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Part IV
CASE STUDIES: DISSECTING COMPLEX PHENOTYPES

The chapters in Part IV provide examples of how scientists are tackling the empirical challenge of dissecting complex phenotypes. In The Origin of Species, Darwin deemed the eye to be an organ of “extreme perfection and complication.” He also wrote, “To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree.” Nonetheless, “reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, … then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable to our imagination, should not be considered subversive of the theory.” In Chapter 1, Ayala mentioned how light-sensing organs in mollusks vary from the simple to the highly complex, each type nonetheless of utility to its bearers. In Chapter 10, Francesca Frentiu and others associated with Adriana Briscoe’s laboratory delve deeper into the molecular basis of vision by discussing the comparative evolution of genes and proteins underlying color-vision phenotypes in primates and butterflies. The research summarized by these authors demonstrates some remarkable parallels in how particular amino acid sites in photopigments can be involved in color perception in both insects and mammals.

Darwin was interested in the close parallels between natural selection and artificial selection, and in 1868 he published a book on the topic



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Part IV CASE STUDIES: DISSECTING COMPLEX PHENOTYPES T he chapters in Part iv provide examples of how scientists are tackling the empirical challenge of dissecting complex phenotypes. in The Origin of Species, Darwin deemed the eye to be an organ of “extreme perfection and complication.” he also wrote, “To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, i freely confess, absurd in the highest degree.” nonetheless, “reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, . . . then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable to our imagination, should not be considered subversive of the theory.” in Chapter 1, Ayala mentioned how light-sensing organs in mollusks vary from the simple to the highly complex, each type nonethe - less of utility to its bearers. in Chapter 10, Francesca Frentiu and others associated with Adriana Briscoe’s laboratory delve deeper into the molec- ular basis of vision by discussing the comparative evolution of genes and proteins underlying color-vision phenotypes in primates and butterflies. The research summarized by these authors demonstrates some remark - able parallels in how particular amino acid sites in photopigments can be involved in color perception in both insects and mammals. Darwin was interested in the close parallels between natural selec- tion and artificial selection, and in 1868 he published a book on the topic 

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 / Part IV of phenotypes in domesticated plants and animals. in Chapter 11, Jeffrey ross-ibara, Peter Morrell, and Brandon Gaut illustrate modern genetic approaches to dissecting important phenotypes that have evolved under human influence, with special reference to domestic corn. They distin - guish top-down genetic approaches (such as QTl mapping) from bottom- up approaches (such as candidate gene assays), and conclude that the latter method, despite some pitfalls, generally holds greater promise for revealing how key phenotypes in crop plants have evolved under domes - tication from their ancestral wild states. in Chapter 12, Al Bennett and richard lenski address a longstanding question: is there a necessary cost to adaptation? in other words, does the evolution of a phenotype that is adaptive to a particular environment necessitate deterioration in other traits? if so, what natural selection can achieve via the adaptive process would inevitably be constrained by such fitness trade-offs. To examine this issue empirically, the authors monitored multigeneration selection responses of bacteria (Escherichia coli) to altered temperature regimes. After 2,000 generations of thermal selection, most colonies that showed improved fitness at low temperatures also showed fitness declines at high temperatures, but this was not invariably the case. The fact that exceptions exist indicates that fitness trade-offs are not an inevitable component of the adaptive evolutionary process. Bacteria such as E. coli are model experimental organisms because they have short generation lengths and are easy to manipulate, but they also have relatively simple phenotypes. near the other end of the continuum is Homo sapiens, which has many complex phenotypes of special inter- est but is far less tractable to experimental manipulation. in Chapter 13, Cynthia Beall describes the adaptations to high-altitude hypoxia (oxygen shortage) displayed by humans indigenous to the Andean and Tibetan plateaus. remarkably, the physiological and molecular adaptations to hypoxia differ dramatically between these two populations, suggesting different evolutionary pathways to the same functional outcome. Beall describes how scientists are currently dissecting the evolutionary genetic responses to oxygen deprivation displayed by these two populations, and in so doing reveals some of the special challenges of working with a nonmodel experimental species. Beetles (Coleoptera) have long been intriguing to biologists. The British geneticist and evolutionist J.B.s. haldane famously remarked that the Creator must have had an inordinate fondness for beetles because he made so many species of them (at least half a million). A century earlier, Darwin had speculated that the oft-ornate horns that many beetles carry on their heads or thorax were favored by sexual selection as weapons, used in jousts between males over mating access to females. Darwin’s fascination with beetles began in childhood and grew in his college years,

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Case Studies /  as indicated in his autobiography: “no pursuit at Cambridge was followed with nearly so much eagerness or gave me so much pleasure as collecting beetles” (Darwin, 1887b). in Chapter 14, Douglas emlen, laura lavine, and Ben ewen-Campen describe modern research on the molecular genet- ics, ontogeny, and phylogenetics of beetle horns. These authors advance fascinating mechanistic scenarios for the evolutionary origins of these peculiar devices, and for subsequent evolutionary alterations in horn shapes, allometries, body locations, and patterns of sexual dimorphism. This volume then concludes with an essay by eugenie scott and nicholas Matzke on the history, philosophy, and societal impact of a reli - gious movement known as intelligent Design, and its sharp contrast with scientific explanations for the appearance of biological design that results inevitably from natural selection.

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