An Introduction to Molecular Ecology

by Beebee, Trevor J. C.; Rowe, Graham

• ISBN13: 9780199248575
• ISBN10: 0199248575
• Format: Paperback
• Copyright: 2004-03-25
• Publisher: Oxford University Press

Summary

Ecology--the study of how individuals and species interact with their surroundings, and each other -- has been revolutionized by a new molecular approach to the subject. By using molecular, biological and molecular genetic techniques, ecological interactions can be investigated in more detail and with more accuracy than ever before. An Introduction to Molecular Ecology makes this fascinating area of research accessible to students for the first time. Beginning with the history of molecular ecology, involving the relationships between natural history, genetics and evolution, the book moves on to discuss the areas of molecular population genetics, phylogeography, and molecular ecology in conservation biology. These are just a few of the ten chapters, which are individually structured to include background information, questions of interest, the underlying theory of the various molecular and analytical approaches, and a range of relevant examples. Two substantial appendices detail accounts of the main practical and analytical methods currently used in molecular ecology.

Author Biography

Professor Trevor Beebee is a Reader in Biochemistry, in the School of Biological Sciences, University of Sussex. Dr Graham Rowe is a Postdoctoral Researcher in the School of Biological Sciences, University of Sussex.

Table of Contents

Preface	xiii
Acknowledgements	xv
List of figures	xvii
List of tables	xxiii
1 A history of molecular ecology
Introduction	1	(1)
An evolutionary perspective for molecular ecology	2	(7)
Systematics, phylogenetics, and the species concept	2	(2)
Variation within species	4	(2)
The origins of modern genetics	6	(1)
The modern synthesis	6	(2)
The neutral theory of molecular evolution	8	(1)
Behavioural ecology	8	(1)
Genetics in ecology	9	(6)
Ecological genetics	9	(3)
Genotype, phenotype, and phenotypic plasticity	12	(1)
What is a molecular marker?	13	(2)
Milestones in molecular ecology	15	(10)
Early days of molecular ecology	16	(1)
Allozyme electrophoresis	16	(1)
Restriction fragment length polymorphism	17	(2)
Minisatellite DNA fingerprinting	19	(1)
The polymerase chain reaction	20	(2)
PCR-based molecular markers	22	(2)
DNA sequencing	24	(1)
Molecular ecology today	25	(1)
SUMMARY	26	(1)
2 Molecular biology for ecologists
Introduction	27	(1)
Nucleic acids and the common origin of life	28	(1)
The structures of DNA and RNA	29	(6)
Primary structure of nucleic acids	29	(2)
Secondary structure of nucleic acids	31	(2)
DNA replication	33	(2)
Protein structure	35	(3)
Basic immunology	38	(1)
The genetic code and gene expression	39	(2)
Genome structure: an overview	41	(2)
Non-coding DNA	43	(4)
Functional (coding) DNA	47	(5)
Ribosomal DNA	47	(1)
Nuclear structural (protein-coding) genes	48	(1)
Mitochondrial DNA	49	(2)
Chloroplast DNA	51	(1)
Plasmids and genetic manipulation in molecular ecology	52	(2)
Mutation	54	(4)
Somatic mutations	54	(1)
Germline mutations	54	(1)
DNA point mutations	55	(2)
Other types of mutation	57	(1)
Evolution and the mutation rate	57	(1)
SUMMARY	58	(3)
3 Molecular identification: species, individuals, and sex
Introduction	61	(1)
The species question	62	(7)
Defining distinctiveness	62	(3)
Hybrids	65	(4)
Dealing with individuals	69	(4)
Basic identification	69	(1)
Competition between toads	69	(1)
Woodland succession	70	(1)
Identification of prey in predator guts	70	(1)
Identification of disease vectors	71	(1)
Forensic investigations	72	(1)
Sex	73	(2)
Bits of individuals	75	(3)
Molecular identification methods: an appraisal	78	(2)
Protein analysis	78	(1)
DNA analysis	78	(2)
SUMMARY	80	(1)
4 Behavioural ecology
Introduction	81	(1)
From monogamy to promiscuity	82	(4)
Animal mating systems	82	(2)
Determining unknown mating systems	84	(2)
Male reproductive success	86	(2)
Sexual dimorphism	86	(1)
Lekking	87	(1)
Female reproductive success	88	(7)
Sperm competition	88	(2)
Why is female promiscuity adaptive?	90	(2)
Mate choice and the MHC	92	(2)
Sexual conflict	94	(1)
Sex ratio biases in offspring	95	(1)
Cooperative behaviour	96	(3)
Cooperative breeding in birds	96	(1)
Social insects	97	(2)
Cheating tactics	99	(2)
Interspecific brood parasitism	99	(1)
Intraspecific brood parasitism	100	(1)
Foraging and dispersal	101	(3)
Foraging	101	(1)
Dispersal	102	(2)
Behaviourally mediated speciation	104	(4)
SUMMARY	108	(3)
5 Population genetics
Introduction	111	(1)
Genetic diversity in natural populations	112	(5)
Some basic concepts	112	(1)
Population size and genetic diversity	113	(2)
Mammalian examples of population size and genetic diversity estimates	115	(2)
Population structure	117	(5)
Assessing where subdivisions occur	117	(1)
Statistical tests for population subdivision	118	(1)
Marker selection for the study of population subdivision	119	(3)
The genetics of metapopulations	122	(5)
Metapopulations	122	(1)
Testing whether metapopulations exist	123	(2)
Distinguishing different types of metapopulations	125	(2)
Gene flow and migration rates	127	(5)
Genetic estimation of gene flow and migration rates	127	(2)
Isolation by distance	129	(2)
Maximum likelihood methods for estimating migration rates	131	(1)
Identification of immigrants	132	(1)
Effective population size	133	(4)
Genetic estimators of effective population size	133	(1)
Determination of effective population size using allele frequency variation between generations	134	(2)
Alternative methods for Ne determination	136	(1)
Population bottlenecks	137	(3)
The significance of population bottlenecks	137	(1)
Genetic tests for population bottlenecks	138	(2)
Molecular markers for population genetics: an appraisal	140	(2)
The basis for choice	140	(1)
Fundamental tests	141	(1)
SUMMARY	142	(3)
6 Molecular and adaptive variation
Introduction	145	(3)
Neutral markers that are not really neutral 141
Allozymes	148	(2)
Nuclear DNA markers	150	(2)
Mitochondrial DNA	152	(1)
Heterozygosity and fitness	152	(5)
Background	152	(1)
Allozyme studies	153	(2)
DNA markers	155	(2)
Molecular approaches to understanding adaptive variation	157	(6)
Comparisons of neutral and adaptive variation	157	(1)
Variation at specific loci	158	(2)
Gene mapping	160	(1)
Quantitative traits and adaptive variation	161	(2)
Genomics and the study of adaptive variation	163	(1)
SUMMARY	164	(1)
7 Phylogeography
Introduction	165	(1)
Molecular markers in phylogeography	166	(4)
Early phylogeography	166	(1)
MtDNA as the standard phylogeographic tool	166	(2)
Alternatives to mtDNA	168	(1)
Genealogies and the coalescent process	169	(1)
Genetic variation in space	170	(11)
Geographic patterns in single populations	170	(3)
Vicariance and dispersal	173	(1)
Divergence between populations: Drift versus gene flow	174	(1)
Gene flow between species	175	(1)
Genetic consequences of the Pleistocene Ice Ages	176	(3)
Phylogeography and coevolution	179	(1)
Nested Glade analysis	179	(2)
Genetic variation in time	181	(4)
Geological events and molecular divergence rates	181	(2)
Measuring lineage divergence in real time	183	(2)
Applied phylogeography	185	(11)
Taxonomic decisions	185	(2)
Determining a species natural range	187	(4)
Finding the source populations of introduced species	191	(3)
Phylogeography and adaptive traits	194	(2)
SUMMARY	196	(3)
8 Conservation genetics
Introduction	199	(3)
The state of the biosphere	200	(2)
Molecular genetics in conservation biology	202	(1)
Genetic diversity as a conservation issue	203	(2)
Inbreeding and genetic load	205	(5)
The basis of inbreeding effects	205	(1)
Inbreeding depression and genetic load in the wild	206	(2)
Purging of genetic load	208	(1)
Outbreeding depression	209	(1)
Genetic restoration	210	(1)
Desperate measures	211	(6)
Plant conservation	212	(2)
Animal conservation	214	(3)
Wildlife forensics	217	(1)
Genetics in conservation biology-a wider role	217	(5)
Systematics and conservation genetics	218	(1)
Phylogeography and conservation genetics	219	(2)
Globally important areas of genetic diversity	221	(1)
Molecular markers in conservation genetics	222	(1)
SUMMARY	222	(3)
9 Microbial ecology
Introduction	225	(2)
Outstanding issues in microbial ecology	227	(5)
The role of microbial communities in nature	227	(3)
Problems for molecular microbiology	230	(2)
Immunological approaches to microbial ecology	232	(10)
Immunological methods	232	(1)
Use of antibody identification in microbial ecology	233	(3)
Ribosomal genes and microbial ecology	236	(1)
Structure and usefulness of ribosomal genes	236	(2)
Identification: the use of sequence-specific oligonucleotide probes in microbial ecology	238	(2)
New developments, problems, and alternative approaches with probes	240	(2)
Ribosomal gene sequencing and community studies	242	(8)
Genetic profiling of microbial communities	244	(3)
Alternatives to ribosomal genes in profiling approaches	247	(3)
Genome analysis and microbial ecology	250	(3)
Sequence complexity and microbial diversity	250	(1)
Microarrays and microbial ecology	251	(1)
Other genomic approaches in microbial ecology	252	(1)
Whole genome separation and viral diversity	253	(1)
Overview of microbial molecular ecology	254	(1)
Molecular markers for microbial ecology: an appraisal	255	(1)
Protein methods	255	(1)
Nucleic acid methods	255	(1)
SUMMARY	256	(3)
10 Molecular ecology and genetically modified organisms
Introduction	259	(2)
Environmental risks from GMO5	261	(1)
The role of molecular ecology in GMO research	262	(1)
Horizontal gene transfer in nature	263	(4)
Conjugation	264	(2)
Transduction	266	(1)
Transformation	266	(1)
Effects of GMOs on natural communities	267	(2)
Transfer of genes from GMOs to other organisms	269	(4)
Vertical gene transfer	269	(2)
Horizontal gene transfer	271	(2)
Effects of introduced genes on other species	273	(3)
Future GMO research and molecular markers	276	(1)
SUMMARY	277	(2)
Appendix 1: Practical aspects of molecular ecology
Sampling and sample treatment	279	(1)
Sampling	279	(1)
Protein and DNA extraction	280	(1)
Protein-based methods	280	(4)
Allozyme analysis and protein polymorphism	280	(2)
Protein profiling	282	(1)
Immunological methods	282	(2)
DNA-based methods	284	(13)
Oligonucleotides for cell identification	284	(1)
Polymerase chain reaction	284	(1)
Restriction fragment length polymorphism (RFLP)	284	(2)
Multilocus minisatellite DNA fingerprinting	286	(1)
RAPD and AFLP analyses	287	(1)
Microsatellite analysis	287	(1)
DNA sequencing	288	(1)
Denaturing gradient gel electrophoresis (DGGE), thermal gradient gel electrophoresis (TGGE) and single strand conformation polymorphism (SSCP)	289	(1)
Primers for PCR-based analyses	290	(3)
Special circumstances: museum material and non-invasive sampling	293	(1)
DNA microarrays	293	(4)
Appendix 2: Analytical methods in molecular ecology
Individual identification and family relationships	297	(3)
Use of multilocus fingerprints	297	(1)
Use of single locus profiling	298	(2)
Assigning individuals to populations	300	(1)
Population diversity and structure	301	(4)
Marker properties	301	(1)
Diversity estimates	301	(1)
Population structure	302	(2)
Population size and history	304	(1)
Phylogeography	305	(1)
Phylogeographic trees	305	(4)
Correlation with geography	306	(1)
Microbial ecology	307	(2)
Glossary	309	(6)
References	315	(20)
Index	335