Bio 20c notes.pdf - Lecture 2 Charles Darwin u2022 born...

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Unformatted text preview: Lecture 2 Charles Darwin: • born 1809, father and grandfather doctor • grew up on farm and went to med school • revolted by surgical procedures • joins natural history society/Scottish coast learning marine science • 1827 transfers to Christ College, to become parson • graduates in 1831 to be a minister Voyage of the Beagle • Henslow recommends Darwin to Captain Fitzroy -­‐ Searching for a naturalist and “gentlemen companion” • Henslow give Darwin copy of Lyell’s principles of Geology as parting • Darwin seasick much of Atlantic • Trip lasted 5 years 1831-­‐1836 • Darwin spend 18 months on board, 39 on shore During voyage of the beagle, Darwin: • Observed rich variety of geologic features, fossils, and living organisms • Methodically collected and described enormous number of specimens • Documented many geologic phenomena which supported Lyell’s views • Developed comprehensive theory to explain coral atoll formation • Documented biogeographic patterns that suggested common ancestry of species -­‐ Rheas -­‐ Mocking birds & finches -­‐ Tortoises Darwin’s rising star • Throughout voyage, sends specimens and notes back to Henslow • Henslow publishes Darwins notes, Darwin becomes well known (Darwin doesn’t know this) • Homeward bound Darwin writes -­‐ “such facts undermine the stability of species” -­‐ “such facts seem to me to throw some light on the origin1 of species” Post Voyage Milestones • Formulation of Natural Selection theory largely compete by 1837 -­‐ kept in secret “B” notebook • Spends next several years working with other scientist to catalog and process specimens • New discoveries -­‐ similarities in fossils to modern S. American fauna -­‐ confirmation of distinct mockingbird finch, and tortoise species • By 1844 230 pages of the book written Alfred Russel Wallace • Born 1823 • Worked as collector of specimens in Amazon Basin and Indonesia • Came up w parallel conclusions to darwin’s with respect to Evolution via Natural Selection • Wrote Darwin about his ideas in 1858 Publication of the theory • Darwin & Wallace jointly present paper on theory of natural selection to Linnean Society in 1858 • Darwin publishes origin of species (the big book) in 1859 Darwin/Russel’s Theory of Evolution • The theory -­‐ Evolution of new species occurs via descent with modification of existing species and the mechanism for this is natural selection • Natural Selection’s two components -­‐ Struggle for existence -­‐ Survival of the fittest Struggle for Existence (Natural Selection) set up that causes competition • Populations can reproduce beyond resources needed to sustain them • Resources become limited • There is competition for those limited resources • Not all individuals will survive & reproduce Survival of the fittest (Natural Selection) the filtration • Members of a population show variation for heritable traits • Some traits give individuals a selective advantage over others • These tend to leave more offspring in next generation (ex: long necks) • Over time the character of the population changes Another way to conceptualize Natural Selection • There is variation for traits within populations • This variation is heritable • Some produce more than others • This is not random-­‐ due to selective advantage of some traits over others Natural Selection and Evolution • Evolution occurs when -­‐ There is differential reproductive success based on heritable traits -­‐ The character of a population changes over time • Population is smallest unit capable of evolution -­‐ Variation! Two important concepts • Fitness: ability of an individual to produce offspring relative to other individuals in population • Adaptation: any trait that increases fitness Evidence for Evolution • Species have changed through time • Species share common ancestor • Vestigial traits • Populations can be observed to change through time Species are related via common ancestry • Closely related species live in the same geographic area (biogeography) • Homologous structures -­‐ Anatomical – hand structure (carpals) -­‐ Embryological – all start w similar embryo -­‐ Molecular-­‐ hox genes Homologous vs Analogous traits -­‐ Homologous: trait shared due to common ancestry -­‐ Analogous: similar traits with independent origins (wings) Molecular basis for evolution • Genotype: determined by genes (DNA) • Phenotype: trait: determined by genotype • Environment: -­‐ Acts directly on phenotype -­‐ Acts indirectly on genotype What Darwin never knew • Genes in DNA are basis for heritable traits • 2 types of changes in DNA can result in changes in phenotype -­‐ can mix up existing DNA • sex -­‐ can alter existing DNA • mutation Lecture 3 Vertical Evolution (normal process) • Evolution of lineage through time • Produces a branching phylogeny -­‐ Common ancestor (single) to branching Horizontal Evolution (separate lineages combining)-­‐ Example: mitochondria • Much rarer than vertical evolution • Involves gene transfer between species • Most common in bacteria • Almost certainly the way eukaryotes evolved from prokaryote ancestors Two Views of Evolution • Change in the character of a population (Darwin-­‐phenotype) • Change in population allele frequencies over time Genetic Concepts • Gene: region of DNA that codes for specific polypeptide (proteins have different codes) • Locus: physical location of a specific gene on a chromosome • Allele: version of a specific gene Causes of change in allele frequencies • Natural selection: dependent on fitness • Genetic drift (random chance, independent from fitness) • Gene flow: genes from other populations; both populations become more similar • Mutation: changing an allele into a brand new one Hardy-­‐Weinberg equation • Explains why allele frequency doesn’t change unless evolution is occurring • Frequencies of all alleles in population add up to 1 (equilibrium) • If you know freq of all alleles in current generation • And population is not evolving • You can predict freq of genotypes in next generation Hardy-­‐Weinberg assumptions (for equilibrium)-­‐ assumes no evolution • No natural selection • No genetic drift • No gene flow • No mutation • Have to have random mating Simple case • Two alleles for a locus in population -­‐ A1 & A2 -­‐ p = freq of A1, q= freq of A2 -­‐ A1A1=2p2, A1A2=2pq (etc.) • Freq of p is p2+(1/2)(2pq) 50% 2 Extreme Cases • If a frequency of an allele is one then it is fixed (fit) • If frequency of allele is 0 the allele is lost (super unfit) • Genetic diversity = number and relative frequency of alleles in population • Lack of genetic diversity usually decrease ability of a population to respond to environmental change • Figure 21.7 Natural Selection – when phenotype has higher fitness than other phenotypes • Phenotype ( and underlying associated genotype) • Four types of natural selection Directional Selection -­‐ decrease genetic diversity • Allele frequencies change in one direction • Where normal frequency vs allele (dome curve) • Favors one extreme of a trait distribution • Where x axis is genetic diversity • Figure 22.12 • Example: giraffe, neck length getting longer & longer (highest fitness), bull horns • Example: flower getting larger Stabilizing Selection – decrease trait and genetic variability • Alleles associated with mean trait values favored • No change in average trait value over time • Example: baby weight Disruptive Selection-­‐ tends to increase genetic diversity • Alleles associated with both extremes of a trait favored • Can result in two species (ex:bill widths for seeds, thick and thin) Sexual Selection – • Special form of selection • Results when individuals in a population differ in their ability to attract mates • Bateman-­‐Trivers: sexual selection acts more strongly on males -­‐ Fundamental asymmetry of sex 2 Types of Sexual Selection • Female choice -­‐ Females respond to some aspect of male phenotype • Male-­‐Male competition -­‐ Males compete with each other for females • Sexual selection leads to sexual dimorphism (male and females look different) • Widow bird example: female favors long tails – female choice • Bright bills (keratin-­‐immune system)-­‐ healthy • Nuptial gift-­‐ brings female food • Males compete to mate w females Lecture 4 Balancing Polymorphism • Maintains less fit alleles in population • Two mechanisms -­‐Heterozygote advantage -­‐frequency dependent selection Heterozygote Advantage • Heterozygotes have higher fitness in some cases • Maintains less fit alleles in population • Examples -­‐Mating success in flying insects: fig 22.19, recessive contributes, more mating than flying -­‐sickle cell anemia: carrier Dd red blood cells have higher resistance against malaria Negative Frequency Dependent Selection • Rare individuals have higher fitness • Examples: -­‐ Scale eating fish: left and right mouthed fish; always changing -­‐ Non-­‐rewarding orchids: beautiful flower and no nectar; yellow and purple flowers increase and decrease in frequency Genetic Drift-­‐ more likely to happen in small populations • Natural selection driven by environment (counterexample) -­‐ Due to random chance -­‐ AKA sampling error (sample size too small) 3 key aspects -­‐ Random with respect to fitness -­‐ Most pronounced in small populations -­‐ Over time can lead to lost or fixed alleles Causes of Genetic Drift • Founder effect -­‐small # of individuals found new population -­‐ may not reflect the allele frequencies of source population • Genetic Bottleneck-­‐ reduces genetic diversity -­‐ Results from drastic and random reduction in population size • Example: founder effect-­‐ fruit fly export all over the world including larvae • Example-­‐ founder effect-­‐ ants from argentina established in 30s coffee shipment • Example-­‐ founder effect-­‐ ellis van creveld syndrome-­‐ omish community small populations • Example: bottleneck-­‐ survive because lucky, chicken hunted; palm tree; cheetah Gene flow • Movement of alleles from one population to another • Functionality -­‐ immigration/emigration -­‐Propagules (gametes, seeds, larvae) • Equalizes allele frequency between populations • Genetic diversity Decreased in donor population Increased in receiving population • Example: plants of near populations Mutation • Production of new allele -­‐ Usually due to damage or replication errors to DNA • Increases genetic diversity • Allele mutation rates are extremely low -­‐ Amplified by large numbers of loci in most genomes • Effect on fitness variable -­‐ Most lower fitness -­‐ Sometimes increases fitness • Natural selection acts on mutations -­‐ Increases frequency of alleles that increase fitness -­‐ Decreases frequency of alleles that lower fitness Inbreeding • Mating between relatives • Example of non-­‐random mating • • • • Increases homozygosity in genotypes Does not alter allele frequencies in gene pool Alters genotype frequency Homozygous recessive genotypes often lower in fitness -­‐subject to subsequent natural selection -­‐ known as inbreeding depression Neutral Evolution • Kimura 1968 • Proposed much of genetic variation is neutral • Neutral mutations do not affect phenotype -­‐either do not alter product of a gene (redundancy of gene code) -­‐affect non-­‐coding regions of DNA • Not subject to natural selection • Useful for reconstructing phylogenies Speciation – undo gene flow • Formation of new species from ancestral species • 2 components -­‐Genetic (reproductive) isolation -­‐genetic divergence • Adds new branch to the tree of life Species Concept • Evolutionarily independent population(s) • Distinguished by common characteristics -­‐ shared amongst members of species -­‐ set them apart from other species Biological species concept • Reproductively isolated • Members of a species -­‐can interbreed -­‐ produce viable offspring • Disadvantages -­‐cant apply to fossils and asexual organisms -­‐can’t apply to geographically isolated populations Morphological Species • Based on differences in morphology • Advantages: -­‐widely applicable to fossils and both sexual ad asexual organisms • Disadvantages -­‐criteria subjective -­‐intra-­‐species morphological variation often greater than inter-­‐species variation Phylogenetic (lineage) species • Based on ancestral analysis -­‐ phylogeny • Smallest identifiable group assigned species status (on tree) -­‐monophyletic group • Advantages -­‐ widely applicable • Disadvantages -­‐ Few thorough phylogenies available Lecture 5 Speciation • Reproductive (genetic) isolation -­‐ Allopatry: populations physically separated -­‐ Sympatry: co-­‐occurring populations become reproductively isolated • Genetic Divergence More on reproductive isolation • Two basic types -­‐prezygotic -­‐postzygotic • Prezygotic isolation -­‐zygote Is never formed • Postzygotic isolation -­‐zygote formed is not viable Causes of prezygotic isolation • Disruptions -­‐temporal; example: spring field/fall field cricket, same place different time -­‐spatial -­‐behavioral; example: mating calls • Gametic Barriers • Mechanical incompatibility; example: flower bending up/down Causes of postzygotic isolation • Results when sufficient genetic divergence of isolated populations has occurred • Hybrid viability -­‐zygote fails to survive • Hybrid sterility; example: male donkey and female horse is a mule (cannot reproduce) -­‐offspring cannot reproduce Gene incompatibilities lead to genetic isolation • Certain mutant alleles at different loci may be incompatible • Dobzhansky-­‐muller model • If all these alleles become fixed, separate populations can become reproductively isolated Mechanisms of Speciation • 2 basic types of speciation • Allopatric speciation -­‐allo=other, patric= country -­‐ occurs between geographically isolated populations • Sympatric barrier -­‐sym=same. Patric= country -­‐occurs within same population Allopatric speciation • Populations become geographically isolated • Gene flow ceases between them • Diverge genetically -­‐natural selection -­‐genetic drift -­‐mutation • Two basic types of allopatric speciation -­‐dispersal/colonization -­‐vicariance Dispersal/colonization – allopatric speciation • Small # of individuals disperse to a new habitat • Founder effect increases likelihood of genetic drift • If environment is different, selective pressure will be different • Especially prevalent in islands • Example: similar mockingbird species on different Galapagos islands Vicariance-­‐ Allopatric speciation • Large population split into 2 or more sub-­‐populations • Usually due to emerging geographic barriers • New populations now isolated genetically -­‐no gene flow • Can diverge genetically -­‐selection, drift, mutation • Example: ratite in southern hemisphere and continents split Sympatric Speciation • Speciation without geographic isolation • Natural selection overwhelms gene flow • Sympatric population mechanisms that reduce gene flow -­‐spatial isolation-­‐ always there a choice to be there -­‐temporal isolation-­‐ -­‐behavioral isolation-­‐ respond to different signals, big beaks low song, small beaks high song; giraffe coat pattern -­‐polyploidy Polyploidy • Special case of sympatric speciation • Polyploidy – more than 2 homologous chromosomes • Usually caused by mutation that creates extra chromosome copy • Two types • Autoploidy-­‐ vertical evolution -­‐mutation doubles chromosomes # -­‐resulting individual can only self-­‐fertilize to produce viable offspring • Alloploidy-­‐ horizontal evolution -­‐two different species mate -­‐mutation in offspring doubles chromosome # -­‐allows self-­‐fertilization Patterns in speciation • Anagenesis -­‐ One species gradually transforms into another -­‐ Doesn’t add a branch to a phylogeny • Cladogenesis -­‐one species gives rise to two or more species -­‐ adds a branch to a phylogeny Hybrids • Formed when isolated populations reconnect • If sufficient genetic divergence has occurred -­‐prezygotic/postzygotic (reproductive) isolation -­‐now separate biological species • If recently separated -­‐lack of genetic divergence should allow gene flow • If viable hybrids form -­‐may have lower fitness than one of both parent species -­‐may have higher fitness than one of both parent species Hybrid zones • Areas of overlap where interbreeding of separate species occur • If hybrid fitness lower than either parent species -­‐predict narrow hybrid zone -­‐reinforcement (selection favors each population’s separate traits) -­‐Example: European fire vs yellow bellied frogs-­‐ • If hybrid fitness higher than one of the parent species -­‐can lead to extinction of species with lower fitness -­‐example: Townsend vs Hermit warblers Lecture 6 Macroevolution Two views of the pace of evolution • Gradualism (example-­‐ molecular data) -­‐ Genetic change continuous -­‐ Accumulates through time -­‐ Leads to change in phenotype and new species -­‐ Predicts transitional form • Punctuated Equilibrium (example fossils) -­‐Change occurs in short burst -­‐long periods of no change -­‐predicts new species to appear rapidly with few or no transitional forms • Microevolution can explain formation of new species • More difficult to explain the origin of new larger taxonomic groups Cambrian Explosion • Major radiation of multicellular animals • Beginning of Paleozoic era • Actually occurred over 40-­‐50 million years • Almost every modern phylum appears during this time Evolutionary – Developmental Biology • Interdisciplinary approach -­‐Paleontology, anatomy, developmental biology, molecular bio, genetics • Attempts to explain rapid development of new body plans Homeotic Genes • Homeobox genes: aka hox genes • Control development • Can be specific to regions of the body • Are turned on/off by their own regulatory genes • Homologous = ortholog-­‐ both have gene by common descent Hox genes and body complexity • More hox genes should allow for more body complexity -­‐Growth direction (up/down/sideways) -­‐body region (front/middle/back) • Gene duplication mutations produce more Hox genes -­‐ Paralogs-­‐ relationship of genes in same organism • Prediction: more complex organisms have more Hox genes • Observed results: true but only to a point Mutations that affect Hox gene expression • Hox genes have their own regulatory genes • These are genes that turn on hox genes • Vary if or when a particular hox gene is turned on • Can result in: -­‐changes in structures -­‐existing structures not to form -­‐existing structures to form in new places • Example: Ubx gene and abdominal leg growth; Mutation in Ubx gene inhibits d-­‐11 gene which causes legs to grow Variation in spatial expression of developmental genes • Changes in when and where regulatory genes are expressed • Can lead to big changes in structure Clawed vs webbed feet in fowl -­‐both chicken and duck feet webbed as embryos -­‐BMP4-­‐ gene that causes tissue to degenerate -­‐gremlin gene produces protein to inhibit BMP4 expression -­‐presence of gremlin results in webbed feet Allometric growth • Differences in growth rates • Example: chimp vs human skull • Genes promoting a skull growth suppressed as chimp grows • Genes promoting jaw growth continue • Result: larger brain cavity in human adults • Paedomorphosis: -­‐retention of larval/juvenile characteristics in adult -­‐can lead to new body plans Fin vs limb bud growth in vertebrates • Both mouse limbs and fish fins form from limb buds in embryos • Hoxd-­‐11 and shh (sonic hedgehog) are both genes that regulate the direction of limb bud growth • Fish fin only express hoxd-­‐11 and shh in rear of limb bud and early • Mouse limb initially similar but there is additional expression in head-­‐tail axis later in development Lecture 7 Developmental genes and molecular evolution • Many structures are similar in organisms • Eg, eyes, wings, legs • Are genes that direct their development evolutionarily related -­‐orthologs • One example-­‐ eyes in insects and mammals -­‐eyeless gene in flies: switch to turn on genes that form eyes in flies -­‐normal gene-­‐n...
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