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This chapter reviews the published data and discusses the taxonomy and population genetics of orangutans. The orangutan was traditionally classified as two separate subspecies, Pongo pygmaeus pygmaeus in Borneo and P. p. abelii in Sumatra. Recent molecular data have suggested a re-classification into two separate species: P. pygmaeus in Borneo and P. abelii in Sumatra. Moreover, three subspecies have been described on Borneo Island: P. p. pygmaeus in Sarawak and west Kalimantan, P. p. morio in Sabah and east Kalimantan and P. p. wurmbii in central and south Kalimantan. Despite this, little is known about the intra-subspecific variation between isolated Bornean populations and among the Sumatran populations. More data are needed, which should include a large sampling of all geographically separated populations in Borneo and Sumatra in order to provide a more complete genetic information database.

Landscape genetics explores how the microevolutionary processes of gene flow, genetic drift, and natural selection interact with environmental heterogeneity to shape population genetic structure. This chapter begins with a review of the various types of genetic data used in population and landscape genetics and discusses how these data are used to estimate genetic variation (heterozygosity) and gene flow among populations. From there, the chapter considers how population genetic structure can be assayed, which then segues into an analysis of the landscape correlates of population genetic structure, the identification of movement corridors and barriers to gene flow, and the relative effects of current versus historical landscape factors on population genetic structure. The chapter concludes with an overview of evolutionary landscape genetics, by considering the adaptive potential of populations in response to future landscape and climatic changes.

This chapter assesses the biogeography of chestnut-backed chickadees using microsatellite analysis, providing alternative scenarios for the glacial refugia and dispersal patterns that could explain the present distribution of distinct, genetic populations. This chapter also considers the potential for hybridization within the brown-capped chickadees to contribute to differentiation among disjunct populations within the chestnut-backed chickadees of northwestern Canada and Alaska. The factors influencing contemporary patterns of population structure in chestnut-backed chickadees are considered, including historical range expansion and geographic distribution, while potential barriers to dispersal are discussed. The patterns found in this western North American species are compared to those of other North American and Eurasian Parids. The population structure of chestnut-backed chickadees, and that of other Parids, appears to be complex and influenced by a variety of factors, most notably postglacial colonization and distribution. Many of the factors limiting dispersal in chestnut-backed chickadees seem to be common in other Parids. These include isolation of peripheral populations, and limited dispersal over large water barriers or other areas of unsuitable habitat.

This chapter considers a general description of natural selection: the Price equation. Developed by George Price in the late 1960s, the Price equation can be applied to the change of any quantity under any selective regime. It is thus not limited to considering simple haploid single-locus traits, unlike the replicator dynamics, and indeed it is not even limited to considering evolutionary selection. The Price equation provides an instantaneous description of selection in action. The simplicity of the equation makes it a useful conceptual tool for understanding selective processes such as natural selection. The chapter first describes the general Price equation before discussing its use to understand genetic selection. It then shows how the Price equation can be used to derive two classical results from population and quantitative genetics: Fisher's “fundamental theorem of natural selection” and the breeder's equation.

This book has examined the genesis, the logic, and the generality of social evolution theory. In particular, it has presented evolutionary explanations of the many social behaviors we observe in the natural world by showing that William D. Hamilton's inclusive fitness theory provides the necessary generalization of classical Darwin–Wallace–Fisher fitness. This concluding chapter discusses the limitations of the analyses presented in this book and assesses the empirical support for inclusive fitness theory, focusing on microbial altruism, help in cooperative breeders, reproductive restraint in eusocial species, and the evolution of eusociality and cooperative breeding. It also considers more advanced topics in social evolution theory, including sex allocation, genetic kin recognition, spite, and the evolution of organismality. Finally, it reviews theoretical approaches to studying social evolution other than replicator dynamics and the Price equation, such as population genetics, class-structured populations, and maximization approaches.

This chapter discusses the population biology and ecological genetics of native species within California grasslands, providing many important insights into the processes of microevolutionary change in plant populations. It describes basic population genetics concepts, ranging from co-adapted gene complexes to evolution of phenotypic plasticity.

This chapter takes a look at genetics and its role in the study of ancient history. Genetics is the study of inheritance, and DNA variation is the essence of heredity. DNA sequence differences underpin genetics overall and population genetics is the study of such diversity in populations and how it changes through time. Reconstructing human history using modern DNA has been a longstanding endeavor rooted in sampling practicality. If a mutational change does not negatively affect the individual's ability to reproduce, it may be passed down to each succeeding generation, eventually becoming established in a population. Such mutations, whether beneficial, harmful, or neutral, can serve as genetic markers.

Its structure, redundancy and plasticity make the genome a dynamic system. This chapter gives an introductory evolutionary view of these genome characteristics focusing on the unanticipated uncoupling between organism complexity and genome size (the C-value paradox). Some approaches to this paradox are presented ranging from genome dynamics to population dynamics. While it may be too early to understand in full the genome dynamics, some case studies in comparative genomics are presented that vindicate the central role of population genetics to understand genome evolution. The roles of duplication, transposition, RNA regulation, and the, recently discovered, structural DNA variants are introduced as examples of the genome evolutionary dynamics and show how the combined population, functional, and structural approaches are enlightening our view on genome evolution. The chapter ends with a deep introductory reflection on the dual role of chance (random variation) and necessity (natural selection) in the building of a dynamic genome.

This chapter examines the field of population genetics as an approach to the origin of the Jews. Most historians study the past by focusing on the period of time that can be documented by textual sources, the past 4,000 years or so. In the past few years, a new form of primordialism has emerged that uses DNA and the brain's evolutionary history to reconstruct demographic history, ancient social interaction, and other insights to shed light on where people come from and how they have evolved. The chapter first provides an overview of genetic history and biological approaches to the origin of the Jews before discussing what genetics research has revealed about the ancestry of the Jews, some of the criticisms hurdled against this research, and whether a genetic approach offers a viable alternative to the constructivist approach employed by many contemporary scholars to address the question of Jewish origins.

Sewall Wright's shifting balance theory remains controversial in part because it is what would today be called a complex systems model that was never developed beyond that of a metaphor. A key component of this theory, the adaptive landscape, has become an important element in population genetics and evolutionary theory. This chapter explores the original metaphor of the adaptive landscape can be modified to make it a usable concept. It suggests that it is useful to consider the landscape to be a very high dimensional space that is conceptually helpful but of little practical use. The high-dimensional landscape potentially includes all aspects of the genotype and phenotype, including aspects of the social and physical environment that affect the phenotype. This broad conceptual visualization of an adaptive landscape is concordant with the diverse uses of this metaphor in evolutionary theory if we consider adaptive landscapes with only a few dimensions to be projections of the high dimension landscape on to the subset that are being used. This modified view of adaptive landscapes is used to discuss Wright's shifting balance theory and how it can be changed to accommodate modern experimental and theoretical findings.

Migration by Odonata may illuminate patterns and evolution of insect migration in general. As aquatic/aerial carnivores dragonflies differ from most migratory insects, and because they are large and diurnal, observational techniques are available that are impossible in most other insects. Geographic analysis of genetic structure and stable and radiogenic isotope composition and use of newly developed radio-tracking techniques has been applied to migration in the North American dragonfly, Anax junius. Southbound migrants move up to 2,800 km. Developmental phenology suggests early (‘resident’) and late (‘migrant’) cohorts at most sites, but these groups appear genetically identical, and the species is essentially panmictic in eastern North America. Apparently environmental cues and physiological responses to photoperiod and temperature engender migratory behaviour. Successful radio-tracking of individual A. junius has revealed alternating periods of migration and energy replenishment, and responses to wind and temperature similar to avian migration.

This chapter discusses the interweaving of problems in ecology and evolution. Early in the history of these fields, topics such as population dynamics were relegated to the realm of ecology, while the fields of evolution and population genetics considered problems like fitness components and methods for their estimation, ignoring ecological context. But over the course of the twentieth century, the evolution of population-growth rates became the focus of experimental studies, as well as the impact of life cycles and population regulation on fitness measurements and evolution. In this chapter, ecological and evolutionary studies of population dynamics are presented. These include studies on population growth, estimation of fitness in populations, and dynamics of populations with age structure.

Darwin's separation between adaptedness and existence entered into modern evolutionary theory at its root, in the population genetics work of Sewall Wright and J. B. S. Haldane. This chapter shows how the teleological aspect of Darwin's theory was translated into the mathematical language of population genetics, particularly by Sewall Wright. This teleology is exemplified by Wright's metaphor of the adaptive landscape; it is absent from R. A. Fisher's fundamental theorem. The chapter also examines the debate over genetic load, showing that the separation of adaptedness from existence is transferred to the mathematical theory most directly in the form of confusion between absolute and relative fitness.

Conservation genetics is a relatively young interdisciplinary field. Essentially, it concerns the application of genetic methods to threatened species. It aims to obtain detailed insights about their evolution, ecology, taxonomy, and population genetics and to inform conservation strategies. This chapter discusses the application of the most commonly used molecular techniques to the conservation of primates, with a focus on non-invasive samples. Recent technological advances in sequencing techniques are allowing the transition from classical population genetic studies, based on few markers, to studies based on whole-genome information. The main techniques and concepts are broadly explored and practical examples are given together with pointers to recent studies and reviews. The aim is to give the reader a general understanding of what the field of conservation genetics is, how it can be applied to primate research and conservation, and how it will likely change in the future.

Two giants of evolutionary theory, Sewall Wright and R. A. Fisher, fought bitterly for over thirty years. The Wright–Fisher controversy forms a cornerstone of the history and philosophy of biology. The chapter argues that the standard interpretations of the Wright–Fisher controversy do not accurately represent the ideas and arguments of these two key historical figures. The usual account contrasts the major slogans attached to each name: Wright's adaptive landscape and shifting balance theory of evolution versus Fisher's fundamental theorem of natural selection. These alternative theories are in fact incommensurable. Wright's theory is a detailed dynamical model of evolutionary change in actual populations. Fisher's theory is an abstract invariance and conservation law that, like all physical laws, captures essential features of a system but does not account for all aspects of dynamics in real examples. This key contrast between embodied theories of real cases and abstract laws is missing from prior analyses of Wright versus Fisher. They never argued about this contrast. Instead, the issue at stake in their arguments concerned the actual dynamics of real populations. Both agreed that fluctuations of nonadditive (epistatic) gene combinations play a central role in evolution. Wright emphasized stochastic fluctuations of gene combinations in small, isolated populations. By contrast, Fisher believed that fluctuating selection in large populations was the main cause of fluctuation in nonadditive gene combinations. Close reading shows that widely cited views attributed to Fisher mostly come from what Wright said about Fisher, whereas Fisher's own writings clearly do not support such views.

Chapter 1, “Introduction: What is molecular population genetics?,” presents the motivations, applications, and historical context for molecular population genetics as a subdiscipline within biology. It describes how changes to DNA are inextricably woven into thinking about evolution and how molecular population genetics can be used to transport our thinking backward and forward through time. Key classic theoretical ideas summarizing allele frequency change, probability of fixation, and the time to fixation are encapsulated in brief vignettes. Both fundamental and applied uses of molecular population genetic perspectives are summarized in this survey of the historical, conceptual, and empirical development of the branch of science that we call population genetics and its integration with DNA sequences.