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ALL of Barrett's Notes - Evolutionary Biology Notes.docx

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Spencer Barrett

Lecture 13 29/10/2012 06:59:00 Theory of evolution  Living things change gradually  Blind mechanistic purpose  Whenever there’s life, it will revolve Jean Baptiste de Lamarck  Pioneer  First person to use the word evolution  Accepted that organisms changed through time  He got the mechanism wrong o Inheritance of acquired characters – wrong idea  He never did experiments o Made observations and made narrative views  Every organisms on earth are inevitably on a linear line of decent o Proceed through series of species over time  RIGHT IDEA – individuals DO NOT evolve o For evolution to occur, it has to have population, as we pass on genes o We are the only one to have these genes, now and forever Charles Darwin and Alfred Russell Wallace – co-discovered mechanism of evolution Recognition of species  Certain type Lecture 14 29/10/2012 06:59:00 Oak woodland in England  Species poor  Low species diversity  Brazil – his first tropical forest o Northern Brazil Diversity of Species Tropical Forests in Brazil  Enormous diversity compared to the temperate zone  Divide environment into factors o Biotic factors  All stuff in environment that is affecting it o Abiotic factors  Temperature, moisture  Result in rapid insect and microbial populations  Pest pressure o Intense on insects  Millions of insects around the world o Plants evolve strategies to deal with pressure from the insets  Darwin saw many trees o Rainforest – up to 300 species o Similar species are far away from each other o Because there’s so many species pact in  Distance between individuals of the same species were really far – conundrum for Darwin  REPRODUCE? CROSS REPRODUCTION  Wind moved pollen around  Large number of species occur together  Together – oak trees – not hard to mate  In brazil – leaves on the trees  Therefore wind is not effective of moving mate  High species diversity  Individuals of same species are widely spread  Evergreen – dense canopy o Therefore, wind is ineffective for pollination o Animals flying long distances pollinate trees  Important pollinators of tropical trees  Animals can remarkably travel long distances  Daniel Janzen o Catch bees – mark them  Research  Single day – a bee can travel up to 23 km a day  TREES REPRODUCING TROUGH TRAPLINE OF BEES  Important in this regard o Pest pressure  Intense in tropical forest  Negative relationship between parent and child proximity  Seedlings land close to the tree more likely to die  Because the mother itself has so many pests  Getting seed further away – the further the seed – the higher the possibility of full term growth and survival  If close to parent  Competing for resources with the parent o Ant-plant mutualism in Acacia  Acacia – legumes – pea family’s  Spinney  Have holes in them  Plant producing home for plants  Also producing sugar water  EXTRAFLORAL  They produce nectar on branches  Leaves – belting bodies – protein  Plant investing quite big for the plants  Divide question to proximate and ultimate  MUTUALISM? Benefits for the plants  Manipulative experiment  What happens to plant without the ants on it?  Bush with ants on it?  Plants with and/or without the ants  Chemical – tangle foot  Put on base of plant and ants leave it – they don’t like it doesn’t affect plant  Control with ants  Independent without plants  After a couple of weeks – defoliated  Harnessed another organism to become a defender  As soon as the beetles land – they would go for them  Love lots of the resources the ants benefit from  Ant-plant mutualism o Megan Frederickson  Peru – had bare areas around the plant DUROIA HIRSUTA  Bare area for what?  If any plants stop to grow in areas  The ants that live in these – ant quirts formic acid on vines and it kills the vines  Why are vines bad for the plants – because they compete for resources  Complicated relationships between plants and animals  Berlin – botanical Garden – in the wild – grassy – holes around the leaf  Protected from pest pressure Famous life forms – epiphytic life forms  Thought to be parasitic  Simply plants that grow on other plants  Grow in different parts of the world in different groups  Australia  Aerial roots  Big tents base to collect water  Absorb nutrients from those medium  Lichens on palm leaf – patchy  Unresolved – so many questions in the tropics  Birds eat the fruits and then poop on other trees or plants and then the seeds in the poop germinates  Flowers change colour – from white to purple or vice versa?  Colour change – pollinator signal  Change colour of their flower once they get pollinated  Juvenile leaf of a plant tend to be red  Red leaf starting off?  Red leaf is when it’s about to fall  Hypothesis – animals can’t see red as well as green leafs  Poinsettias – red bracts? o Because relatively small flowers? Red leafs to attract pollinators o Great for manipulative experiments Patagonia  Part of Argentina and part of Chile  Completely different from the amazons  Different landscape  Cold windy, snowy place  Darwin impressed with abiotic factors o Severity of the climate o Geology – young area – geologically speaking o See the force of the weather there and the climate o Physical factors causing strong impacts on organisms o Saw animals that were different o Saw black necked swan o Species differentiate o Bumblebee o Clove of plant – bumblebees – different than the ones in Ontario and Europe o Bumblebees very dark – they need to warm up o In cool climates have hairs in dark orange colours to keep warm o Similar in other countries o Darwin’s rhea – south Africa – flightiness evolved  Evolved more than one time in birds  Closely related to the camel  Animals that are relative to animals in other parts of the words  World is not stable  Things happening all the time Galapagos Islands  Islands relatively young  Volcanic – islands  5-10 million years old  Lava flows, wood, materials washing up ashore  No big mammals – no large NATIVE large animals  Big mammals  Distinct races and subspecies when moved to different islands  In between species in different areas  Hard to say what he was looking at  Made him think about the history  Views – forming basic views of forming basic views of evolution  Evolution laboratory  Evolution in action  Certain parts of the island where we can’t go  Lots of galapogos is volcanic rock and shrubs  Environments and organisms here  Long distance dispersal – how did they get there?  Get there on their own o Some organisms make it and some don’t prickly pear cacti o 15 species o middle east – often eaten there o big fruites o freshy red fruit o prickly pear to reproduce o poop of bird – seeds germinate  Galapagos finches – Darwin’s finches o Made mistakes o Mixed up some of his collections o Forgot to mention which island he got certain birds from o Messed up searches o Different billows  Evolution of different species  Best example of evolution on earth o Every year in galapago  Measured natural selections for 35 years each year  Over 35 years – best evidence  14 galapagos finches  ADAPTIVE RADIATION  The evolution of ecological and phenotypic diversity from a common ancestor  Start with one species – over time – cahgnes differentiates into 14 species  Each adaptive to different environments  Happen to all types of organism – especially in islands  Common ancestor  Correlation between phenotype and environment  Trait of functional beats the non functional  Rapid species – relatively  Largest tortoise – highly conserved  Different tortoises with different shell shapes  Eating seaweed all the time  Special glands that expel salt  Terrestrial iguana – eat the prickly pear from the cacti  High frequencies of flightless birds Austraila  Unique adaptations  Endemic species o Species restricted to a strickly geographical region or habitat o Lots of it in austrailea o Tropical forests  Species in the forests are different  Although life forms are the same  Evolve the life form  83 hours in Sidney blue mountains  forest dominated by one genous  gum tree o 700 species of gum trees in austrailia o survival rate high in dry areas o KOALA – there is one organism that can eat gum trees o Koala in zoos – shipping gum leaves and trees  Happy eating these leaves than the leaves in the local area  RODENT POLLINATED BANKSIA  One example  Come at night  Lots of nectar here  Darwin - Down Lecture 3 29/10/2012 06:59:00 Variation  Issues to do with genetics  View evolutionas 2 dimensional o Ecological dimension  Natural selection  Darwin’s theory  No genetic basis of the many ideas of his theories o Genetic dimension  Became integrated with ideas in evolution Requirements for darwin’s theory  Variation and Heredity – genetics  Selection – Ecological Basic Terms of Genetics  Genotype o Is the genetic constitution of an individual  With reference to a particular gene  Ex. Aa – genotype  2 alleles – one dominant and one submissive  multi-locus genotype  idea of one with two genes  interact with envirionment to react with phenotypes  Phenotype o Organism as observed o What we see in the organism o Physical features  Genome o Entire DNA  Both genes and non-coding regions  DNA – chemicals/ compounds that are responsible for inheritance  A lot of DNA are non-coding  Doesn’t code for protein Gene  Functional unit of inheritance  Codon – sequence of 3 nucleotides that makes up the genetic codes Where does genetic variation come from?  Mutation  Recombination  Gene Flow – how genes move from one population to another o Increase genetic variation because of immigration and emmigration  Hybridization – different genetic makeup, increase genetic variability Independdent assortment and recombination  Mix up of genes during sex and recombination o Genetic variation  Recombination – way more important o It shuffles up and puts different genes together o Enormous source of new genetic combinations o Occurs through miosis  Mechanism of shuffling up of genes  Results from sex  Everbody have a special type of genotype that nobody has ever had before  Offspring – half of mother and father  Variation Mutaiton  Barbara McClintock o There are certain mutations DNA sequences hop around the genomes  Jumping genes  Idea that mutation involves jumping around  Mutation of the figmentation of the petal  Random processes  Genes low frequency lst more often in genetic flow  Fitness benefits to muoj  Average better  Two forms o Mutation is neutral or it could be o They both have similar benefits   SUMMAY o Ultimate source of genetic variation o Occus in a slowr rate o Fitness  How many good genes are trafer  Dominant lethal mutations  Hang around in the organish Whevere there is life there is mutation  Why design a system that will be perfect?  Fidelity of replication does not need to be 100% Somall number of processes in evolution that are rajdom Point mutations  Most importatnt for form of mutation  Change of bases  Gene is replaced Insertions/deletions – also includes jumping genes  ATCVAGT -> ATGGCAGT Changes in repeat numner  ATGATGATG -> Chromosomrearrangemets  Where taking a section of mutations and take it and jumble it all up/ Motoo Kimura  First person that a lot of mutations that occur in our genomes or  Mathematics  Theory – theoretical o Drive our understanding Mutation rates  Vary of genome from one to the rest Transmission of genes from one generation to the next  How many genes control a trait?  Finding disorders and disorders are sipimoh is  Height not controlled by a single  2 pure different lines o cross o Onw ro 1 row o Half ar herte o 30 phenotypes o allele  every gene that  alleles  compy of a gene  AA  Whati  Gametes have two copies  Miosis – keeps the chromosomal number stable at certain times Discrete vs, continuous traits  Character traits – there are two kinds of research programs depending on which types of research o Blue and red – mandialian genetics – classic gene o Trait o Colours – body weight – o Humans  Tall people and short people  Quantitavive inheritant  Createll  Genetic Poly morphism  Two pheonotypes o Whte coloured o Bluey grey o Pehonotype o Genetic morphism  Sex  Female  Male Gladioulus  Flowers o White and pink  Polymorphisms  For flower colour Variation in human height  Genetic polymorphism  How tall you are is 65% genetic o Others are fromt eh environemtn o Formalize the idea that as we increase the number of genes controlling a trait  Go from discontinuous to vontinous  Always just dominance or submissive o Co-dominant  As number of genes increases – moves towards continuous discontinuations  Paradimes in genetics  Dominance and resistance  Genetic variation  Discontinuous variation – mendelian genetics   Quantitive genetics o Plant and animal production o Lipid content of something  Look at selection  Fisher – how fast popluations evolves is mathematical of how much genetics will variate. Rate of increase of fitness – ithat rate is genetically equal the genetic variation  How they adapt Lecture 4 29/10/2012 06:59:00 Some genes that are invariable  Invariable vs. variable o All of us have samples of invariance genes o Monomorphic genes Foundations of population genetics  Fisher, Haldane, Wright o Mathematical foundation of evolutionary biology o Fused genetics to Darwin’s evolutionary ideas  Wright vs fisher o Diabolical views  Especially on genetic drifts Model systems in ecological genetics  Find organisms to test theories KEY QUESTIONS IN ECOLOGICAL AND EVOLUTIONARY GENETICS  Process?  How much and type?  Measurments? Perameters  Polymorphism (P) o Proportion of the genes o More than one different type of Allele o Opposite?  Monomorphism o More than one type of allele  Aa o Measured by going out sampling a large number of individuals and sample them  What amount is variable  Heterozygosity (H) o Looking at frequency of individuals  Mutation o Genesis – variable o New allele  Errors o Various forces acting on variation  Recombination o Different variability o Shuffled up o Different combinations of allele o Not new mutations  Taking the new mtations and shuffling them up  Random  Random genetic dift o Due to random sampling effect o Variability gets lost o Process whereby variation is lost  Natural selection (purifying) o Negative selection o Taking out the mutation  Natural selection o Positive selection (adaption) o Form mutations to better adapt habit  Natural selection (balancing selection) o Two forms being maintained o Inferences – balancing selection o Maintains diversity o Heterozygous diversity better than homozygous  Heterozygous balance because it is better because of allele o Can’t never fix heterozygous o Heterozygous advantage  Mutation (+)  Recombination (+)  Genetic drift (-)  Natural selection (+/-) Diverse mechanisms maintain genetic variation within populations  Three classes of explanation as to how genetic diversity is maintained  Identify 3 classes o MUTATION-SELECTION BALANCE  If we have a balance that is going on mutation, bringing alleles in, and selection, getting allele or rid allele, likelihood of maintenance between variability.  Rate of speciation (more species)  Extinction rate (loss of speciations) o DIFFERENT SELECTIVE FORCES  Maintain variability  Heterozygous advantage  Fitter than heterozygous = more balance  Frequency-dependent  Fitness and survival depends on frequency  Depends on whatever is out there  Sex ratio o Classic example of frequency o 1:1 – too much of one sex equal too much competition  fitness varies in space or time  individual that is fittest over there may not be fit here  certain genotypes specialize in special places  environments are always heterogeneous o maintains individuals  special and temperal act to maintain genetic variablitllity o VARIATION SELECTIVELY NEUTRAL  No fitness effect.  Neutral EARLY EVIDENCE FOR THE EXISTENCE OF GENETIC VARIATION  Improve animal and plants o Can only improve them from natural selection  Artificial selection o Do we get a response to the selection that we impose  This is considerate only of quantitative genetics o Traits with a bell curve  Exposes the fact that there is genetic variable  There is genes for flower size o Is able to split o Amount of variability Want measures of (P and H)  General statements  For all organisms  Quantative – specific details of a specific organisms  Predicted Morgan and Muller  Mutationist Balance school  Genetics ] Different view poins  Classical o World view o Labs o Mutants o Most fit genotype o Notion that somewhere in the population there will be a fitness character o Most individual is the same o Mutation – introduced – increases – replace the alleles  Balance o Real worlds o Seeing all the variability o How much of it was genetic variability o No such thing as fittest genotype o Idea genotype for one patch is different than another If it is a metamorphic individual  2 alleles but in same position  homozygous o stronger  allele – migrating allel  Balance school was right o There was a lot more gent Co diominant gene  Count genotypes Species go extinct for two reasons  Low amounts of genetic variablility  Lots of spread o Genera at different ages  SNP o Singular nucleotype microorganisms o How many polymorphism in the DNA  Humans o 1 in 1000 base pairs  during domestication Lecture 5 29/10/2012 06:59:00 Organismal Reproductive diversity  Flying – birds get away from predators  Adapted to stay on the islands Sex, recombination – reproduction systems we see on earth today  Many different ways to reproduce o Explain diversity of reproduction methods o Different facets of reproduction Why did sex evolve?  Simple scheme o Remember terms on diagram PAGE 3 o Whether offspring is reproduced sexually or asexually  If reproduction  Diecious or hermaphrodite  Diecious – have 2 sexes  Hermaphrodite – 90% plants are diecious o Cross-fertilization or self- fertilization o Does offspring produced by it arise from either one? o cross fertilization o self – fertilization - mixing of the genes – sex with the self Darwin on Sex  Identify problem PAGE 4  Sexual occurs in turbulent water  Asexual occurs in calm water  There are some species do both at the same time o Asexual and sexual o Water Hyacinth  Roots – asexual Costs of sex  Early forms of organisms reproduce through mitosis – copy of itself  Why is sex maintained? o Costs? o Takes time and energy to find mate o Energetic costs  Growing – stuff involved in sex o Risk of predation & predation  Mind on somewhere else – especially vulnerable during copulation o Cost of producing males  Producing gametes  Engage in sex and take off o Asexual – every individual creates offspring  Transmission of genes o Sexual vs. asexual  50% less genetic transmission – sexual  why risk sharing genes when less fit  asexual – 100% genetic transmissions  sharing genes – breaking up gene combination  offspring less fit  why not asexual if it gives all their fitness? The two-fold cost meiosis  Meiosis vs. mitosis  Sex = 2 parents o Sexual – half of genes  no sex = 1 parent o asexuality – transmission bias – bias own transmission to next generation o fitter – more gene copies to the next generation o Gene counting – how many copies of things o Quantity isn’t everything – quality counts Hypotheses for the advantages of sex  Maintenance of sex might be for a variety of explanations  Benefit in sex o Bringing together in desirable mutations in different paretns  Do not get this by cloning  Sex – variable offspring  Asexual – one offspring  Temporal heterogeneous o Some organism evolve faster than others o Variability through time o Pests and diseases evolve fast  Spatial o How variable the environment differences Favourable combinations of mutations brought together more rapidly by sex  Asexual – ABC – fittest  Probability of three favourable will arise will only take mutation  Environmental factors Sex and recombination – shuffle around – get to ABC a lot quicker  Sex is good o Get rid of bad mutations quicker Lottery- model  How theoreticians – think about 2 alternative forms of reproduction o Environment as a lottery  Small number of wins  Just like environments  Produce thousands offspring – online a few makes it  Every organism replace itself with one offspring – then it will stay stable  Best way to win a lottery?  Buy thousands of tickets?  Copy of same ticket thousands of time?  Sexual?  Asexual?  Heterogenous environment – changing environment – n
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