Evolutionary Biology

by Clegg, Michael T.; Hecht, Max K.; Macintyre, Ross J.

• ISBN13: 9780306462276
• ISBN10: 0306462273
• Format: Hardcover
• Copyright: 2000-09-30
• Publisher: Plenum Pub Corp

Summary

After volume 33, this book series was replaced by the journal "Evolutionary Biology." Please visit www.springer.com/11692 for further information. The nature of science is to work on the boundaries between the known and the unknown. These boundaries shift as new methods are developed and as new concepts are elaborated (e.g., the theory of the gene, or more recently, the coalescence framework in population genetics). These tools allow us to address questions that were previously outside the realm of science, and, as a consequence, the boundary between the knowable and unknowable has shifted. A study of limits should reveal and clarify the boundaries and make sharper the set of questions. This book examines and analyzes these new limits as they are applied to evolutionary biology and population genetics. It does this by framing the analysis within four major classes of problems - establishing the fact of evolution; understanding the evolutionary pathways that led to today's biological world; mechanisms of evolutionary change (e.g., models of social behavior, sexual selection, macro evolution); and, finally, prediction.

Table of Contents

I. Limits to Knowledge: An Introduction
Limits to Our Knowledge of Evolution
Michael Ruse
Introduction	3	(1)
The Fact of Evolution	3	(11)
The Path of Evolution	14	(3)
The Causes of Evolution	17	(3)
Macroevolution	20	(2)
Human Evolution	22	(2)
Alternative Theories?	24	(4)
References	28	(7)
Limits to Knowledge in Population Genetics
Michael T. Clegg
Introduction	35	(3)
A Classification of Limits to Knowledge in Population Genetics	37	(1)
The Analysis of Gene Genealogies	38	(4)
Inferences Based on Coalescence Theory	40	(1)
Some Empirical Data	41	(1)
Adaptive Evolution in Complex Biological Systems	42	(6)
Chalcone Synthase Genes in Morning Glory	43	(1)
Gene Duplication and Divergence in Evolution	44	(3)
Interlocus Gene Conversion-Recombination	47	(1)
Genetics and Population Biology of White Flower Color Phenotypes in Morning Glory	47	(1)
Summary	48	(2)
References	50	(21)
II. The Philosophy of Biology, Paradigms, and Paradigm Shifts
Laws, History, and the Nature of Biological Understanding
Alex Rosenberg
References	71	(2)
Avoiding Paradigm-Based Limits to Knowledge of Evolution
Ward B. Watt
Introduction	73	(2)
Paradigms and Worldviews in Biology	75	(1)
The Amechanistic Paradigm in Evolutionary Study	76	(3)
Crisis in the Amechanistic Evolutionary Paradigm	79	(2)
Intellectual Confinement by the Amechanistic Paradigm	79	(1)
Evidence for Paradigm Crisis	80	(1)
Adaptation, Not Adaptationism: Avoiding Another Limiting Paradigm	81	(3)
Are There Philosophical Limits to Knowledge of Evolution?	84	(2)
Prospects for Extending the Limits to Knowledge of Evolution	86	(5)
Examples of the Feasibility of Reintegrating Evolutionary Studies	86	(2)
Conflict or Synergism? The Continued Utility of Subdisciplines	88	(1)
``Complexity Problems'' in Adaptive Studies and Strategy to Address Them	88	(2)
Broad Evolutionary Time Scales	90	(1)
The Possible Generality of Evolutionary Study	91	(1)
Conclusions	91	(1)
References	92	(5)
Anticipating Scientific Revolutions in Evolutionary Genetics
Jody Hey
Introduction	97	(1)
Questions Clear and Questions Not	98	(2)
Scientific Revolutions and How We Do Not See Them	100	(2)
Scientific Revolutions in Progress	102	(7)
Rejecting the Neutral Model	103	(1)
The Rediscovery of the Hill-Robertson Effect	103	(2)
The Seeds of a Revolution	105	(4)
Conclusions	109	(1)
References	110	(7)
III. Limits to Historical Inference and Prediction
Inferring Ancestral Character States
Gary A. Churchill
Introduction	117	(2)
Methods	119	(3)
Model	119	(1)
Prior Distributions	120	(1)
Posterior Distributions	121	(1)
Computing	122	(1)
Results	122	(7)
One Branch	122	(2)
Star Phylogeny with Clock	124	(2)
Star Phylogeny with No Clock	126	(3)
A Clocklike Tree	129	(5)
Two Trees	131	(3)
Conclusions	134	(1)
References	134	(1)
The Problem of Inferring Selection and Evolutionary History from Molecular Data
Charles F. Aquadro
Introduction	135	(2)
Why Is Evolution So Difficult to Study Experimentally?	137	(1)
Recapturing Evolutionary History	138	(1)
Are There Significant New Insights to Be Gained in Population Genetics?	139	(1)
The Problem of Weak or Recent Selection	140	(1)
How Do We Increase the Signal?	141	(1)
Issues of Linkage Disequilibrium	142	(1)
Will the Ability Technically to Obtain Large Sample Sizes Extend the Limits of What We Can Rigorously Distinguish?	143	(1)
Prospects for the Future	144	(1)
References	145	(6)
Evolutionary Genetics of Primate Color Vision: Recent Progress and Potential Limits to Knowledge
Wen-Hsiung Li
Stephane Boissinot
Ying Tan
Song-Kun Shyue
David Hewett-Emmett
Introduction	151	(2)
Color Vision Systems in Primates	153	(2)
Critical Amino Acid Residues for Spectral Tuning	155	(6)
Frequent Gene Conversion between X-Linked Opsin Alleles or Genes	161	(4)
Origins of Color Vision Systems in Higher Primates	165	(6)
Evolutionary Mechanisms	171	(2)
Concluding Remarks	173	(2)
References	175	(4)
The Limits to Knowledge in Conservation Genetics: The Value of Effective Population Size
Leonard Nunney
Introduction	179	(2)
The Parameters of Genetic Planning	181	(2)
Measuring Effective Population Size	183	(2)
Population Fragmentation---The Island Model	185	(2)
Population Fragmentation---The Interdemic Model	187	(1)
Movement among Reserves	188	(2)
Conclusion	190	(2)
References	192	(3)
What Is the Structure of Human Populations?
Bruce S. Weir
Introduction	195	(1)
Human Disease Gene Mapping	196	(2)
Human Identification	198	(1)
Hierarchical Model of Human Evolution	199	(2)
Conclusion	201	(1)
References	202	(3)
IV. Quantitative Genetics and the Prediction of Phenotype from Genotype
Limits to Prediction of Phenotypes from Knowledge of Genotypes
Andrew G. Clark
The Problem	205	(3)
Genetic Heterogeneity	208	(1)
Multiplicity of Small Effects	209	(1)
Epistatic Interactions	210	(2)
Simpson's Paradox: Complex Systems Viewed from the Margins	212	(2)
The NK Model Viewed at the Margins	214	(2)
N-Locus Diploid Epistasis Viewed from the Margins	216	(4)
Genotype x Environment Interaction	220	(1)
Recommendation	221	(1)
References	222	(3)
The Limits to Knowledge in Quantitative Genetics
Michael Lynch
Introduction	225	(1)
Phenotypes versus Genetic Values	226	(1)
The Nature of Quantitative Variation	227	(2)
The Meaning of Quantitative Variation	229	(3)
Population Genetics and Population Dynamics	232	(1)
Issues Concerning Outbreeding Depression and Species Incompatibilities	233	(1)
Summary	234	(1)
References	235	(4)
Genetics of Species Differentiation: What Is Unknown and What Will Be Unknowable?
Chung-I Wu
Musings about Generality in Biology	239	(2)
Haldane's Rule and the Peril of Overgeneralization	241	(2)
Species Differentiation and the Uncertainty in Extrapolation from Population Genetic Variation	243	(4)
Conclusions	247	(1)
References	247	(2)
Conclusions	249	(2)
Michael T. Clegg
Index	251