Bioinformatics A Practical Guide to the Analysis of Genes and Proteins. Edited by Andreas D. Baxevanis and B. F. Francis Ouellette. New York John Wiley and Sons. 2001. 649 pp. ISBN 0-471-38390-2код для вставкиСкачать
AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 127:124 –127 (2005) Book Reviews MONOGAMY: MATING STRATEGIES AND PARTNERSHIPS IN BIRDS, HUMANS AND OTHER MAMMALS. Edited by Ulrich H. Reichard and Christophe Boesch. New York: Cambridge University Press. 2003. 267 pp. ISBN 0-521-52577-2. $40.00 (paper). Because this book largely succeeds in summarizing the state of the bird and mammal monogamous union, it may prove the new standard-bearer for research on monogamy. This book contains 16 chapters addressing both the theoretical foundations for monogamy and a rich taxonomic spread of bird and mammalian natural history on the topic. The data presented tend to derive from quantitative behavioral and demographic ﬁeld studies, sometimes supplemented by genetic paternity analyses. Analyses relying on phylogenetic patterns of mating systems are also used to reconstruct evolutionary scenarios of monogamy. The introductory chapter provides a dense, welldocumented discussion of social monogamy that anchors the volume. It shows the value of distinguishing social, sexual, and genetic monogamy. It argues for three main contributors to social monogamy: paternal care, access to resources, and partner choice. It discusses how genetic paternity studies documenting extrapair fertilizations (EPFs) in the context of social monogamy have stimulated research into monogamy. The chapter concludes that there are multiple pathways to monogamy rather than a uniform process. This chapter opens into Part 1 of the volume, “Evolution of Social Monogamy,” presenting further theoretical foundations for the study of monogamy. Some of this material overlaps too much with the introductory chapter, despite adding theoretical force. Moller’s chapter focuses on the role of extrapair paternity (EPP) in the evolution of social monogamy in birds. The chapter by Brotherton and Komers (well-illustrated with data on Kirk’s dik-dik, a socially and genetically monogamous antelope from Africa) concludes that mate guarding represents the best general model of mammalian monogamy. Van Schaik and Kappeler champion infanticide as the main cause of social monogamy in primates, relying primarily on phylogenetic analyses to support their views. Ribble focuses on the genus Peromyscus, and particularly the socially monogamous California mouse, describing male removal experiments, and discrepancies between laboratory and ﬁeld data. This chapter also points to the distinction between the origin and maintenance of social monogamy. Part 2, “Reproductive Strategies of Socially Monogamous Males and Females,” will be least inter© 2004 WILEY-LISS, INC. esting to physical anthropologists. Its ﬁve chapters document various aspects of reproductive strategies related to monogamy. Wagner’s chapter highlights the social functions of copulation among a species of socially monogamous birds (razorbills) visiting mating arenas. Somner looks at the nature and causes of social monogamy of the Malagasy jumping rat. Kays uses radio telemetric, night vision, and molecular data to study monogamy among the kinkajou, a mammalian carnivore of Panama. Sun presents demographic and behavioral data on beavers. Finally, Kishimoto examines monogamy among the solitary ungulate, the serow, of Japan. In addition to the introductory chapters, those in Part 3 (“Reproductive Strategies of Human and Non-Human Primates”) will be of greatest interest to physical anthropologists. Low begins this section by considering human monogamy in cross-cultural perspective. She provides a discussion of the challenges comparing human with nonhuman data on mating systems, and presents cross-cultural patterns of monogamy and its social correlates, such as dowry. Strassman’s chapter contains fantastic descriptive ethnography and quantitative data on the Dogon of Mali. These data suggest an interesting story, including costs to Dogon women of polygynous, as opposed to monogamous, marriage. Reichard’s chapter on gibbons adopts a male perspective, presenting data largely from Thai ﬁeld studies. He ﬁnds quantitative support for the potential for polygyny; since gibbons are nonetheless socially monogamous, he attempts to advance alternative means of understanding this pattern. Fietz focuses on the dwarf lemur, which hibernates 7 months annually and caches its offspring. This species is socially monogamous but appears to engage in a high frequency of EPFs. Goldizen’s chapter on callitrichids provides a review of relevant demographic and behavioral data illustrating, among other topics, the costs of infant care. Lastly, Heymann presents interesting data on New World primates and olfactory communication, tentatively showing links between male care and both calling and scent marking. As impressive as the theoretical and empirical content of this volume is, unanswered questions remain. For instance, why focus on monogamy rather than mating systems more broadly? Many of the chapters discuss both monogamy and polygyny, and key models for monogamy view it as the inability of males to achieve polygyny given female distributions. Considerations like these show how intertwined monogamy and polygyny may be. More clearly stating in the Introduction, or in a concluding chapter (which the volume lacks), the reasons for focusing on monogamy would have helped. 125 BOOK REVIEWS Second, how does one convincingly test alternative hypotheses of monogamy? This is no trivial question when authors within the same volume reach drastically different views regarding the relative merits of alternative hypotheses (e.g., contrasting the infanticide hypothesis for primate monogamy favored by van Schaik and Kappeler with Brotherton and Komers discounting it among mammals generally). Experimental studies described in the volume, including male removal studies, manipulations of sexually selected characteristics, and playback experiments, enable the most robust tests. For ethical and logistical reasons, most ﬁeld studies surveyed in this volume relied on phenotypic correlations with small sample sizes. Authors of various chapters point toward further work on genetic paternity analyses and ﬁeld endocrine studies as ways to better test alternatives, and such additional techniques may help avoid a confusing morass of alternative interpretations of similar data (which plagued the discussion of infanticide in this volume). Third, how relevant is this volume to physical anthropologists? For researchers interested in the evolution and ecology of primate monogamy or human mating systems, this book is an excellent reference. Although many of the empirical examples BIOINFORMATICS: A PRACTICAL GUIDE TO THE ANALYSIS OF GENES AND PROTEINS. Edited by Andreas D. Baxevanis and B.F. Francis Ouellette. New York: John Wiley and Sons. 2001. 649 pp. ISBN 0-47138390-2. $69.95 (paper). Although bioinformatics is advancing at a rapid pace, Baxevanis and Ouellette’s edited volume, published in 2001, still provides an excellent introduction to the many methods utilized in the ﬁeld. The volume aims to educate scientists on how to mine, analyze, and interact with DNA, gene expression, and protein data. The book provides a detailed explanation of a wide range of analytical techniques in a clear and methodical framework, including lists of websites, recommended computer programs, and ﬂowcharts. The text’s strength, its stepwise approach, will provide a useful introduction for scientists wishing to learn bioinformatics. However, the text does not provide an in-depth mathematical or statistical treatment of any the individual analyses. Therefore, anthropologists should look to this book as a vehicle for learning a bioinformatics analysis or technique, but not for gaining additional expertise in an already familiar area. Interestingly, most authors provided some treatment of the biological and evolutionary context for each individual analysis—a welcome surprise that both enhanced the readability of the book and also hinted at applications of these techniques beyond bioinformatics. and even some of the theoretical foundations fall outside a primate scope, this body of work may stimulate fresh approaches to human and nonhuman primate data. For example, a repeated conclusion is that paternal care in mammals appears to represent the maintenance, rather than the origin, of social monogamy. Such an inference casts doubt on scenarios of human pair bonding that view the origin of such bonds as caused by direct paternal care (of, say, large-brained altricial offspring). For those seeking a useful teaching reference for undergraduate and graduate anthropology courses on primate mating systems, chapters in this volume may be very helpful, but the volume as a whole contains too many nonprimate chapters for such ends. PETER GRAY Division of Endocrinology, Metabolism, and Molecular Medicine Charles Drew University of Medicine and Science Los Angeles, California DOI 10.1002/ajpa.20028 Published online 31 August (www.interscience.wiley.com). 2004 in Wiley InterScience The text opens with the chapter “Bioinformatics and the Internet,” parts of which seem to be directed to computer neophytes (e.g., a discussion on the advantages of e-mail, p. 7), an unlikely audience for this text. Still, other discussions are surprisingly helpful, such as the description of ﬁle transfer protocol (FTP) (p. 10). Chapters 2– 6 are dedicated to understanding public DNA and protein databases. These chapters are useful because they explain each component of the current data models and databases, which are rife with abbreviations and obscure elements. Even anthropologists familiar with the National Center for Biotechnology (NCBI) databases are likely to learn something useful from these chapters. Chapters 7–9 treat information retrieval and alignment of DNA and protein data. These chapters focus on the available computational tools and applications to be utilized for collating and searching these data, and provide a straightforward guide for how to conduct these data-mining and analytical techniques. Most of the techniques addressed are immediately useful for molecular anthropologists, though it was disappointing not to ﬁnd discussion of local blast searching, a technique which searches a locally made database of sequences. Instead, the usefulness of not maintaining local databases of DNA sequences is emphasized. For many anthropological questions, making and searching a local database would be very helpful, such as a local database of all primate mitochondrial genomes. This 126 BOOK REVIEWS database could be searched locally, without sending multiple queries to the entire NCBI database. The remaining chapters, save the ﬁnal one, all deal with bioinformatics data analyses. Physical anthropologists will doubtlessly be most familiar and interested with the material presented in “Phylogenetic Analysis.” As found in many of the other chapters, a methodical approach to phylogenetics is given, including a comprehensive listing of applicable computer programs such as PAUP. Though the chapter would be a useful introduction to the analytical aspects of molecular phylogenetics for a physical anthropology graduate student, practicing phylogeneticists would require a more in-depth and substantial treatment of the topic, addressing more of the methodological and epistemological issues surrounding phylogenetic analysis. This is not a failing on the author’s part, but rather a reﬂection of the existing strengths many anthropologists would bring to this book. Meltzer’s chapter, “Large-Scale Genome Analysis,” is a helpful introduction to the generation and nature of gene expression data. Understanding gene expression has been an area of special interest to physical anthropologists since the hypothesis of King and Wilson (1975) that changes in gene regulation are the major driver of phenotypic change in the hominid lineage, not individual amino acid replacements. Today the methodological description in this chapter would require supplementation with a description of recent statistical advances in the treatment of gene expression data, only available since publication of the text. The ﬁnal chapter describes Perl, a computing language with the power to turn tedious computing tasks into simple algorithmic scripts. An unacknowledged issue with this chapter is its assumption that readers are comfortable with operating at a computer’s command line, which may not be true for most readers. Perhaps Stein could have spent additional time describing this, or pointed readers toward a website or another introductory text. A second minor issue is the outdated description of MacPerl as the Macintosh interface with Perl. Since the introduction of the UNIX- COMPARATIVE BIOMECHANICS: LIFE’S PHYSICAL WORLD: By Steven Vogel. Princeton, NJ: Princeton University Press. 2003. 582 pp. ISBN 0 – 691-11297-5. $60.00 (cloth). Anyone with an interest in understanding organismal form and function will enjoy Steven Vogel’s comprehensive new text on comparative biomechanics. For most undergraduate and graduate students (and some professors), and particularly for those who are not mathematically inclined, the prospect of reading a new text on biomechanics may seem about as appealing as reading a dictionary or yellow pages. However, these readers will be pleasantly surprised based OSX operating system, Macintosh users would actually ﬁnd the UNIX instructions most helpful. Nevertheless, this chapter was an outstanding introduction to the power of Perl for bioinformatics, and it is also apparent that Perl is a perfect tool for any anthropologist analyzing large amounts of data. For example, a Perl script could help a morphologist create a new forelimb-only data matrix from a large spreadsheet of characters. If similarly convinced of Perl’s usefulness, readers may want to supplement this chapter with an entire book devoted to the programming language, along with a text on basic UNIX commands. Bioinformatics is a well-written and organized guide to mining and analyzing both the mountains of publicly available genetic and protein data as well as one’s own data sets. For most molecular anthropologists, this text would be an excellent reference for a wide range of techniques. Pedagogically, this volume would serve well as part of a graduate-level course in molecular methods or as a primer for new graduate students interested in molecular anthropology. However, as investigators gain expertise in a particular bioinformatics tool or procedure, the text would require supplementation with additional technical readings. MICHAEL E. STEIPER Department of Anthropology Hunter College of City University of New York & Doctoral Faculty in Biology Graduate Center of City University of New York New York, New York LITERATURE CITED King M-C, Wilson AC. 1975. Evolution at two levels in humans and chimpanzees. Science 188:107–116. DOI 10.1002/ajpa.20029 Published online 31 August 2004 in Wiley InterScience (www. interscience.wiley.com). by Vogel’s skill in conveying complex material in an intuitive, informative, entertaining, and thorough way. The principal difﬁculty in writing a biomechanics text is striking the appropriate balance between mechanical and biological components. Erring on the side of too much mechanics (i.e., math) can lead to a useful text for advanced students and professionals, but such a text may be too difﬁcult or too dry for introductory students. In contrast, texts that emphasize the biological component of biomechanics (i.e., how animals and plants cope with their physical environment) provide many fascinating examples of structural and functional adaptation in the BOOK REVIEWS plant and animal world, but may leave advanced students wanting more mechanical detail in order to apply these principles to their own research. The balance that is struck in this text is close to ideal for undergraduates and early graduate students. There is thorough explanation of the mathematical and mechanical concepts and these concepts are illustrated by many intriguing examples of plant and animal adaptation, allowing students to gain an appreciation for mechanical principles and their application in a diverse set of biological situations. The text, by necessity, has a very broad scope and is divided into four main sections comprising 25 chapters. The ﬁrst four chapters deal with the essential background material, the basic physical and mechanical concepts (e.g., physical variables, forces, moments, units, scaling, dimensional analysis) that are required to understand the remainder of the text. The second and third sections make up the bulk of the text, and discuss ﬂuids (10 chapters) and solids and structures (10 chapters), respectively, while the fourth section is a summary chapter and Vogel’s perspective on safety factors, morphological adaptation, and convergence. The large amount of text devoted to organisms in ﬂuids (and ﬂuids in organisms) may not have direct relevance to anthropologists, but there is plenty of material here that will satisfy or stimulate most people’s curiosity about how animals and plants cope with liquid and gaseous substances and environments. Topics in the section on ﬂuids range widely from surface tension, and bird and ﬁsh locomotion, to ﬂuid ﬂow in open and closed vascular systems, as well as moving at the air-water interface (among others). The chapters on solids and structures will be most relevant to anthropologists with an interest in the mechanics of biological materials, and how animals make use of these to support themselves (physically) and move around in nonaquatic environments. Chapters cover the mechanics of materials, how these materials have been modiﬁed by natural selection to perform their biological roles, viscoelasticity, structural consequences of differing bone shape (e.g., trusses and cross-sectional properties), hydrostatic structures, adhesion, and achieving motility. There is even a short section on making effective use of mucus (primarily of interest to slugs). There are very good introductory sections on the structural composition and properties of bone, muscle, and tendon, and Vogel provides many conventional and nonconventional examples of how biological tissues function within the organisms that possess them as well as in devices that humans have constructed (e.g., taking advantage of the elastic properties of mammalian tendons in constructing Roman-era ballistic weapons). Whether the examples are conventional or not, Vogel’s writing style makes reading a pleasure. 127 Anthropologists interested in the mechanics of primate locomotion may be disappointed by the brief space devoted to nonaquatic locomotion. There are a few pages devoted to the major gaits in bipeds and quadrupeds, and discussion is focused on techniques for saving energy during walking (inverted pendulum) and running (elastic energy storage). There is no discussion of the determinants of gait to explain why bipedal walking is not a simple inverted pendulum. Nor is there any discussion of recent research on nonsteady state gaits, or mathematical modeling of human locomotion. Most surprisingly, given the comprehensive treatment of other nonterrestrial forms of locomotion in earlier chapters, there is no discussion of the mechanical consequences of arboreal substrate use. Leaping is considered only for kangaroos, and both brachiation and multilimbed locomotion are covered in a perfunctory manner. Some of these topics are covered in other recent texts by R. McNeill Alexander and Andrew Biewener, and while Vogel admits that his text will be updated in the future, these omissions prevent me from recommending the entire text to most biological anthropologists for use in courses on primate or human functional morphology and biomechanics. Of course, this text is not aimed primarily at anthropologists, and I should reiterate that the book’s strengths lie in its vast biological breadth, and the ease with which Vogel conveys general biomechanical principles. Finally, Vogel has created a set of helpful teaching aids that could facilitate the use of his text in classrooms. These teaching aids are available from the author upon request, and come in an 87-page document that includes a sample syllabus, problem sets and practical assignments (with solutions) for each chapter, additional sources, useful websites, and (brief) errata in the text. In summary, this is an excellent, well-referenced, and comprehensive introduction to biomechanics for comparative biologists. The broad scope leaves little space for terrestrial and arboreal animals, but mechanically inclined anthropology students will ﬁnd a thorough treatment of basic biomechanical concepts as well as structural and material properties of biological tissues, and all readers will learn a great deal about the mechanical inﬂuences on the organisms in our world. JOHN D. POLK Department of Anthropology University of Illinois, Urbana-Champaign Urbana, Illinois DOI 10.1002/ajpa.20030 Published online 31 August 2004 in Wiley InterScience (www. interscience.wiley.com).