BIOS101 W10: Microevolution to Speciation & Natural Selection in Genetics PDF

FROM MICROEVOLUTION TO SPECIATION. NATURAL SELECTION IN GENETICS - Microevolution speciation - Apply genetics to Darwin and other aspects of evolution, see how evolution works when we understand genetics and diversity - Evolution is change over time - Within the species, over a short...

FROM MICROEVOLUTION TO SPECIATION. NATURAL SELECTION IN GENETICS - Microevolution speciation - Apply genetics to Darwin and other aspects of evolution, see how evolution works when we understand genetics and diversity - Evolution is change over time - Within the species, over a short period of time -- in the gene pool - microevolution - Or evolution in the type and number of species, over a longer period of time -- macroevolution - Macroevolution is how and when everything came about - Microevolution Is about evolution within a species -- why did z change happen in the peppered moth? Why can only some people drink milk? - Differences between species -- two variating species, what processes made them different - How did humans and chimpanzees come to be different, even though they have the same common ancestor? - Why does variation exist, in spite of natural selection? - What are the evolution processes going on within species that lead to species differing from each other and their phenotype and their adaptation? - Microevolution is about all of these questions A screenshot of a cell phone Description automatically generated PROBLEMS WITH DARWIN'S MODEL OF NATURAL SELECTION - Wrong with the assumptions he made, but when you add genetics, these assumptions now work - Genetics rescues Darwin's assumptions -- give examples, proof - Natural selection happens, but not under the conditions he imagined - Natural selection says -- you take a trait, which is good, it's selected on because it's good, everyone becomes of that form - Produces the same form, optimal phenotype - Why it is that despite natural selection promoting the best form, actually everybody is different - Natural selection, as Darwin thought of it: - If variation exists in populations -- things look and behave differently - If some of this variation is heritable -- parents and offspring were more like each other - If some variants survive better than others -- there is a better form of organisms to survive and reproduce better, depending on their biochemistry and physiology - THEN, next generation of population will be biased to variants that are better adapted, have the better form =\> a greater mean number of offspring - They become better adapted over many generations Major Problems 1. Process gets rid of genetic variation - By the end of natural selection, every peppered moth is the same - Darwin's model doesn't have variation, everything becomes the same, the better form - Therefore, naturals election can't happen again, it can only happen once - There is no typical form left - The best form is gone to fixation 2. His model of inheritance wasn't very good -- blending inheritance destroys existing variation - Blending inheritance -- everything comes out as the average of their parents - Red and white parents produce a pink progeny, no genetics, everything was a mean of their parents - Without any form of natural selection, everything becomes the same -- if you leave different species to go through natural selection, if every offspring is an average mean, in the end, they would all be the same - THINGS MUST VARY in order for natural selection to happen, but Blending inheritance gets rid of variance - Everything he says in his book about genetic and natural selection gets rid of variation, which is the first IF for natural selection to happen - He creates a thing that can happen once, but never again - His theory didn't work with his assumptions - We can make it work, add genetics and knowledge of DNA -- how our phenotype is underpinned by our genes - Mutation generates variation, permits novelty (mutation) - Mutation = Latin for change - Phenotype isn't constant - Mutation -- progeny has a part, which is from neither parent - We are a combination of our parents' genes, but we have some, which are unique - Mutation generates novelty outside of inheritance - If you keep fruit flies in the lab for long enough, you'll see visible mutations, which have never been before - Mutation saves Darwin -- novelty is constantly being generated, particularly during meiosis - If you keep fruit flies in the lab long enough, you'll see physical mutations between generations - Novelty is continuously generated - You are copies of your parents with changes - Mendelian genetics maintains variation, doesn't just disappear by averaging -- add Mendel's model to Darwin's assumptions and it works - Darwin's ideas + Mutation + Mendel solve Darwin's genetic variance problem - Mendelian genetics say that variation is preserved, it's not just removed by averaging - In Mendel's model, if you have your red and white parent, you get pink progeny - Cross the pink progeny -- you can get red and white again -- variation is preserved - The fact that natural selection gets rid of novelty doesn't really matter anymore because there are mutation and Mendelian genetics EVOLUTION IN THE ERA OF GENETICS 1: MUTATION - How traits form from genes -- Darwin didn't have that - Population size is one of the most important things to promote evolution because it promotes mutations Types of Mutation - In terms of DNA, gene expression, genes - When you look at a chromosome, 99% of it doesn't really make a protein, just little regions (genes) - Genes are in big islands of DNA sequences - Genetic code is degenerate -- 64 different triplets, 20 amino acids -- many of the amino acids are encoded by the same triplet - Mutations in exons (coding regions) can be 3 types - Silent -- no effect on the protein, a single change, change in heredity material, but doesn't affect the protein produced because the amino acid is identical, no phenotypic effect - Missense -- when you change the base, which changes the whole amino acid sequence, adds a different amino acid may have a phenotypic effect - Nonsense -- knockout mutation, stops the protein being produced, adds a stop codon, knockout the presence of the protein  A diagram of a sequence of dna sequence Description automatically generated Other Mutations May Affect Gene Expression - Change the gene expression (when and where the gene is produced), not the sequence - Gene, encoding the protein - To make a protein, we need to have RNA polymerase to bind, it requires a transcription factor to be present, - The transcription factor sits against the promoter - It may also be activated by a factor, called enhancer/activator, or the silencer, which prevents transcription - Changes in these sequences - silencer, enhancer or the promoter, can change when and where the genes are transcribed, changing the phenotype - Changes in any of the three can change whether the protein is produced or not, and when and where - Quite a lot of genetic variation is how much of a specific thing is produced - Many of us may have the same genes for particular things - But whether or not this gene is expressed and when and where varies - Our genome is 99% identical to chimpanzees' genome -- the differences come in when and where these genes are expressed - Changes in exons may affect the whole protein, changes in gene expression affect whether that protein is produced or not - Gene expression is key in development - It determines when in development is the protein produced - Which cells and tissues it is produced in - How much of that protein is produced - Key differences between us and chimps is when and where the genes are expressed, even though we share 99% of genes -- what microevolution is all about - A lot of variation between individuals is variation in gene expression Other Mutational Events Have a Larger Effect - Macromutations -- big changes, big mutations - Gene duplication -- gene duplicated, 2 copies instead of 1 - Novel genes -- not today (some genes are present in humans, but not in yeast, and the reverse) - Endosymbiosis -- mitochondria and chloroplasts were big genetic events through endosymbiosis - Changes in karyotype -- we have a different chromosome number than chimpanzees, most taxa vary in their chromosome number from their neighbors - Polyploidy -- genome doubles, genome duplication (jawed vertebrates erose from a genome duplication event) DOES EVOLUTION USE SMALL OF LARGE EFFECT MUTATUONS - Which types of mutation are important for evolution? -- Mutation varies from very small changes to profoundly big consequences - Normally, the small things - Big mutations screw up the organism, it dies and gets selected out -- not able to keep the change going - Most large-effect things are deleterious, big screw-ups - Even when natural selection gets rid of variation, mutations are constantly reintroducing it, so that we never get rid of all variation Dogma: - Small effects allow for gradual evolution of a time - Small effects are much more likely to be beneficial -- small effects bring small changes, allowing for a gradual evolution over time - Big changes make organisms die off and not keep the heredity line - Most selection on mutations of small effect -- gradual, slow changes - Large things are usually screw-ups Macromutations are important in Microbes (An exception) - Analysis of microbial genomes -- they have a different way of mutation - They have the classic mutation -- individual base pairs change, but - They can also acquire a bit of genetic material from the outside world at a fast rate - Widespread genetic material transfer between microbes - Microbes acquire a lot of DNA, which sometimes stays in their heredity material - When this happens, you get whole different genes being introduced to them at one point in time - These sets already had a complete function microbes acquire that function - Example: Antibiotic resistance spreads commonly because it spreads as a block, as a complete function, which is beneficial for microbes - It's not that all different bacteria/microbes are evolving antibiotic resistance, they acquire it as a w hole -- DNA has gone in one, which spreads it to another one\... - That's a case of macromutation -- a whole DNA segment, which is beneficial And Sometimes in Eukaryotes - Symbiosis -- origin of eukaryotes and photosynthetic eukaryotes - Acquisition of a bacterium, which did a particularly good evolutionary function - Genome duplication -- created hox gene complexity in jawed fish, enabling vertebrate evolution complexity - Big things are bad in eukaryotes, on little occasions they are important in the history of life, evolution INFLUENCE OF POPULATION SIZE ON MUTATION AND ADAPTATION -- - Population size is one of the most important things, underpinning how evolution happens - Every time meiosis happens, there are some errors, some mutations -- mutations happen every meiotic division - In humans, there are 40-50 errors in a meiotic event - Increases with age in males - This means that the number of mutations in a population is a product of the size of that population - Each individual has meiotic events, each meiotic event creates mutations more people = more meiotic events = more mutations - The more individuals, the more meiotic events, the more mutations - Humans have a massive population size -- more chances and less time to acquire a mutation - Each base has a mutation rate of one in a million - If you have a population of 1000 people, a particular mutation to occur needs 10 x 10\^6 years - Because there are 7 billion people in the world, every nucleotide that can change, does change in at least one person every generation - Any single nucleotide mutation that can happen, does happen within our human population - If you take a smaller animal population, mutation isn't happening enough -- evolution is constrained, slowed down - Not enough errors occurring - If variant does not exist in a population, if there is a novel threat, if the population didn't have the variant to kill it, then - The population will wait for the mutation to happen -- the mutation to fight the threat - A small population will wait a very long time - So, a small population size have slower adaptations by lower mutation rates - More meiosis = more errors, more errors = mutations happen more rapidly - Large populations have more meiotic divisions, more chances of mutations more changes HIV Example -- Useful Small Populations - This can be very useful in medicine -- HIV therapy - In 1987, the first drug came out, which suppressed virus for 22 weeks before HIV evolved resistance to it - HIV is a very fast evolving virus, emerged in the 1980s, very lethal - We can invent drugs, but the virus will develop resistance to it because they have a higher mutation rate - The drugs, which knock HIV out, if used in combination, will knock out the infected cells and tissues so low, that mutation rate became very low, and the virus didn't evolve in response - How, we use triple therapy -- 3 drugs at once, which acts very differently, so that resistance takes a long time to evolve, virus has to evolve 3 different mutations to become resistant, virus doesn't evolve drug resistance - Anti-evolution therapy -- knocking down population sizes to tremendously small numbers to constrain mutation of the virus EVOLUTION IN THE ERA OF GENETICS 2: MENDEL AND INHERITANCE - Natural selection when variation exists in populations - We never get rid of variation - Mendel's idea is that some variation is heritable, and the population starts to look like those variants - Some variants survive better than others - Genotype underpins phenotype - Traits are underpinned by variations between loci - Simple genetic basis -- traits are underpinned by one or a few loci (particular bits in the genome) - Complex genetic basis -- traits are underpinned by variation in many loci, we call them quantitative traits - Population genetics -- Measure the frequency of differences between loci, use segregation patterns and mathematical biology to work out how evolution is going to happen - Complex genetic basis -- underpinned by genes of many loci - At a genetic level, traits would come from bits of different genes - We call them quantitative traits -- height (underpinned by 12 000 different loci) - Can't track individual loci, that's why we track the entire phenotype Simple Genetic Traits - We can measure frequency of alleles from data, and observe changes over time - We can do that by directly genotyping people -- sequence a person, tell directly what they are going to be - Score genotype of individuals calculate frequency of alleles - F (A) = 20 x w + 10/(35x30=50/70v= 0.71 -  Example to do: - Photo - Fruit flies are very alcohol-resistant - Alcohols resistance is underpinned in a locus, called ADH (Alcohol dehydrogenase, detoxifies alcohols) - It does it fast or slow - F -- fast enzyme - S -- slow enzyme - See the changes in allele frequencies happening over time -- the basic way to understand evolution for particular simple genes, we see the change happening A close-up of a bug Description automatically generated - Year 0: (2x2 + 1x5) / 30 x2 = 9/60 = 0.15 - Year 10: (2x20 + 1x7) / 30x2 = 47/60 = 0.783 Modelling Selection on Mendelian Loci - In 1930, 3 different people (Wright, Fisher, Haldane) said that -- if you understood genetics and natural selection, put them together, you could model the evolution of individual traits, called population genetics - You needed to know genetic basis of the trait, selection, whether or not there was sex, to work out evolution - The thing that matters most on evolution is whether a TRAIT IS DOMINANT OR RECESSIVE - Dominant alleles -- phenotype when heterozygous, phenotype seen when allele is rare, can be selected when rare - Recessive alleles -- phenotype only as homozygous, don't have a phenotype, when rare, spreads slowly - If something is dominant and beneficial, it spreads really fast, but if something is recessive and beneficial, it spreads very slowly - =\> Evolution is strongly biased to mutations and traits, which are dominant  Quantitative/Complex Traits - Height varies amongst all of use -- there are 12000 loci that affect our height - Many aspects of phenotype are the sum of many genetic loci - Heritability -- how close are you to the midpoint of your parents - We can model heritability - If something is truly heritable, our phenotypic value will be the same as the value of the parents -- if you have 2 tall parents, you'd most likely be tall - You can have quantitative traits, where your parents really matter and some, where they don't - Parent-offspring correlation - If a trait Is 10% heritable, then the correlation to your parents would be a lot weaker - When you have that value and natural selection, you can model evolution - The response to natural selection is related to the selective coefficient of heritability - Stronger the selection, the higher the heritability, the stronger the response - Even if the selection as strong, if the heritability is weak, the response will also be weak -- only a certain amount of variation exists because of genes - R=h2S -- change in phenotype between generations is a response - Response = heritability x selection - magnitude of selection is heritability In reality, Complex to Model - However, the model works on 1-2 generations, then it stops working - Reason 1 - as you select on the trait, you get rid of a genetic variation. What heritability is in one generation, is NOT at another -- quite a lot of genes are removed - Reason 2 -- Heritability depends on the environment. H\^2 varies between environments. People, who came out of WW2 because of the food rationing were quite short -- not enough food. After the war, where there is no rationing, people came out taller. Heritability depended on how much food there was -- the environment - As selection proceeds, genetic variation reduces heritability declines - Heritability depends on the environment - Heritability can vary between the generations Summary - Incorporating mutation and Mendel into the theory of natural selection makes the process work - Variation is generated and maintained in the absence of selection - Mutation rekindles variation - The process of natural selection works really well with Mendelian inheritance UNDERSTANDING GENETIC DIVERSITY - Things do look different; we are all different from each other - In every 300 base pairs, there is a difference between us - Things are extremely variable Paradox of Genetic Diversity - Natural selection should drive good things through fixation - If it drives bad things, we should get rid of it, if it drives good things, we keep it - Natural selection is both positive selection and purifying selection -- drives beneficial things through and gets rid of bad stuff, which make us less well - This naturally gets rid of variation - Every organism on the planet has genetic diversity - NT tells us that variation shouldn't be variable - Genetic diversity is abundant! -- How do we explain it? Different Types of Genetic Diversity - Some changes are bad, make us less good -- a stop codon on a protein, which is bad - Three types of variations: Deleterious, neutral, advantageous - Bad, neutral/don't affect fitness or usually phenotype, good/beneficial - Look at the genetic diversity and look for answer to understand why we have these variations, which are bad -- why genetic diseases persists? Diversity and Different Forms of Variant - Deleterious mutations - Natural selection should get rid of them; they are making us worse - If natural selection is so good, then why do genetic diseases persist? - Neutral mutations - Not subject to selection - Why more in large populations? - Advantageous mutations - Subject to positive selection - The things that are most likely to be beneficial are changes in amino acid sequences or changes in gene expression - Why do some remain variable? WHY DO GENETIC DISEASES PERSIST? - On average, each person carries 4 lethal/deleterious mutations - Usually, such mutations are recessive -- changes of function, which lose a particular aspect, they have little phenotypic effect - They get dangerous when they are homozygous recessive - As long as we have one working gene that makes the protein, we are ok - Most people are carriers, or the deleterious mutations have a little phenotypic effect, make a bit less healthy - Mostly, individuals have different lethal mutations -- each genetic disease is rare - 2 people may have all 4 deleterious mutations different - Most of the mutations are on carriers, make us a bit less healthy, but don't kill us - Mutation is a selected equilibrium - New deleterious mutations happen every meiosis - 40 mutations per meiotic event, 1 of those is likely to be deleterious - Selection removes them because they are bad, BUT -- it removes them very slowly because they are always recessive - Dominant traits, which are advantageous spread very quickly; recessive advantageous traits spread slowly -- this works in reverse in genetic diseases - In genetic diseases, because it's recessive, it is selected against very slowly to start with because it's not matching itself -- it's not producing a homozygote, and therefore, it's not producing a phenotype to be selected against, whereas a dominant one would be - So, we get a genetic load - in any natural population, most individuals carry 4/5 deleterious mutations - Most people carry different deleterious mutations each genetic disease is rare Some Genetic Disease are Quite Common - Some genetic diseases are quite common in certain populations - Different populations have different genetic diseases commonly - Cystic fibrosis is the most common disease in Europeans -- a single autosomal recessive - Allele frequency is 2% - quite high - 1/25 people are carriers - 1/625 pairs of parents both carry the mutation - 1/2500 births - A recessive trait, the only way of getting that is to have 2 carrier parents A diagram of a family Description automatically generated How can Something That Bad Can Get That Common? - Selection is weak to start with - People go through population bottlenecks - We start with a large population with large genetic diversity - At some point of time, the numbers of individuals go down (due to movement, famine, death...) - At some point, number of people shrinks and some of the variance becomes high frequency, by virtue of being in the individuals, which survive - After population size recovers due to breeding, you get a genetically simplified population - Quite commonly, in animal populations, things go through bottlenecks -- periods of time when the population size is small, during that time genetic diversity is lost, and what's left goes up in frequency - Bottleneck effects produce higher variation of genetic disease, just by chance - Genetic diversity is lost, what's left goes in a bottleneck - This is seen mostly in small, closed societies, where breeding is present - Amish -- Ellis-van Creveld syndrome, common in the Amish because they almost always marry another Amish person - 1 in 8 founding fathers of the Amish had this mutation - 1 in 8 males are heterozygous for this mutation - This allele expanded - Ashkenazi Jews -- Tay-Sachs disease - Often, they get tested whether they are carriers before marriage, if they are, they don't get married - When individuals come out of the bottlenecks, they come out with many genetic diseases  A baby\'s hand and a diagram Description automatically generated Summary - Alleles, causing genetic diseases are present because mutation is recurrent - Selection removes them, but does so slowly when the diseases are rare (most of them are recessive) - Therefore, there are many different mutations, all rare - Founder effects make particular genetic diseases more common NEUTRAL MUTATIONS NOT SUBJECT TO SELECTION - Majority of variation is neutral - Neutral mutations don't affect phenotype - Outside of genic regions - In introns - In third base pair positions, no aa change affect phenotype in insignificant ways - Small populations have least diversity - As population size increases, the difference between 2 individuals increases - Large populations have more genetic diversity -- needs explanation - The answer comes in an evolutionary process, which is NOT natural selection - It is the genetic drift - How does the frequency of neutral variants change? - Genetic drift -- the random sampling between 2 populations (some individuals reproduce, some don't, or die in random ways) - All that randomness does produce changes in allele frequency - Every neutral mutation has a chance of spreading into a population - Eventually, every neutral mutation will be fixed or lost - Either all individuals will look like it, or it will just get lost - How quickly that happens depends on population size - The randomness in smaller populations is much bigger than in bigger populations -- more chances of getting a significant change (tossing a coin 10,50,100 times -- chance plays role in more long-term and bigger events) - Magnitude of the drifts is much bigger in small populations - In small populations, neutral mutations are fixed or lost very quickly -- they don't hang around for a very long time, but in large populations, they hang around for a lot longer time because the random processes are weak - This explains why large populations have so much variation - Small populations have lots of sampling and lots of sampling errors because there are only a few reproduction events going on -- large amounts of randomness - Large populations -- less randomness neutral mutations hang around for a longer period of time - That can be lost very quickly -- bottlenecks, things go down to small populations, which tend to dominate the amount of genetic diversity - Variation reflects history of population size, not current size Consequences - Things with very small population sizes will have a very small genetic diversity - When things change and some of the diversity is useful, the things become less evolutionary responsive - In nature, if you see a difference, it's going to affect fitness in some way - Classic model of natural selection: beneficial mutation - Positive selection -- mutation increases in frequency - Everyone has it in the end - What is it about natural selection that allows us to maintain diversity of phenotype for stuff that is obviously affecting us how well we survive, or solve certain environmental problems - One solution -- as soon as the problem is solved, the problem changes -- evolutionary lag, evolution lags behind the environment - Best phenotypes may change over time - It takes time for nature to promote the best form - Peppered moth takes 50 generations to promote the best form - So, if the environment is changing all the time, natural selection doesn't have time to fix the best trait. By the time it has a form to high frequency, the best form has changed - Evolutionary lag - maintaining phenotypic variation because what's best is changing over time - There are certain circumstances in nature, where there is change ALL the time - Cases, where different species interact with each other - Example -- parasites and pathogens in their hosts - Tapeworm -- its fitness depends on eating food in your gut, its eggs go into your poo, they are taken somewhere else and go onwards. A good parasite uses you and doesn't get cleared out - Parasites' interests are feeding off of you without being recognized - That's bad for us -- we need to get rid of it - The parasite evolves to exploit the host better, the host evolves to get rid of the parasite -- as the parasite evolves, it produces selection on the host to get rid of the parasite better. Selection in one party is bad for the other - They drive each other's evolution - Coevolution/cyclical evolution - This gives rise to the idea of the "Red Queen effect" - even if the environment was completely static, parasites would evolve to better exploit the host, and the hosts would evolve to get rid of the parasites better. Evolution would continue, natural selection is ALWAYS happening - The metaphor -- run to stay still. We need to change, otherwise we'll get exploited - In evolution, if you don't run, you get exploited, things will get badly wrong - If we want to continue our lineage and don't get exploited or die out, we run, evolve and adapt Other solution: Balanced Polymorphism - Variation is maintained by natural selection - 3 circumstances when that happens: - Segregated variation (genetics), heterozygote advantage - Environmental variation with gene flow (in any particular population, what's best varies over space, animals move) - Frequency-depended selection (some things are good, but only when rare) - Segregated variation -- when heterozygous is the best form - Best form has both alleles, producing a heterozygote advantage - Sickle cell anemia -- happens when humans are homozygous recessive - In West Africa, heterozygotes allow resistance for malaria AND defense against sickle cell anemia -- allow for highest fitness - Individuals that are heterozygote are best fit - Individuals homozygous dominant are resistant to anemia, but have no defense against malaria - Best form -- heterozygote, has both forms - When the heterozygotes breed, they produce the other 2 forms -- maintain variation - This explain why sickle cell anemia is common in West Africa - That allele isn't advantageous in Europe because we don't have malaria, but it IS in West Africa  - Spatially divergent selection with gene flow - An animal form lives in more than one place, different environments, so there are different phenotypic solutions to these environments - Sugar content of milk is lactose - Digestion of lactose requires lactase enzyme - Every infant has lactase -- we are mammals, BUT - Adults vary -- persistent in some, not in others (Lactose intolerance). Variation whether lactase is STILL produced - In some people, lactase is produced in the first 2 years of life, then it stops -- if they drink lactose products, they get very bad - All due to the point mutation lactase persistence - Various human societies keep cattle -- lactase persistence is very common - Yellow are cattle-keepers -- they drink milk all the time, they are used and developed to drinking it, others not - Societies, which didn't drink milk ancestrally, they haven't evolved lactase persistence -- why would they? No lactose to digest - In Japan, it's hard to buy milk -- there is a lot of lactose intolerance A collage of people in different clothes Description automatically generated - Mutation spread only in human populations where cattle domesticated - Lack of fixation in these populations: incoming genes from people coming from the outside - Presence in other populations: movement out of pastoralist societies Frequency-Dependent Selection - Things are good, only when rare - E.g. predators learn to detect common prey: snail - If you make yourself look different from everybody else, predators don't look at you because they aren't used to you. Only when you are common, they'd figure out you are edible - When things are rare, they aren't predated - Rare cryptic types can invade -- when rare, predators don't attack them - Rare things have an advantage -- we get diversity because new rare things are coming all the time - Handedness in humans -- a possible example - LH -\> 10% is heritable - A strong genetic presence - 82% concordance between identical twins - If you have a left-handed parent, you are most likely to be left-handed - Left-handedness is inconvenient in different ways -- why is it there? - It must be that it has had some advantage at some point in time - Left-handedness has persisted at exactly the same frequency between the Paleolithic and now - Left-handedness is most common in violent societies - if people are coming at you with a sword or a stick and they presume you\'re right handed, left handed more likely survive because they do the wrong thing  SUMMARY - Genetic diversity is high: - This is mostly associated with neutral mutations, whose frequencies undergo a random walk "genetic drift", producing diversity in large populations, compared to smaller - Deleterious mutations persist across multiple loci at low frequency -- mutation-selection equilibrium - Natural selection can also maintain diversity NATURAL SELECTION: BEYOND THE BASIC MODEL SEXUAL SELECTION Session 2 27/11/2024 COMPLEXITIES OF NATURAL SELECTION - Explain why in nature, you find animals being nice to each ither -- altruistic, behavior - How do organisms adapt to varying environments? - Is natural selection perfect? WHY DO WE SEE ANIMALS BEING "NICE"? - Darwin couldn't explain why did he observe animals being altruistic - Competitive struggle -- massive reproduction, lots of dying, fierce competition for food - Individuals would directly fight for food, they would be out for themselves - Those, which were good at outcompeting the others, were the ones to leave their genes to the next generation - This suggests a lot of selfishness -- animals are out for themselves - However, we see quite often animal behaviors, which are helping other individuals - How can we have a competitive struggle, but also be nice and helpful to others? - How do we explain being nice? -- altruism - Behavior beneficial to others, but costly to the individual - Example: termites - The queen termites is an egg machine -- she just reproduces eggs and gets fed - The other sibling termites take care of her and her eggs, take them away, but never reproduce themselves - This is a problem worldwide -- what's the point of being nice? The Problem of Being Nice - Costly to ourselves - A selfish individual produces at the maximum rate (4 babies, for example), an individual, which helps others would produce 1 baby - The next generation would be found by the babies of the selfish individual - In general, natural selection would produce individuals, which are selfish, invest in themselves to survive and reproduce, instead of others - Most animal species show some level pf altruism - 2 types of altruism: - Helping relative -- helping your genes, helping your sister to reproduce conservates your genes. Helping your genes to reproduce. A dominant way, which individuals have evolved to do altruism. Your reproduction and genes are not just in you - Give now, receive later/reciprocal altruism -- mutual benefit, forming coalitions with other individuals. A diagram of a diagram Description automatically generated Answer 1 -- Be Nice to Relatives - W D Hamilton (British scientist, 1960s) -- genetic inheritance goes on not only from individual reproduction, but from the reproduction of your relatives - 100 years after Darwin - Not only can you gain fitness through your own progeny, but you can also gain it from your siblings because they are 50% related to you - Siblings have similar genetics to you -- if you help them, you help your genes to be preserved, you help yourself - Hamilton's rule: - Fitness benefits can be gained: - Directly, through producing and raising own offspring (selfish) - Indirectly, through helping to raise offspring of related individuals (kin selection) - Total/Inclusive fitness = direct fitness + indirect fitness - Inclusive fitness -- total fitness for yourself, a combination of direct and indirect - In genetics, not only your own reproduction matters, but the reproduction of your siblings matters - In nature, most of the help comes from relatives, not random individuals Answer 2 -- Reciprocal altruism - Not all altruism involves relatives - If you scratch my back, I'll scratch yours - Private grooming -- removing ticks on the backs from other primates - An individual can't do this themselves - Being nice to other individuals, so that they are nice to you later - Integrated for lot of periods of time - Many primate species and species beyond primates show reciprocal altruism - Many primates watch behavior of individuals - If an individual decides to not return the favor, they are never going to be groomed again - The bad individual develops a bad reputation - Relationships breaks down -- the bad one won't get the niceness back - The bad individual will be known by the others as a deal-breaker and won't be helped - I do this to you now, you'll help me later - Cooperation between individuals, who interact on a daily basis -- needs recognition - Only if you can recognize the other individual, then you could have reciprocity Summary - Although there is a competitive struggle for existence, it's not the only way of getting fitness - In the struggle for existence, we must remember that: - Extended families, kin selection and maximization of inclusive fitness -- natural selection optimizes inclusive fitness, not individual fitness. We should be nice to our relatives - Benefits from reciprocal actions -- reputation and reciprocal actions produces an alliance for future cooperation in the long-term, producing higher fitness HOW DO ORGANISMS ADAPT TO CHANGING ENVIRONMENTS? - Natural selection produces adaptation over many generations - Natural selection is good for long-term changes in alleles -- next generations are more adaptive, survival goes up - But organisms live in variable environments - Within generations: - Seasonality -- winter and summer, different conditions. Natural selection has to produce an organism, which can cope with both winter and summer - Heat waves and cold snaps -- organisms need to survive these extreme conditions - Between generations: - Light/shade environments for plants -- better environment for germination - High/Low predation environments -- more safety - An organism has to live and solve the problem of variable environments -- it doesn't know in what conditions it will be born How does natural selection maximize fitness in changing environments? - Best form is one that can change to suit to the environment, not a fixed one - A form that can change its biology, in association to its environment - Adaptive phenotypic plasticity -- a property of an organism to change its phenotype so that it's more fit to the environment - Change in phenotype, NOT genes!!! - Plasticity - change - Natural selection selects genes, which can do that - Genes that are good in winter, but can also change in the summer - Obvious example of phenotypic plasticity: - Mountain hare (rabbit) -- the form that is best against predators in summertime is different than the form that is best in the winter - When there is snow, it is white, when it is summer, it regrows its color to brown - White is hard to see in the snow, brown is hard to see in the summer - What natural selection has produced is a gene expression change in losing white hair in the summer and losing brown hair in the winter - White hair is produced in the summer through a particular gene expression, brown hair is produced in the summer through a change in the gene expression - This adapts the hare to the environment - Adaptive phenotypic plasticity ensures that hair is adapted in all scenarios, camouflaged in all seasons Some Vary Between Generations - These adaptations vary between generations -- mountain hare changes every generation, every year - Example - water fleas develop with "helmets" if predators are present in the water during development - Sometimes the water has predators, sometimes it doesn't - If it senses predators early on, it changes its phenotype - The evolved form requires the predators to have a bigger mouth to eat it - Predators leave chemicals in the water, the water fleas smell it during development, which tells it whether to develop in a different way - One has been exposed to a predator early in development and grows and develops into a much different form, but they have the same genotype, no change in gene frequencies - Same genes, phenotype change, based on the environment - Same genes, but different expression of these genes, tailored to enhance survival for the environment encountered - Genetic systems that produce epigenetic variation -- variation in DNA sequences, whether or not a gene is expressed, depending on the environment (usually by methylation) - Adaptive epigenetic variation produces adaptive phenotypic plasticity - Phenotypic plasticity leaves epigenetic marks on certain genes, which tells them whether they are expressed, or not expressed, depending on the environment  Learning the Ultimate Plasticity A diagram of a blue arrow Description automatically generated - In nature, completely unpredictable things could happen -- animals need complicated cognition to solve these problems - We have a brain system, which doesn't need to have seen a particular problem before in evolutionary terms, in order to solve it - Our brain systems can assess environments never see before and alter behavior dynamically to optimize our survival in these environments - Learning and complicated cognition is the ultimate plasticity that natural selection comes up with - 2 types of behavioral learning: - Associative learning -- when animals spot patterns and respond to those patterns in the future to maximize their survival - Insight learning -- experimentation/play to solve a problem, more complicated than associative learning - Associative learning is found in most mammals, birds, fish, cephalopods - Takes 3 forms: - Observational learning -- learned by direct copying. If an individual has seen another one solving a problem, it will copy the solving mechanism - Classical conditioning -- if an animal is exposed to a certain thing, like the sound of a farmer rustling outside in the morning, the chicken works out that this is the time for feeding, the chicken will go to the door at the sound of the rustle, not at the sound of the food - Operant conditioning -- giving a reward, in response to a particular behavior, used in training animals - Insight learning - Most complex cognition evolved - Found in birds, some mammals and cephalopods - Applying knowledge of the world to solve a problem without trial and error - Crows, solving many problems and tasks -- learning to use a curved wire to pick up food. If you give it a straight wire, it will learn to curve the wire, so that it can pick up the food again - This has never happened in nature, but the crow is using its brain and map of the world to solve the problem - Complex cognition allows for animals to solve a problem they've never seen before  A bird pouring a glass of water into a container Description automatically generated Conclusion - Natural selection is good for adaptation to a constant challenge -- favorable mutations that increase survival in that environment - Mostly, natural selection produces organisms, which can fit in every environment they are put in - One of the ways it does that is through adaptive phenotypic plasticity, where gene expression changes according to the environment -- not a particular environment, across all environments - It also -- adaptation to varying challenges -- favoring mutations that alter gene expression to produce phenotypes that fit the current status of a variable environment - Selection can produce complex cognition -- Learning and complex behavior to maximize fitness in changing worlds HOW GOOD IS NATURAL SELECTION? - Does it produce perfection? -- NO Case of "Bad" Design - Cases, where natural selection produces solutions that are better than no solution, but not the best solution - Oesophagus and trachea - We have a mouth -- it goes to one of 2 tubes -- for breathing and for eating - This is a solution, which sort of does the job, but then it could lead to choking -- it is dangerous - Far from the best - Natural selection doesn't produce perfection, but if you made the selection strong enough, it would produce a two-tubed system -- whales - Whales' mouths are in water for feeding -- they don't want mouths for breathing, too much pressure between air and water, they don't water to go into their body - So, they have a separate breathing tube that comes up on the top of their heads, where the oesophagus goes - Natural selection is much stronger in whales, in humans it isn't as strong whales have a two-tubed system - Natural selection doesn't produce perfection, but it could produce change - Selection is stronger in whales - Natural selection works on genetic variation, and with some constraints, not perfect solutions all the time. Reasons why: - Population size limits efficiency of selection - Poor fitness of intermediate form - Best form is not genetically pure Efficiency of selection - Evolution can proceed by genetic drift or by selection - Genetic drift -- random changes over generations - Magnitude of drift (amount of change) depends on population size - Large changes in frequency at small population size - Natural selection needs to be thinking of a big enough magnitude to overcome the wobbling around allele frequencies - As well as neutral mutations, we have "effectively neutral mutations", which have a much smaller selective coefficient - Natural selection as a force is much weaker than the genetic drift - In small populations - purifying selection is less efficient accumulate mildly deleterious mutations - If something has a 0.1% deleterious effect on your fitness and the population, small natural selection may not be able to get rid of it - Small populations will accumulate mild deleterious mutations - Positive selection is also impacted -- early beneficial alleles may not spread - If your population\'s too small, genetic drift stops advantageous things being spread and stops disadvantageous things disappearing. Impacts - Perfection of adaptation is much higher in large populations - As populations get bigger and bigger, the effect of the genetic drift goes down, natural selection becomes much stronger - Degree of adaptation highest in large populations -- bacteria - If you take a bacteria population, which has millions of individuals, then natural selection is a very good optimization process because even mild deleterious mutations can be gotten rid of, and mild advantageous mutations will spread - As population size declines, things are more susceptible to acquiring deleterious mutations, and not spreading beneficial ones - On Earth, the most highly adapted things in terms of natural selection, are bacteria - We are used to natural selection spreading good things and getting rid of bad things, but this can't happen in small populations Less Fit Intermediate Forms - Sometimes there is a better form, but natural election needs a few steps to acquire it, but the intermediates between the steps are less good - NS could only work efficiently only if it affected different loci -- additive - If instead they had an interaction (epistasis, you need both A and B to be good), natural selection can't produce the optimization, becomes a poor force  Genetic architecture: Sickle Cell Anemia - The third thing that can stop optimization, is when the best form isn't genetically pure - Sickle cell anemia is maintained in West Africa because it provides malaria resistance. In that case, the best form wasn't genetically pure -- bad forms (RBCS that couldn't resist malaria) persisted by genetic segregation - Natural selection couldn't produce perfection because the best form was genetically mixed - When something is genetically mixed, when you breed it, all the bad forms come out together DOES ADAPTATION AND COMPLEXITY IMPLY A DESIGNER? - Paley's blind watchmaker argument -- complexity is not possible as a random event - Whenever you see big complexity in nature, it couldn't just have been created by itself out of nowhere - Complex forms, for which you can't find a natural selection pathway to get to, so they must have had a designer - If you see complexity in nature, it doesn't seem likely as a random event - When Paley was going across Hampsted Heath in London, and he saw a rock, he thought nothing of it - Rocks could be produced by simple physical processes - If he came across a watch, for example, it is much more complex, so that must have had some sort of higher level of learning and cognition to produce. You can't see how it could be produced in just a few steps, or physical forces - He looked at the eye -- it was too very complicated, like the watch, therefore, there is a designer, it can't just be produced by physical forces - Whenever he saw complexity, he thought they are made by a designer, a higher level of cognition -- it's too complicated Irreducible Complexity - Eyes and body parts, which give a sense of orientation, are produced as a gradual process, through gradual natural selection - You CAN find a natural selection progression from simple to complex, where each form in turn has a single reason for it - Not necessarily rejected by particular case studies, in which natural selection is a good explanation - Is it confirmed when we can't explain them - We can evolve complexity by natural selection in a stepwise fashion, you just have to find the intermediate steps that exist between the two ends -- no designer DARWIN'S SECOND PROCESS: SEXUAL SELECTION - Darwin's second big idea - Evolution didn't just work on survival, but actually worked on the capacity to get mates - Fitness differences associated with acquisition of mates -- sexual selection - Selection, related to sex - In sexual selection, the variation of fitness comes from the acquisition of mates, not survival - An individual, who can acquire more matings, will pass their genes to more individuals Sexual Dimorphism - A wide diversity in males and females -- how similar or different they are - One of the biggest variations in nature is sexual dimorphism -- how sexually dimorphic animals are - There are animals, where boys and girls look just the same -- an expert is needed to distinguish them - There are some with similar morphology and outside looks, but different "boy and girl parts - There are some extreme cases, who have extreme visible differences -- bird colors, feathers, lions - Dimorphic traits beyond the sexual apparatus - There are some, where females are 10 000 times larger than males - Sexual dimorphism varies -- there are some animals, which are dimorphic, and some, which aren't INTRODUCTION TO SEXUAL SELECTION - When does sexual selection occur? - IF: - There is variation in the phenotype - Some of this variation is heritable - The phenotype is associated with the ability to secure mates - THEN: - The next generation will be biased towards individuals with higher ability to secure mates - ULTIMATELY: - The population is dominated by individuals with traits that enable them to secure mates - Sexual selection is like natural selection, but for the ability to secure mates Sexual Selection Happens, Where There is Variation in Mating Success - There is variation in mating success - It varies between a mating system - Monogamy -- little capacity of variation in mating success - Swans -- only 1 mating partner, male and female bond for the entire life - Polygyny -- lots of capacity for mating variation - One male acquires many different female for mating - Variation of mating success between males - Largest individual becomes the winner, and the winner gets most of the mating - Polyandry -- lots of capacity for mating variation - One female acquires multiple males for mating - Found in some birds - Females acquire males to do parental care for them for the babies - 1:1 sex ratio -- some females will be left with no males for mating Where Sexual Selection Occurs, the Outcome Varies by Sex - Sexual selection tends to occur more in males - Females -- fewer potential offspring - Invest more in outcome of each, invest more in the offspring - Fitness is defined by mate quality - Choosy about potential mates - Males -- many potential offspring - Invest little in each - Fitness is defined by mate quantity, not quality - Compete for access - The more mates they get, the more genes the males leave for the next generation - In general, one sex invests more in the progeny than the other Two Forms of Sexual Selection - Intrasexual "male-male competition" - Males compete for access to females - Within the same sex, competing for access to the other sex - Intersexual "female choice" - Females choose males on basis of phenotype - The rare sex makes her choice for individuals of the other sex - Males are displaying traits and trying to persuade the females to mate with them - Because one sex is very abundant in the mating pool because it is not doing any parental care, the rare sex (female in this case) can make their choice amongst the individuals of the other sex, who she can mate with A couple of animals fighting Description automatically generated Intrasexual Sexual Selection - Male-male competition large males win guard access to females - Classic outcome of male-male competition is that males are way larger than females - Armaments -- males become not just bigger, but ready to fight -- this helps them win over other males in terms of guarding access to females and getting extra matings - Outputs - Sexual dimorphism in body size -- where males fight with each other for females, they have evolved to be bigger than female - In monogamous animals, males are the same size as females, no dimorphism - When there is sexual selection, males are 40%-60% bigger than females - Dimorphism in weapons -- canines (teeth), antlers. Males are trying to fight over males -- weapons (armaments) help them, weapons aren't there because of diet, etc. - Primates are vegetarians -- they don't need large, big front teeth (canines) for eating, but use them for fighting - Sexual dimorphism as an adaptation for acquiring mates, to being better in fighting with other males  A close up of a monkey\'s mouth Description automatically generated Sexual Selection Like This is in Opposition to Natural Selection - Growing teeth and weapons is costly to the individual in terms of mortality - Practically, there are always males dying before females - Sexual selection in body size and armaments translates into an effect on death rates and aging - Where sexual selection is strong, males die young, before females - Some deer die in the first two years - They put all their energy into going big, and not to health, infection, dealing with famine... - Adaptation to fighting is having a cost on their survival - Natural selection produces well-designed individuals, not well-designed overall species - That's good for getting mates and bad for surviving Sexual Selection Can Promote Diversity - There is more than one way to get a female - Male-male competition produces a lot of strategies that males use for acquiring females - Orangutans have a troop -- one large male controls the troop, needs to get rid of the other males - In this situation, some of the males retain juvenile features, which makes them look more female-like - This allows them to be tolerated in the troop and not seen by the large male, they sneak matings - Instead of growing big, they maintain their juvenile form -- dominant male doesn't recognize them - When the dominant male dies, the "hidden" males develop into a dominant form - This is the way Darwin saw sexual selection - 100 years later, Jeff Parker came, who studied sperm: Male-male competition goes beyond acquiring mates - The competition that males undergo with each other to gain access to mates will also happen within females, when they mate with multiple males - Where a female mates with more than 1 male, she has sperm from more than one male in her reproductive tract - The competition for fertilization wouldn't just be about getting the mate, it will be about which sperm fertilizes the female - This leads to sperm competition - Most species mate multiply - Fitness is not just acquiring mates; it is acquiring fertilization -- competition with the sperm of other males - Intrasexual selection happens not just before copulation, but also happens after copulation -- the sperm of multiple males inside a female will compete with each other to get fertilization - In nature, males should be adapted to not just acquiring mates, but also to acquire fertilization within the female through sperm competition Adaptations - In nature, males produce sperm massively, have large testes - One egg, many millions of sperm cells, but only 1 sperm fertilizes the egg - Animals have a lot of sperm because they need to compete with the sperm of other males - The male that puts more sperm inside the female, will have a higher chance of fertilization - The male that puts more sperm, would have a higher chance to fertilize the female - In monogamous species, males form less sperm, have smaller testes for their body size - Zebras invest a lot of sperm -- 30 x 10\^12 sperm cells per an ejaculation - Zebras have 10 times the testes size that they should have, if they were monogamous - Co-operative sperm behavior: - Sperm of a particular species of mouse swim in packs - Sperm cooperatively swim to the egg -- together, they swim faster and are more likely to reach the egg before sperm of the other male Getting rid of previous sperm... - Males will evolve to get rid of previous sperm - When a male bird returns to the nest to his female, he would peck her genitals, so that any other sperm gets out - Insects could have extraordinarily long mating - Drosophila can mate in 30 seconds, another species of drosophila can mate for 3 hours - Why do they mate for so long? -- males get rid of previous sperm, it takes time - Getting rid of other sperm as a competitor, and then putting in your own Preventing Females From Mating - Males puts a plug of sperm inside the female, makes her think she is giving birth -- she won't make with others - Evolve very big testes - Drosophila evolve to have testes, which are 15% of its body mass Summary -- Intrasexual selection - It may occur for: - Access to mates (Darwin) -- leads to sexual dimorphism - Access to fertilization (Parker) -- sperm and testes size and reproductive behavior INTERSEXUAL SEXUAL SELECTION: FEMALE CHOICE - Peacocks use their tails, animals will call/produce sounds to attract females - A member of the rare sex chooses the member of the other sex Where is female choice most commonly found? - Where females care for progeny and males don't - Where males cannot physically monopolize access to females - A bird can just fly away if it doesn't want to mate - Females choose: - Arbitrary -- they just like the male for some particular reason - Direct benefits -- a male is going to provide a good environment and support for the progeny - Genetic benefits -- best progeny from best genes - Zebra finch (bird species): - Females prefers males with bright beaks - Also, prefer males with the most leg bands (females liked brightness of bands) -- people put small bounds on the legs of the finches, so that they know which bird is which - Satin bowerbird - Females like blue stuff - Males find and take everything blue and put it in a nest -- collect plastic, paper, everything they can find - Females go to the nests, which have the most blue stuff  Direct Benefits - Female mates with a male, who is going to give direct resources for the progeny - Good territory, good provisioning, good protection - Females pick males, who will provide for progeny - Nuptial gifts in insects - Good Territory, provisioning, protection Indirect (genetic) benefits - What is the female choosing, if she isn't looking for direct benefits or fancying? - Exaggerated traits are a way of telling males with "good genes" from "bad genes" - Long tails, long distance between the eyes - Males find something, which isn't usually present in nature, unless they are very fit -- condition-dependent trait - The progeny will get good genes -- females want good progeny - They represent an "honest signal" of male quality - If you have parasites, unwell, you don't have the energy to produce a particular difficult trait - Females choose males with very big and visible traits because only the fittest males will be able to produce those things - Peacock's tail: - An honest signal of quality - Males with large eyespots on the tail produces the fittest progeny -- more protection, more life - Selecting genes, which fit very well in the environment, the progeny with those genes will do better -- good for the female choice How About Humans? - Females advertise youth and beauty - "Stunning, smart, blond female seeks \_\_\_" - Males advertise resources - "Owns care, has good job, lives in \_\_\_" - However, this isn't the good way to go -- people aren't attracted by specifically these things - Humans are very cultural Summary A close-up of a chart Description automatically generated SEXUAL CONFLICT - Sometimes, sexual selection can produce conflict - Males and females interests in reproduction can differ from each other - Females may wish to remate, current male prefers they don't - In drosophila, females, which mate every 5 days have a higher fitness than females, which mate only once or rarer - However, the current male doesn't want his female to remate - Males need to persuade the female not to remate - In drosophila, this involves putting a chemical into the female, called sex peptide, which acts on her brain and makes her less likely to remate - Drosophila males: sex peptide - Chemical chastity belt -- refractoriness to remating - Also, damages females - Females want one thing, males want another thing -- sexual conflict - Females' adaptation is to mate, males' adaptation is to persuade the female not to, using a chemical, which damages the female, actually - Male-female interactions can produce a cycle -- the Red Queen effect - Males tries to persuade the female to mate with him, not to remate with his rivals -- that's good for him - Female has an advantage in remating, so she adapts to avoid being manipulated by the male - We get a cyclical evolution of males exploiting females, and females resisting exploitation and getting their own fitness back through natural and sexual selection - A never-ending Red Queen effect - Evolution of males -- evolution of females - Continuous diversification - Reproductive systems are forever evolving, have the fastest evolution - Anything that involves sex, evolves faster than anything to do with survival - Sex is the fastest evolving thing in all of zoology - Males are running continuously to get their fitness interests in females, and the females are continuously running to get their fitness interests in males - RUN TO STAY STILL!!!! Summary - Male-female interactions produce: - Sexual selection - Which leads to: - Sexual dimorphism - The forces are strong and continuous - =\> the reproductive systems are incredibly diverse, odd and fast evolving  SPECIATION AND THE ORIGINS OF BIODIVERSITY 29/11/2024 Session 3 - How species split into two? - One lineages splits into two, going different ways, becoming different species -- speciation - Without speciation and lineage splitting, you can't have a tree of life - How can a lineage split into two? - What determines the rate at which this happens? -- happens in different rates, in different points of time and history Darwin's view of speciation - Darwin's first book was called "On the Origin of Species" -- all about how you get species - How thing adapted to different environments, he argued that species will become different in different places/environments -- what he saw as speciation - His book was based on geographical isolation in different places - Species in these different places would go down different evolutionary routes because they were adapted to different environments, they would diverge, in the end, this divergence would create different species - Variation over space Variation in best form Divergence - One of the problems with the book is that it doesn't actually define what is a species - You know what a species is, but you have to define it, which is very difficult - Darwin wasn't defining what is a species - Darwin had a verbal model of a species -- discontinuity of forms, things that looked different - Species are related, but separated - Nature is divided into different clusters of morphology and biology - You don't see anything in-between -- you don't see half-blue and half-grey tit -- they are either fully black with a white stripe and yellow on the sides, or they are white, blue and yellow - Tits are related, but separated A bird on a branch Description automatically generated Phenotypic Discontinuities Can Be Misleading - There can be cryptic species -- look very similar, but actually genetically independent from each other - Oak titmouse and Juniper titmouse -- look the same, but were sequenced and discovered that they are different with different gene pools  - There are also polytypic species -- look different, but are actually the same species - Lots of morphological diversity, but actually they are all interbreeding in the same gene pool - Asian harlequin beetle - Diversity of form doesn't actually define species WHAT ARE SPECIES AND WHAT KEEP THEM APART? - Most operational and universal definition of species - units with independent evolution because of barriers to gene flow - Doesn't work for bacteria -- WE FOCUS ON ANIMALS - Mayr's biological species concept - based on genetics - A species are a set of individuals or a population that can interbreed with other members of the population and cannot produce viable offspring with members of other species -- a variant and a mutation in one can't spread into the other - There is genetic isolation - Species are evolutionary independent -- a mutation in one species can't change the other species - Over time, they will become discontinuous - Species diversity is caused at some level by genetic isolation of units -- things that stop genes flowing between populations - A variant and mutation in one can't spread to another Gene Flow Definition -- What stops genes from flowing? - Species are distinct in genetic composition of populations - In species, there is absence of viable, fertile hybrids -- individual between species - Species are the result of barriers of gene flow - What stops gene flow: - Barriers before fertilization -- pre-zygotic isolation - Zygotes can't physically be formed, they don't come together - In nature, there are 5 things that produce pre-zygotic isolation - Temporal -- don't meet in time - The 2 species mate in different times of the year, or in the day - Different from species mate in different times of the year -- February, April/May, October/November. Even if they could form hybrids, they don't because they mate at different times of the year - Ecological -- don't meet in space - Live in different places (continents, countries) or even planets - Northern spotted owls live in the West Coast of USA and Mexican spotted owls live in Mexico -- there is a lot of space in-between, therefore, they won't mate and have separate gene pools - Some flies may mate on apples, some on hawthorns -- mate in different microplaces in the same habitat, but still don't see each other and don't exchange genes - Behavioural -- don't want to mate - They don't fancy each other -- either sexual selection (picking the best mate), or making sure mating is with the right species - Very common and very diverse -- mating signal divergence -- songs, dancing, color, smell. - Bird songs are specific to species, attracting females of the same species. Females will mate with males, whose song/tweet is the same as theirs - Fruit flies dance, males will chase the females in various ways and if the female is happy that the male is the right species, she will allow the male to mate with her - Different species have different frequencies of tweets, different genital smells... - It's very important for the female to know she is mating with the right species - Mechanical -- can't physically mate - Genital morphologies -- sexual organs aren't physically compatible, stopping things physically from mating - Spiders have variation in their genital parts -- from very small and thin to very big. Not all of them will fit into the female species - Lock and key system - A pollen may not be viable on the stigma - Sexual conflict drives genital morphologies to diverge - Gametic -- gametes won't find and fuse - Sperm of wrong species may have gone inside the female -- no fertilization. In insects, sperm competition is biased to the sperm of own species - Sperm may be transferred, but the sperm and the egg aren't compatible, the egg needs to internalize the sperm - When the sperm touches the egg, the egg needs to internalize the sperm -- a physiological response the egg makes to the sperm, based on a chemical signal from the sperm - A pollen from of some species, if put on the stigma of another species, may stop it from growing and fertilizing - Where there is sperm competition (insects) females will keep the sperm of only their own species - In oceans, sperm of only the right species has the capability to internalize the laid eggs - Barriers after fertilization -- post-zygotic isolation - Produces hybrid infertility -- the babies are sterile - Produces reduced hybrid viability: Fertilization happens, zygotes are formed, but they are infertile and don't develop, sterile babies, they die very young. Fertilization doesn't proceed very well - Things either can't develop properly, or can't make sperm Summary - Genetic isolation takes many forms - All of these forms create species' evolutionary integrity -- basically what that means, is that a mutation in a species stays in that species. Species go down different evolutionary routes and become different. Species are defined by gene flow and evolutionary independence - Separate evolutionary trajectory WHAT EVOLUTIONARY PROCESSES LEAD TO SPECIATION? - How do species form? - How one thing becomes 2 isolated things - How do you go from interbreeding to isolated? - In the tree of life, one things has become two on many occasions -- one lineage from another lineage - At some point one thing has interbred and exchanged genes, but suddenly stopped gene flow and became isolated species Easiest Way To Conceptualize -- Complete geographical isolation (allopatric speciation) - We are taught this way because it is easy to conceptualize - Vicariance event -- At some point, one species is split into two by a barrier. This barrier could be a river, mountain, etc. - Now, the two species are separated into two units. - Over time, these units evolve differently because they are not exchanging genes because of the barrier - The primary thing, which stops gene flow and creates isolation, is the barrier - Over time, the two units come together again, but are sufficiently different - All the things that stopped exchanging genes (the barrier, mating choice, temporal isolation) have made the species divergent - Now, they can no longer exchange genes - Over time, you get divergence and that divergence is sufficient, so that when you put them back together, they no longer exchange genes -- core model of speciation - One population that has been physically cleaved in two, which gives the primary barriers to gene flow - Initial barrier is just a random event that has happened to the species - Now, species are 2 units, but they are not exchanging genes because of the barrier - Separately, they evolve, and when they come back together, they can't breed because they are too different - Barrier to gene flow Genetic Differentiation Reproductive Isolation Evidence - Sibling species pairs were found in Pacific/Atlantic sides of Isthmus of Panama - Isthmus closed 3 MY ago, when NA and SA hit each other - Until 3 MYA, there was water flowing between Atlantic and the Pacific -- gene exchange - When the Isthmus closed, this cleaved all the species of fish into two parts -- land went across the ocean - The land went across the ocean, different sides of the ocean weren't exchanging fish - They evolved to go different directions because they ere no longer exchanging genes - They became gemini species -- twin species, which are created at the same time, associated to a particular event - In fish, you find one on one side and another one on the other side -- Atlantic form and Pacific form A map of the caribbean islands Description automatically generated The Paradigm - Spatial isolation produces independent gene pools - They diverge over time - When things diverge over time in their own evolutionary trajectories, they would eventually evolve by various means, and there will be reproductive isolation -- they can't exchange genes, even if they see each other "Peripatric geographical isolation"/ Dispersal geographical isolation - Vicariance is not the only way for reproductive isolation - Peripatric isolation is the most common way - Peri -- away from the homeland - In peripartic isolation: - A new habitat arrives on the other side of a barrier that already exists - A few individuals cross that barrier and found a population on the other side - The barrier is big enough, so that there is no gene flow going across - The crossed individuals diverge into different species - This generates large amounts of biodiversity - This is the most common way for reproductive isolation because new isolated landscapes are occurring all the time in geology: - Volcanic islands -- they have nothing on them to start off with but generate a lot of biodiversity because things fly to them accidentally or get picked up in strong winds. They pop down on the island, found a population, which is genetically isolated - "Sky islands" - habitat areas which are isolated because they\'re high up and high up on the top of mountains. Each individual mountain peak becomes a little island because things that can live high in the mountains can't live a level below - Glacial lakes -- when glaciation happens, it weighs down the land. When the glacier retreats, it leaves a lot of lakes -- Finland and Sweden have a lot of lakes, formed since the last Ice Age with nothing in it. Everything inside them has come through dispersal. - Geology and geological processes form new habitats all the time, which get colonized by animal species, so we know that dispersal mediated speciation is very common Many Mammal Radiations Come After the Landscape, Implying Dispersal - Old vs New World monkeys -- 40 MYA - One set of monkeys went from the Old World to the New World - They are different -- the entire New World Monkeys Clade was formed by dispersal mediated speciation - Madagascar is 150 MYA old - Same thing as the New World Monkeys - Lemurs radiated there 60 MYA - They must have got there again by dispersal - We have isolated habitats, animals or plants arriving there, creating speciation - NOT a physical cleavage - It is actually movement of rare individuals to new places, which are then isolated Sympatric Speciation -- Final form of speciation - Reproductive isolation without geographical separation - Usually, about evolution to live on new foods - Consider a mutation, which: - The apple tree was taken from Europe to America because of high demand - Americans started growing trees, but with no insects in them - The apple maggot fly in America evolved a mutation, which allowed it to eat apples because it originally lived on hawthorne - Species split into two -- ancestral form, which lived on hawthorns and the new form that had evolved to eat apples - Flies mated on their fruit no longer could exchange genes, weren't mating with each other anymore - Apple maggot flies' preference to lay eggs on new host plant - This gives genetic isolation when mating occurs on a host plant - The populations have become divergent from each other - One beneficial mutation giving the ability to eat apples, gave the reproductive isolation as an accidental byproduct - We call these things "magic traits" -- a single bit of natural selection creates new species - Single beneficial mutation -- instantaneous mating barrier - Snails have evolved to be left-handed -- these can't mate with right-handed ones - Evolution on living on heavy metal soils produces speciation -- plants evolved various detoxification mechanisms and could now live on metal-rich soils. This automatically produces reproductive isolation as a byproduct because they flowered in different times of the year because of the different soil - A single beneficial mutation split populations and created barriers to gene flow - First event is biologically driven - Moving to a new host plant -- genetic isolation as mate is on plant - Able to grow on heavy metal soil -- genetic isolation as flowering time is different - Left-handed shell -- genetic isolation by physical incompatibility with right-handed snails - In these cases, reproductive isolation is a byproduct of adaptive evolution, creating species -- sympatric speciation, not geological change So, - You can get initial separation due to vicariance - Or sympatric through magic traits - Or dispersal to new habitat -- peripatric Why Does Reproductive Isolation Develop? - New species are kept apart by barriers to gene flow - What processes lead to these barriers? - Temporal isolation -- divergence on seasonality and mating time - Ecological isolation -- divergence in place (or host plant) - Sexual selection -- males-type females prefer, genital anatomy, evolution of female choices, male strategies - Sexual conflict -- post-mating isolation - Sexual selection creates: Behavioral isolation (different cues of mating), Mechanical isolation (male and female morphology), Gametic isolation - What does natural selection do to create these barriers? - Lots of natural and sexual selection processes will diverge if things are isolated, and when they come back again, the processes of finding mates don't work as before, either because of time or because of space or sexual selection Postzygotic Isolation - Commonly considered to be genetic incompatibilities between components of cellular/developmental pathways - Processes, associated with making sperm/eggs -- quite complicated developmentally - Developing from a single cell to an adult organism - As you go to different systems and with different morphologies, such systems and processes will change and when they come back again, they would be too different Unselected Incompatibilities - As things diverge over time, aspects of development arise, where gene combinations unseen each other before, may go different -- untested gene interactions - New variation will be added to isolated populations via mutation, drift and selection - Therefore, untested gene interactions will come in contact - When systems develop differently in different places, they may be incompatible together - Post-zygotic isolation can also be ecological - Selection for traits that help individuals deal with local environment - When things can produce hybrids, but they are less fit - Hybrids are viable, but less fit - Benthic and limnetic sticklebacks - Sticklebacks have evolved a benthic form, which allows them to live at the bottom of lakes -- it's big and fat - The limnetic form lives in the water -- it swims well, it's well-defended against predators - If you hybridize these two, you get a form, which is neither good at the bottom, or at the top  A close-up of a fish Description automatically generated A and B have never seen each other before -- 2 populations, where A and B evolve So, - There is an initial event -- vicariance, sympatric, peripatric - Things diverge - You get reproductive isolation because things have diverged separately GENERATING BIODIVERSITY - Speciation processes + Maintenance of species - Whether the thing that has split, will split again - Whether or not they will be maintained - It's not only about when and how it would split, but whether or not it will be maintained or split again Generating Biodiversity is More than Just Speciation - After you create new species, they need to be able to coexist - If you get species A and B and they live in the same habitat, eat the same food, there will be competition Only 1 of them is maintained So, to create diversification, you require not only just reproductive isolation, but you need ecological separation (living in a different way so that one doesn't exclude the other) - You may get genetic isolation without actually strong amounts of ecological diversification - Divergence in allotropy may be: - Changes in diet/reproductive preferences - Do not interfere when making contact - Two things doing the same thing in the same space can't coexist - So, things evolve to be different, to eat different things and have different niches -- ecological character displacement - Selection for each species to utilize different niches - Two things can happen: - Competitive exclusion -- one species predominates over the other because it's better - Ecological character displacement - species evolve to be different, eat different things, natural selection could promote them to being parted and have different niches - If you have 2 things doing the same thing, one of them will go extinct - If there are sufficient resources, natural selection will drive them apart and differentiate them, so that they don't have to go through competition - Less competition = more opportunities to maintain the new species niche separation is encouraged Darwin's Finches - The above explain Galapagos' finches - They are a set of species, all of which come from one ancestor, who flew to Galapagos from Ecuador, and formed all the different forms - Therefore, they evolved different beak size - What you can see on the Galapagos is that the radiation was enabled because there was a lot of food because it was a new island - Seeds of different sizes, different-sized insects - Finches evolved to eat different things, so that they don't compete with each other and become diverse and persist Corollary/Opposite -- Diversification will be constrained when there are no free niches, no new way of eating - Species can't evolve in a direction because there are other species, which eat the same things, out of the two species, one of them will go extinct - When there isn't a new food, you may get reproductive isolation, but not diversity because there isn't enough niche space, not enough ways for species to make a living - Generation of biodiversity requires not only geographical isolation, but also distinction between species that permit coexistence - Natural selection may produce these through the process of Character Displacement  So, - Generation of biodiversity requires not only geographical and reproductive isolation, but it also requires distinction between species that come out, so that they can coexist - Reproductive isolation -- Allopatry, peripatry, divergence - Distinction between species, allowing coexistence -- resource use, mate choice IS THE RATE OF SPECIATION CONSTANT, OR VARIABLE? - It is VARIABLE - Diversification depends on niche space - To start, there is a lot of energy, lots of resources -- you get diversification - Where new habitat is created, - Lots of diversification to start with -- adaptive radiation - Over time, you get more species, they all have different ways of feeding, at some point of time, you fill up these ways of feeding, you've eaten all seeds of all shapes, and you get to the point, where new species can't form - If they do form, they coalesce, one of them becomes extinct - Diversification slows as niches become filled Price' Himalayan Songbird Study -- Exemplifies the above mentioned - Himalayas formed 34 MYA - India wasn't a part of Asia, 35 MYA it hit the Asian subcontinent, and the Himalayas formed, creating a vast amount of new habitats - Lots of diversification to start with -- lots of habitats, empty niches, new ecological zones going up the hills - Lots of energy, lots of free food - When looking in diversification of birds, which flew into the Himalayas from India and Asia, speciated - In the phylogeny of Himalayan birds, there are massive amounts of diversification to start with - But there haven't been any new species in the last 5 MY - Speciation stops because there is no free food and space left - Starts with lots of energy and lots of ways of living, new species could persist by dragging themselves into different parts with different food to eat or in different geographical environments - Eventually, all niches were used up, radiation and speciation stopped - Amount of diversification that happens is basically related to food -- around 2000 meters there was the most food, best environment for insects (food for birds), and most species formed at around 2000 meters - Generation of reproductive isolation is initially important - Later, there is saturation -- new species are limited by niche availability - Once all the food and free space is sued up, everything stays in one place, diversification stops The Largest Radiation is New Habitats - Largest radiations observed are all in new habitats - Rift valley lakes and cichlid fish adaptive radiation - The Great African lakes formed, and they are very big and nutrient-rich - Remarkable diversity of fish, despite they are 2 MYO - 2 MYA, but have an incredible diversity - All of the fish originate from 2 other (river fish), which will reach the isolated lakes, where there are lots of different energy sources and habitats they will diverge and speciate there are over 200 species of cichlid, arisen from 2 species - Where there is lots of energy, you evolve massive radiations So, - We get a burst of speciation -- adaptive radiation -- in the new unexploited habitats, as any new species formed can find new niches - The diversity in nature is based on the diversification of ways of feeding DOES THE RATE OF SPECIATION VARY BETWEEN TAXA? - Is there variation between taxa in: - Initial barriers that allow divergence -- what are the things that allow one thing to split into two in the beginning of speciation? - Speed of divergence when separate -- how quickly can reproductive isolation evolve? - Creation of new niche space and capacity for radiation -- how can this species live in different ways? - Not all taxa have the same biodiversity -- 300 000 species of beetles... - What is causing this biodiversity? Initial Barriers - For everything, accept sympatric speciation, they are breaking gene flow -- very important - The most important way of breaking gene flow is dispersing into a new habitat - The ability of an organism to disperse is related to its ability to speciate - What that predicts is that the ability for an organism to disperse, is related to speciation - No dispersion - Vicariance is the only source of isolation - Kiwi bird -- can't fly, low mobility, harder dispersal - You have to physically split the kiwi population to get a new species - Low dispersion - Can reach new places occasionally, but population has integrity vs gene flow, vicariance is viable as well - High dispersion - Can reach new places easily, but these have gene flow to source - They can go back and forth, not very convenient to speciation - Vicariance is unlikely, dispersal doesn't work because they can come back again - PREDICTION -- Dispersal rate of the species should predict its biodiversity -- the hotspot is at low dispersal - Low dispersal can have vicariance events - Low dispersal can reach new environments, but it is hard to go back Case Study -- Amazonian Birds - Quite a lot of Amazonian biodiversity is created by the rivers - They act as physical barriers, cleaving the environment in bits - The capacity of birds allows them to fly across - Experiment - they took a lot of birds, let them go in the middle of the river, and saw whether they can go across the river to the other side - Rescued the ones, which didn't make it - Some species just can't make it across the river, some can make it across the river very easily -- there is an intrinsic variation between species of whether they can get across a river - That creates a prediction that: - Birds that live in the lower canopy of trees evolve stubbier and smaller wings (big wings would mean that birds would bash them into the tree branches ) - Birds that live in the top canopy of trees evolve big wings (they can't hit them in the tree branches) - Understory birds don't fly at all and couldn't cross the river - Therefore, birds that live in the understory should be more speciated because they are the ones at this hotspot, where they can disperse a bit, but not a lot - The most biodiverse taxa are the ones that live in the understory and can't disperse very well - IF YOU LIVE IN THE UNDERSTORY OF TREES, YOU HAVE POOR DISPERSAL, IF YOU HAVE VERY POOR DISPERSAL, YOU WILL BE MORE LIKELY TO SPECIATE BECAUSE YOU WON'T GO ACROSS THE RIVER THAT OFTEN. WHEN YOU DO GO ACROSS, YOU'LL BE GENETICALLY ISOALTED FROM OTHERS. - As dispersal biology evolves, so does the chance of speciation - How quickly, when isolated, things become reproductively isolated? - How long does it take for things to not be able to produce a fertile and viable offspring? - This varies between taxa - Mammals: very low tolerance to hybridization - Mammals evolve reproductive isolation faster than any other taxa - Hybrid in unviability evolves quickly - Max 3 MYA in mammals - Amphibians, birds, plants can create hybrids, they aren't fully reproductively isolated - Why fast in mammals? - Mammals aren't defined by pregnancy, BUT - Most mammals are placental -- hold inside them a fetus, which is 50% not them, genetically not fully similar to it - You can't hold another organ, which is 50% not you, but you can hold an entire fetus -- a lot of evolution is required to make this work - One of them is immunosuppression -- your immune system is repressed for that thing and can't reject the fetus -- that's why infections and other weaknesses are more common during pregnancy - In hybridization, with this, it becomes very different - Hypothesis -- mammals have a low tolerance for hybridization because pregnancy fails due to rejection because hybrids are too genetically different for mammals. Pregnancy creates a tolerance such that genetic divergence doesn't develop very well over 3 million years - Fetal viability requires both internal development and correct interface with mother - Immunological tolerance is too stretched for a mother to keep a hybrid inside -- her tolerance can keep a fetus, but not a more genetically distinct organism - Hybrids are genetically distinct, therefore, rejected Biological Change and Adaptive Radiation - Biological innovation can allow new ways of living -- beetles created their own energy space by evolving to eat flowering plants - When they evolved, they had this massive amount of energy that they can use in a massive amount of niches - New beetle species evolved multiple new ways of living and speciated directly - The plants were like a new island to the beetles - Biological evolution led to new niche space -- lead to diversification - In evolution before, many cases have been because of biological evolution -- evolution of beetles, flowering plants, creating new niche space OVERALL SUMMARY - Species are defined by genetic isolation - Darwin had his verbal model of species, which was just about difference - There are many sources of genetic isolation - Pre-zygotic -- most common form is usually to do with mating -- whether things can or want to mate with each other - Post-zygotic - Speciation -- processes producing isolation - May occur due to vicariance events, or more commonly due to dispersal, and sometimes it can be sympatric (mutations within the same geographical space) - Speciation rates are variable over space and time, depending on opportunity and biology -- some things are biologically more likely to radiate from others - Diversification requires more niche space overall - There are geographically more species in the tropics because there is more energy and more different habitats and more land - Temporarily, we get a burst of new species, when we have a new habitat and adaptive radiation on islands, lakes, mountain tops - We can also get a new habitat through biological innovation -- the ability to eat new plants - Taxa vary intrinsically in speciation rate - Dispersal capacity produces barriers to gene flow --dispersal capacity can evolve with adaptation - There are features of biology, which can affect reproductive isolation -- pregnancy, affecting speciation rates A black and white text Description automatically generated