Bio 1B Evolution Study Guide PDF

1️⃣ Lecture 1 Notes The logic of evolution by natural selection Key Questions What are the five properties that led Darwin and Wallace to conclude that we might expect species to change with time? 1. Many more ind...

1️⃣ Lecture 1 Notes The logic of evolution by natural selection Key Questions What are the five properties that led Darwin and Wallace to conclude that we might expect species to change with time? 1. Many more individuals of each species are born than can possibly survive 2. If there is a struggle for existence 3. If Phenotypes are variable 4. If existence depends even a little bit on phenotypes 5. If phenotypic attributes are heritable then we can expect descent w/modification Why is each important? That is, why if one was missing would we not expect species to change with time? (ask) * Inheritance (If phenotypic attributes are heritable): It allows us to connect the outcome of selection in one generation to the following generation. Why is inheritance important to the evolutionary process? Because it allows us to connect the outcome of selection in one generation to the following generation. Vocabulary Phenotype - The outer or inner appearance of the a individual. Struggle for existence - Over-reproduction leaves individuals of a species struggling to exist because of the limited resources in their environment. Lecture 1 Notes 1  Heredity/Inheritance - the process by which genes are passed down from one generation to the next. Natural Selection - The process by which individuals in a species succumb to their environment because of the fecundity of nature. “We produce too many, and they get driven hard against the limited resources of the world”. Evolution - basically descent with modification, where a species transforms over time. Microevolution - within Macro- betweeng Lecture 1 Notes 2  3️⃣ Lecture 3 Key Questions Why are snout proportions in dogs more evolvable than in cats? Because dogs already have a range of snout lengths it is easy to breed dogs of different snout lengths. With cats you have to wait till you get a random genetic variation. What is the relationship between adaptation and fitness? Adaptation increases the fitness of the species. It is often said that variation is random. In what way is this true, and in what way not. Variation (they just pop up without thinking, they don’t really care) is random in the aspect of the needs of the organism but not random to what can happen (we aren’t just going to sprout wings.. For instance, in humans, there is random variation in height but there is no random variation in the number of limbs we have. Why can it be difficult to identify the target(s) of selection? Make sure you mention evolutionary hitchhiking. Traits are often correlated, thus non-selected traits can hitchhike along with the selected traits. That is called evolutionary hitchhiking. Can natural selection occur without evolution? Give an example. Yes! when extreme phenotypes are selected against there is a stabilizing selections and no evolution. What are three types of selection on traits? Stabilizing - the middle phenotype is favored Directional - one side or the other is favored Lecture 3 1  Disruptive - the extremes are favored. What is the name for selection when it concerns access to mates? Sexual selection What are three ways that evolution can occur without selection (can you explain how they work)? 1. Genetic Drift 2. Bottleneck Effect 3. Founder Effect So, then, can you list the various mechanisms that can lead to evolutionary change? 1. Adaptive change driven by selection a. Disruptive b. Directional c. Sexual 2. Non-adaptive change driven by chance a. Genetic Drift b. Bottleneck Effect c. Founder Effect 3. New Mutations 4. Genetic Flow How do most mutations arise in the genome? Most arise due to replication errors in the DNA but also environmental damages. Why do fast rates of mutation enable drug resistance to evolve? A fast mutation rate means faster adaption, which means that the viruses adapt very fast to drug resistance which mean they need to be fast. Lecture 3 2  The Hardy-Weinberg model is very simple, yet its simplicity enables us to determine whether one or more mechanisms of evolution has occurred. Explain how. How allele frequencies compare to genetic frequencies. [Exit Ticket] What is genetic drift? Genetic drift is the change in frequency of an existing gene variant (allele) in a population due to random chance Vocabulary Evolutionary hitchhiking - A trait hitchhiking on the back of a positively selected trait and survives through the ages. Ex: Stabilizing Selection - the middle phenotype is favored Directional Selection - one side or the other is favored Disruptive Selection - the extremes are favored. Balancing selection (see also Lecture 2) - Comes through genetics versus stabilizing that’s more phenotypical. Sexual selection - When selection is directly related to access to mates Drift/Phenotypic drift/Genetic drift - a random change in the frequency of a gene variant in a population Bottlenecks - population size reduced in the home range Founder effect - small subset of individuals establish [found] a new colony. Adaptive change - A change driven by selection Non-adaptive change - A change driven by chance. Mutation/Mutation rate - replication errors as the DNA is duplicated during cell division. The rate that happens. Immigrations - The movement of individuals from one place to another. Gene flow -the movement of genetic material between populations, also known as gene migration Lecture 3 3  Hardy-Weinberg - how allele frequencies (like S [sickle cell anemia], H [‘normal’ red blood cells]) translate into genotype frequencies (SS, HH, SH/HS) Allele frequency - (S (sickle cell anemia) or H (normal red blood cells)) Genotype frequency - (SS, HH, SH/HS) Lecture 3 4  2️⃣ Lecture 2 Notes Unpacking how Evolution works Key Questions Describe how selected traits might be viewed as ‘profitable. If the traits are useful and help them survive like claws or camouflage they can be viewed as profitable. What drives evolution? The fecundity of nature drives evolution. Over reproduction drives the pressure of selection. Evolution can be viewed as repeated rounds of a two-step process. What are the two steps Variation to Selection This repeats every generation How can evolution be re-cast in terms of development and ecology? Variation arises through development Natural selection plays out in the arena of ecology So evolution can be viewed as repeated rounds of the filtering of development by ecology. How are natural selection, adaptation, and fitness related? Natural selection is the only force of evolution that results in adaptation. Lecture 2 Notes 1  Natural Selection increases the fitness of the population. If a long neck is good for the giraffe, why don’t we see long necks in other species? We expect to see extreme morphologies in already extreme species. Why can’t/doesn’t evolution lead to perfectly fit species? Trade Offs and The “appropriate” variation might not be avalible. The sickle cell anemia allele is a genetic disease, yet the allele can also be selected for. Explain. The sickle cell anemia is linked with an increase immunity for malaria, so in populations where malaria is present, the allele is selected for to increase the chance of survival against Malaria. While experiments suggest that widow birds with longer tails would be more reproductively successful, why don’t we see these longer tails in the wild? The longer tails means it’s harder to flyer and easier for prey to detect them, thus decreasing the chance that they reproduce and spread those genes. In computer simulations of plant evolution what were the consequences of increasing the number of selective pressures, that is, the number of trade-offs the plants had to deal with? When there are many trade off’s there are many good solutions to those trade offs, and therefore many complex morphologies. It is often said that variation is random. In what way is this statement true, and in what way is it not? Variation (they just pop up without thinking, they don’t really care) is random in the aspect of the needs of the organism but not random to what can happen (we aren’t just going to sprout wings.. For instance, in humans, there is random variation in height but there is no random variation in the number of limbs we have. Lecture 2 Notes 2  Vocabulary Variation Development Ecology - the branch of biology that deals with the relations of organisms to one another and to their physical surroundings. Adaptation - a beneficial trait or characteristic that an organism develops through natural selection, Fitness - The ability of the organisms to survive. Trade-off - a situation in which evolution improves one part of a biological system at the expense of another part Genetic disease - mutation in a allele that causes a disorder. Sickle cell anemia - a chronic, inherited blood disorder that causes red blood cells to become rigid and sickle-shaped, which can block blood flow and lead to serious health problems Chromosome - a structure found inside the nucleus of a cell, composed of DNA and proteins, which carries genetic information for an organism Allele - one of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome. Balancing selection - There's a balance between these two alleles because neither on their own are perfect. Genetic Variance between Lecture 2 Notes 3  4️⃣ Lecture 4 Key Questions Darwin’s ‘syllogism’ consists of five parts; which ones are needed to explain phenotypic evolution by drift? (Genetics Drift) Variable Phenotypes - Need to have a difference Inheritance - Need to pass it down What is the Biological Species Concept? Give an example where it is hard to apply. A species consists of a population that can interbreed with each out but is reproductively isolated from others populations. Difficult to apply with Ring species. What is the Morphological Species Concept? Why do we think there should be good agreement with species defined using the Biological Species Concept? Groups of individuals that are morphologically similar to one another What are Chronospecies? where there is a continuity in the phenotype over time, but where the ends don’t overlap. What are cryptic species? What type of data are used to identify them? A cryptic species is one of two or more morphologically indistinguishable populations where DNA data imply that they can’t interbreed. DNA data suggest there are two species of living elephant in Africa. Why do we think there are different enough to call different species? Because there is a fixed difference between all three species of elephant. Lecture 4 1  What are type specimens? a preserved specimen designated as a permanent reference for a new species, new genus or some other taxon. Like a perfect specimen that can be compared to. What is a synonymy? Why are synonymies needed? A document with synonyms of species names, they are needed to make sure we aren’t double downing on species. Because it is easier to miss older literature if you are unaware of name changes (the older literature is often used to estimate temporal and spatial ranges, for example) Why are species especially hard to diagnose in the fossil record? because we can’t see them behave, we have less specimens, and much of the phenotype is not preserved Do you think, given the data shown in lecture, there are three or just one species of Tyrannosaurus? one Vocabulary Parthenogenesis - Asexual reproduction without males. Bacteria - A species separate from Archaea. Archaea - the other type of prokaryotes other than Bacteria. Eukaryotes - what we descend from. Biological Species Concept - A species consists of a population that can interbreed with each out but is reproductively isolated from others populations. Difficult to apply with Ring species. Ring species - The species can only interbreed in a ring. Cryptic species - one of two or more morphologically indistinguishable populations where DNA data imply that they can’t interbreed. Lecture 4 2  Morphological Species Concept - Species are the distinct if they are morphologically distinct from other populations. Chronospecies - a species that evolves over time from an ancestral form through a series of uniform changes. The changes can be physical, genetic, behavioral, or morphological. Type specimen - The best comparable specimen for the species. Synonymy - A list of different names for the same species. Lecture 4 3  5️⃣ Lecture 5 How are species maintained, how they form Key Questions Why do we typically use the Morphological Species Concept rather than the Biological Species Concept (BSC) “its difficult to test every species to see if they interbreed” and also it is easy to see the difference rather than test the difference. What is allopatric speciation? What are the two primary mechanisms of this type of speciation? Can you provide examples? Speciation that occurs because of a geographical or otherwise physical distance between the two groups. The two specific types are dispersal and vicariance; disperal is through movement (can lead to rapid evolution because of the small population that disperses) (Dodo bird), and vicariance is through geographic separation (i.e Isthmus of Panama.) What is parapatric speciation? Can you give an example? A niche within a population becomes separated and then fully becomes a reproductively isolated. The monkey flowers that were in the copper soil, became reproductively isolated from the monkey flowers in the normal soil, because of their immunity to the copper in the soil. What is sympatric speciation? Can you give an example? Speciation that occurs in the middle of a population without leaving. (Not Common) The speciation of the fruit fly to the hawthorne versus the apple. When there are no physical barriers preventing any members of a species from mating with another, with all members in close proximity to one Lecture 5 1  another. A new species, perhaps based on a different food source or characteristic, develops spontaneously. Why do we think sympatric speciation is uncommon? Because if things can interbreed, statistically they will. Creatures want to survive, and they will do so in anyway they can. What is difference between prezygotic and postzygotic barriers to reproduction? Can you give some examples? One happens before fertilization and intercourse, and one happens post intercourse/fertilization. A mule is a postzygotic barrier while different penis lengths are a pre-zygotic barrier. In the context of hybrid zones, what is reinforcement? Basically when the organisms in the hybrid zone can still reproduce with the non-hybrid zones but prefer to stay within their own zone. How does the development of reproductive barriers increase fitness to local environments? when a new species forms, it will lack the moderating effects of interbreeding and so can morphologically specialize. On longer timescales, why is there an evolutionary tension between widespread generalists and geographically restricted specialists? Because the specialists can only work in a specific environment but do really really well there, however generalists can work averagely in multiple places. Vocabulary Speciation - the emergence of a new species (new lineages) Phyletic change - the changes within a species over time Anagenesis - a synoym of phyletic change, the changes/ new developments in a species over time. the change in a chronospecies is anagenesis Lecture 5 2  Cladogenesis - The splitting of lineages over time; achieved through speciation. Allopatric speciation - The creation of a species due to geographic separation. Parapatric speciation - The creation of a new species due a niche becoming reproductively isolated. Sympatric speciation - A new species, perhaps based on a different food source or characteristic, develops spontaneously. Dispersal - A group migrates to a new place is not isolated Vicariance - A group is geographically separated (out of their control) and speciation occurs. Polyploidy - where failure of cell division can lead to extra sets of chromosomes (mostly in plants) Zygote - a fertilized egg. Prezygotic barrier (to reproduction) - A barrier that prohibits two populations from getting to the intercourse stage. Postzygotic barrier (to reproduction) - A barrier that keeps the zygote from developing into a viable thing. Habitat isolation - Rhagoletis pomonella flies mate and feed on different plants: hawthorn & apple trees (the plants are their habitat). When the habitats become isolated. Temporal isolation - They are isolated by the time they breed (spring vs winter). Behavioral isolation - They are isolated because of the why they behave (the meadowlark song) Mechanical isolation - Different genital morphologies Gametic isolation (name omitted by mistake from slide 49) - Many marine invertebrates have external fertilization, so reproductive isolation can occur if the Lecture 5 3  egg rejects sperm based on the sperm’s genotype, as is known to happen, e.g., in some sea urchin Sterility - the organism can’t reproduce. Hybrid zone - two incipient species (i.e., that are only partially reproductively isolated) come into contact. (A little hybrid zone can form). Reinforcement - Sometimes “reinforcement” occurs – the strengthening of mating isolation in response to selection against unfit hybrids. If an individual mates with an individual from the other species, and if the fitness of the offspring is lowered, then any genes that led to the preference for mating with the other species will be lost. Thus, there is selection for those that prefer to mate with their own kind. Lecture 5 4  6️⃣ Lecture 6 Key Questions Why do we think allopatry is the most common mode of speciation? Speciation requires interrupting gene flow. This is easiest when the populations are separated, so allopatric speciation seems likely to be most common. What are the 3 goals of systematics? Be sure to mention phylogenetics. 1. Identifying and naming spcies 2. Establishing the evolutionary relationships between taxa 3. Developing classifications What is a cladogram? Diagrams that depict the relative degree of relatedness among taxa, nothing more. How are cladograms made? Be sure to mention the character matrix and the principle of parsimony. They are made to be the parsimonious and the character matrix might support differing trees. The cladograms are usually the trees with the least changes and switches. What is the role of the outgroup? The outgroup is a species or group of species used in phylogenetic analysis to determine the evolutionary relationships among other groups being studied. It serves as a reference point for comparison, helping to establish which traits are ancestral and which are derived within the ingroup (the taxa of primary interest). How can evolutionary relationships be masked by evolutionary change? Lecture 6 1  Because you’ve evolved to lose something, and that something was what made you related to something else. You lose the evolution evidence and the relationship is then masked. How can the fossil record help (what do mean when we say the fossil record can be evolution’s time machine)? Given an example. The fossil records can reveal ancestral morphologies, before they become to different to recognize like the Cretans. How do we use DNA data to build evolutionary trees? With parsimony the DNA data matrix is treated exactly like a morphological data matrix. How can parsimony be fooled, that is, what is long-branch attraction? How is it related to statistical inconsistency? They can be fooled because the characters of DNA. The species that mutated the most and been around a lot created long branches. Then those branches could have more similar DNA. We use maximum consistency to weight them down. How (qualitatively) does Likelihood analysis deal with the problem of long- branch attraction? For each pair of sequences, the more different they are, the greater the chance that candidate synapomorphies, will have arisen by chance. Likelihood analysis weights each candidate synapomorphy in the data matrix by the probability that it was generated by chance given the amount of evolution. Vocabulary Taxon - any rank, species, genera, families, orders, classes, phyla, etc. Cladogram - diagrams that depict the relative degree of relatedness among taxa, nothing more. Phylogenetics- determining the evolutionary relationships between species (and higher taxa) Sister group - Branches that share a node Lecture 6 2  Node - branch points Apomorphy - derived evolutionary stat (e.g. Feathers) Synapomorphy - Shared evolutionary innovation such as feather and the base of the node. Plesiomorphy - An ancestor trait; At least two nodes down. Symplesiomorphy - A shared ancestoral trait, bascially a plesiomorphy that’s shared. Autapomorphy - Evolutionary innovation present on only one branch on a cladogram. Homoplasy - A character that evolves more than once on a cladogram, or evolves and is lost. Outgroup - The outgroup is a species or group of species used in phylogenetic analysis to determine the evolutionary relationships among other groups being studied. Character matrix - A matrix with similarities between species being marked with 1 or 0 in binary. Principle of Parsimony - The simplest cladogram will be made. Cetacean - Whales Long branch attraction - Statistical inconsistency - Maximum Likelihood.- Maximum likelihood adjusts the weight of the synapamorphy based on the chance that the change is accidental by chance. Lecture 6 3  7️⃣ Lecture 7 Key Questions What distinguishes phylograms and phylogenies from cladograms? Cladogram branches have no meaning and are just relative, phylograms the branches are related to the number of changes the species went through, and the phylogenies the branches are related to time. What are monophyletic, paraphyletic, and polyphyletic groups? Can you give examples? Monophyletic groups contain all the groups from a shared common ancestor. Paraphyletic groups contains an ancestral species and some but not all of its descendants. Polyphyletic groups contains distantly related species but not their most recent common ancestor. Taxonomic groups should be named based on which type of group? many believe we should name with the monophyletic groups however the paraphyletic naming are popular as well. What are the relationships between synapomorphies, homologies, homoplasies, and convergences (parallelisms)? Synapomorphies are homologs, are signatures of shared ancestry. Homoplasies are traits that when viewed in isolation appear to be homologs, but on the weight of other evidence may not to be. So homoplasies are convergences. Can you give some examples of convergences? bat and insect wings What is the Phylogenetic Species Concept? Lecture 7 1  A species is the smallest monophyletic group (lineage) distinguishable by a unique set of typically genetic (but can be morphological) traits, that is, synapomorphies) Why might the Phylogenetic Species Concept lead to the recognition of more species than the Biological and Morphological Species Concepts there is a time lag between the allopatric event and when the lineage will be recognized as a separate phylogenetic species, the time for plesiomorphic alleles to go extinct [Exit Ticket] What is the relationship between homology, synapomorphy and homoplasy? Synapomorphies are homologs, for example the limbs of tetrapods. Homoplasies are characters that in isolation we might have thought were homologs but turn out not be (typically representing convergences). Vocabulary Phylogram - a graph with branches related to the number of changes made. Phylogeny - a graph with branches related to time. Taxonomies - a graph that reflected genealogy. Monophyletic Group - Monophyletic groups contain all the groups from a shared common ancestor. Also called a clade. Paraphyletic Group - contains an ancestral species and some but not all of its descendants. Polyphyletic Group - contains distantly related species but not their most recent common ancestor. Homology - the similar positioning and maintaining of structures. Convergence/Parallelism - The parallel evolution of traits. Phylogenetic Species Concept - A species is the smallest monophyletic group (lineage) distinguishable by a unique set of typically genetic (but can be morphological) traits, that is, synapomorphies) Lecture 7 2  8️⃣ Lecture 8 Key Questions How were phylogenies used: – to make better flu vaccines? The flu evolves at a very fast rate and that’s why we need a new vaccine each year. However when a tree was finally built the CDC learned to only make vaccines out of the strands with the longest branches. – to determine where the HIV virus came from, and how many times it crossed over into humans? The HIV virus looks like SIV and when comparing a phylogeny of humans and primates it looks like the virus are polyphyletic, which means they evolved differently from different places. However there are a lot of origins from bush meat It also came from the Caribbean to the US – determine whether a dentist infected his patients with HIV? the dentist, and several controls (LCXs) shows that the virus in some of these patients was most closely related to the dentist’s virus, providing evidence of transmission. Lead the wearing of more gloves. – in a law case where a doctor was accused of injecting his girlfriend with HIV? Phylogenetic analyses of HIV-1 sequences were used as evidence the victim, the patient, and some local HIV-1-positive people showed the victim’s HIV-1 sequences nested within a lineage comprised of the patient’s Lecture 8 1  HIV-1 sequences – the paraphyly of the patient’s sequences implied transmission from the patient to the victim What was the hypothesis of the molecular clock? – How did it change our view of human origins? Homo and Pan (chimps) were (1) sister groups and (2) only diverged 4-5 million years ago! – Is there a universal rate of DNA change? No – If not, why not? While the rate of DNA changes are relatively constant within clades there is no universal rate of DNA change. Neutral rates of evolution: – What does this mean? those that are neutral with respect to selection, i.e., not subject to selection. – What is the difference between synonymous and non-synonymous mutations? Synonymous are changes that mean the same thing happens when a mutation happens. With proteins like three different patterns code for the protein. Non-synonymous mean that the mutations code for different proteins. – What is the difference between a mutation and a substitution? Mutations are changes in the DNA and Substitutions are mutations that become fixed in a population Can we use DNA distances to estimate divergence times even if there is no universal clock? There is a molecular clock – What technique is used to do this? rate smoothing - just average the rates and the differences. Lecture 8 2  Why has the SSU rRNA been such a valuable phylogenetic tool? All organisms have it, so we can trace it very easily. – What did it reveal about the origin of mitochondria & chloroplasts? The mitochondria group with the purple bacteria (which include E. coli).The chloroplasts group with the cyanobacteria. Vocabulary Molecular clock - the number of DNA changes was used to infer the amount of time elapsed, allowing us to date nodes on the tree the hope that differences in the DNA between species accumulate at a universal (stochastically) constant rate, and thus that the DNA differences between living species could be used to date their times of divergence (analogous to radioactive decay). Neutral evolution - those that are neutral with respect to selection, i.e., not subject to selection. Mutation versus substitution - Synonymous versus nonsynonymous mutation - Synonymous are changes that mean the same thing happens when a mutation happens. With proteins like three different patterns code for the protein. Non-synonymous mean that the mutations code for different proteins. Rate smoothing/relaxed clock analysis - we take our phylogram (the cladogram with the branch lengths measured in DNA changes) and ‘rate smooth’ it, to convert it into a phylogeny Time tree/Chronogram - gives the relative divergence times between the lineages based on the molecular data. Mitochondria - The powerhouse of the cell. Chloroplast.- The way plants can be green. Lecture 8 3  9️⃣ Lecture 9 Key Questions What is the difference between microevolution and macroevolution?- Evolution at or above the species-level is macroevolution and microevolution is evolution under the species level. Does the range of variation present at any given time put a hard cap on how far evolutionary change can proceed? Give an example. the evolutionary response to the directional selection was not limited to the range of variation seen at the beginning of the experiment. What is pre-adaptation? New morphologies are built upon previous innovations. How do the eyes of living mollusks help support the scenario for the major steps in the evolution of complex eyes? They provide living examples of every step of evolution. Did the vertebrate invasion of land involve pre-adaptation? Explain. Yes it is said that the legs that helped us to get onto land. Limbs and feet evolved in an aquatic environment, which later turned out to be very useful for walking on dry land. Where did our middle ear bones come from? Was preadaptation involved? Explain. The mammalian middle ear bones came from the reptilian lower jaw. The lower jaw was already being used for hearing so it is not a pre- adaptation. Birds evolved from whom? Was preadaptation involved? Explain. Lecture 9 1  The capacity for flight was built on many pre-adaptations Early meat-eating dinosaurs to the first birds Feathers evolved before flight. What is character analysis? What does this imply about the biology of LUCA? Explain? The process of identifying homologs based on morphology alone. Vocabulary Macroevolution - Evolution at or above the species-level Microevolution - Evolution under the species - level Pre-adaptation - New morphologies are built upon previous innovations. Vertebrate - that has a backbone and a skeleton Tetrapod - it has 4 feet Lobe-finned fish - fish with the fins have muscle and bone inside the fins Acanthostega - It is a tetrapod but it has a full set of gills, tail fin and lateral lines (sensory organs used by fish) Lateral line - sensory organs used by fish Archaeopteryx - The first bird Character analysis - The process of identifying homologs based on morphology alone Compound eye - Eyes that are made up of a lot of components. Lecture 9 2  Last Universal Common Ancestor (LUCA) - Literally the definition in the word Hydrothermal vent - milder vents some distance from the active spreading ridges Lecture 9 3  🔟 Lecure 10 Key Questions Difference between anagenesis and cladogenesis Anagenesis is change without new lineages and branches Cladogenesis is change with new lineages and branches What features suggest that the first tetrapod, Acanthostega, lived in water? A full set of gills, fins, and lateral lines. Can selection operate at the species-level? Explain with an example. The planktotrophic speciation, which favored planktotrophic larvae and not non-planktotrophic, because of the species-level trait of geographic range, and not the individual level trait of feeding type. What is the theory of punctuated equilibrium? Do we see the punctuated pattern in the fossil record? Do we see other patterns? Morphological change occurred rapidly during speciation, followed by long periods of stasis We can see a lot in the fossil record, the forum fossil has an example of punctuated anagenesis. Can we see micro-evolutionary change in the fossil record? Give an example. Is this common or rare? Yes, stickleback fish losing their spines. Why don’t we usually expect to see morphological change that occurred at the time of speciation in the fossil record? Just because of the time difference between the fossil records. Explain how the basic elements of microevolution scale up to macroevolution. Lecure 10 1  How can evolutionary trends be created at the clade-level? Use the fossil record of horses to explain. Was the selective regime during the end-Cretaceous mass extinction different from the non-mass extinction regime? Give an example. Not simply an extensions of natural selection during background times – it removed groups (such as the major dinosaur groups) that (we suspect) would have otherwise continued to be evolutionarily successful. Why do we think understanding mass extinctions are crucial to understanding the current composition of the biosphere? Restructured global ecosystems and in doing so played a major role in shaping the history of life. Can the evolutionary process be viewed as simply repeated rounds of microevolution? we cannot explain why the biosphere has the species that it currently has via a micro evolutionary account of evolution alone. Because of the events of our planet. Vocabulary Planktotrophic larvae - Larvae that eat plankton and have a larger geographic range. Non-planktotrophic larvae - Larvae that don’t eat plankton and have a smaller geographic range. Punctuated equilibrium - morphologies which features stasis. Phyletic gradualism - gradually changing morphologies, with many intermediates. Varves - Annual sedimentary layers) from glacial lakes Species sorting - Cause of ‘differential replication’ Directed speciation - When, on average, the direction of speciation is biased, Lecure 10 2  Asymmetric increase in variance - When the clade begins close to a boundary (e.g., a minimum body size), so that over time it will move on average to larger body sizes, even if there is no bias in the size of each new species. End-Permian mass extinction - a complete restructuring of the terrestrial and marine ecosystem, might have happened because of a LIP. End-Cretaceous mass extinction - meteor event, which killed the dinosaurs, short- term climate change, disruption of the base of the food chain; ocean acidification? Iridium (anomaly) - a huge concentration of iridium (Ir), which largely comes from meteorites, in the so-called boundary clay between the Cretaceous (K) and Paleogene (Pg) Chicxulub crater - The place where we believe the meteorite to have struck Mantle plume - a hypothetical column of hot, solid material that rises from the Earth's mantle to the surface, creating stationary hot spots Large Igneous Province (LIP) - a GIANT mantle plume eruption Siberian traps - a large region of volcanic rock, known as a large igneous province, in Siberia, Russia Lecure 10 3  🕚 Lecture 11 Key Questions Why is it so hard to see into the Earth’s earliest history? Because all of our data is coming from a sparse collection. Like of meteorites or carbon dating that could or could not be needed. Why is evolution important to the geologic timescale? The timescale is built around the evolution of life, What is the timeline for the origin of the Earth, of life, rise of oxygen, the first eukaryotes, origin of animals and our own genus? 4.65 Billion years ago the Earth booted up, life came around ~4 billion years ago, oxygen rate started increasing ~2.5 billion years ago. First Eukaryotes around ~2.1 billion years ago, then multicellularity came up ~1.6 billion years ago. The first animals popped up ~0.6 billion years ago and our own genus around 2.5 million years ago. How did the Moon form? Why are there seasons? There is a theory that a smaller proto planet (theia) crashed into the earth and them became our moon, probably after the formation of the core. The crash lead to the tilt of the Earth and that lead to seasons. What are Pallasite meteorites? Meteorites that are from the core of destroyed planets, that we use to date the formation of the earth and it’s core. If the oldest evidence of rocks on Earth is 4.4 Ga years old, why do we think the Earth formed at about 4.56 Ga ago? Because we found a pallasite meteorite What is one piece of geologic evidence for the rise of oxygen? Lecture 11 1  The amount of iron and and uranium deposits. The iron and the uranium were oxidized to things that are insoluble and they sunk and we still see them. Why might we call the ‘Great Oxygenation Event’ the ‘Great Poisoning’? We didn’t need oxygen before and now we are dependent on it which inhibits us from doing things like a poison. Animal life evolved very late, give one reason. Because the earth was very unstable, and then there wasn’t enough oxygen and then it was too cold, and there was no food. Vocabulary Multicellularity - more than one cell types. Cyanobacteria - multicellular organisms Brown Algae (e.g., kelp) - other independent multicellular organism (not close to plants). Red Algae - other independent multicellular organism (not close to plants). Golden Algae - other independent multicellular organism (not close to plants). Slime molds - organisms that start at single celled organism and then move to multicellular to reproduce and then switch back to single celled. Theia - proto-planet that was thought to crash into the earth and then become a part of the moon. Pallasite meteorites - meteorites with mantle remnants embedded in a matrix of iron-nickel (Fe Ni) matrix derived from the core Sedimentary rock - Faint Early Sun - Luminosity increased by ~50% over the last 4 Ga Stromatolites - Layered structures made by the binding and cementation of sedimentary grains by biofilms of microorganisms Great Oxygenation Event - The amount of oxygen in the atmosphere went up a lot and thus lead to the emergence to the eukaryotes. Lecture 11 2  Snowball Earths - An extended cold spell that lead to the oceans freezing over. Slushball Earth - An extend cold front that lead to the oceans becoming like slushies that allow a bit of sunlight through. Cambrian ‘Explosion’ - The emergence of more animals and more genuses around Lecture 11 3  🕛 Lecture 12 Key Questions Give the approximate times of origin of these intermediates between us and our last common ancestor with chimpanzees: Sahelanthropus, Homo erectus, and H. sapiens. Sahelanthropus was around 7 million years ago, Homo Erectus was around 1.6 million years ago, and Homo Sapiens was around 200,000 years ago It appears that the genus Homo dispersed out of Africa many times. When was the first (and what species was it)? When was the last (this is a trick question)? The first time was with Homo Erectus and the last time was probably like an hour ago. How does the practice of naming species hide the true nature of the brain-size increase in our lineage? When did tool use begin in our lineage? 2.6 – 1.7 Ma The mitochondrial DNA tree of living humans shows that sub-Saharan Africans are paraphyletic. What does this imply about the origin of living people? They are all evolving separately except that we are all descendants of sub- saharan african. Homo erectus developed a unique ability for a primate. What was it? List 4 relevant morphological innovations. Why do we think it evolved? What was an evolutionary consequence? Lecture 12 1  They could run very well. They had a swivel head, and long legs, and shock absorption feet, and our heel structure. Why is Homo erectus reconstructed without extensive hair/fur? Because it didn’t have that much fur it probably traded for sweat glands as the weather got warmer. The human brain grows significantly after birth, increasing the cost of parenting. List other aspects of human reproductive biology that require increased parental investment compared with chimps and gorillas. A hidden menstrual period, menopause, the parental investment. How has our species accommodated this increased cost? How was this solution already foreshadowed with the evolution of hunter-gathering? Our species have accommodated by becoming more of a social tribe member What is the oldest evidence of engravings? Who was responsible? On clams and it was by Homo Erectus What is an evolutionary mismatch disease? Give an example. Type two diabetes, an evolutionary mismatch disease is a disease that came about because of the misuse of an adaptation. Vocabulary Sahelanthropus - The currently oldest fossil of our lineage, the ~7 million-year-old Ardipithecus - Oldest bipedal ancestor and an ancestor to Lucy and the homo genus. Australopithecus afarensis (“Lucy”)- Pretty old bipedal, ancestor to the modern human but not homo. Homo erectus (Narikotome Boy) - The type of homo that left Africa, was kinda tall, and made tools, and maybe wrote stuff down. Homo sapiens - Us! Oldowan tools - oldest tools probably made by homo habilis Lecture 12 2  Acheulean tools - (1.7 Ma to 100,000 years ago) Coalescence time - the time when we had the same thing, genetic common ancestors or last names etc. Hunter-gatherers - People who hunted and gathered for their food, pre- agriculture. Childhood - When you are a child and your brain is still growing. Menopause - A point where women stop being able to reproduce. Group selection - A selection will not be what helps the individual survive it is what helps the group survive. Non-infectious mismatch diseases - Type 2 diabetes, Heart disease, stroke, High blood pressure Lecture 12 3