MOLECULAR ECOLOGY

By MATTHEW CLARK

CONTENTS 1 MOLECULAR GENETICS IN ECOLOGY WHAT IS MOLECULAR ECOLOGY? THE EMERGENCE OF MOLECULAR ECOLOGY PROTEIN ALLOZYMES AN UNLIMITED SOURCE OF DATA MUTATION AND RECOMBINATION POLYMERASE CHAIN REACTION SOURCES OF DNA GETTING DATA FROM PCR OVERVIEW CHAPTER SUMMARY USEFUL WEBSITES AND SOFTWARE FURTHER READING REVIEW QUESTIONS 2 MOLECULAR MARKERS IN ECOLOGY UNDERSTANDING MOLECULAR MARKERS MODES OF INHERITANCE NUCLEAR VERSUS ORGANELLE HAPLOID CHROMOSOMES UNIPARENTAL MARKERS: A CAUTIONARY NOTE MOLECULAR MARKERS CO-DOMINANT MARKERS DOMINANT MARKERS 3 GENETIC ANALYSIS OF SINGLE POPULATIONS WHY STUDY SINGLE POPULATIONS? WHAT IS A POPULATION? QUANTIFYING GENETIC DIVERSITY HARDY--WEINBERG EQUILIBRIUM ESTIMATES OF GENETIC DIVERSITY CHOICE OF MARKER WHAT INFLUENCES GENETIC DIVERSITY? GENETIC DRIFT POPULATION BOTTLENECKS NATURAL SELECTION REPRODUCTION 4 GENETIC ANALYSIS OF MULTIPLE POPULATIONS WHY STUDY MULTIPLE POPULATIONS? QUANTIFYING POPULATION SUBDIVISION GENETIC DISTANCE F-STATISTICS QUANTIFYING GENE FLOW DIRECT METHODS INDIRECT METHODS ASSIGNMENT TESTS GENE FLOW DISCREPANCIES WHAT INFLUENCES GENE FLOW? DISPERSAL ABILITY BARRIERS TO DISPERSAL FRAGMENTED HABITATS AND METAPOPULATIONS INTERSPECIFIC INTERACTIONS POPULATION DIFFERENTIATION: GENETIC DRIFT AND NATURAL SELECTION GENE FLOW AND GENETIC DRIFT GENE FLOW AND LOCAL ADAPTATION 5 PHYLOGEOGRAPHY WHAT IS PHYLOGEOGRAPHY? MOLECULAR MARKERS IN PHYLOGEOGRAPHY MOLECULAR CLOCKS BIFURCATING TREES THE COALESCENT APPLYING THE COALESCENT NETWORKS NESTED CLADE PHYLOGEOGRAPHIC ANALYSIS AND STATISTICAL PHYLOGEOGRAPHY DISTRIBUTION OF GENETIC LINEAGES SUBDIVIDED POPULATIONS LINEAGE SORTING HYBRIDIZATION COMPARATIVE PHYLOGEOGRAPHY REGIONAL CONCORDANCE CONTINENTAL CONCORDANCE INTRODUCED SPECIES 6 MOLECULAR APPROACHES TO BEHAVIOURAL ECOLOGY USING MOLECULES TO STUDY BEHAVIOUR MATING SYSTEMS MONOGAMY, POLYGAMY AND PROMISCUITY PARENTAGE ANALYSIS MATE CHOICE SOCIAL BREEDING MANIPULATION OF SEX RATIO ADAPTIVE SEX RATIOS SEX RATIO CONFLICTS SEX-BIASED DISPERSAL NUCLEAR VERSUS MITOCHONDRIAL MARKERS RELATEDNESS FST VALUES CONCORDANT RESULTS FORAGING IDENTIFYING PREY IN SEARCH OF FOOD 7 CONSERVATION GENETICS THE NEED FOR CONSERVATION TAXONOMY SPECIES CONCEPTS GENETIC BARCODES SUBSPECIES CONSERVATION UNITS POPULATION SIZE, GENETIC DIVERSITY AND INBREEDING INBREEDING DEPRESSION TRANSLOCATIONS OUTBREEDING DEPRESSION CAPTIVE BREEDING MAXIMIZING GENETIC DIVERSITY GENETIC DIVERSITY BANKS 8 MOLECULAR ECOLOGY IN A WIDER CONTEXT APPLICATIONS OF MOLECULAR ECOLOGY WILDLIFE FORENSICS POACHING ILLEGAL TRADE NON-HUMAN PERPETRATORS AGRICULTURE PESTS AND DISEASES LAW ENFORCEMENT GENE FLOW BETWEEN GENETICALLY MODIFIED CROPS AND WILD RELATIVES FISHING OVERFISHING STOCK ENHANCEMENT THE FUTURE OF MOLECULAR ECOLOGY