Evolution (Uni Additions).pdf

 Chapter 1 Insects (arthropods) - basic insect body plan : 1. head 2. thorax ↳ three pairs of legs - one/two p...

 Chapter 1 Insects (arthropods) - basic insect body plan : 1. head 2. thorax ↳ three pairs of legs - one/two pairs of wings 3. abdomen - insects found abt habitat every in Adaption > - a trait (characteristic) that contributes to fitness by improving an individual's chances of surviving/reproducing - can be physical or behavioral Origin of Adaptations -natural selection - in each generation , new traits and combinations are created in a population mutations recombination by and > - mutations : genetic "errors" > - recombination : mixing of genes through sex - leads to some individuals to possess traits that are more adapted to the current environment allowing them to survive and reproduce better "These individuals higher fitness have > - fitness : measured the as # of offspring an individual produces relative to other individuals in the population Natural Selection - results from variation among individuals in the # of surviving offspring that contribute to the next generation -advantageous traits that are hentable will be passed down , making them more present in the next generation - evolution : change over generations in the proportion of individuals o a certain trait requirements for a trait to evolve by natural selection 1. trait heritable is 1. variation present blu individuals win a population for the trait. 3 variation trait in leads to some individuals leaving more offspring than others - some traits are neutral for fitness - not all differences in traits blw populations arise from natural selection  Lecture 1 Theory of Evolution. 1 Living things change over time. 2 adaptations have arisen through natural selection the special creation * evolution challenges view of descent in modification Conclusions - organisms changed throughout time have , giving rise to new species ↳ gradual changes Lineages split by speciation biodiversity biodiversity adaptation - + * + - all species share a common ancestor are products of - adaptations result from natural selection evolution * Biodiversity : diversity of life on Earth > - # and kinds of living organisms In a area given Adaptation : a) any trait that increases an fitness organisms 6) evolutionary process that leads to the and maintenance of such origin traits of evolutionary study Major areas evolutionary history · · evolutionary mechanics Microevolution : evolutionary patterns and processes observed within species Macroevolution : evolutionary patterns and processes observed among species Evolutionary History -Genealogy info represented cladogram as a ↳ cladogram set to time scale phylogenetic free = evolutionary tree phylogenetic tree ↳ = phylogeny = a A B C DE clade : branch +each branch represents a common ancestor combatability of ancestries to determine of * check their common combatability evolutionary trees. Evolutionary Mechanics - - > determine processes responsible for evolutionary change ↳ identify major forces of evolution * Scientific theories have testable and falsifiable hypotheses as opposed , to fath and belief Revelance of Evolution 1. children questions. 2 medicine 3. agriculture 4. environment. 5 biology  Lecture 2 Bio blf Darwin's time Paley's argument from design - an object that function must have has a creator/designer a - an object that has deliberate function don't no need to invoke a designer , for this rock might have - from natural processes arisen - for living thingshave have deliberate functions to them, there must be which God. a designer is - didn't consider variation Lamrack TRUE need to changing environmental conditions adapt to - organisms - aquired traits (phenotypic changes) from generation hereditary one is life starts simple and createsmea - evolves into complex beings , God then simple beings once they are all evolved ↳ Germplasm Theory (discovered aft. Lamarck 3 Darwin) -inhentance works through germ cells (gametes) only ; somatic cells don't function as agents of heredity > - genetic info flows in one direction only => DNA to mRNA to protein 4 Central Dogma Darwin and Wallace : Development of their idea - D. developed first comprehensive theory of evolution - D. 3 W. independently discovered the chief mechanism of evolution ↳ Natural Selection (NS) > - their theory of evolution :. 1 all have descended in modification from organisms a common ancestor > - living things change over time. 2 process leading to evolution NS is operating on variation among individuals - exploration : voyage on the H M.. S Beagle around the world - D. made numerous observations and collections of plants , animals 3 fossils - development of D. ideas Gradualism > - "Principles of Geology" ↳ implications for Di 1. world is dynamic , not static 2. changes are built up gradually - development of D. ideas= Species Vary - variation patterns of Galapagos mockingbirds => 4 similar species endemia to the Islands descended from a South American mainland ancestor ↳ D. doubts fixity of species - development of D. ideas= Struggle for Existence ↳ reproduction for a population should grow exponentially but , resources don't exponentially > populations who stronger (more well grow are - * adapted to the environment) will survive while the others perish only favorable variants tend to be preserved while unfavorable ones be eliminated of evolution theory selection of natural. D Mechanism NS by 3 -variation : individual variation in a population -heredity : progeny resemble their parents more than unrelated individuals -fitness :someforms aremoresuccessfulat and reprodu, surviving is * ↑ natural selection is heritable variation in fitness Elements of D. theory. 1 evolution occurs primarily at the population level 2. variation isn't directed by the environment. 3 fitness depends environment on 4. "Survival of the fitter" " can't acheive perfection > - Implications ↳ changing universe ↳ evolution is a phenomenon e no purpose -once antibiotics are applied fitness for , a resistance against the antibiotics increases leading to resistance of bacteria to antibiotics -thetime scaleandmagni t udeinwhich e organisms volvevary a great of => mutations organisms - a character change caused by a mutation occurs at a single individual for many generations ↳ other processes must cause it to increase in free within the population to result in an evolutionary change ENS is a process - the of freg of variants that survival process increase in improve or reproductive success - explains the evolution of adaptivecharacteristics better > => performance of the individual's body or behavior will generally contribute to greater fitness  - Genetic Drift : the change in the freg of an existing gene variant in a population due to random chance ↳ this variation when there selective progeny can cause in is neutral variability=> in the absence of selection the offspring , genes in population are a random sampling of genes in the parent population - species : a population that interbreed/ have the ability to interbreed in each other-> leads to diff evolutionary , paths > - formation of new species must involve the evolution of barriers to interbreeding related populationsE allows for blu divergence under mutation, selection and genetic drift= leads to diversity , - speciation : process by which new species form through reproductive isolation  Lecture 3 Evidence for evolution 1. Geology - D. observed fossils on the Beagle ↳ South America finds fossils of extinct mammals - realizes its similarities to current armadillo's ↳ Tiktaalik Roseau fossil transitional fossil = posseses features of both tetrapods and fish - Earth Old =allows time for evolution to is occur - intermediate forms transitional fossils linking features of seemingly dissimilar relatives - fossils in strata increasingly resemble modern species the younger in same region 2. Homology : ↳ features inherited from common ancestors in two or more species vestigial structures : inherited but reduced morphology function homologies and - in , > - ex Mainland cormorants and Galapagos : flightless cormorant - homologous structures : anatomical features in different species that share a G have common ancestry evolved to serve very diff. functions 3. Biogeography ~ colonization - patterns of variation => diversity of traits for similar species ↳ galapagos finch beak size high unique adaptations - Australia endemism and : have animals similar to animals from other parts of the worlda minor differencesI close resemble each other organisms 4. Domestication - vast amounts of heritable variation found within species ↳ artificial selection can occur - differential fitness : some forms successful at and reproducing than more surviving are others a environment in given Animal Phyla Classification 1. Porifera 1. Domain 2. Cnidaria 2. Kingdom. 3 Arthropoda 3. Phylum largest 4. Mollusca 4. Class to. 5 Annelida 5. Order smallest 6. Platyhelminthes. 6 Family 7. Chordata 7. Genus. 8 Nematoma. 8 Species V. 9 Echinodermata Naming and genus species Homo Sapiens => Homo Sapiens -account for hierarchial patterns of similarities blu through organisms evolution time  Embryonic Development 3 Vestigial Organs > - ED. provides many similarities blu diff. groups of organisms -> suggest descent from common ancestor descent from ancestor > - vestigial organs => show common Similarities in cells and cellular functions - Endosymbiotic Theory ↳ cells mitochondria and chloroplast => descended from bacteria that colonized cells and integrated into them Metabolic Pathway - Anabolic : synthesis of complex molecules from simple ones ↳ require input of energy - Catabolic : break down complex molecules to simple ones ↳ releases energy Feedback Inhibition : cellular control mechanism the activity of an enzyme , inhibited by the end product of is biochemical pathway a theorine A BCDIsoleveesct) ↳ ex : > enzyme 1 ES as isoleucine levels rise it will incr , In therefore incr the chances it will # ,. bind to the allosteria site on E13 inhibit it Inhibition > - cell chemistry (p 22). Protein Synthesis > - Genetics Inheritance (p 46-52). ↳ across the entire range of living organisms , the genetic code differs only slightly that all life very - suggests Earth on may have a common ancestor Mendel = Genetics & Inheritance (p 54). Many bacteria have just circular DNA molecule their genetic - one as material - some bacteria have genes made of RNA ↳ proof-reading process doesn't occur in RNA > - leads to high mutation rates + can evolve rapidly in hosts bodies - If a mutation results in an AA change changing , the polypeptide chain of a protein = protein may malfunction Molecular Clock - DNA sequences of a will be most similar for more given gene closely related species and vice-versa - the amt of diff. increases roughly proportionally to the amount of time separating two sequences being compared ↳ allows evolutionary biologists to estimate times of events that can't be studied in fossils  Lesson 4 - Genotype : genetic constitution of an organism Phenotype : feature of the organism observed (traits - as ↳ individuals have phenotype based on their genotype of - Genome : entirety an organisms DNA Sources of Genetic Variation. 1 Mutation - stable change in DNA sequence= occurs at low rates > - mutation rates vary in ways that are partially predictable depends ↳ on type of mutation and environment effects fitness codon : mutation - - mutation mutation - on ↓a p > - ↓ TTTE GGT landed outside neutral gene a · no effect ↳ · deleterious Chromosomal DNA · beneficial mon-coding on L > - mutations are inevitable not directed , Genes Types : a) point ATGCAGT - ATCCAGT b) insertions/deletions ("indels") ATGCAGT > - ATGGCAGT C) changes in repeat #'s ATGATGATG > - ATGATGATGATG ↳ repeating seg. ↑ mistakes ↑ chances of mutations d) chromosomal rearrangements ATGCAGT > - TGACGTA ↳ ex : double-strand break =DNA repairs don't know orientation of strands - Identify ↳ sequence parentsgenome and then the 'targets' - a nucleotide that can't be traced to either parent is caused by a mutation Fitness Affecting Mutations ex1 : fly's legs place of antennas grow in ex 2 : human = GGPD deficiency = enzyme deficiency that causes anemia ↳ protects agst malaria > - 2 mutations (2 At subs ). = disease allele (At = phenotype is fully active 'wild type' enzyme (no anemia , ↑ malaria susceptibility A- 3 malaria resistance due to reduced activity ↑ anemia enzyme protein BVal ASee ↑ LeuM DNA 13 A - GTG ATG AAT GAT CA CTG S sentation > - on no effect fitness. 2 Independent Assortment - Meiosis = Genetics and Inheritance (p 44 -46). - inheritance of one trait doesn't influence the inheritance of another trait > - random orientation of chromosome during metaphase I of pairs meiosis results in various combos of maternal and paternal chromosomes in the gametes Parent 1 Parent 2 can haploid from one parent i another to make new diploid zygotes Aa Bb C Dd of 16 diff. combinations melos IS ↓ ↓ ed gamete types AB Ab ab CD Cd cD =4 possible haploid aB Diversity (possible zygote comb ). = 2 > - a = # of chromosome sets Astronger force than mutation in next. 3 Recombination (crossing-over) generation - as homologous pairs more closer together , the chromatids may exchange genes non-sister but chromathe ↳ here same gene may diff. alleles Sister tids Performationism parent + one to inheritance Theory of Blind Inheritance phenotype from both + parents are mixed together to create an offspring Inheritance by Mendel = Genetics 3 Inheritance (p. 54). 1 Inheritance is determined by discrete particles. 2 each diploid two copiesCalleles) of each organism carries gene ↳ alleles can be dominant/recessive ↳ gametes contain only one allele per gene 3. gametes fuse to make offspring inherit from each parent at random 4. offspring one gamete ↳ allele at random from each parent one per gene Partial dominance > - show continuous traits aa AA/Aa 1 locus(discrete aa Aa AA partial dominance (continuous aabb Aabb AaBb AAaB AABB + 1 locus (continuous  Discrete variation > - measure recessiveness 3 dominance , spread of alleles Continuous variation -many genes each , w alleles of small effect, important environmental effects > measure - selection response as change in trait value avg Fossil formation - soft parts of organisms decay rapidly - only in unusual environments are microbes unable to break them ↳ and atmosphere of desert - preservative chemicals of amber - slow rate of for skeletal structures allow minerals to dissapearance infiltrate them and replace the original material in mineralized replica a - fossilization occurs under water deposition of sediment 3 precipitation of minerals > - fossil records are based Coelacanth (fish) -> thought to be extinct but wasn't left no fossil record due to low abundanced depth they live fossil records of time -freg gaps in over great periods  Lecture 5 Factors that change can Allele Frequencies 1. Mutation (* diversity - ultimate source of genetic variation -not directedI caused by during errors replication 2 Recombination -creates new combinations of mutations. 3 Genetic drift ( ↓ diversity > - change in freg of an allele due to random chance - random sampling affects every generation - affect smaller populations - If there is change next To effect fitness it is gen a i no on ,. mostlikelycausedby Gendrif population for at least one. gen ↳ founder effect : new population established by very small a # of individuals from a larger population 4. Natural selection a) purifying selection (negative) > - selection agst mutations that will reduce fitness (d diversity) b) directional (positive) selection- fixation of mutations that will increase fitness (t diversity) ↳ fixation : occurs when polymorphic locus a becomes monomorphic due to loss of all but one allele e) selection favoring diversity- natural selection that acts to favor diversity over the long-term ; heterozygote advantage (4/retains diversity. 5 Gene Flow ; migration ↳ movement of genetic material from population to another one - increase diversity win a population ; potentially reduces diversity blo them effect link 2 pop -homogenizing. lead to evolution migration changes allele freg. > - Metrics of Genetic Variation - Heterozygosity (H) ↳ proportion of individuals in a population that are heterozygous (possess two alleles) at a specific gene locus or across multiple loc Polymorphism (P) - ↳ proportion of loc that have two more alleles the gene or in population > a - locus can be polymorphic wout being heterozygous Mutation-selection balance model = Classical School -variation from genetic mutation and usually bad ; followed rose is by selection acting to remove them - Low H ↳ low P Selection Maintaining Variation - E Balance School - heterozygote advantage - fitness varies in space and time , resulting in a preference for individuals to have variation H ↳ high ↳ high P Neutral Theory- most molecular variation may be selectively neutral - negative selection rapidly eliminates detrimental functions - positive selection rapidly fixes beneficial mutations - only selectively neutral mutations are left to create genetic variation - allyzomes : diff allelic forms of same protein. #example Fruit flies - scientist selected for #'s of bristles , in flies showing the vast amt of variations present win the population > - after selection relaxed the # of bristles decreased drastically ,  Lecture 6 Reproductive system asexual sexual dioecious hermaphrodite crossing selfing Sexual Reproduction - 2 parents contribute their genetic material to offspring state -meosis toform game Asexual Reproduction -one parent contributes all meiotic their genetic material - no reductive division - offspring are genetic replicas of parents a clones female at Form Costs. two 1 fold cost of Menosis > - transmission bas - favors asexuals in competition o sexual asexual female -> contributes all of her genes - sexual female + contributes 50 % of her gene - ↳ sexualreproduction uses same amt of energy as asexual reproduction but produces only half as many offsprings capable of breeding asexual Invest in resources to make 4 eggs asexualtwiethegene ftness ↳ amt of of the sexual ferase genes - ↑ in freg of genes in next generation - important evolutionary change efitness advantage ↳ sexual half of opportunity to leave behind genes for a investment - give away your given  can't this also be true * for unfavorable combos. 2 a sexual reproduction maintains favorable allele combos > in short-term ↳ sexual can continually re-create unfavorable combos - ex : Al-adapt to wet habitat aat" "dry " Aat" "neither-basexual heterozygote - terrible fitness Costs In some cases -> time I to find s attract mates energy > - increased energetic cost of mating > - risk of predation 3 infection > - cost of producing males > two-fold cost - Benefits of sex 1. favorable combinations of mutations are formed more quickly by sex ↳ bring together favorable mutations and eliminate harmful mutations ↳ recombination E creates combinations of through 3 new genes crossing over independent assortment > - bring to ether beneficial mutations from diff. parents increasing overall fitness of offspring= deleterious combinations > are eliminated through NS  Hypothesis for advantages of sex > - benefits of genetic variation in diff /unpredictable environments. ↳ spacially heterogeneous environments - "tangled bank hypothesis" - ecological specialization - temporally heterogenous environments + "red queen hypothesis" time often due to temporal changes - change over E Harmful Mutations - a sexual -> more "premature" stop codon mutations -> leads to dysfunctional proteins evolution accumulation => higher rates of protein of deleterious mutations seq , = greater -higher rates of sex maintained in populations involving heterogeneous habitats > - sex t rapidly in homogeneous environments + sex persisted at a much higher level on spacial heterogenity Macroevolutionary history of asexuality - asexuality by parthenogenesis rarely just = a sexual esperatically distributed across the animal kingdom - asexual propagation by clonal - usexual species usually at the top of phylogenesis are ↳ macro-evolutionary patterns indicate higher extinction rate ↳ low chance of long-term evolutionary persistence due to extremely => low genetic variation 3 the accumulation of deleterious mutations  Outbreeding -mates are less closely related than random Inbreeding related than random -mates are more closely relatives > in - small populations , even random mating can lead to mating among - outcrossing > - mateI someone else through outbreeding/inbreeding fusion of from two parents > gametes - -selfing > - mate i urself- only possible in hermaphrodites of (NOT asexual reproduction ↳ extreme form inbreeding > - fusion of gametes from one parent Inbreeding Avoidance - Plants * -timing offset blu male & female reproduction - diverse morphological 3 physiological mechanisms to avoid selfing ↳ self-incompatability - Animals - dispersal by one sex - delayed maturation -less likely for parents 3 offspring to mate -extra-pair copulatione cheating - diversify mates - kin avoidancea recognition - inbreeding by itself doesn't change the frequency of alleles and polymorphism e changes heterozygosity inbred have their polymorphism changed but its not caused by pop usually ↳. inbreeding itselfI usually caused by downstream negative consequences 1 allele zalleles 1 allele ↓ ↓ (AiAi 3 genotypes , A Az , , AzAz) 2 pop : random and inbreed of - random E square of overall global freq an genotype frequency allele = > - inbred decrease heterozygotes and in increase in homozygotes > doesn't change freg of A and As allele - , inbreeding decreases in heterozygotes and increases in homozygotes > - effects are cumulative ↳ keep losing heterozygosity until you stop inbreeding a closer inbreeding is worse (selfing Inbreeding Depression ↳ reduction in fitness of inbred offspring compared to outcrossed offspring - leads to nasty effectsE lowering fitness - lower viability - lower fertility > - lead to the loss of polymorphism Reduction of fitness - recessive deleteriors alleles= mostly always in heterozygous condition leads to the deleterious traits to ↳ inbreeding populations become homozygous = recessive alleles can then make phenotypes > - It reduced by 50 % per germination i selfing Why is selfing still present inbreeding bias - - outcrossed individual will invest in a seed then cheap pollen - leave 2 gene copies -selfer will invest in an ovule Cand pollinate it i its own pollen and send pollen out into the world -> leaves 3 gene copies ↳ has transmission advantage outcrosser selfer 1 2 seed pollen 1 I totalgenea 3 Consequences -selfing have advantages the short-term = lack of pollinators /mates can major over , transmission bias= could be good if population has low inbreeding depression - selfing tends to lead to low diversity and inefficient selection =drive higher extinction rates  Lesson 7 -fitness : genetic contribution of individuals to next generation , relative to other individuals , as a result of diff. in variability and fertility relative quantity -Selective advantage amt by which individuals of better given genotype : some a are adapted to a given environment - Adaptation : a) a trait that contributes to fitness by making an better able to organism survive or reproduce a environment given in b) the evolutionary that leads to the and maintenance of such traits process origin - Artificial selection : selection by humans - Natural selection : selection by abiotic and biotic environment I not directed Natural Selection on Alleles 1. negative (purifying) selection-↓ > diversity > - eliminates mutations that will reduce fitness 2. directional (positive) selection t diversity > - fixes mutations that will increase fitness. 3 selection to maintain variationE retains/4 diversity > - selection that favors diversity over the long-term ↳ heterozygote advantage Selective pressure/modes of selection. 1 disruptive > - split into two different pop, groups selection agst - mean - often leads to speciation => If trait divergence causes reduction flow gene a in -ori. pop , will ↓ 2. directional -> evolve towards one extreme · stabilizing e favors individuals ; reduces extremes avg..  ex : human birth weight , beak size study adaptation - test for correlations of alleles/trats = environment over space and time ↳ analyze genomic diversity targeted by selection will show distinctive patterns -genes - experimental manipulations in field 3 lab Ex : evolution to pollution - evolution of industrial melanism in peppered moths evolution of heavy metal tolerance in grasses - > trees - near industrial pollution blackened ↑ dark variant is - In > - in city trees were normal (birch; white color) light moth + - selection mechanism = predation Ex : evolution of heavy metal tolerance in plants ↳ zinc tolerance grasses in humans Ex : GGPD deficiency in - causes severe anemia ; protect agst malaria Malaria Freg of A-. selection absent to agst anemia present ↑selectionrence GGPD Deficiency alleles genetic sequence - signature of NS > - strong " relatively recent NS = It increases its freg rly rapidly.. 1 heterozygosity goes down ; homozygosity goes up selection allele will 2. strong enough 3 sweep dramatic enough the good bring the genes its linked to along i it > - selective sweep : occurs when selection causes a new mutation to increase in freq so quickly that nearby alleles "hitchhike" along and also increase in frequency  Lecture S -population : of individuals of single species a occupying a group a at the time given area same - migration : movement of individuals from one population to another flow : movement of alleles from population to another -gene one Gene Flow - hold populations together > - reduces differences blu populations that have migrated - establish two populations fixed for alternative alleles separated by a given distance ↳ freq of heterozygosity in offspring = estimate of an gene flow - most gene flow occurs over a short distance selection & Genetic Drift = cause divergence in populations - Stochastic Crandom) evolutionary forces ·mutation · recombination · genetic drift - deterministic (non-random) evolutionary force · NS Genetic drift - random changes allele freg indue. to random variation in mortality and reproduction > - important small populations in ↳ fluctuations more drastic each generation ; more rapid loss of diversity - bottleneck effect : sharp reduction in population size for at least one generation = usually followed by rebound > - loss of diversity - founder events : colonization by a few individuals that start new population > - contains limited diversity compared to source population Ex : human genetic variation -humans show a loss of genetic variation o increasing distance from East Africa => reflect serial founder events as humans migrated from source population sequence divergence DNA High gene flow - alleles make it across the barrier , but won't reach fixation bl population will have a hard time differentiating shared polymorphisms Low flow gene polymorphisms and fixed differences forces - gain unique - diverging are dominant Genetic differentiation -further we are from our ancestor the , more genetically differentiated we are E monotonic increase Phenotypic differences blu populations win a species may be... - adaptive genome environment - due to genetic drift ↓ factor ↓ phenotypic plasticity gene A, B - , C 3D 1 2 3 34 , , ,