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This chapter examines selection at the level of species and clades. The history of the species selection debate, including its conceptual link to the idea that species are individuals, is outlined. The issue of how to distinguish ‘real’ species selection from ‘species sorting’ (i.e., differential speciation/extinction that is a side effect of causal processes at other levels) is analyzed. It is argued that clade-level selection is conceptually problematic given that clades, being monophyletic by definition, cannot form parent-offspring lineages.

First life-forms appeared at least as early as 3.5 billion years ago in the form of prokaryotes. Some of these species developed oxygenic photosynthesis, which resulted in the presence of oxygen gas in the atmosphere. Later, eukaryotes appeared and diversified through mutation and gene duplication (including mutation and duplication of master genes), which led to the rewiring of entire gene networks. The chapter shows that there is no fundamental difference between macroevolution and microevolution. It shows that making artificial life in the lab as well as transgenic life-forms would be impossible if the Intelligent Design scenario were correct. Indeed, ID posits that living systems were holistically designed and thus cannot be constructed in a piecemeal fashion.

The Crustacea represents one of the major branches in the tree of animal life, displaying diversity in form and lifestyle that rival those of the vertebrates and insects. But perhaps because of the primarily aquatic habits of crustaceans, they have received much less attention in evolutionary ecology than mostly terrestrial taxa. The chapters in this book make clear the richness of adaptations of crustaceans to social and sexual life, and their still largely untapped potential to test fundamental theory in behavioral ecology and evolution. Kinship, cooperation, and conflict play an important role in social evolution, modulated by extrinsic factors (resource competition, predation or parasitism), some of which have only recently begun to be studied. There are rich opportunities awaiting the student willing to pursue them, both in clarifying the social and sexual biology of individual crustacean species and in exploiting the Crustacea in broad comparative approaches to testing evolutionary theory.

Engaging in tree thinking (using phylogenetic diagrams to interpret and infer historical processes) is a prerequisite for understanding macroevolution. Tree thinking has become increasingly important in biology, with important ramifications for applied fields such as genomics, conservation, epidemiology, and pharmacology. Focusing on what is currently known about cognitive and perceptual constraints on students' tree-thinking skills the chapter reports on the effectiveness of business-as-usual instructional units on tree-thinking concepts in two upper-level classes for Biology majors and discussing how this knowledge can be used to inform curriculum development. The chapter argues for a paradigm shift in the way evolution is taught — from a strong focus on natural selection to a model that visualizes evolution as a broad hierarchical continuum which integrates both micro and macro processes with critical scientific reasoning skills.

Evolution education has been hampered by two conditions. The first is the perception that there is no need to understand anything beyond the short-term processes of evolution (microevolution) to be a functional citizen. The second is the overwhelming focus on microevolution in the biology curriculum — if evolution is taught, typically only microevolution is addressed. This chapter begins our chapter by building a case for the importance of student understanding of both micro- and macroevolution. Following this discussion, the chapter offers a description of a course designed using the findings of a wide body of research (cognitive science, nature of science, evolution education) that employs an intentional conceptual change approach to the learning of both micro and macroevolutionary concepts.

Interacting groups with patterns of codiversification are powerful arenas for testing the influence of selection, dispersal, and other processes on lineage diversification. When reproduction in one group is linked to reproduction in another group, codiversification may occur. For example, parasite dispersal is often linked to host dispersal, with barriers to host movement also influencing the movement of their parasites. This linkage of host and parasite dispersal is particularly common in permanent parasites, such as lice, which complete all stages of their life cycle on the body of the host. If barriers to movement contribute to lineage diversification in both host and parasite, then they will codiversify. If codiversification is simultaneous, then the host and parasite may undergo cospeciation. In this chapter we review the five main macroevolutionary events that govern patterns of cophylogenetic history. These processes are cospeciation, host switching, duplication, sorting events, and parasite cohesion. Each of these processes can influence copylogenetic patterns in different ways.

Cophylogenetic patterns are central to the study of coevolution in the broad sense because they document codiversification, which is the correlated diversification of interacting lineages. In the last chapter, the macroevolutionary events that govern the cophylogenetic dynamics of codiversifying groups were reviewed. Given the complexity of these processes, it can be difficult to identify ecological or other factors influencing macroevolutionary events and cophylogenetic processes. Comparisons of related groups of organisms can be very helpful. This comparative approach has the power to pinpoint ecological or other differences between groups that may be responsible for different patterns of codiversification. In this chapter, the comparative approach is applied to groups of lice with different cophylogenetic histories. These case studies illustrate some of the ways in which to integrate cophylogenetic analyses with ecological data. They also illustrate the importance of understanding the basic natural history of the system being studied.

This chapter summarizes the book using a graphical framework that integrates the coadaption and codiversification ends of coevolution with five “zones” of coevolution. This framework can be applied to any host-parasite system. Indeed, it can be used with any coevolving system. Differences in the five coevolutionary zones are operational, yet subtle. Delineating these different zones helps to clarify the ways in which dispersal and selection influence the adapation, coadapation, diversification, and codiversification of interacting groups. Coevolution in this framework varies from a purely microevolutionary focus in the case of coadapation, to a purely macroevolutionary focus in the case of codiversification. These extremes are first considered in more detail. Then the three combinations of adaptation and diversification that comprise the middle portions of the framework are discussed. The importance of integrating phylogenetic, comparative, and experimental approaches cannot be overstated in studies of coevolution, or evolutionary ecology in general.

This chapter is designed to push community ecologists to re-consider how they are using phylogenetic information in their research. The research path that I present as a much more interesting, valuable and viable phylogenetic approach to community ecology is not novel. It has been running in parallel with occasional cross-pollination with the phylogenetic proxy literature for decades. Furthermore, this approach has the ability to make more meaningful inferences regarding the intersection of evolutionary history, biogeography and community ecology. Lost in the critiques of the phylogenetic proxy approach that focus on the proxy itself and inferring a process from a pattern is one of the more damning critiques of this literature—it has largely failed to fully integrate evolutionary history and community ecology. Without knowing such information it becomes hard to identify any generalities emerging across taxa and ecosystems, which would greatly help in the formation of a true synthesis between evolution and community ecology.

Macroevolutionary theory incorporates issues of scale and hierarchy, and thus includes the origin and fates of evolutionary novelties, the evolutionary role of rare events ranging from the internal redeployment of gene regulatory networks to externally driven mass extinctions, and the potential for emergent properties or dynamics at different hierarchical levels to shape large-scale patterns. Developmental factors impose non-linear relationships between magnitudes of genetic change and their phenotypic expression, an uneven probability distribution of evolutionary changes around any given phenotypic starting point, and the potential for coordinated changes among traits that can accommodate change via epigenetic mechanisms. Large-scale sorting of these biased inputs – clade dynamics – are often shaped by differential origination and extinction, including strict-sense species selection, in which rate differentials are governed by emergent, species-level traits such as geographic range size, and effect macroevolution, in which rates are governed by organism-level traits such as body size. Both processes can create hitchhiking effects, indirectly causing proliferation or decline of other traits. The nonlinear, sometimes temporally discordant, relationships among macroevolutionary currencies (taxonomic, morphologic, functional) are crucial for understanding the nature of evolutionary diversification; e.g. taxonomic diversifications can lag behind, occur in concert with, or precede, increases in disparity.

This chapter starts out with a review of what is known about the potential for evolutionary change, the strength and pattern of selection on phenotypic traits, and rates of evolution and adaptation. This is then used to discuss and evaluate quantitative genetics models for evolution on an adaptive landscape. It is argued that the predicted dynamics is too fast to adequately represent patterns of macroevolution. Instead macroevolutionary dynamics must reflect long-term changes in the adaptive landscape itself. Models and theories about the evolution of the adaptive landscape are then reviewed and critically evaluated.

Fitness and adaptive landscapes have theoretical limitations, but they have played a valuable role in integrating population genetics and macroevolution. Sewall Wright introduced fitness landscapes in 1931 to describe the relationship between genotypes and fitness, and George G. Simpson modified and popularized the concept of landscapes in evolutionary biology in 1944 as adaptive landscapes to illustrate the evolutionary response of fossil lineages to natural selection. Patterns of sediment and fossil accumulation impose practical limitations on the use of adaptive landscapes to analyze fossil data. Phenotypic evolution can occur too rapidly to resolve in the stratigraphic record, hindering observation of movement of lineages upward on an adaptive peak. Use of the null hypothesis of a random phenotypic walk through time (i.e., genetic drift) to test for adaptation in the trajectory of change in fossil lineages has consistently led to rejection of adaptation, but recent methods, including a maximum likelihood procedure for individual lineages and simultaneous analysis of multiple species and traits, indicate that fossil lineages have ascended adaptive peaks and remained at their summits as they shift position through time. Recognition of the limits to temporal resolution in fossil lineages provide guidance for the selection of fossil lineages to study, and development of new statistical tools have enhanced the value of adaptive landscapes to analyze the fossil record.

Organisms—biology begins with organisms, and indeed a great deal of the history of biology is a trek through progressively finer subdivisions of organisms. When “forefronts” of biology are listed these days, nearly all concern the molecular biology of intracellular (and intraorganelle) physicochemical processes—and quite rightly so. But the ontology of units larger than organisms, while not wholly neglected, is at least as difficult a problem. Organisms are by far the easiest of biological units for us to see, to probe, to conceptualize as “individuals.” But, in the present context, organisms pose a unique problem all their own: they constitute the only class of individuals to be found in both the genealogical and ecological hierarchies. Consider the confusion that permeates even the recent explicitly hierarchical literature: ecology and evolution (as in the quote from Valentine that stands at this chapter’s head) are generally seen as separate areas of inquiry, but the choice of the higher-level individuals to be incorporated into one’s hierarchy very much depends upon one’s point of view. Below the organism level, of course, the distinction between the somatic and germ lines (i.e., in multicellular organisms) once again ensures a clean separation of the elements of the two hierarchies. Hence the conclusion (Eldredge and Salthe 1984) that there must in fact be two independent, yet parallel and interacting, process hierarchies that together combine to yield evolution. Organisms, as members of both hierarchies, threaten to muddy the picture. It is possible, of course, to distinguish between the economic and reproductive functions of organisms, as I have done at length in the preceding chapter. Physiologists, after all, have long been telling their students that reproduction is the one physiological process not essential to the survival of an organism; thus, it is no surprise that it is invariably the first such process to be dispensed with when the organism is stressed. It is easy to distinguish the economic from the reproductive functions of the vast majority of organisms, but in many vertebrates, most especially Homo sapiens, sexuality has clear economic implications, obscuring the distinction between the two hierarchies perhaps even more.

This chapter addresses how we can talk about macroevolution without lapsing into teleology, and shows that the principle of the conditions for existence can play a key role here, first discussing how natural selection enters into explanations of macroevolutionary changes. It then looks at a simple example of macroevolution—evolution of bird flight—and considers the question of how the process of evolutionary adaptation should be represented. In particular, the chapter addresses how the role of narrow sense natural selection and of the conditions for existence in this process should be represented.