Molecular Markers, Natural History, and Evolution

by Avise, John C.

• ISBN13: 9780878930418
• ISBN10: 0878930418
• Edition: 2nd
• Format: Paperback
• Copyright: 2004-03-01
• Publisher: Sinauer Associates Inc

Summary

Univ. of Georgia, Athens. Updated and expanded, text covers new laboratory methods for uncovering molecular markers, statistical and conceptual approaches for estimating intraspecific genealogy, and interspecific phylogeny. Offers a vast array of empirical examples. Abundant halftone illustrations. Previous edition: c1994. Softcover.

Table of Contents

PART I Background
CHAPTER 1: Introduction	1	(22)
Why Employ Molecular Genetic Markers?	5	(15)
Molecular data are genetic	6	(1)
Molecular methods open the entire biological world for genetic scrutiny	6	(1)
Molecular methods access a nearly unlimited pool of genetic variability	7	(1)
Molecular data can distinguish homology from analogy	8	(1)
Molecular data provide common yardsticks for measuring divergence	9	(5)
Molecular approaches facilitate mechanistic appraisals of evolution	14	(3)
Molecular approaches are challenging and exciting	17	(3)
Why Not Employ Molecular Genetic Markers?	20	(3)
CHAPTER 2: The History of Interest in Genetic Variation	23	(32)
The Classical-Balance Debate	24	(6)
Classical versus balance views of genome structure	24	(2)
Molecular input to the debate	26	(3)
Questions of empirical refinement	29	(1)
The Neutralist-Selectionist Debate	30	(17)
Multi-locus allozyme heterozygosity and organismal fitness	36	(4)
Single-locus allozyme variation and the vertical approach	40	(1)
Selection at the level of DNA	41	(3)
The unresolved status of the controversy	44	(3)
Must Molecular Markers Be Neutral To Be Informative?	47	(1)
The Molecule-Morphology Debate	48	(1)
Molecular Phylogenetics	49	(6)
CHAPTER 3: Molecular Techniques	55	(60)
Protein Immunology	55	(2)
Protein Electrophoresis	57	(6)
Mendelian markers	59	(2)
Idiosyncratic protein features	61	(2)
DNA-DNA Hybridization	63	(4)
Restriction Analyses	67	(20)
Animal mitochondrial DNA	70	(8)
Plant organelle DNA	78	(1)
Single-copy nuclear DNA	79	(4)
Moderately repetitive gene families	83	(1)
Minisatellites and DNA fingerprinting	84	(3)
Polymerase Chain Reaction	87	(14)
RAPDs	91	(1)
STRs (microsatellites)	92	(2)
AFLPs	94	(1)
SINEs	95	(2)
SSCPs	97	(1)
SNPs	97	(1)
HAPSTRs and SNPSTRs	98	(1)
DNA sequencing	98	(3)
Categorical Breakdowns of Molecular Methods	101	(14)
Protein versus DNA information	104	(1)
Discrete versus distance data	105	(5)
Detached versus connectable information	110	(1)
Single-locus versus multi-locus data	111	(1)
Utility of data along the phylogenetic hierarchy	111	(4)
CHAPTER FOUR: Philosophies and Methods of Molecular Data Analysis	115	(46)
Cladistics versus Phenetics	115	(5)
Molecular Clocks	120	(12)
History of clock calibrations and controversies	123	(5)
Absolute and relative rate comparisons	128	(3)
Closing thoughts on clocks	131	(1)
Phylogenetic Reconstruction	132	(11)
Distance-based approaches	134	(5)
Character-state approaches	139	(3)
Conclusions about phylogenetic procedures	142	(1)
Gene Trees versus Species Trees	143	(18)
PART II Applications
CHAPTER FIVE: Individuality and Parentage	161	(70)
Human Forensics	161	(8)
History of laboratory approaches	162	(3)
History of controversies	165	(2)
Empirical examples	167	(2)
Ramets and Genets	169	(25)
Background	169	(3)
Spatial Distributions of Clones	172	(7)
Ages of clones	179	(4)
Clonal reproduction in microorganisms	183	(9)
Genetic chimeras	192	(2)
Gender Ascertainment	194	(2)
Genetic Parentage	196	(35)
Behavioral and evolutionary contexts	202	(2)
Selected empirical examples by taxa	204	(17)
Selected empirical examples by topic	221	(10)
CHAPTER SIX: Kinship and Intraspecific Genealogy	231	(90)
Close Kinship and Family Structure	231	(17)
Eusocial colonies	235	(6)
Non-eusocial groups	241	(3)
Kin recognition	244	(1)
Genetic relationships of specific individuals	245	(3)
Geographic Population Structure and Gene Flow	248	(35)
Autogamous mating systems	249	(8)
Gametic and zygotic dispersal	257	(9)
Direct estimates of dispersal distances	266	(1)
Vagility,philopatry,and dispersal scale	267	(10)
Non-neutrality of some molecular markers	277	(2)
Historical demographic events	279	(1)
Population assignments	280	(3)
Phylogeography	283	(33)
History and background	285	(4)
Case studies on particular populations or species	289	(12)
Genealogical concordance	301	(13)
Genealogical discordance	314	(2)
Microtemporal Phylogeny	316	(5)
CHAPTER SEVEN: Speciation and Hybridization	321	(80)
The Speciation Process	325	(38)
How much genetic change accompanies speciation?	325	(13)
Do founder-induced speciations leave definitive genetic signatures?	338	(3)
What other kinds of phylogenetic signatures do past speciations provide?	341	(1)
Are speciation rates and divergence rates correlated?	342	(4)
Can speciation occur sympatrically?	346	(5)
What are the temporal durations of speciation processes?	351	(2)
How prevalent is co-speciation?	353	(3)
Can morphologically cryptic species be diagnosed?	356	(5)
Should a phylogenetic species concept replace the BSC?	361	(2)
Hybridization and Introgression	363	(25)
Frequencies and geographic settings of hybridization	363	(4)
Sexual asymmetries in hybrid zones	367	(3)
More hybrid zone asymmetries	370	(15)
More hybrid zone phenomena	385	(3)
Speciation by hybridization	388	(13)
CHAPTER EIGHT: Species Phylogenies and Macroevolution	401	(74)
Rationales for Phylogeny Estimation	402	(31)
Phylogenetic character mapping 402 Biogeographic assessment	418	(13)
Academic pursuit of genealogical roots	431	(2)
Some Special Topics in Phylogeny Estimation	433	(11)
DNA hybridization and avian systematics	433	(1)
Mitochondrial DNA and the higher systematics of animals	434	(4)
Chloroplast DNA and the higher systematics of plants	438	(5)
Ribosomal gene sequences and deep phylogenies	443	(1)
Genomic Mergers, DNA Transfers, and Life's Early History	444	(16)
From ancient endosymbioses to recent intergenomic transfers	448	(5)
Horizontal gene transfer	453	(6)
Relationships between retroviruses and transposable elements	459	(1)
Further Topics in Molecular Phylogenetics	460	(15)
Toward a global phylogeny and universal systematics	460	(6)
Molecular paleontology	466	(9)
CHAPTER NINE: Molecular Markers in Conservation Genetics	475	(68)
Within-Population Heterozygosity Issues	478	(13)
Molecular variability in rare and threatened species	479	(5)
Does reduced molecular variability matter?	484	(7)
Genealogy at the Microevolutionary Scale	491	(6)
Tracking individuals in wildlife management	491	(1)
Parentage and kinship	492	(3)
Gender identification	495	(1)
Estimating historical population size	495	(1)
Dispersal and gene flow	496	(1)
Population Structure and Phylogeography	497	(18)
Genetics-demography connections	497	(3)
Inherited versus acquired markers	500	(2)
Mixed-stock assessment	502	(3)
Shallow versus deep population structures	505	(5)
Lessons from intraspecific phylogeography	510	(5)
Issues At and Beyond the Species Level	515	(25)
Speciation and conservation biology	515	(12)
Hybridization and introgression	527	(5)
Species phylogenies and macroevolution	532	(8)
Conclusion	540	(3)
Literature Cited	543	(120)
Taxonomic Index	663	(6)
Subject Index	669