An introduction to ecological genomics

374 Pages·2012·11.22 MB·English

by  Nico M. van Straalen, Dick Roelofs

An Introduction to Ecological Genomics
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An Introduction to
Ecological Genomics
Second Edition
N ico M . van S traalen and D ick R oelofs
VU University Amsterdam
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3

Great Clarendon Street, Oxford ox2 6dp
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Preface to the second edition
How fast ecological genomics has moved forward tecture in relation to gene expression and epigenetic
since the fi rst edition of this book! The few years regulation of genes. Altogether we believe that this
that have elapsed since then (2006–2011) have not new chapter has expanded the scope of the book to
only seen the rise of extremely fast, so-called ‘next- include a wider variety of topics of interest to evo-
generation’ DNA sequencing technology, but also a lutionary ecologists.
host of excellent new studies in which genomics We have retained our ‘problem-orientated’
technology has been applied to address ecological approach to introduce each chapter, plus an
questions. We are particularly impressed by the appraisal section at the end. With this design we
massive progress in comparative genomics, phyl- want to emphasize that, in the end, ecological
ogenomics, population genomics, and metagenom- genomics is just another branch of ecology and that
ics. We tried to pay particular attention to the new it addresses questions that all ecologists ask, only
frontiers created by these fi elds as we prepared the with different technology. On the other hand, it is
second edition of this book. our opinion that ecological genomics also brings
In comparison to the previous edition, we new questions to the discourse that were not raised
skipped the ‘Genome analysis’ chapter, as the before or could not be answered by more traditional
technology has moved forward to such an extent ecological approaches.
that a great deal of that chapter was considered What was marginally doable in 2005 has now
outdated. Instead, we added a separate section on become an impossibility: to summarize all publica-
methodology and data analysis to Chapter 1 , in tions of relevance to ecological genomics in a single
which we also treat the new-generation sequenc- book. We hope that the reader may fi nd guidance
ing technologies. and inspiration in this book to further study more
Furthermore, we have included a completely new specialized areas of their interest that we could not
chapter on variation and adaptation, in which we cover.
treat the various aspects of genome variability, and We hope this book will support graduate pro-
pay a good deal of attention to population genom- grammes of Ecology, Evolutionary Biology, or simi-
ics, a topic of increasing popularity among popula- lar programmes, and stimulate students to proceed
tion-oriented ecological genomicists. In this chapter with their career in the exciting fi eld of ecological
the reader may also fi nd extensive reference to the genomics, while it is—still—relatively new.
issue of neutrality in molecular evolution. In addi- Nico M. van Straalen and Dick Roelofs
tion we discuss the various aspects of genome archi- Amsterdam, February 2011
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Preface to the fi rst edition
This book is an introduction to the exciting new encompassed by evolutionary genomics, such as
field of ecological genomics, for use in MSc courses comparative genomics, phylogenetic analysis, and
and by those beginning their PhD studies. molecular evolution, can now be considered as
When we became involved in a national research fields in their own right. They are certainly too large
programme on ecological genomics, or ecogenom- to be covered in an introductory book on ecological
ics as it became known, we realized that informa- genomics; indeed, evolutionary genomics deserves
tion on this newly emerging subject needed to be a textbook of its own.
brought together. In order to start up a research pro- We have organized this book around three issues
gramme in such a new discipline, not only the stu- important in modern ecology, choosing questions
dents, but also we as teachers, had to get to grips for which the links to genomics are best developed.
with the subject. Furthermore, although obtaining a At the outset, we perhaps use rather ambitious
PhD implies mastering a specialized field, the PhD phrasing to announce the genomics approach to
student must be able to place this field in a broader these ecological questions. Maybe our questions
context if he or she is to become a mature scientist. cannot be answered at this stage. However, we
This approach may be called the T-model of educa- decided not to suppress unanswered, and thus
tion; the horizontal bar of the T representing a broad open, issues. Instead we hope to stimulate discus-
understanding, and the vertical bar an investigation sion as well as provide factual information. We have
in depth, going down to the root of the problem. included an appraisal section at the end of each
Our book uses this approach. chapter to emphasize this question-orientated
We assume a basic level of knowledge in the bio- approach. Combined with information given in the
logical sciences to BSc level: ecology, evolutionary introductory section, this allows the reader to grasp
biology, microbiology, plant physiology, animal the main points of each chapter, even if the detailed
physiology, genetics, and molecular biology. We treatment of molecular principles and case studies
have tried to link up with the content of the most are left aside.
common textbooks in these fields, at the same time Case studies are taken from literature published
realizing that students of ecological genomics have since the year 2000. Nevertheless, a book on genom-
a variety of backgrounds. However, our main tar- ics runs the risk of becoming outdated very quickly:
gets are students with subjects closely related to the rate at which knowledge is being accrued and
ecology and evolutionary biology, which is why we insight developed is unprecedented. However, we
place the emphasis on aspects that we judge to be hope that our question-orientated set-up will be
particularly new to them. useful for some years to come, even when new and
Evolutionary genomics and bioinformatics are better case studies are available.
companion disciplines to ecological genomics. In Before this book was written, journal articles
the last 10 years interest in both disciplines has comprised the only literature on ecological genom-
grown enormously. Several textbooks on bioinfor- ics. These, although very inspiring, were scattered
matics have already been published and subjects widely. Today, most textbooks on genetics and evo-
viii PREFACE TO THE FIRST EDITION
lution have a chapter on genomics. Gibson and Röling, and Martijn Timmermans. We thank Desirée
Muse published a primer on genome science in Hoonhout and Karin Uyldert for checking the refer-
2002, but this did not cover ecological questions. So, ence list, and Nico Schaefers, for preparation of the
for us, writing this book was ploughing unknown figures. Ian Sherman at Oxford University Press
ground. We have attempted to add structure to the provided us with stimulating discussion. We thank
field, and hopefully have put ecological genomics members of the Animal Ecology Department at the
on the map. However, we welcome constructive Vrije Universiteit for your friendship and encour-
criticism and suggestions from our readers. agement. N.M.vS. also thanks the Faculty of Earth
We thank the colleagues who reviewed parts of and Life Sciences of the Vrije Universiteit for grant-
the book, suggested issues that had escaped us, or ing the sabbatical leave during which most of this
helped with correcting the English: Martin Feder, book was written.
Claire Hengeveld, Jan Kammenga, René Klein Nico M. van Straalen and Dick Roelofs,
Lankhorst, Bas Kooijman, Jan Kooter, Wilfred Amsterdam, July 2005
Contents
1 Ecological genomics and genome analysis 1
1.1 The genomics revolution invading ecology 1
1.2 Yeast, fl y, worm, and weed 3
1.3 -Omics speak 9
1.4 Genome analysis 15
2 C omparing genomes 38
2.1 Properties of genomes 38
2.2 Prokaryotic genomes 52
2.3 Eukaryotic genomes 64
3 S tructure and function in communities 96
3.1 The biodiversity and ecosystem functioning synthetic framework 96
3.2 Measurement of microbial biodiversity 98
3.3 Microbial genomics of biogeochemical cycles 113
3.4 Reconstruction of functions from environmental genomes 129
3.5 Genomic approaches to biodiversity and ecosystem function: an appraisal 146
4 L ife-history patterns 148
4.1 The core of life-history theory 148
4.2 Longevity and aging 153
4.3 Gene-expression profi les in the life cycle 167
4.4 Phenotypic plasticity of life-history traits 182
4.5 Genomic approaches to life-history patterns: an appraisal 192
5 S tress responses 195
5.1 Stress and the ecological niche 195
5.2 The main defence mechanisms against cellular stress 198
5.3 Heat, cold, drought, salt, and hypoxia 217
5.4 Herbivory and microbial infection 226
5.5 Toxic substances 234
5.6 Genomic approaches to ecological stress: an appraisal 243
6 Variation and adaptation 245
6.1 The internal tangled bank 245
6.2 Genomic polymorphisms 247
6.3 Regulatory and structural change 267
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