- Email: [email protected]
Molecular Markers, Natural History and Evolution. By John C. Avise.
MOLECULAR PHYLOGENETICS AND EVOLUTION
Vol. 5, No. 2, April, pp. 441–442, 1996 ARTICLE NO. 0023
BOOK REVIEW Molecular Markers, Natural History and Evolution. By John C. Avise. Chapman & Hall, New York, 1994. 511 pp. Paperback, $37.50. According to the author this book is designed to provide an overview of how molecular markers can be used to study the natural history and evolution of organisms. The intended audience consists of advanced undergraduates, graduate students, and scientists interested in a general introduction to how one can apply molecular markers to problems in their respective disciplines. The book is subdivided into two major sections titled Background and Applications. The first section is subdivided into four chapters that address several topics including: (1) the justification for the use of molecular markers in studies of natural history and evolution; (2) the history of the use of molecular markers in evolutionary studies and how such markers have been used to test hypotheses concerning the role of selection at the level of the gene; (3) molecular markers in phylogeny reconstruction; (4) the types of molecular markers available and the methods used to obtain molecular data as well as the underlying principles associated with those data; and (5) the analysis of molecular data in terms of examining the overall processes of molecular evolution that might influence the ability to obtain a pattern reflecting the evolutionary and natural histories of the taxa under study. The second section contains five chapters that span an ever-increasing level of evolutionary divergence, beginning with issues of individuality and parentage and continuing through species phylogenies and macroevolution. The final chapter in this section pertains to issues of conservation and how genetic approaches can be used in conservation biology. Throughout this second section, Avise provides a wealth of well-illustrated case studies that are used to describe how long-standing hypotheses in behavior, ecology, population biology, phylogeny, etc. can be addressed using various molecular approaches. As is Avise’s style, this section is well written and easy to follow. By far the most exciting part of this book is the second section, especially the chapters dealing with species, populations, and individuals. Avise is a population geneticist, and in these sections he brings his training to bear on questions of mating systems, kinship, population structure, geographic variation, gene flow, and speciation. The first section is less exciting. For instance, the chapters on molecular tools and interpre-
tive tools are incomplete and lacking in detail. Given the recent treatments by Hillis and Moritz (1990) and Miyamoto and Cracraft (1991), one wonders why Avise chose to dedicate so much space to the same issues discussed at length in these other texts. The first section also is where I had the most difficulty appreciating many of the points raised by Avise regarding systematics and phylogeny reconstruction. Although Avise indicates that molecular markers may provide a link between the major areas of evolutionary research, those related to populations and higher taxa, he fails to provide such an integration. I believe this failure is in part a result of Avise’s misunderstanding of systematics, past and present. Let me provide a few examples. First, in Avise’s discussion as to why molecular genetic markers should be employed, he suggests that they can distinguish homology from analogy, a statement first made by Gould (1985) regarding the DNA–DNA hybridization data for birds. Are molecular data less subject to homoplasy? Although there are examples to the contrary, molecules may be less subject to convergence and parallelism (if one assumes a molecular clock) but reversals are a real problem. Thus, one must evaluate the evolution of molecular characters the same way one evaluates morphological characters, that is, on a phylogenetic tree. Second, in several places Avise alludes to the use of a ‘‘molecular yard stick,’’ which will allow for the derivation of a taxonomy using overall magnitude of divergence. Although this might simplify taxonomy, in that no specialists would be necessary, this overall concept is flawed from the beginning simply because taxonomists define the groups, and categories of equal rank that represent different groups of taxa may not be similar in terms of rates of evolution, time since divergence, etc. This approach is not phylogenetic, and instead of a ‘‘universal tapestry linking all life forms,’’ one would get a rag quilt. Finally, Avise confuses issues pertaining to the cladistics/phenetics debate, arguments for a classification based on a phylogeny, and phylogeny reconstruction. Throughout the section on systematic philosophy and the phenetic/cladistic debate, Avise downplays the real issues related to why a phenetic approach (or numerical taxonomic approach), especially one using tree construction methods that assume rate homogeneity (e.g., UPGMA), provides an inferior method for either phylogeny reconstruction or the derivation of a classification. Cladists have argued, and rightly so, that relationships in a phylogeny should be based on shared de-
441
1055-7903/96 $18.00 Copyright 1996 by Academic Press, Inc. All rights of reproduction in any form reserved.
442
BOOK REVIEW
rived characters, a requirement that Avise states may lead to ‘‘authoritarianism.’’ Overall similarity can be misleading because the similarity can be based on shared primitive characters, convergence, and parallelism. Cladistic methodology is about hypothesis testing, whereby many characters are examined. The major criterion is to obtain a phylogeny with the least amount of homoplasy, and all types of characters (morphological, behavioral, genetical, etc.) should be evaluated using a consistent and objective methodology. With regard to the phylogenetic procedures to be used, Avise states (p. 124) ‘‘Secondly, it generally is advisable to attempt multiple methods of data analysis, particularly if these entail philosophically distinct approaches. For example, both UPGMA clustering (a distance-based method epitomizing the phenetic philosophy) and Wagner parsimony (a character-state approach more akin to cladistic thought) reasonably can be applied to many molecular data sets and the results compared.’’ What happens when the results differ among the different procedures? The first section also provides a discussion (Chapter 4) of the utility of particular types of molecular data obtained at different levels of evolutionary divergence. The issue of finding the appropriate molecular marker for a particular question is important. Nevertheless, Avise’s guideline is arbitrary. For instance, what is an ‘‘intermediate taxonomic level’’ and what gene should be sequenced? As indicated by Avise later in this sec-
tion, differential rates of sequence evolution allow one to pick a region that is appropriate for a particular time scale. This assumes, of course, that different DNA sequences evolve in a clock-like manner within groups. Although I have provided some critical comments on this book, especially with respect to the first section, I consider it to be worthwhile reading for individuals seeking an introduction to the general field of evolutionary genetics. The unique part of the book is the second section. This is where Avise provides a wealth of examples and interesting comments regarding the use of molecular markers to interpret both evolutionary pattern and process. REFERENCES Gould, S. J. (1985). A clock of evolution. Nat. Hist. 94: 12–25. Hillis, D. M., and Moritz, C. (1990). ‘‘Molecular Systematics,’’ Sinauer Press, Sunderland, MA. Miyamoto, M. M., and Cracraft, J. (1991). ‘‘Phylogenetic Analysis of DNA Sequences,’’ Oxford Univ. Press, New York.
RODNEY L. HONEYCUTT Department of Wildlife & Fisheries and the Faculty of Genetics Texas A&M University 210 Nagle Hall College Station, Texas 77843
Vol. 5, No. 2, April, pp. 441–442, 1996 ARTICLE NO. 0023
BOOK REVIEW Molecular Markers, Natural History and Evolution. By John C. Avise. Chapman & Hall, New York, 1994. 511 pp. Paperback, $37.50. According to the author this book is designed to provide an overview of how molecular markers can be used to study the natural history and evolution of organisms. The intended audience consists of advanced undergraduates, graduate students, and scientists interested in a general introduction to how one can apply molecular markers to problems in their respective disciplines. The book is subdivided into two major sections titled Background and Applications. The first section is subdivided into four chapters that address several topics including: (1) the justification for the use of molecular markers in studies of natural history and evolution; (2) the history of the use of molecular markers in evolutionary studies and how such markers have been used to test hypotheses concerning the role of selection at the level of the gene; (3) molecular markers in phylogeny reconstruction; (4) the types of molecular markers available and the methods used to obtain molecular data as well as the underlying principles associated with those data; and (5) the analysis of molecular data in terms of examining the overall processes of molecular evolution that might influence the ability to obtain a pattern reflecting the evolutionary and natural histories of the taxa under study. The second section contains five chapters that span an ever-increasing level of evolutionary divergence, beginning with issues of individuality and parentage and continuing through species phylogenies and macroevolution. The final chapter in this section pertains to issues of conservation and how genetic approaches can be used in conservation biology. Throughout this second section, Avise provides a wealth of well-illustrated case studies that are used to describe how long-standing hypotheses in behavior, ecology, population biology, phylogeny, etc. can be addressed using various molecular approaches. As is Avise’s style, this section is well written and easy to follow. By far the most exciting part of this book is the second section, especially the chapters dealing with species, populations, and individuals. Avise is a population geneticist, and in these sections he brings his training to bear on questions of mating systems, kinship, population structure, geographic variation, gene flow, and speciation. The first section is less exciting. For instance, the chapters on molecular tools and interpre-
tive tools are incomplete and lacking in detail. Given the recent treatments by Hillis and Moritz (1990) and Miyamoto and Cracraft (1991), one wonders why Avise chose to dedicate so much space to the same issues discussed at length in these other texts. The first section also is where I had the most difficulty appreciating many of the points raised by Avise regarding systematics and phylogeny reconstruction. Although Avise indicates that molecular markers may provide a link between the major areas of evolutionary research, those related to populations and higher taxa, he fails to provide such an integration. I believe this failure is in part a result of Avise’s misunderstanding of systematics, past and present. Let me provide a few examples. First, in Avise’s discussion as to why molecular genetic markers should be employed, he suggests that they can distinguish homology from analogy, a statement first made by Gould (1985) regarding the DNA–DNA hybridization data for birds. Are molecular data less subject to homoplasy? Although there are examples to the contrary, molecules may be less subject to convergence and parallelism (if one assumes a molecular clock) but reversals are a real problem. Thus, one must evaluate the evolution of molecular characters the same way one evaluates morphological characters, that is, on a phylogenetic tree. Second, in several places Avise alludes to the use of a ‘‘molecular yard stick,’’ which will allow for the derivation of a taxonomy using overall magnitude of divergence. Although this might simplify taxonomy, in that no specialists would be necessary, this overall concept is flawed from the beginning simply because taxonomists define the groups, and categories of equal rank that represent different groups of taxa may not be similar in terms of rates of evolution, time since divergence, etc. This approach is not phylogenetic, and instead of a ‘‘universal tapestry linking all life forms,’’ one would get a rag quilt. Finally, Avise confuses issues pertaining to the cladistics/phenetics debate, arguments for a classification based on a phylogeny, and phylogeny reconstruction. Throughout the section on systematic philosophy and the phenetic/cladistic debate, Avise downplays the real issues related to why a phenetic approach (or numerical taxonomic approach), especially one using tree construction methods that assume rate homogeneity (e.g., UPGMA), provides an inferior method for either phylogeny reconstruction or the derivation of a classification. Cladists have argued, and rightly so, that relationships in a phylogeny should be based on shared de-
441
1055-7903/96 $18.00 Copyright 1996 by Academic Press, Inc. All rights of reproduction in any form reserved.
442
BOOK REVIEW
rived characters, a requirement that Avise states may lead to ‘‘authoritarianism.’’ Overall similarity can be misleading because the similarity can be based on shared primitive characters, convergence, and parallelism. Cladistic methodology is about hypothesis testing, whereby many characters are examined. The major criterion is to obtain a phylogeny with the least amount of homoplasy, and all types of characters (morphological, behavioral, genetical, etc.) should be evaluated using a consistent and objective methodology. With regard to the phylogenetic procedures to be used, Avise states (p. 124) ‘‘Secondly, it generally is advisable to attempt multiple methods of data analysis, particularly if these entail philosophically distinct approaches. For example, both UPGMA clustering (a distance-based method epitomizing the phenetic philosophy) and Wagner parsimony (a character-state approach more akin to cladistic thought) reasonably can be applied to many molecular data sets and the results compared.’’ What happens when the results differ among the different procedures? The first section also provides a discussion (Chapter 4) of the utility of particular types of molecular data obtained at different levels of evolutionary divergence. The issue of finding the appropriate molecular marker for a particular question is important. Nevertheless, Avise’s guideline is arbitrary. For instance, what is an ‘‘intermediate taxonomic level’’ and what gene should be sequenced? As indicated by Avise later in this sec-
tion, differential rates of sequence evolution allow one to pick a region that is appropriate for a particular time scale. This assumes, of course, that different DNA sequences evolve in a clock-like manner within groups. Although I have provided some critical comments on this book, especially with respect to the first section, I consider it to be worthwhile reading for individuals seeking an introduction to the general field of evolutionary genetics. The unique part of the book is the second section. This is where Avise provides a wealth of examples and interesting comments regarding the use of molecular markers to interpret both evolutionary pattern and process. REFERENCES Gould, S. J. (1985). A clock of evolution. Nat. Hist. 94: 12–25. Hillis, D. M., and Moritz, C. (1990). ‘‘Molecular Systematics,’’ Sinauer Press, Sunderland, MA. Miyamoto, M. M., and Cracraft, J. (1991). ‘‘Phylogenetic Analysis of DNA Sequences,’’ Oxford Univ. Press, New York.
RODNEY L. HONEYCUTT Department of Wildlife & Fisheries and the Faculty of Genetics Texas A&M University 210 Nagle Hall College Station, Texas 77843