Human Evolution Summary PDF HS 2021

BIO 115 Annik W. Human Evolution – Summary L1: Basic Evolution Theory 1.1 What is evolution Biological evolution is the change in the properties (Eigenschaften) of organisms over the course of generations. The c...

BIO 115 Annik W. Human Evolution – Summary L1: Basic Evolution Theory 1.1 What is evolution Biological evolution is the change in the properties (Eigenschaften) of organisms over the course of generations. The changes are passed via genetic material into the next generation. Ontogeny (development/growth) of organisms is not evolution. f.e: antibiotic resistance 1.2 Different evolution theories Plato: Variation is accidental imperfection Aristotle: Species have fixed properties (human f.e: talking, walk on two feet) Christians believe: Gods creation, „great chain of being” must be permanent/unchanging as change implies imperfection Carolus Linnaeus: catalogue plan of creation, systema naturae, classification of animals and plants 1.2.1 Lamarck (1809) Species originated spontaneously Evolution aims to get more complex (always climbing up the scale of organization) No common ancestors between species Species differ because of their different needs Alternations are inherited No sorting process Organic progression à nervous fluid Transformational evolution: organisms can pass on traits that they acquired during their lifetime to their offspring (à if one has muscles, all offspring have muscles) Transformational evolution says that a population simultaneously acquire the same structures and adaptations as the result of an inherent progressive tendency which drives them continuously towards greater complexity 1.2.2 Darwin(1809-1882) On his voyage: mockingbirds on different islands look different à adaptations 2 breakthroughs Descent with modification: all species have descended from one “original” forms of life Natural selection 5 theories 1. Characteristics of lineages change over time 2. Common descent: Different species arose from one single common ancestor 3. Gradualism (changes occur step by step) 4. Individuals of a species can vary from each other (have different characteristics) 5. Natural selection: only those individuals who are adapted best will survive and get into the next generationà survival of the fittest / best adapted Variational evolution implies that individuals in an evolving population vary from one to another, and that these variations may accumulate during evolution due to a sorting process by which some variants become either more or less common. Evolution is not goal-oriented (not aimed to be more complex) 1.3 Phylogeny (evolutionary tree) A phylogeny, or evolutionary tree, represents the evolutionary relationships among a set of organisms, called taxa. The tips of the tree represent groups of descendent taxa (often species) and the nodes on the tree represent the common ancestors of those descendants. BIO 115 Annik W. History of events by which species have originated from common ancestor Each branch point (node) represents the division of an ancestral lineage into two or more lineages Closely related species have more recent common ancestor The longer a branch, the more time has passed and the more mutations taken place (genetic change over time may happen faster on one species than on others) Tree based on parsimony (Sparsamkeit) only as much branches as needed May include reticulation (Vernetzung) because of hybridisation Phenotypic similarity is not always phylogenetic similarity. Some individuals may look pretty similar, so phenotypically they are alike but they may not be closely related (shark and dolphin look alike, but dolphin and hippo are closer because they are both mammals). Coalescence analysis: Coalescence analysis allows tracking back to the most recent common ancestor. By the coalescent tree we can track the sampled (erfasste) lineages (no chance to track all lineages) and then represent all as good as possible 1.4 Difference between homology and analogy Homology: structures that are similar in related organisms. Homologous means that sth had the same basic plan and the same phylogenetic origin but they can now have specific adaptions and different functions. f.e.: construction of bones the same as the common ancestor had Analogy: structures that are similar in unrelated organisms. They had different basic plans but now have similarities in adaption and function (homoplasy). The phylogenetic development that was independent but lead to a similar result is called convergent evolution. (only because they look the same doesn’t mean they have the same ancestor) f.e.: Wings make both able to fly but they achieved it in independent pathways of evolution (so birds have feathers, bats have skin) 1.5 Adaptive radiation Adaptive radiation is a process in which numerous related lineages arise and diversify rapidly from an ancestral species into a multiple new forms in a really short time. Particularly when a change in the environment makes new resources available or opens new environmental niches. Evolve into different directions as they adapt to different habitats à most common pattern of evolution 1.6 Darwin’s difficulties explaining variation new species and other evolutionary changes arise by the accumulation of small variations blending inheritance and selection would destroy variations in population => natural selection can’t continue ð Darwin had no answer to that BIO 115 Annik W. L2: Genetic variation 2.1 The problem with “blending inheritance” The theory assumes that both parental substances mix to determine offspring characteristic, so offspring is an intermediate of parents. But by that, all variation would disappear + selection would also remove variants. à how is variation maintained? 2.2 Mendel’s experiment Mendel isolated traits of a pea plant with only two forms (variants) and bred them to make heterozygous offspring. The breeding between the heterozygous plants lead to a predictable mixture of genotypes. Mendel found out that characteristics are determined by two particles, one from the mother and one of the father, that equally likely to be transmitted when gametes are formed. The particles are chromosomes. 2.3 What creates genetic variations? Gene-mixing by segregation: both alleles segregate independently Gene-mixing by recombination: Crossovers between genes leads to recombinant chromosomes => new combinations Independent assortment of homologous chromosomes during meiosis Mutations: change in the DNA (mutation rate varies between species) Point mutation Structural mutation (Deletion, Duplication, Inversion) Genome duplication ð Mutations can affect fitness of an individual Pleiotropic effects: A pleiotropic gene is a gene that controls more than one gene, so if there is a mutation in a gene it can have impact on many other functions of an organism à great for evolution to act upon 2.4 Linkage disequilibrium When two loci are found inherited together more than expected it’s called linkage disequilibrium. The closer two Loci are, the lower the possibility that they get separated because of crossing-over Recombination rate “r”: probability that recombination takes place Large distance = high possibility that two Alleles are separated through cross-over à low LD Short distance = little possibility that two Alleles are separated à high LD 2.5 Solving Darwin’s Problem Problem 1: Selection will remove variants from population: New variants arise in every generation (segregation, recombination) Mutations Changes in gene regulation Pleiotropic effect Problem 2: If blending inheritance was true: natural selection would destroy variation “Blending” is not the right word, an offspring receives 50% of the mother’s DNA and 50% of the father’s DNA but they remain separate and don’t blend. BIO 115 Annik W. L4: Selection and adaption in humans 4.1Natural and artificial selection Nature: Peppered moth: mutation of Melanin, dark mutant à decreasing pollution, less dark trunks Cockroaches: different taste receptors à some can avoid traps set by humans Artificial: Rapid evolution when humans select traits à chicken selection (their weight within 60 days in different years) 4.2 Selection and fitness Trait will evolve if These is a correlation between phenotype in parents and in their offspring There is a correlation between phenotype of parents and their number of offspring (their fitness) ð Without selection, no evolution (stay as it is) ð Selection can affect fitness in different stages of life Fitness: number of offspring an individual leaves to next generation !"#$. '(")*)+, -#.+-("*-/ Absolute Fitness (w): number of zygotes produced by one individual W= 01!02-.3(.$0" #44'!"*35 Relative fitness (wpop): average number of offspring in a population f.e: W = 2 wpop = 1 à Individual has good fitness compared to others wpop = 4 àIndividual has bad fitness compared to others ð relative fitness plays important role in determining speed and result of evolution by selection 4.3 Selection and reducing variation: Selective sweep: Process through which a new beneficial mutation that increases its frequency and becomes fixated (reaches frequency = 1). Selective sweeps eliminate polymorphisms at near regions of the mutation and thus variation is reduced. Neutral sites close to the loci “hitchhike” and get fixated as well because they are linked. Positive selection: occurs whenever one allele has a higher fitness à allele frequency of beneficial mutation increases in order to reach fixation (alleles can hitchhike an also become fixated) Selective coefficient “s”: measure of strength of selection that favours beneficial allele (the stronger the quicker it will take over a population. => Evolution is proportional to strength of selection (s) and amount of genetic variation (depends on allele frequencies) 4.4 Dominance and time within fixation: Relation between s and time: how many generations until fixed (the higher “s” the faster) Dominant: frequency increases rapidly Recessive: frequency spreads slowly No dominance: intermediate Deleterious mutations: “s” is negative à change in allele frequency is negative Difficult to remove recessive disease because most people are heterozygous (Carrier) and don’t die Many genes have evolved in response to strong natural selection BIO 115 Annik W. Lactose tolerance: our ancestor could not digest lactose, now we can (beneficial mutation) à different alleles lead to lactase persistence = convergent evolution Golden Gene: Mutation decreasing skin pigmentation à lighter skin 4.5 Selection and preserving variation: Standing genetic variation: Environmental change suddenly gives fitness advantage to a mutation that is already present in the population.. Region of reduced variation is smaller than if mutation had an advantage from the beginning. Balancing selection: maintains genetic variation à polymorphic equilibrium f.e: mutation in a gene makes bad erythrocytes but protection against malaria 4.6 Selection and Allele frequency changes Positive: positive selection favours one specific allele à fixation (go to top, independent on start frequency) Overdominance (balancing): heterozygote has higher fitness à polymorphic equilibrium and maintaining genetic variation (get to the middle) Underdominance: heterozygous has lowest fitness à fixated or lost (depending on start frequency) 4.7 Population genetics: Fst: is a measure of genetic differentiation between population Fst = 0 no difference Fst = 1 complete differentiation Detect selection: compare two population. Big difference in Fst shows, that selection was active and some allele was more efficient and now has a higher frequency than in the other population f.e: comparison between Inuit, Chinese and European: branch between Chinese/european and inuit is long: big amount of mutations that took place à adaption to arctic environment (temperature, marine food) Tibetans show very high level of differentiation from Chinese people à adaption to high altitude 4.8 Summary Natural selection is any consistent difference in fitness among different phenotypes (selection acts on phenotype) Rate at which beneficial mutations spread depends on s and the amount of genetic variation present in the population Selective sweeps reduce genetic variation in region close to selected locus Selection can maintain genetic diversity à overdominance Deleterious mutations occur frequently à are maintained in population by mutation even if selection want to remove them BIO 115 Annik W. L12: Genetic drift & human evolution Loss of genetic diversity: Small population: little option of interaction Harmen structure: one male with many females 12.1 Genetic drift Genetic drift is the change in the frequency of an existing gene variant (allele) in a population due to random sampling of organisms Genetic change between generations also happens when selection is not at work Mutations can change allele frequencies Chance plays a big role in evolution (survival, reproduction, meiosis) only one allele in heterozygotes gets passed on => proof by in-silico experiment In-silico evolution (experiment) 5 populations with two qual alleles, each generation starts with a given number of individuals, there’s no selection on survival nor on reproductive success, all adults die after reproduction. Result: Random fluctuations are larger in smaller populations Genetic drift causes genetic variation to be lost Genetic drift causes populations that are identical to become different Alleles can become fixed without the benefit of selection (random allele is fixed, not the better one) ð The smaller the population is, the bigger the chance that alleles get lost by random occasion ð Other allele got extinct because it was not inherited anymore 12.2 Genealogy of genes For any given locus in the human genome, there was a copy of that gene in the past that was the ancestor of all copies of the gene now carried by all living humans. When lineages of two gene copies merge they coalesce => shows most recent common ancestor (MRCA) of that gene. Due to chance many lineages become extinct after time, depending on how strong the drift is, it takes longer. 12.3 Genetic drift and effective population size: The strength of random genetic drift in a population is measured by effective population size Ne. Ne is the number of individuals that would give an idealised population (individuals have same chance of leaving offspring) the same strength of random drift as the actual population. Average time back to common acestror is 2Ne What affects drift: Size (large population => small drift => maintain genetic variation) Changes in size => bottleneck: when part of a society leaves there’s is reduced option for mating => genetic diversity decreases with further distance from Africa Age demography Unequal reproduction (f.e. harem) Ne varies between species and depends on History of species Variation in mutation rates BIO 115 Annik W. Selective sweeps Background selection Reproduction 12.4 Genetic diversity of great apes vs humans Genetic variation within orangutan and gorillas is much higher than in humans despite the much smaller population size because it takes a long time for genetic variation to build up: mutations take time to evolve =>Most human diversity occurs in Africa (genetic splits much deeper in Africa) =>Genetic splits in Great Apes deeper than in humans Why are humans genetically less diverse than other great apes? Very recent speciation event: Great apes are way older than humans are Genetic diversity and size of ancestral population Demographic events: bottlenecks f.e. migration and thus split of a group Stochastic events: genetic drift (and chance) shape our genetic variation 12.5 Genetic diversity within the modern human Linnaeus (1756): described different human “races” due to different looks but also on intellectual and cultural characteristics. Race: natural subdivision of a s species in biologically distinct groups forming incipient subspecies. => is there enough genetic diversity for human “races”? Human ó Great Apes Variation within population Variation between population Humans: two Europeans have more differences than a European and an Asian Great Apes: Are genetically more diverse both within and between subspecies than humans but more different between groups (narrow within group but big step to next group) 12.6 Structure analysis of human genetic diversity Algorithm that classifies humans into wanted number of groups (K) and see how different “races” based on genetic diversity would be put together. Result: Difference between clusters is very small Shows us that European, Middle East and C/S Asia are genetically similar => genetic variation WITHIN population: 93-95% => genetic variation BETWEEN population: 3-5% => To justify “races” it should be around 30% between groups => no genetical races! Furthermore: Humans are much less differentiated than other mammals (FST very low, even though we are widely spread) Genetic diversity in human follows a gradient => not “fixed” classification possible BIO 115 Annik W. V5: Mismatches 5.1 Evolutionary Mismatch What: State of disequilibrium whereby a trait that evolved in one environment becomes maladaptive in another environment Integral part of evolution in changing environment Important to humans as environment changes drastically Can occur through cultural evolution in addition to genetic evolution When: Adaptation evolve in context of selective pressure = adaptively relevant past environment “Ancestral environment” doesn’t imply that relevant selection pressures were homogenous à is becoming increasingly common as our environment is changing rapidly 5.2 The way evolution shapes our health goes far back in past Humans are apes with derived adaptations (f.e. pelvis that is smaller due to upright walking, brain got bigger (4x bigger) obstetric dilemma: contra productive evolutionary development as pelvic got smaller but head got bigger =>stabilizing selection for birth weight Maternal and neonatal mortality as consequence of obstructed labour: survival and reproduction are at stake 5.3 Mismatches and major cultural transitions Hunter-gatherers: Humans evolved their derived characteristics as hunter-gatherers Hu-gath. today are not a perfect representation of early homo sapiens because they adapted as well but still closest to how our ancestors lived o Bayaka o Agta What was important: Food availability is unpredictable (low resource predictability) low environmental carrying capacity (number of people that can be sustained at a steady state with the available resources) craved food that was energetic and versatile but hard to get physical work to get food ð consequences of low carrying capacity: high mobility, no possession ð cooperation becomes important Adaptions of hunter-gatherers: group structure and kinship system egalitarianism (equality) variety of tools to process foods cooperation and equality running and throwing ð increased reproductive success than ancestors BIO 115 Annik W. 1.Transition to farming Mismatches: Quality of food decreased: loss of variety and more carbohydrates o Dental caries, abscesses, tooth decay visible on skeleton Increased parasite loads / viral infection Animal domestication was bad for health Mortality rate increased But why was farming evolutionary successful? Quantity of food increased Predictability of food Starch and baby food lead to less mortality of baby Carrying capacity increased because of more productive land and storage possibility physical work increased long-term immunity ð fertility rate increased à reproductive success was higher ð fertility > mortality à population size increased à fast expansion ð BUT: sex equality decreased First transition: Demographic: caused by increased quantity and predictability of food Epidemiological: increased of communicable diseases and less diverse food 2. Transition to modern life started recently in comparison to transition to farming Solving problems brought by agriculture: Fighting communicable (übertragbare) diseases with vaccination, hygiene, medicine, more food variety First from high mortality to low mortality Then from high fertility to low fertility (less offspring) Life expectancy improved (living longer) à population still grows because mortality decreased before fertility decreased What were new mismatches? New non-communicable diseases (Alzheimer, Diabetes, Osteoporosis, heart diseases) “Having too much”: Significant health problem are increasing from easy availability of high-calorie food (carbs, fat, sugar, fibre) => diabetes “Doing too little”: decreasing of physical work “Environment of evolutionary adaptedness” à human is genetically adapted to a hunting-gatherer way of life not to modern life à Not because of the consequence that humans live longer, but of the drastic change of the environment BIO 115 Annik W. L7: Life History and Reproductive Health 7.1 What is life history theory? Life history studies the changes organisms undergo through lifetime from birth to death Focus on reproduction and survival (offspring vs soma, see L6) Explains phases of life cycle as a consequence of evolution by natural selection 7.2 Trade-offs: Time invested in growth and somatic maintenance length of reproductive span Trade-off determines the optimal age at first reproduction (Energy switched from growth to reproduction) -Different body sizes have different life schedules: Elephant: big, needs much time to grow -> reproduction late Mouse: small, doesn’t need much time to grow -> reproduction early Trade off and different extrinsic mortalities create continuum: Increased extrinsic mortality Decreases extrinsic mortality Great number of offspring less offspring Shorter lifespan longer lifespan Fast growth slow growth Early reproduction late reproduction Early sexual maturation late sexual maturation Small body size => fast living big body size => slow living 7.3 Slow life history of human: Investing in quality: 1. Gestation: long period of pregnancy 2. Birth: larges and fattest babies of all mammals -> proportionally expensive 3. Long-term dependent children (because brain and body need time to grow) ð Mortality rate is low ð Humans adopted the extreme of the slow life history stragety adopted by Apes 7.4 Menstruation and Menopause Menstruation: Because human babies are energetically expensive humans are one of few species that evolved menstruation to eliminate abnormal embryos When ovulation high inflammatory response to select good embroys over bad ones (body attacks everything but only good embryos are selected) After ovulation: anti-inflammatory response that embryo can attach to endometrium If no embryo “good enough” and no attachment -> menstruation (elimination of bad embryos) à Due to menstruation women are in control over embryo unlike in other species where embryo has control Why Menopause? Human have a long lifespan but our post reproductive span can be longer than reproductive span. Menopause is the result of a mismatch between the rates of reproductive and somatic senescence. longer lifespan than expected for our body size ó stop reproducing earlier than expected for our lifespan BIO 115 Annik W. Why not selection for longer reproductive span if we life longer? 1. Theory “good mother”: If a mother of old age has a baby she may not be able to raise the child until independence, so there needs to be a menopause to minimize that risk =>but post-productive time is way longer than the time it takes for an independent child 2.Theory: “Grandmother hypothesis” -Short IBI (fast new baby) ó still investing in quality -Grandmothers have important role because they help raising grandchildren -> we can wean (entwöhnen) infants way faster so we can reproduce again faster -> Menopause to help family and that women can contain high fertility 7.5 Difference between humans and apes who also have “slow life history” Shorter lactation period (breastfeeding period) Shorter interbirth interval (IBI) fertility is much higher (quantity high) => fast life Paradox: We adapted in ways to invest in quality (trough menstruation) and in quantity (through menopause) Slow life history Fast life history Long pregnancy high fertility Large & fat babies short breastfeeding period Long-term dependent children early weaning (entwöhnen) Low mortality rates short interbirth interval (IBI) = investment in quality = investment in high quantity à MENSTRUATION àMENOPAUSE 7.6 Mismatches and Diseases in female reproduction Although menstruation and menopause are important life history adaptions to ensure quality and quantity of offspring, changes in current reproductive patterns lead to maladaptation (mismatches) in western society. Not present in hunter-gatherers Changes in reproductive traits lead to mismatches - Early Menarche (first period 1860: 15, today: 12) - Menopause late - Lactation phase shorter - Less pregnancies à More menstrual cycles (450 today, 160 in hunter-gatherers) = More inflammatory cycles à increased risk of mutation lead to higher risk of reproductive cancer Cancer: Endometrial cancer (Gebärmutterschleimhaut): Oestrogen promotes proliferation, also it has inflammatory effect on body, so the more menstrual cycles woman has, the more inflammatory processes take place à can lead to cancer Ovarian cancer: multiple ovulations injures the ovarian epithelium Breast cancer: Women who breastfeed longer have more differentiated cells and less undifferentiated cells. Undifferentiated cells suspected to mutate and become cancer cell Birth control pill leads to 12-13 menstruations a year which keeps oestrogen level really high, may lead to health risk in later life BIO 115 Annik W. à Progesterone has protective effect on body, so rather than simulating menstruation, pills should simulate pregnancy because while being pregnant, progesterone level high àMenopausal symptoms are result of sudden decrease of very high lifetime oestrogen level to zero when menopause comes. Auto Immune Diseases: Increased immune reactivity (ups and downs all the time) lead to excess production of antibody, coupled with fewer immune challenges due to cleaner environment lead to increased susceptibility (Anfälligkeit) to autoimmune diseases for women (pregnancy improves symptoms in autoimmune disease). BIO 115 Annik W. L6: Senescence (ageing) If there is so much variation natural selection could select extreme longevity? All living organisms will die, but lifespan is extremely variable Natural variation in the population => selection of the fittest 6.1 What is ageing? Is the process of declining in fertility and survivorship rates with age leading to increasing mortality rate Decrease of physical function Decrease in reproductive rate Increase in age-specific mortality rate => ageing seriously reduces individual fitness and therefore should be opposed by natural selection. why do we still age? Positive senescence: mortality arises with age (mammals) Negative senescence: mortality sinks with age (the older the less risk to die) No senescence: age-specific mortality does not increase If humans maintained tiny mortality rate -> average person could last up to 1200 years 6.2 Different ageing-theories 1. Programmed ageing-group selection Ageing evolved by “group selection” => Idea of altruism For the benefit of a group the old individuals would be replaced by new ones Ageing and death are themselves adaptive Evidence for the theory: o telomeres are parts of a chromosome. As cell divides over time they get shorter, causing cells to stop functioning and then lead to ageing o Lemmings who commited suicide as benefit for the group o Senescence protects population from epidemics by controlling population density BUT: Natural selection acts upon one individual not on a group. There’s no benefit for one individual if it has to die for a group (only disadvantage) No theoretical reason to explain why ageing would be programmed 2. Rate-of-living-theory: Non-adaptive theory Death and senescence are not determined by natural selection Ageing is caused by accumulation of irreparable damages of cell that happen as a by-product of normal metabolic process When the damage overcomes the rates of repair mechanisms à ageing Reduce caloric intake should reduce metabolic rates leading to less oxidative stress and slow ageing Animals with higher metabolism should age faster (mouse has higher metabolism compared to body size than an elephant) -> large animals tend to live longer because of the slower metabolism Reducing calory intake should reduce metabolic rate -> slow ageing -> increased lifespan BIO 115 Annik W. BUT: Ageing cannot be a direct by-product of metabolic rate because all animals of the same size would then have the same lifespan Animals that have higher metabolic rate for same size would age faster and die earlier (compore bat to a mouse) Since species are set to be as efficient as possible in repairing damages, they should not be able to evolve longer lifespan (but they are) Can be selected for and thus an adaptive trait, not just a by-product => All these theories imply that we die because we age, different rates of ageing lead to different ages of death 3. Life-history-theory (Reproduction versus Soma) Ageing is consequence of accumulation of mutation (cell damage) at different rates according to extrinsic mortality Focus either on reproduction or Soma -> Trade-off When focused on reproduction rather than somatic maintenance than errors accumulate fast -> leads to strong senescence and shorter lifespan Mutation that affects individual late in life have no effect on reproductive success (because offspring were already made) =>“Charnov’s theory”: we age because we die (senescence as a consequence of death) External/extrinsic factor: Each environment gives different ecological risk to die (extrinsic mortality) Animals lifespan depends on external factor an environment has (death through predators, diseases, starvation, accidents Death is an external factor that cannot completely be controlled => is inevitable Time is a limited resource 6.3 Why does selection not produce eternal lives? Extrinsic mortality cannot be completely controlled (external factor). The higher the extrinsic mortality, the faster will the animal age and then die because it rather invests in reproducing early than in somatic maintenance. Individuals adapt to extrinsic mortality rate. 6.4 Correlation between mortality, fertility and ageing: high mortality => fertility high in early age (offspring early) => ageing faster as focus on reproduction than on somatic maintenance Species with different extrinsic mortality should have different probabilities of surviving (independent of senescence) 6.5 Senescence as an evolutionary consequence Average lifespan is a consequence of the ecological mortality rate Senescence is the evolutionary consequence of the inevitable death Why? 1. Removing deleterious mutations decreases as chances of accidental death increases 2. Every mutation that kills you in young age will not be passed to next generation -> selection has less power to eliminate bad mutations in later life BIO 115 Annik W. => ageing means we accumulate bad mutations that we cannot eliminate through selection in old ages, because it’s always passed to the next generation =>old age: garbage bin of all accumulated deleterious mutations that selection couldn’t eliminate 6.7 Why are genes associated with aging diseases selected for? Antagonistic pleiotropy: Pleiotropy: one gene has more than one effect on phenotype Antagonistic: one effect is beneficial, one is detrimental Organisms that need to have offspring as early as possible, genes favouring early reproduction are selected at cost of effect in later life. Reproduction is favoured over soma. Anything that provides having offspring early will be selected even if its detrimental when older. o Testosterone: high levels early lead to high fitness but decreased fitness later à will be selected for because it provides good fitness when young à Age can be accelerated by antagonistic pleiotropy, where genes that have an advantageous effect at early age can be selected for even if they have negative effect later on BIO 115 Annik W. L8: Human brain and cognition 8.1 Brain sizes and body size Brain size: Different primates have different brain sizes. Great Apes have a wide range but they don’t overlap with other other primates. Humans have a very large brain. We evolved from an ancestor that already had a big brain but we took it to a new level. Body size: Most variation in brain size is explained by different body sizes. Brain responds to body size. But it’s only the expected brain size compared to body size of a species, not the absolute number. => body size scaling Encephalisation &EQ: Encephalisation is measured by encephalisation-quotiend (EQ) EQ = observed brain size / expected brain size EQ = 3 => 3 times larger brain than expected for body size => species is encephalised Primates are highly encephalised => cat and capuchin monkey weigh the same but monkey has a 3 times bigger brain Humans are the most encephalised species (dolphins after us) => EQ = 6-7 8.2 Brain structure Neocortex ration: Brains vary in structures. Key difference is „neocortex ratio“ (associated with higher functions. => Primates have high neocortex ratio. Brain connectivity: ratio of white (connection) /grey matter (functional modules) small brains are mostly grey Humans have a lot of white matter (but whales have even more) Humans are no exception, we follow the general scaling But big brains cause a problem: obstetrical dilemma 8.3 Obstetrical dilemma: Brains need to fit inside a skull and skull needs to fit through hips of a mother. => encephalisation vs pelvic adaption. Solution: reduce space of the brain by packing and folding the grey matter, increase brain convolution. But result is that convolution reduces the amount of white matter required to connect functional modules. But because of the shape we have a large surface (many other species have smooth brain) convolution correlates with absolute brain size (dolphins and whales have more convoluted brains) Summary: what makes a human brain special? Humans… Have large brains (but not the largest, primate brains were large before human brains were) Are highly encephalised (we had encephalised ancestor but we took it even further) Have a lot of white matter (but it’s not an exception) Have higly convoluted brains (as a consequence of high encephalisation) Have a unique structured brain with large neocortex ratio 8.4 Brains and minds Lobes: Neocortex is divided into 4 units /lobes: frontal, parietal, temporal, occipital Sensory function (vision, hearing) are processed in the posterior regions sensory information are transmitted from raw input into primary area (V1) to secondary area (V2,3) Damage of primary: total blindness Damage of secondary: specific visual deficit (f.e colour blindness) BIO 115 Annik W. Vision involves significant processing and interpretation of raw inputs Somatosensory information is sent from thalamus to somatosensory cortex (S1) Movement is commanded by the primary motor cortex (frontal lobe) 8.5 Association areas: Cortical regions that are not primary sensory (input) / motor (output) => association area („thinking“ and high cognition part) Mammals: Association parts are rather small (input / output) Human: Most of the brain is association part Cross-modal information: Association area put sensory information together: vision, sound, smell to recognise object => can lead to disagreement (video with dada, baba) => human brain is very visual (see the sound rather than hear it) 8.6 Working memory: Is the set of mental processes holding limited information in a temporarily accessible state (here and now) Many regions in the neocortex are activated by working memory tasks Hippocampus (not neocortex): long-term memory, only fraction of our experiences is filtered into „past“ memory Damaged Hippocampus: only presence is available, facts remain (semantic memory) but personal experiences are gone (episodic memory), reality based on 10-30 sec windows Learning without episodic memory is possible (handshake with pin) Link between memory (real experience) and imagination (constructed experience) => experiment of words on a list and the picture the mind makes, mind „makes things up“ that were not reality Constructive memory: memory is re-imagined every time its recalled BIO 115 Annik W. L3: Cooperation 3.1 Major transition in evolution require cooperation single-cells à multicell-systems RNA as gene à DNA solitary individuals à colonies with task specialisation =>Natural selection favours individuals that maximise their fitness: competition “struggle for existence” / “survival of the fittest” => How can natural selection then favour cooperative traits that benefit others? 3.2 Problem with cooperation: Cooperation is observed everywhere in nature, but it’s not compatible with Darwin’s theory of natural selection and adaption (survival of the fittest) 3.3 Hamilton’s rule Hamilton’s rule: helps to classify social behaviour (not only cooperation) rb > c c= cost of actor b= benefit of receiver r = relatedness between actor and receiver Relatedness: is a measure of interaction probability high relatedness: interactions occurs more often among individuals that are alike than expected low relatedness: interaction occurs as often among individuals that are alike as expected The 4 cases of interaction mutually beneficial cooperation (beneficial for both => r= low ) § cooperative agreements between people § group hunting Altruism (reduces my own fitness but benefits someone else => relatedness must be high) § worker bees that help the queen producing offspring § menopause: help the daughters to raise their offspring selfish behaviour (benefits me but harms the other => r=low ) § lions kill young offspring of previous males § stag fights: one can stay with the female, other has to go spite (harms both => r= must be low) § warfare: both are likely to be killed § toxin production in bacteria: kill the acter and recipient Personal fitness: number of offspring that one individual leaves Inclusive fitness: number of offspring that are supported / hindered through behaviour of one individual Summary: it matters with whom you interact and what the cost and benefit is natural selection favours individuals that maximise their inclusive fitness inclusive fitness theory explains any social interaction, not only cooperation between relatives 3.4 Relatedness(r) and kin discrimination High relatedness through BIO 115 Annik W. limited dispersal => keeps relatives together and favours indiscriminate cooperation (no discrimination is required) Kin discrimination: allows individuals to selectively cooperate directly with relatives: kind recognition is an individual’s ability to distinguish between genetic related and non-related individuals. o Primates and humans have cognitive ability to recognize each other o Ants form odour (Gestalt) to recognize colony member o amoeba green beard effect: mechanism to recognize other carriers of the cooperative allele. The cooperative allel is here linked to the “green beard”, no common ancestry. o r = 1at green beard locus o r= low at the rest of the genome 3.5 High relatedness and kin competition: High relatedness can promote kin competition and cancel out cooperative benefits. inelastic population (can’t grow): by helping on, one indirectly harms other elastic population: extra offspring by cooperation global competition: cooperation will lead to higher success probability Selection mainly acts on the individual as the carrier of genes and not on a whole group! 3.6 Conditional cooperation: Individuals can decide whether to cooperate or not Prisoner’s dilemma: Snowdrift game better if you defect in both scenarios! Here it depends on what the other does! Other typical human interaction Iteration: learning and reciprocal interaction Tit-for-tat: players react to opponents last move (cooperate first and then copy other) Win-stay-lose-shift: players react to the opponents and their own last move (if you win you repeat, if you lose you change strategy) Indirect reciprocity: observer recognizes what others are doing and pick who cooperates Generalized reciprocity: own decisions are based on previous positive interaction Costly punishment: punishment and threat are strategies to enforce cooperation => Conditional strategies occur outside of human o Rats groom if they were groomed by another => Require cognitive abilities and memory => Repeated interactions foster cooperation BIO 115 Annik W. L9: Humans & infectious diseases Pathogens: virus, bacteria, protists, micro parasites Obligate: relies on a host for replication and transmission Opportunistic: replicate in environmental habitats 9.1 Transmission routes: Environmentally acquired: food, water Vector: mosquito, tick Horizontal: via sex, blood, aerosols Vertically: from mother to offspring Nosocominal: through hospitalisation Ethiology: Study of the causes and origin of diseases Epidemiology: Study of distribution (frequency and pattern) and causes of a diseases in order to control it Endemic: local outbreaks, easy to control Epidemic: large outbreak (f.e. Influenza) Pandemic: affect large part of worldwide population (swine flu, corona) 9.2Correlation vs Causation Correlation: means something is linked but one does not have to be the „trigger“ for other Causation: One thing only happens because of other thing Distribution of diseases worldwide: Disease diversity: more diseases at equator than in colder regions Disease composition: many diseases have limited distribution range (only few occur worldwide, many locally (mostly at equator)) ð Equator: Diverse but local ð Temperate zone: Few but more globally spread Migration patterns correlate with fewer but more widespread pathogens (out of Africa) => Globalisation: dispersal is a key parameter for epidemiology 9.3 Where do human infectious diseases originate from? Correlation with wild animals: higher probability for multi-host and zoonotic pathogens to emerge when there‘s a high diversity of animals Correlation with domesticated animals: domestication leads to close interaction with animals which increases the possibility for pathogens to hop from animals to humans => positive correlation between years since domestication and shared pathogens Correlation to agriculture: Agriculture lead to higher density, larger groups, closer interaction, increased transmission opportunities o African hunter-gatherers: big reservoir of wild animals, many local pathogens, less acute but stay for long o Temperate-zone agriculture: domesticated animals, fewer pathogens but more globally spread, acute (either recover or die), longlasting immunity Diseases in temperate-zone: acute, long-lasting immunity, genetic adaption to diseases => lead to drastic historical change: europeans came to America with diseases they were not immune to (pox) => many died BIO 115 Annik W. 9.4 5 stages from animal to human pathogen: 1. Only among animals 2. Primary infection 3. Limited outbreak (among human) 4. Large outbreak (among human) 5. Exclusive human agent (only human) ð Not every pathogen will go through all stages! Step 1 to 2: Reasons: Land use Agriculture Livestock (Viehzucht) Bush meat use ð Higher jumping rate Step 2 to 4: Ecological: Urbanization Travel and migration Hygiene practice Climate change Evolutionary: Genetic change in pathogen in reservoir Genetic change in pathogens within human ð Increased transmission within human ð Threshold effect (Schwelle, R0 of pathogen) 9.5 Pathogen reproduction number R0 R0: average number of secondary cases generated by a single primary case introduced into a large population of hosts. R0 < 1 => infected individuals infect less than one other individual as secondary infect (low level of transmission but extinct over time) R0 = 1 => low levels of transmission, infection might persist at low frequency R0 > 1 => spread of infection through population (over 1 can lead to epidemic spread) ð R0 < 1 will not lead to mutation within pathogen (in order to stop mutations, R0 must be below 1) ð R0 > 1 evolution can act upon the pathogen Factors that increase R0 Mass breeding => high contact rate => international trading Migration of virus from remote places to cities due to increased mobility Higher transmission due to higher sexual partner change Evolutionary change in the virus (outside and inside the host) Increased bush meat trades Human expansion into natural habitat Traditional health care and funeral practice Spread in hospitals BIO 115 Annik W. Spreading and virulence of viruses The more virulent a pathogen is, the less it can be spread because the individuals rapidly die or because people can get isolated quickly because they notice that they are sick => extinct Less virulent pathogens have a higher risk to be globally spread because transmission rate is higher f.e: Ebola: very virulent, people quickly died thus not globally spread SARS-2003: spread rapidly but very virulent (immediately sick) => could get extinct => could not evolve SARS-CoV-2: spreads rapidly and is not as virulent as SARS-2003 => transmission rate is high because a lot of carriers don’t know they are sick => many infected people => high chance for virus to evolve / adapt Influenza: seasonal flu due to variation in antigenetic properties from year to year (antigenic drift) ð Antigenic drift: accumulation of small mutation in antigenic properties ð Antigenic shift: major, radical change in antigens Summary: Human history, migration, agriculture, and domestication of animals explain pathogen origin and distribution Emerging pathogens help us to understand how diseases evolve, when pathogens climb up the pyramid and what human activities promote or hinder their spread Pathogen reproduction number R0 is a key parameter, determine the success (transmission) of a pathogen => but not yet a good understanding of evolution between host and pathogen => L10 BIO 115 Annik W. L10: Human-Pathogen Co-evolution 10.1 Co-evolution: evolutionary changes that occur within two or more organisms as a response to interaction between them, and the mutual selective pressures that those interaction causes. Mutualistic co-evolution: interaction is beneficial for both (humming bird – plant) Antagonistic co-evolution: interaction is harmful for at least one organism (lynx – snow hare) 10.2 Antagonistic co-evolution: Evolutionary change in one partner can have dramatic negative fitness consequences for opponent To alleviate (lindern) the negative fitness consequence, the opponent has to counter adapt Low evolutionary potential in one partner can lead to its extinction Population number within interaction comes in “waves”: o Lot of hare => lynx population will go up => more hares hunted => hare population decreases => lynx have less to eat and decrease as well => hare population goes up again Red-queen hypothesis: If one partner adapts, other partner counteradapts and this leads to new selection pressure for first partner to adapt again. If one improves, other improves as well => running but staying in the same place 10.3 Co-evolution can lead to….. …different population dynamics: Selective sweep: alleles get fixated => accumulated improvements in both populaitons Dynamic polymorphism: fluncuation in allele frequencies (Schwankung) …local adaption: Evolutionary changes differ within different “patches”. In one patch maybe well adapted and in another patch it would be maladapted. Local adaption Is often taken as evidence for antagonistic co-evolution Gene x Environment interaction (GxE): When two different phenotypes respond to environmental variation in different ways. A good allele in one time and place may be a bad allele in another time and place 10.4 Host vs. pathogen and their adaptation Evolvability: is the ability of a biological system to produce phenotypic variation that is both heritable and adaptive Human Pathogens Mutation rate: low high Generation time long short Population size small large Selective spread low high =>human have no chance to keep pace with rapid evolution of pathogens => adaptive immunity: protection of the host from pathogens/toxins by immunological memory BIO 115 Annik W. 10.5 Human adaptation to disease Finding association between allele frequencies in humans and diseases: Selecting on standing genetic variation Arising of new allels by mutation Sickle cell allele (HbS) distribution “Sick” allele HbS is recessive and should be selected against and go extinct but HbS is maintained. There is a co-occurrence between malaria and HbS => Heterozygous HbA/HbS individuals have a selective advantage = beter fitness because it reduces the risk of malaria. ð Many mutations in red blood cell genes are associated with malaria resistance Human leukocyte antigen (HLA) selection HLA are part the immune response, as they expose non-self structures on the surface. Enormous allele diversity on human population => Correlation between viral species richness and HLA diversity. Balancing selection leads to dynamic polymorphism in populations => maintains diversity. ð Enormous diversity at HLA / MHC loci evolved in response to pathogen diversity and is maintained by balancing selection 10.6 HLA & Mate choice experiment Better partner if he has dissimilar HLA /MHC profiles ð Sex is good for mixing diversity ð Natural selection acts on behavioural traits ð Pathogens seem to exert selection on human bevahiour (mate choice) Liffe history traits: describe a species / populations strategies related to reproduction (fitness) f.e: number of offspring, timing of reproduction, duration of reproductive period, 10.7 Pathogen adaptation to humans Important pathogen traits: finding a host, infectivity, growth within host, virulence factors & transmission => all these factors contribute to virulence and affect pathogen fitness BUT not all traits can be optimized which leads to trade-offs between growth and transmission rate Too virulent = host dies too soon = resources not used efficiently Low virulence: host survival is too long = no transmission Phases Phase 1: accidental infection, not adapted to the host Phase 2: phatogen starts to transmitting, still maladapted with regard to virulence, rapid evolution Phase 3: virulence settles as an intermediate level where the pathogens transmission success is maximized 10.8 Treatment agains pathogenes Vaccines: injection of pathogen antigen/toxins à adaptive immune system produces antibodies à immune agains infection Response to vaccination: Pathogenes adapt their surface proteins in order to not be recognized by the immune system that were injected with the vaccine => no immunity => new vaccine needs to be made. Or phages lose the “virulent” DNA and become avirulent and thus won’t be attacked ð Vaccination causes arms race, increasing virulence and fatalities for unvaccinated individuals ð Natural selection has favoured pathogen traits (high antigen variation) that allow pathogens to escape vaccines BIO 115 Annik W. Antibiotics The evolution of antibiotic resistance is the result of natural selection. When there’s a antibiotic treatment and only one pathogen with a mutation survives, all new pathogenes will be the adapted mutated version => selection for the adapted. Mechanism of resistance: Prevent drug entry Increase drug efflux Enzymatic activation that cleave antibiotic Modification of the antibiotic to inhibit its action =>Here again, not all traits can be optimizes which lead to trade-offs between susceptible and resistant bacteria =>removing antibiotics after treatment will leave bacteria with bad fitness, as they adapted, which costed and then they are maladapted New approaches: Combinatory therapy: combine two antibiotics because the chance of two random mutations that lead to resistance is very low Phage therapy: page kill bacteria very efficiently BIO 115 Annik W. L11: Microbiome & Cancer evolution 11.1 Introduction to microbiome Higher Organisms Bacteria Fixed set of genes that evolves within organism genes and genetic elements move Share genes with closest relatives share a core genome, differ in accessory genome 20’000 genes 2’000’000 genes =>similar genes =>different genes Microbiome: the collection of microbial organisms within a community 11.2 Characterize a microbiome: Microbes colonize all our external body surface Can be collected by cultivating on media or by sequencing o 16S rRNA by PCR amplification: useful for bacterial identification & phylogeny o shotgun metagenomics without cultivating 11.3 The human microbiome Our body offers many different ecological niches, each selecting for a specific microbial community. High variation in the microbiome composition between individual at all body sites but the functions performed are constant across individuals Positive correlation between microbiome dissimilarity and phylogenetic divergence over time (the bigger the divergence, the more dissimilarity) Diet plays important role to our microbiome How do we acquire the microbiome and how does it change? 1. Pregnancy: microbiome diversity of vagina and gut 2. Delivery: natural birth => Vaginal microbiome, caesarean section => skin microbiome (clear differences) 3. Baby: enrichment, milk digestion 4. Child: diversification of microbiome, digest carbohdydrates =>Microbiome develops from birth to childhood and is influenced by many factors Antibiotic treatments and diet Antibiotics long-term reduce the diversity of microbiome significantly Antibiotic resistance appears and persists after treatment Gut microbiome differs between Western and non-western societies => reduced in western =>Our gut microbiome affects physiology, vegetative nervous systeme and the brain 11.4 Microbiome and human disease: Many links between the microbiome and diseases (correlation vs. causation) o Causation: the shift in the microbiome that causes a disease o Correlation: a disease leads to current inflammation which then selects for another microbiome (its not the microbiome to cause the disease) Mouse model to establish causalities o Change in microbiome causes disease X => infect mice to find out if mouse is diseased or not Microbiome can be used as biomarker for treatments (fecal transplant) BIO 115 Annik W. 11.5 Microbial interaction Assembly of microbiomes Top-down approach: complex sample -> sequencing -> descriptive analyses -> correlation with disease Bottom-up-approach: assembly of microbiomes -> ecological dynamics (interaction) -> evolutionary dynamics -> identify forces that lead to healthy microbiomes Interaction: Bacteria often interact through the secretion of small molecules competition: release toxins to fight each other Cooperation: share resources through enzymes =>difficult to find out which factors lead to a dynamic and stable microbiome 11.6 Cancer evolution What leads to cancer: Germ cells: genetic predisposition to develop cancer Somatic cells: cancer is a somatic process of mutation-accumulation and selection => a sequence of events is needed for a healthy cell to turn into a cancer cell Key mutational targets: Oncogenes: control cell growth => mutation leads to uncontrolled growth Tumor suppressor gene: removes damaged cells => mutation leads to proliferation of damaged cells DNA repair genes: DNA errors are fixed => Mutation leads to remaining DNA errors Carcinogenesis: development of cancer Multistep mutational process Associated with chromosomal insability Tumor mutations need to be on both copies to be harmful (one can partly compensate for the mutated gene) 11.7 Tumors: Tumors consist of multiple cell lineages => own little ecosystem Each tumor is unique => makes it hard for therapy Social interaction between tumor lineages o Negative interaction: one is harmed (competition) o Positive interaction: one is benefited (cooperation, synergism) =>interaction is very important for tumors: tumor growth, metastasis, therapeutic resistance Therapy: Targeting selfish or neutral cells Targeting cooperational cell lines, which provide servise to others 11.8 Cancer lottery The cancer lottery: given ó lottery ó consequence Given: Lifestyle: diet, smoking Genetic disposition Exposure to mutagenic agents (radioactive radiation, UV, chemicals) Evolutionary trade-offs: Consequence: BIO 115 Annik W. Mutational patterns Selection Cancer adaption Fatale consequences 11.9 Trade-offs: 1. Evolutionary trade-offs: DNA double strand breaks: recombination is beneficial ó chromosome instability Tissue regeneration: regeneration capacity of stemcells ó immortal cells that replicate Inflammation: remove pathogens ó causing DNA damage =>either get rid of these characteristics or have cancer under control => has no eyes for the future, selects for what is best in the moment => winners of today are the loosers of tomorrow 2.Life history trade-offs: Dark skin -> out of Africa -> light skin -> Australia -> maladapted -> increased skin cancer risk Women have less babies -> less pregnancies -> different hormone levels -> breast & ovarian cancer Growing up in clean environment -> low exposure to pathogenes -> evolutionary mismatch -> modern disease like asthma, allergies, diabetes and leukemia Why is cancer not selected against? Cancer mostly evolves in older people after they had offspring (after reproductive period). Natural selection selects for good fitness of individual. Selection against any kind of disease that manifests after reproductive period is absent or weak! Peto’s paradox: no correlation between cancer incidences and body mass longevity What we think: Elephant has a higher risk of cancer than mouse has. => Wrong! Elephants have 20 tumorsuppressor genes Elephants have a better DNA repair mechanism than a mouse => less mutations