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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 0-471-38390-2

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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).
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practical, francis, 471, baxevanis, 649, isbn, sons, 2001, new, john, ouellette, andreas, york, 38390, protein, guide, edited, analysis, genes, bioinformatics, wiley
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