BIOL2609_L1_2007 - Molecular Ecology Lecture 1 What is...

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Unformatted text preview: Molecular Ecology Lecture 1 What is molecular ecology ? • Teacher: Dr Steve Pointing Department of Ecology & Biodiversity • Contact: via the website supporting this course • Course clinic (optional): Thursdays 10:30-11:30 Kadoorie Building Room 2S-09 • Teaching – Lectures • All lecture notes can be downloaded as PDF files from website – Self-learning via website • Download lectures supplementary information, browse on-line book, consult glossary of terms, chat and debate with classmates • Assessment – Two-hour MCQ examination • 50% weighting – Coursework • 25% weighting for laboratory reports • 25% weighting for laboratory MCQ examination – Download instructions from website What is molecular ecology? • A broad definition: The application of molecular genetic methods to ecological problems – But this is rather too vague to have any real meaning! • To understand what molecular ecology is we need to view developments from a historical perspective … • Basically advances in two areas have driven the emergence of molecular ecology: – Evolutionary theory – Molecular techniques Evolutionary theory 1) Systematics • 1500 BC – Attempts at formal systematics were first recorded by Aristotle and Pliny in ancient Greece • 1758 – Carl Linnaeus (a doctor by training) applies the binomial method – Each species identified by a generic and specific name (eg: Homo sapiens) • Linnaeus provided a concise and usable survey of all known animals and plants in the 18th century – ~7,700 plant species – ~4,400 animal species • Species Plantarum 10th edition, volume 1 (1758) – accepted by international agreement as the official starting points for botanical and zoological nomenclature – scientific names published before then have no validity unless adopted by Linnaeus or by later authors 2) Evolution by natural selection • 1858 – Darwin and Wallace propose the theory of evolution by natural selection to the Linnean society • Darwin publishes in 1859 • His book ‘On the Origin of Species by Means of Natural Selection’ is available on-line at: Charles Darwin He used observations of 13 endemic finch species to illustrate his theory of natural selection Darwin’s 1859 theory of evolution by natural selection • Individuals within a species are variable • Some of these variations are passed on to offspring • In every generation, more offspring are produced than survive • Survival and reproduction are not random – the individuals that survive and go on to reproduce, or reproduce the most, are those with the most favourable variations They are naturally selected! 3) Mechanism of heredity • 1865 – Gregor Mendel (a monk) presents his results and publishes in 1866 but is largely ignored, even by Darwin to whom he sent a copy! – He was interested in how ‘traits’ (physical characters) were passed from parents to offspring – He His work is the basis of all our current knowledge of heredity » The principle of segregation » The principle of independent assortment He experimented using pea plants in the monastery gardens! – He identified pairs of heredity factors (alleles of a gene) in each parent that separate during gamete formation (we now know this is meiosis) – With each gamete contributing one heredity factor (allele) to the zygote • This is called the principle of segregation – Heredity factors for different traits (eg: flower colour, seed texture) segregate independantly from eachother during gamete formation (they are on separate chromosomes) • This is the theory of independent assortment 4) Population genetics • 1908 – Hardy (England) and Weinberg (Germany) re-discover Mendel’s work and come up with equilibrium theory – Basis of population genetics The mathematician Godfrey Harold Hardy • Hardy-Weinberg equilibrium principle – They demonstrated mathematically that in a population where individuals mate randomly there is no change in gene frequencies from one generation to the next – This provides a null hypothesis with which to test the effects of mutation, natural selection, genetic drift etc 5) Neutral theory of evolution • Haldane 1932, Kimura 1968 – Haldane observes that some traits had no adaptive value and so variants (polymorphisms) must be equally fit – He conclude that much of this variation must be neutral in terms of selection • Ie: it was gained or lost over time purely by chance – Formulated into the neutral theory of evolution by Mootoo Kimura • So natural selection is not evolution by itself, just one type of evolution! At any point in time, many genes are randomly on their way to loss/fixation in a population Frequency Time 6) Behaviour • 1976 Richard Dawkins – synthesized the work of several workers to show how behaviour affected selection • Individual selection and kin selection • Inclusive fitness (combined effects of these) Phenotype v genotype • Most of these advances were made without any realization that DNA was the genetic material – morphological characters (phenotype) were used to make deductions – These have limited power of resolution for many ecological problems • Some definitions – Phenotype • Set of morphological, physiological, biochemical and behavioural characteristics of an organism – Genotype • Set of genes possessed by an organism • Variability in an individual arises from the combined effects of genotypic differences and environmental influences – Nature v nuture! – Phentotypic variation is not necessarily inherited in a simple ‘Mendelian’ way • Examples from nature: – Among ‘sibling’ species (arising recently from a common ancestor) genetic variation can occur with minimal morphological changes • Eg: bats – In other cases rates of change in genotype and phenotype are roughly equivalent • Eg: Caribbean lizards – Where there is strong directional selection large morphological differences can be associated with minimal genetic divergence • Eg: African cichlid fishes • Phenotypic plasticity – Local conditions affect phenotype – Eg: the noctuid moth (Pseudaletia unipuncta) • Caterpillars reared on hard grasses develop twice the head mass of those fed on soft diets, even though overall body size is the same • Why? Because they developed big jaw muscles! – Even though this appears to be a purely environmental influence, it can be traced to altered patterns of gene expression • There is probably therefore also a genetic component • Polymorphic morphological traits are therefore not ideal characters for investigating many aspects of population ecology – They can be strongly influenced by natural selection, local environment, or both! • Much of molecular ecology has been concerned with identifying neutral genetic markers – Regions of the genome that can be informative about population structure and history but with less bias from these complicating effects of selection and environment • The concept of comparing molecular characters was not completely unknown in the past! • 1867 Church records certain pigments in feathers found only in birds of the Musophigadae family, and inferred a common evolutionary link from this – But of course the power of resolution using such molecular markers is weak (to family level in this case) • Early clues about DNA – 1873 Chromosomes first observed – 1903 Link between chromosomes and Mendels theories made • Ie: chromosomes contain the hereditary factors The structure of DNA • James Watson & Francis Crick (1959) Cambridge, UK – Elucidated structure of DNA – Also based upon XRD work of Rosalind Franklin at KCL, UK • The genetic code is made up of genes encoding sequences of triplet bases (codons) that are translated into proteins – Plus other control and redundant sequences – Examples: • • • • AAU = asparagine AAG = lysine UGG = tryptophan UUU = phenylalanine But what is a molecular marker? • A molecular marker is: – A relatively short DNA sequence in the genome – Chosen as representative of a much larger section – Each is called a ‘locus’ • But this may or may not be a functional gene • They have the potential to address ecological questions that cannot be solved in any other way • Since their precision is far greater than any phenotypic marker • Not all sections of the genome are equally useful as markers – An important requirement is that alternate sequences at a locus (alleles) are easily recognizable – Most eukaryotes are diploid and so have 2 alleles per locus • 2 identical alleles = homozygous • Different alleles = heterozygous • At any individual marker locus the level of polymorphism ranges from zero to perhaps hundreds of alternative alleles in a species – It is the isolation and characterization of a wide variety of molecular markers with different levels of polymorphism that is the central development of molecular ecology • Eg: behavioural studies are best achieved with highly polymorphic markers as you need to discriminate between individuals • Alternatively population studies are better with lowmoderate levels of polymorphism since you can generate a larger sample size for statistical analysis • Marker choice has changed as molecular techniques have improved Molecular techniques in ecology • Earliest approach was using allozymes (‘alleles’ of proteins) – But severe limitations make them obsolete in modern research • Destructive • Limited range of expression in tissues • DNA based markers are therefore preferred in modern studies – This course will focus on genome-based molecular ecology • A brief history of DNA markers (we will cover these in depth later) – Early studies focused upon DNA fingerprinting (RFLP, minisatellites, microsatellites) • Lots of data that greatly advanced our understanding from earlier morphological studies • But limitations due to interpreting fingerprints and in reproducibility • An RFLP fingerprint – Here the genome is cut at random locations with restriction enzymes that recogize a specific sequence • Eg: GGCC (a single locus) RFLP of protozoan clone library – This produces fragments of DNA of different length according to gain/loss of sites due to mutation – Level of resolution is low • But can be used to differentiate haplotypes such as in mtDNA • Good for phylogeography studies as we will see later • Minisatellites and (later) microsatellites – RFLP differences are suitable for detecting population differences but are not sensitive enough to detect differences among individuals (not polymorphic enough) – Microsatellites are randomly dispersed short repetitive sequences in the genome • Highly polymorphic and so better for behavioural ecology studies – Eg: sexual selection studies where we want to know parentage so we can determine breeding success • Multilocus microsatellite fingerprints can also be obtained – But problems in assigning bands to loci Microsatellite fingerprint of the european lobster (Homarus Gammarus) • PCR-based techniques – The PCR reaction revolutionized molecular ecology • First used in 1987, so a relatively recent advance! • Allows analysis of tiny tissue fragments • Microsatellite PCR, RAPD PCR fingerprints – DNA sequencing technology • Allows the greatest possible level of resolution in a marker – Ie: single base polymorphisms! • New advances in multiplexing and genomics will be discussed in later lectures Directed reading An Introduction to Molecular Ecology Beebee & Rowe (2004) Chapter 1 ...
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This note was uploaded on 03/19/2010 for the course DEB BIOL2609 taught by Professor Drstephenb.pointing during the Spring '10 term at HKU.

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