Non-Neutral Evolution: Theories and Molecular DataBrian Golding All organisms--from the AIDS virus, to bacteria, to fish, to humans--must evolve to survive. Despite the central place of evolution within biology, there are many things that are still poorly understood. For Charles Darwin, the driving force behind all evolution was natural selection. More recently, evolutionary biologists have considered that many mutations are essentially neutral with respect to natural selection. Many questions remain. Are molecular differences between species adaptive? Are differences within species adaptive? Modern biotechnology has enabled us to identify precisely the actual DNA structure from many individuals within a population, and thus to see how these DNA sequences have changed over time and to answer some of these questions. At the same time, this knowledge poses new challenges to our ability to understand the observed patterns. This exciting volume outlines the biological problems, provides new perspectives on theoretical treatments of the consequences of natural selection, examines the consequences of molecular data, and relates molecular events to speciation. Every evolutionary biologist will find it of interest. |
Contents
Alternatives to the Neutral Theory | 1 |
Patterns of Polymorphism and Between Species Divergence in the Enzymes of Central Metabolism | 18 |
Molecular Population Genetics in Drosophila Pseudoobscura Three Future Directions | 29 |
Selection Recombination and DNA Polymorphism in Drosophila | 46 |
Effects of Genetic Recombination and Population Subdivision on Nucleotide Sequence Variation in Drosophila ananassae | 57 |
Polymorphism and Divergence in Regions of Low Recombination in Drosophila | 67 |
Inferring Selection and Mutation from DNA Sequences The McDonaldKreitman Test Revisited | 77 |
Detecting Natural Selection by Comparing Geographic Variation in Protein and DNA Polymorphisms | 88 |
Gene Trees with Background Selection | 140 |
Phylogenetic Analysis on the Edge The Application of Cladistic Techniques at the Population Level | 154 |
The Divergence of Halophilic Superoxide Dismutase Gene Sequences Molecular Adaptation to High Salt Environments | 175 |
Mitochondrial Haplotype Frequencies in Oysters Neutral Alternatives to Selection Models | 188 |
Gene Duplication Gene Conversion and Codon Bias | 199 |
Genealogical Portraits of Speciation in the Drosophila melanogaster Species Complex | 208 |
Genetic Divergence Reproductive Isolation and Speciation | 217 |
Polymorphism at Mhc Loci and Isolation by the Immune System in Vertebrates | 233 |
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Common terms and phrases
Aguadé allele frequencies allozyme amino acid analysis ananassae ancestor autosomal background selection Biol Biology C. F. Aquadro C. H. Langley characters chromosome cladistic coalescent theory codon codon bias codon positions correlation covariance deleterious distribution divergence DNA polymorphisms DNA sequence Drosophila melanogaster effective population effective population size enzyme estimate Evol evolutionary expected Figure fixation function G6PD gametes GC content genome geographic variation halophilic haplotypes heterozygosity hitchhiking hybrid sterility individuals interspecific Kreitman large number lineages locus mauritiana method Mhc loci molecular evolution molecules mutation rate natural selection neutral model nucleotide diversity observed overdominance pairs parameters pattern phylogenetic phylogeny polymorphisms population genetics protein pseudoobscura R. R. Hudson random region reproductive isolation sample SAS-CFF sechellia secondary structure selective sweeps sequence data silent sites simulans simulations sod genes speciation species statistical studies substitutions Table Tajima's Tajima's D tion tree two-allele underdominance variance X chromosome