horned lizards. It discusses adaptive radiation, an evolutionary process that enabled horned lizards to diversify into a number of closely related species of similar form. It is believed that the ancestral group of horned lizards separated into what later became a southern group of species (southern radiation) and a northern group of species (northern radiation).

This chapter focuses on the evolutionary history of lizards. It first examines aspects of the fossil record and then reviews the morphological, behavioral, physiological, and ecological aspects of lizards within the context of their evolutionary history. The chapter also examines the evolution of major lizard clades and appraise diversification within each. Finally, the chapter speculates on global scenarios and suggests a working hypothesis for the evolution of diversity within lizards.

This chapter discusses the role of evolutionary biology as a historical science, and attempts to understand how and why evolutionary diversification has occurred. It is important to know what processes occurred in the past and how these they shaped the diversity we see today. Depending on the quality of the historical record, we can infer, with a greater or lesser degree of confidence, what happened. Historical analysis (either examination of fossils or phylogenetic inference) can investigate the evolutionary history of a group, or whether evolutionary diversification has occurred.

This chapter explains how phylogenetic information can be used to make better conservation decisions. Evidence shows that human-caused climate change is likely to be the dominant cause of extinction in the near future. Phylogeny can provide a powerful tool for aiding decision making in species conservation. The chapter first considers the importance of preserving evolutionary history by focusing on the tree of life, the phylogenetic tree connecting all living organisms that provides a powerful metaphor for conservation biology. It then examines phylogenetically based metrics for quantifying evolutionary history, including phylogenetic diversity for evaluating sites and evolutionary distinctiveness for comparing species. It also discusses the integration of evolutionary history with extinction probabilities for conservation prioritization using relative extinction risk to weight evolutionary distinctiveness, or EDGE (evolutionarily distinct and globally endangered). Finally, it describes how to prioritize biodiversity hotspots of evolutionary distinctiveness and how to apply metrics to conservation prioritization.

This chapter explores the emergence of adaptation within the evolutionary domain. Charles Darwin, convinced of an impending rise of a natural law of adaptation, relates adaptation with two scenarios: progressive change and speciation in isolation. After formulating natural selection and recognizing the fact that paleontologists have failed to find any convincing evidence of gradual progressive change, Darwin acknowledges a conflict wherein adaptation becomes a problem. As a result, he feels obliged to choose between adaptive change associated with the origin of species in isolation, or an image of gradual wholesale transformation of species. Darwin resolves the conflict by insisting that gradual evolutionary change must be the general rule, since there is a lack of evidence to the contrary. The chapter closes with an examination of why Darwin saw the two scenarios as opposing forces in evolutionary history.

This chapter describes the simpler, more durable, but equally important relationships cows develop with one another. The forebears of bison cows must have experienced both plenty and scarcity in their evolutionary history — times when dominance was worth fighting for and times when it wasn't. Changing circumstances select for changeable behavior, with different strategies for different times and places. The bison pay the costs of striving for dominance when the benefits are high, and don't when the benefits are low. Being a dominant member of a group has high potential payoff. In Yellowstone Park, subordinates searched more and harvested less than dominants. A dominant will eat everything it clears and some that it doesn't clear. A subordinate will eat only part of what it clears.