- Email: [email protected]
Flowers and Flowering
Update
Trends in Ecology and Evolution Vol.24 No.3
Book review
Flowers and Flowering Understanding Flowers and Flowering: An Integrated Approach by Beverley Glover, Oxford University Press, 2008, £75.00/£32.50 hbk/ pbk (240 pages) ISBN 978-0-198-56597-0/978-0-198-56596-3
Douglas E. Soltis Department of Botany, University of Florida, Gainesville, FL 32611, USA
In the Epilogue of Understanding Flowers and Flowering, Beverley Glover states that the book ‘was conceived with a single clear aim: to link what we know of the molecular and genetic control of how flowers come to look as they do with what we know from evolutionary and ecological perspectives about why they look as they do.’ This is an ambitious undertaking; Glover attempts to bring together diverse fields including flower induction, floral pigmentation, pollination biology, development and developmental genetics. As a major goal, she states ‘that if nothing else, this book will serve to show each sort of specialist the complexity of the rest of the field.’ By touching on such a diverse array of topics in one volume, the author has accomplished this important goal; in this broad sense, Understanding Flowers and Flowering is valuable as a compendium of diverse information. It should appeal to a broad audience, including specialists and nonspecialists, and might be particularly helpful for those interested in interdisciplinary research. Strengths of Understanding Flowers and Flowering include the useful overviews of pathways for floral induction, floral inhibition, vernalization and genes controlling flowering and floral organ identity. The chapter on flower induction is a good overview for those not familiar with the various standard approaches used in the study of Arabidopsis. Useful sections are given on generating mutants, complementation analysis, gene cloning and reverse genetics. The discussion of individual genes involved in flowering and the control of floral organ identity are particularly useful to evolutionary biologists. The individual sections on genes such as FLC, FT, LFY, AP1 and CAL are also helpful, and readers not familiar with them (but always hearing the names rattled off by Arabidopsis researchers) can quickly find out about each, with descriptions that are easy to read. In fact, the entire book is well written and easy to follow. However, given that this review is for an ecology and evolutionary biology audience, some comments are necessary that would not be applicable for a general readership. For evolutionary biologists and ecologists, a weakness of the book is that it lacks a firm evolutionary foundation. For example, a better overview of the phylogenetic framework of relationships now available for flowering plants (e.g. a figure of a simple summary evolutionary tree) would be a Corresponding author: Soltis, D.E. ([email protected]).
124
great help to readers, particularly when the author mentions eudicots, rosids and asterids, but these terms are not really explained [1]. The overview of the ‘evolution of flowers’ is also very general and not really up to date. The author writes ‘the oldest fossil families suggest that the early angiosperms were primarily understory plants.’ But the author does not note that the earliest unequivocal fossils are actually aquatic [2,3], and it remains unclear whether the earliest flowering plants were aquatic or understory shrubs or trees [1]. The author also paints a picture of conflict between age estimates for the origin of the angiosperms based on fossils versus molecular data, but no such conflict now exists. Recent molecular estimates more closely agree with the fossil record [4]. Understandably, much of the coverage of morphology, development and developmental genetics focuses on the model plant Arabidopsis. However, to give a broader evolutionary overview, additional information could have been provided on the morphology of basal angiosperm flowers. An important point that is not stressed is that, although non-monocot basal angiosperms represent only 3% of angiosperm species diversity [5], they display enormous floral diversity; many basal angiosperms have flower parts that are spirally arranged, rather than the typical whorled arrangement with a gradual transition from one floral part to the next through this spiral [1,6]. Similarly, in the discussion of the development of floral organs and the ABC model of flower development [7], a broader evolutionary perspective could again be given. Excellent reviews of flower development and evolution have been provided on a broad scale across the diversity of flowering plants [6]. It is now clear that the classic ABC model of floral organ identity as proposed for Arabidopsis is evolutionarily derived. Basal angiosperms have broader patterns of expression of floral organ identity genes, and this appears to be the ancestral condition [8]. In summary, this is a useful, well-written book that compiles a lot of information from diverse areas. It serves the important purpose of illustrating to researchers the complexities and difficult problems that are faced in other areas of research and also highlights the interconnection among these diverse areas as we strive for synthesis. References 1 Soltis, D.E. et al. (2005) Phylogeny and Evolution of the Angiosperms. Sinauer Associates 2 Sun, G. et al. (2002) Archaefructaceae, a new basal angiosperm family. Science 296, 899–904 3 Friis, E.M. et al. (2001) Fossil evidence of waterlilies (Nymphaeales) in the Early Cretaceous. Nature 410, 357–360
Update 4 Bell, C.D. et al. (2005) The age of the angiosperms: a molecular timescale without a clock. Evolution 59, 1245–1258 5 Drinnan, A.N. et al. (1994) Patterns of floral evolution in the early diversification of non-magnoliid dicotyledons (eudicots). Plant Syst. Evol. 8 (Suppl.), 93–122 6 Endress, P.K. (2006) Angiosperm floral evolution: morphological developmental framework. In Advances in Botanical Research (Soltis, D.E. et al., eds), pp. 2–36, Elsevier
Trends in Ecology and Evolution
Vol.24 No.3
7 Coen, H.S. and Meyerowitz, E.M. (1991) The war of the whorls: genetic interactions controlling flower development. Nature 353, 31–37 8 Kim, S.H. et al. (2005) Expression of floral MADS-box genes in basal angiosperms: implications for the evolution of floral regulators. Plant J. 43, 724–744 0169-5347/$ – see front matter ß 2009 Elsevier Ltd. All rights reserved. doi:10.1016/j.tree.2008.10.010 Available online 29 January 2009
Book Review
Modeling the past: a resource for the future Coalescent Theory: An Introduction by John Wakeley, Roberts & Company Publishers, 2008. US $59.95 (326 pages) ISBN 978-0-97470775-4
Laura S. Kubatko Departments of Statistics and Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
Coalescent theory has served as the foundation for most analyses in population genetics since its initial development by Kingman and others during the early 1980s [1–4] because it provides a mathematical model for the shared ancestry of a collection of individuals in a framework that enables computation. Recent advances in sequencing technology coupled with the development of computational techniques that enable the implementation of models of growing complexity have led coalescent modeling to become perhaps the most rapidly expanding area of research focus in the field of population genetics. Thus, Coalescent Theory: An Introduction provides an extremely timely and much-needed resource for those wanting to enter into research in this field. It is just the second textbook devoted solely to the coalescent, the other being the text by Hein et al. [5] and, similar to the Hein et al. text, it provides a thorough introduction to the subject. Because the coalescent is a quantitative model for the genealogical relationships of a sample traced back in time, a certain amount of mathematical and statistical background is required to fully appreciate the model. Thus, the two books will be equally challenging for those who do not recall fundamental ideas from their calculus training and who have not been exposed to basic concepts in probability and statistics. However, Coalescent Theory provides an entire chapter devoted to reviewing the mathematical and statistical ideas required to work through the derivations included in much of the remainder of the book. This mathematical review follows a brief introduction to the typical biological settings to which the coalescent model is applied in Chapter 1. Chapters 3 and 4 build on this introductory material by providing detailed derivations of the coalescent under standard population models, such as the Wright-Fisher and Moran models, as well as results that follow from these models under the standard coalescent. Corresponding author: Kubatko, L.S. ([email protected]).
The self-contained nature of these chapters is a feature that should have widespread appeal, and the researcher who works through them carefully will be firmly grounded in the theoretical underpinnings of Kingman’s coalescent. Chapters 5–8 proceed to more advanced topics, and readers without a background in areas such as Markov processes might find the material more challenging in some places. Nonetheless, the brief introduction to these topics provided at the beginning of Chapter 5 will be helpful to those who have been exposed to such topics in the past. Throughout the text, emphasis is placed on the cultivation of a set of tools that are commonly applied in coalescent modeling. A nice example of this is the detailed discussion of ‘first-step analysis’ for Markov chains, a technique that is repeatedly used to derive useful recursive relationships in the coalescent framework. Similarly, Chapter 7 includes thorough discussions of ancestral graphs that incorporate either selection or recombination. Both topics are currently gaining prominence; in particular, the ancestral recombination graph is increasingly being used as a tool in genetic mapping via linkage disequilibrium. Also valuable is the separate treatment of mating systems that do not result in an exchangeable breeding structure, as would be the case, for example, in a diploid, biparental system. Because such considerations are often omitted from introductory writings in this field, the full exposition of these results is a clear strength of this text. A further strength of Coalescent Theory is that many details of the historical development of the methodology are given throughout the text. It is therefore fitting that the book should close with an excellent discussion of the current state of the field. This final chapter clearly lays out the fundamental ideas involved in statistical analyses in very general settings, before moving on to describe the particular challenges associated with analysis in the context of the coalescent. It is the kind of chapter that I have seen included in only a few textbooks, but one that should become standard for books in these emerging areas, where the biggest challenge facing progress is often the ability to implement analyses efficiently using realistic models. It is a delight to read such a carefully written volume by one of the leaders in this field. Coalescent Theory will serve 125
Trends in Ecology and Evolution Vol.24 No.3
Book review
Flowers and Flowering Understanding Flowers and Flowering: An Integrated Approach by Beverley Glover, Oxford University Press, 2008, £75.00/£32.50 hbk/ pbk (240 pages) ISBN 978-0-198-56597-0/978-0-198-56596-3
Douglas E. Soltis Department of Botany, University of Florida, Gainesville, FL 32611, USA
In the Epilogue of Understanding Flowers and Flowering, Beverley Glover states that the book ‘was conceived with a single clear aim: to link what we know of the molecular and genetic control of how flowers come to look as they do with what we know from evolutionary and ecological perspectives about why they look as they do.’ This is an ambitious undertaking; Glover attempts to bring together diverse fields including flower induction, floral pigmentation, pollination biology, development and developmental genetics. As a major goal, she states ‘that if nothing else, this book will serve to show each sort of specialist the complexity of the rest of the field.’ By touching on such a diverse array of topics in one volume, the author has accomplished this important goal; in this broad sense, Understanding Flowers and Flowering is valuable as a compendium of diverse information. It should appeal to a broad audience, including specialists and nonspecialists, and might be particularly helpful for those interested in interdisciplinary research. Strengths of Understanding Flowers and Flowering include the useful overviews of pathways for floral induction, floral inhibition, vernalization and genes controlling flowering and floral organ identity. The chapter on flower induction is a good overview for those not familiar with the various standard approaches used in the study of Arabidopsis. Useful sections are given on generating mutants, complementation analysis, gene cloning and reverse genetics. The discussion of individual genes involved in flowering and the control of floral organ identity are particularly useful to evolutionary biologists. The individual sections on genes such as FLC, FT, LFY, AP1 and CAL are also helpful, and readers not familiar with them (but always hearing the names rattled off by Arabidopsis researchers) can quickly find out about each, with descriptions that are easy to read. In fact, the entire book is well written and easy to follow. However, given that this review is for an ecology and evolutionary biology audience, some comments are necessary that would not be applicable for a general readership. For evolutionary biologists and ecologists, a weakness of the book is that it lacks a firm evolutionary foundation. For example, a better overview of the phylogenetic framework of relationships now available for flowering plants (e.g. a figure of a simple summary evolutionary tree) would be a Corresponding author: Soltis, D.E. ([email protected]).
124
great help to readers, particularly when the author mentions eudicots, rosids and asterids, but these terms are not really explained [1]. The overview of the ‘evolution of flowers’ is also very general and not really up to date. The author writes ‘the oldest fossil families suggest that the early angiosperms were primarily understory plants.’ But the author does not note that the earliest unequivocal fossils are actually aquatic [2,3], and it remains unclear whether the earliest flowering plants were aquatic or understory shrubs or trees [1]. The author also paints a picture of conflict between age estimates for the origin of the angiosperms based on fossils versus molecular data, but no such conflict now exists. Recent molecular estimates more closely agree with the fossil record [4]. Understandably, much of the coverage of morphology, development and developmental genetics focuses on the model plant Arabidopsis. However, to give a broader evolutionary overview, additional information could have been provided on the morphology of basal angiosperm flowers. An important point that is not stressed is that, although non-monocot basal angiosperms represent only 3% of angiosperm species diversity [5], they display enormous floral diversity; many basal angiosperms have flower parts that are spirally arranged, rather than the typical whorled arrangement with a gradual transition from one floral part to the next through this spiral [1,6]. Similarly, in the discussion of the development of floral organs and the ABC model of flower development [7], a broader evolutionary perspective could again be given. Excellent reviews of flower development and evolution have been provided on a broad scale across the diversity of flowering plants [6]. It is now clear that the classic ABC model of floral organ identity as proposed for Arabidopsis is evolutionarily derived. Basal angiosperms have broader patterns of expression of floral organ identity genes, and this appears to be the ancestral condition [8]. In summary, this is a useful, well-written book that compiles a lot of information from diverse areas. It serves the important purpose of illustrating to researchers the complexities and difficult problems that are faced in other areas of research and also highlights the interconnection among these diverse areas as we strive for synthesis. References 1 Soltis, D.E. et al. (2005) Phylogeny and Evolution of the Angiosperms. Sinauer Associates 2 Sun, G. et al. (2002) Archaefructaceae, a new basal angiosperm family. Science 296, 899–904 3 Friis, E.M. et al. (2001) Fossil evidence of waterlilies (Nymphaeales) in the Early Cretaceous. Nature 410, 357–360
Update 4 Bell, C.D. et al. (2005) The age of the angiosperms: a molecular timescale without a clock. Evolution 59, 1245–1258 5 Drinnan, A.N. et al. (1994) Patterns of floral evolution in the early diversification of non-magnoliid dicotyledons (eudicots). Plant Syst. Evol. 8 (Suppl.), 93–122 6 Endress, P.K. (2006) Angiosperm floral evolution: morphological developmental framework. In Advances in Botanical Research (Soltis, D.E. et al., eds), pp. 2–36, Elsevier
Trends in Ecology and Evolution
Vol.24 No.3
7 Coen, H.S. and Meyerowitz, E.M. (1991) The war of the whorls: genetic interactions controlling flower development. Nature 353, 31–37 8 Kim, S.H. et al. (2005) Expression of floral MADS-box genes in basal angiosperms: implications for the evolution of floral regulators. Plant J. 43, 724–744 0169-5347/$ – see front matter ß 2009 Elsevier Ltd. All rights reserved. doi:10.1016/j.tree.2008.10.010 Available online 29 January 2009
Book Review
Modeling the past: a resource for the future Coalescent Theory: An Introduction by John Wakeley, Roberts & Company Publishers, 2008. US $59.95 (326 pages) ISBN 978-0-97470775-4
Laura S. Kubatko Departments of Statistics and Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
Coalescent theory has served as the foundation for most analyses in population genetics since its initial development by Kingman and others during the early 1980s [1–4] because it provides a mathematical model for the shared ancestry of a collection of individuals in a framework that enables computation. Recent advances in sequencing technology coupled with the development of computational techniques that enable the implementation of models of growing complexity have led coalescent modeling to become perhaps the most rapidly expanding area of research focus in the field of population genetics. Thus, Coalescent Theory: An Introduction provides an extremely timely and much-needed resource for those wanting to enter into research in this field. It is just the second textbook devoted solely to the coalescent, the other being the text by Hein et al. [5] and, similar to the Hein et al. text, it provides a thorough introduction to the subject. Because the coalescent is a quantitative model for the genealogical relationships of a sample traced back in time, a certain amount of mathematical and statistical background is required to fully appreciate the model. Thus, the two books will be equally challenging for those who do not recall fundamental ideas from their calculus training and who have not been exposed to basic concepts in probability and statistics. However, Coalescent Theory provides an entire chapter devoted to reviewing the mathematical and statistical ideas required to work through the derivations included in much of the remainder of the book. This mathematical review follows a brief introduction to the typical biological settings to which the coalescent model is applied in Chapter 1. Chapters 3 and 4 build on this introductory material by providing detailed derivations of the coalescent under standard population models, such as the Wright-Fisher and Moran models, as well as results that follow from these models under the standard coalescent. Corresponding author: Kubatko, L.S. ([email protected]).
The self-contained nature of these chapters is a feature that should have widespread appeal, and the researcher who works through them carefully will be firmly grounded in the theoretical underpinnings of Kingman’s coalescent. Chapters 5–8 proceed to more advanced topics, and readers without a background in areas such as Markov processes might find the material more challenging in some places. Nonetheless, the brief introduction to these topics provided at the beginning of Chapter 5 will be helpful to those who have been exposed to such topics in the past. Throughout the text, emphasis is placed on the cultivation of a set of tools that are commonly applied in coalescent modeling. A nice example of this is the detailed discussion of ‘first-step analysis’ for Markov chains, a technique that is repeatedly used to derive useful recursive relationships in the coalescent framework. Similarly, Chapter 7 includes thorough discussions of ancestral graphs that incorporate either selection or recombination. Both topics are currently gaining prominence; in particular, the ancestral recombination graph is increasingly being used as a tool in genetic mapping via linkage disequilibrium. Also valuable is the separate treatment of mating systems that do not result in an exchangeable breeding structure, as would be the case, for example, in a diploid, biparental system. Because such considerations are often omitted from introductory writings in this field, the full exposition of these results is a clear strength of this text. A further strength of Coalescent Theory is that many details of the historical development of the methodology are given throughout the text. It is therefore fitting that the book should close with an excellent discussion of the current state of the field. This final chapter clearly lays out the fundamental ideas involved in statistical analyses in very general settings, before moving on to describe the particular challenges associated with analysis in the context of the coalescent. It is the kind of chapter that I have seen included in only a few textbooks, but one that should become standard for books in these emerging areas, where the biggest challenge facing progress is often the ability to implement analyses efficiently using realistic models. It is a delight to read such a carefully written volume by one of the leaders in this field. Coalescent Theory will serve 125