Evolution Final Exam

Named taxonomic units are legitimate only if they represent a clade (monophyletic group)

A monophyletic group includes an ancestor and all of its descendants. Modern taxonomists make an effort to only name groups that are monophyletic, so that the groups we talk about when classifying organisms reflect evolutionary relationships. There are two ways named groups may be non-monophyletic (and thus fail to reflect evolutionary relatedness). A paraphyletic group includes an ancestor and some, but not all, of its descendants. A polyphyletic group includes descendants from very distant lineages and excludes their common ancestor. For example, the group "pandas" is polyphyletic, in that giant pandas are bears and red pandas are more closely related to raccoons. The common ancestor of red pandas and giant pandas is also the common ancestor of bears, weasels, raccoons, and skunks - no one classifies that extinct species as a "panda."

A phylogeny is similar to a family tree

A phylogeny is similar to a family tree in that it portrays relationships of different degrees of closeness. You and your sibling shared common ancestors (your parents) more recently than you and your cousin (your common ancestors with your cousin are your grandparents). However, sexual reproduction means that human family trees are different from phylogenetic trees. Two humans need to come together to produce a new human, but two species don't need to come together to produce a new species. Also, the species represented by the nodes in a phylogeny no longer exist, but at least in humans and other species with overlapping generations, it's common for parents, grandparents, and sometimes great-grandparents to be alive at the same time as their descendents. Finally, if more than two branches are coming out of a node in a phylogenetic tree, that's a polytomy and indicates that more information is needed to resolve the relationships among those taxa. If more than two branches arise from a "node" (i.e., pairing) in a family tree, that just means the couple had more than two children.

#1: Evolution is "just" a theory

A scientific theory- set of mechanisms or principles that explain a major aspect of nature Hypothesis- a proposed explanation for a phenomenon that can be tested Like cells, evolution itself is a phenomenon we can observe. The theory of evolution seeks to explain how the process of evolution gave rise to the diversity of life on Earth In principle, the cell theory, the theory of gravity, the Big Bang theory, and the theory of evolution could all be disproven, but it would take truly extraordinary, hard-toimagine observations to do so.

Biologists since Darwin have realized evolution is a branching process

"As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it have been with the great Tree of Life, whihc fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications." -Darwin, 1859

Neither "reptiles" nor "fish" are monophyletic

"Fish" is not a monophyletic group unless it includes all other vertebrates (including humans). "Reptiles" is not monophyletic unless it includes birds. On the right, you can see a revised classification system for the vertebrates that uses only monophyletic groups. The convention among scientists when using the names of commonly recognized but non-monophyletic groups is to put the name in quotation marks. That's what I've done here, and you may see it in other papers you read.

Many traits are influenced by multiple genes

"Quantitative traits" with continuous distribution of phenotypes Example, imagine three loci, at each of which the dominant allele increases height slightly As with coat color in Labrador retrievers, many traits are influenced by more than one genetic locus. In some cases, though, the effects of those loci are largely additive, which means that many loci influence the phenotypic trait, but the loci don't interact with each other. When that's true, we often see a fairly continuous, bell-curveshaped frequency distribution of trait values in a population. One example of this kind of trait is human height. One reason why we see a fairly continuous distribution of heights in the human population is because there are several loci influencing that trait, each with a small effect on height. There's also environmental influence on height, although that's fairly minimal in societies where most people are well-nourished.

Evolutionary biology can trace the origin and spread of human disease

Here's a more recent paper published since Zika virus became a major public health concern (note the much more prestigious journal, Science) investigating the evolutionary history of Zika virus and how it may have arrived in Brazil. The researchers used an approach called a "molecular clock" to measure how many changes separated virus strains from different regions and predict how long ago the common ancestor of those strains probably existed. This kind of research may help determine how Zika virus spread across the world. This recent burst of research on Zika virus, however, would have been much more difficult if not for the work done when Zika was still a "neglected tropical disease."

Fossils can help infer the timing of branching events

Here, finding fossil F tells us that its direct ancestors, X and Y, must have lived more than 50 million years ago. However, it tells us nothing about when Z was last alive, because species Z is neither an ancestor nor a descendant of species F. Either the scenario shown in part C or part D of the figure could have occurred - we don't know

Sometimes, we don't show all species included in a tree

In figure A, the researcher might only have data for species B, E, F, and G, and therefore decide to leave species A, C, and D off the tree he or she was using in the analysis. This is still an accurate tree, in that it correctly shows the relationships between species B, E, F, and G, but it's not complete. Figure B shows a common way of simplifying phylogenies when drawing them, so that we're only showing the relationships among higher taxa, not individual species. You should only collapse a group like this if it's a monophyletic group, however

Dominance is a continuum, not an absolute

Incomplete dominance: phenotype of heterozygote is intermediate between phenotypes of the two homozygotes Incomplete dominance might result if having a single copy of a gene involved in the synthesis of red pigment didn't allow a plant to make enough pigment to produce red flowers, but only pink flowers. Two copies might be needed to produce enough pigment to make the flowers red. Again, dominance is usually a result of interactions between the proteins generated by different alleles of the same gene. Proteins can interact in many different ways, so there isn't always a clear dichotomy between dominant vs. recessive alleles.

#6: Evolution is the result of individuals adapting to their environment

Individuals do change in response to environmental conditions, but only changes that are passed on to offspring result in evolution The photos show Arnold Schwarzenegger and his actual children, demonstrating that, although individual humans can drastically change their muscle phenotype during their lifetimes, those changes are not passed on to offspring. As students correctly answered, you would not expect the population in the question to evolve to have more green-haired babies. There aren't any alleles in the human gene pool that code for green hair, so there would be no way for the green hair trait to be passed from parents to offspring. This is an example of selection that does not result in evolution. If only green-haired individuals can reproduce, that's strong selection in favor of green hair. However, if green hair is a phenotype that results only from environmental variation, with no genetic component, the population will not evolve in response to that selection. It's also important to recognize that the situation in the question (only green-haired individuals can mate) would also not make a mutation causing an allele for green hair any more likely to arise in that population than that mutation would be to arise in any other human population.

Evolution of insects is tied to evolution of plants

Insects emerged ~400 mya, but most current lineages appear much later As with fungi, the diversification of insects is tied to the diversification of plants, especially flowering plants, because insects interact with plants both as herbivores and as mutualists (mostly through pollination).

First terrestrial animal life

Invertebrate trackways date to 480 mya Probably relatives of insects and spiders Not clear whether they lived on land permanently Oldest fossil of fully terrestrial animal from 428 mya, appear to be relatives of millipeds The oldest known fully terrestrial animals appear to be relatives of millipedes

#8: Evolution always promotes selfishness and cruelty

It is possible for individual-level population to evolve, but they do not evolve because of their benefit to the population or species Under some circumstances, cooperation among individuals can be adaptive, but these cases must always be explained in terms of benefits to individuals We'll talk more about what can select for cooperation later in this class, but the key thing to remember is to always frame arguments about why a particular trait is adaptive in terms of benefits to individuals. The trait may sometimes also benefit the population or species of which those individuals are members, but the reason why a trait increases in frequency relates to its benefits to the individuals that have it.

Which species are "primative" vs. "advanced" depends on which traits you look at...

It's more accurate to say a particular trait or version of a trait is basal or ancestral (similar to a trait present in a group's ancestor) vs. derived (evolved after the species diverged from other members of its group) You sometimes still see the words "primitive" and "advanced" used to refer to ancestral or derived versions of traits, especially in older scientific papers or in papers from fields of biology other than evolution. However, most evolutionary biology researchers have switched to the words ancestral vs. derived, to avoid contributing to the incorrect idea that some species are in some way objectively more "primitive" or "advanced" than others. Certainly, some species are more complex than others in their physiology, morphology, or neurobiology. Some species are also more closely related to humans than others. Usually, if someone says a species is "evolutionarily advanced," what they really mean is that it has a complex biology or is closely related to humans. However, like all other living species, our own species descends from a lineage that has been evolving since the origin of life on Earth.

Phylogeny: A visual representation of the evolutionary history of genes, populations, species, or higher taxa

It's possible to make phylogenies of individual genes, showing which alleles arose from other alleles by mutations. It's also possible to make a phylogeny of populations within a species, although when members of different populations reproduce with each other occasionally, this can be complicated. Many phylogenies show relationships between different species (you'll probably mostly see phylogenies like this). However, you can also look at relatedness between higher level taxa (like genera, families, orders, etc.).

Diversification of mammals Mammals diversified after non-avian dinosaurs went extinct (~65 mya), with whales & bats both emerging around 50 mya

It's thought that the extinction of the dinosaurs left many open niches, into which surviving mammals radiated.

Geologists recognized that the Earth itself had changed gradually over long periods of time

James Hutton & Charles Lyell • Uniformitarianism: the same processes observed today (erosion, volcanoes, etc.) are responsible for events in the past • The earth must be old The idea that geological features of Earth have changed gradually over long periods of time is similar to the idea that gradual changes in the proportions of traits present in populations over time can lead to the evolution of new traits and, eventually, the divergence of an ancestral species into descendant species. In order for the subtle changes we can observe during our lifetimes to add up to the drastic changes we know have occurred, however, the Earth must be very old. Independent sources of evidence (mostly from the decay of radioactive elements in rocks) have now confirmed that the Earth is billions of years old, not thousands of years old as early philosophers though. The idea of uniformitarianism provided the first hint at how truly ancient the Earth must be, however.

Chromosomes contain genes, which are often "intructions" for making proteins

Locus= physical location on a chromosome Plural loci Alleles= versions of a gene that may generate different versions of a phenotypic train At some loci on a chromosome, there are genes, but many loci do not code for proteins. A locus is any physical location on a chromosome, whether or not that location is part of a gene. We'll discuss the functions of non-coding DNA frequently in this class.

#2: Scientists routinely "prove" scientific hypothesis or theories to be correct

Never, ever use the phrase "prove my hypothesis to be correct" in any kind of science writing We may find data that are consistent with, support, or strongly suggest a particular hypothesis We can almost never imagine, let alone test and falsify, all possible alternative hypotheses that might explain our results If we find results that are completely inconsistent with our hypothesis, we may be able to disprove it, but it is extremely rare to prove a hypothesis I'm adding an essay from the journal The American Biology Teacher to Blackboard that expands on this topic. The use of the phrase "prove X to be true" has been so common in term papers and assignments in various classes I've taught that I've decided to push hard against it. Let's say, for example, that one semester's Evolution class did better, on average, than a previous semester's class on the Natural Selection Concept Inventory pre-test. We can argue that this result disproves the hypothesis that the two sections' scores were the same. However, there are several different alternative hypotheses that might account for the difference: 1. Students in the better-scoring section of Evolution are smarter, on average, than students in the lower-scoring section. 2. Students in the better-scoring section of Evolution took their last biology class more recently than students in the lower-scoring section did, so they remember more, on average. 3. There were more seniors in the better-scoring section of Evolution than in the lower-scoring section, so they had studied more biology and had more outside knowledge. The results of our "experiment" are consistent with all those hypotheses, and probably many others that you can imagine. To "prove" any particular alternative hypothesis to be correct, we would need to test and disprove not only the null hypothesis, but also all other possible alternative hypotheses. Very, very few scientific studies can do this, so it's virtually never correct to say you've "proven" (or "will prove," if you're writing a proposal) a particular hypothesis to be correct. For the purposes of this class, just don't do it.

Fossils sometimes document the loss of synapomorphies

Not all taxa have a detailed enough fossil record to document the loss of synapomorphies, but whales do. We can see through a series of transitional fossils that whales descended from four-legged ancestors, and that their hind limbs gradually became more reduced over time. Living whales do have a few of the bones that were once part of their hind limbs, which are homologous to similar bones in other tetrapods. However, these bones no longer function, making them a vestigial trait.

The co-discoverer of evolution by natural selection

Alfred Russel Wallace focused more on geographic patterns than Darwin, so he is often called the "father of biogeography," or the study of why we find particular species of organisms where we find them. One of his key observations was what's now known as the "Wallace Line" between southeast Asia and Australia. Islands on the northwestern side of the line have flora and fauna that more closely resemble those on the Asian mainland, while islands on the southeastern side of the line have flora and fauna that more closely resemble those of Australia. This is in spite of the fact that the climate, seasonality, etc. of those islands are similar and they're geographically close to each other. We now know that Wallace's Line is mostly a result of the fact that, in the past, sea levels were lower, and islands near Southeast Asia were part of that continent. Similarly, islands near Australia were part of that continent (areas of ocean that were previously dry land are shown by the shaded areas on the map). Wallace's line represents deep water, where land was never exposed, even during periods of extremely low sea levels. There has thus been more exchange of genes between populations living on the same side of Wallace's line than between populations living on different sides of Wallace's line, even if populations living on different sides of the line are in similar environments.

#4: Evolution proceeds in "stages," with some species "more evolved" than others

All species living on Earth are equally evolved, in that all descend from a universal common ancestor and have been evoling since the origin of life of earth Similarly, evolution can't predict the future- neither humans nor any other species are passing through particular "evolutionary stages" A student during a previous semester asked a good question about the X-Men analogy. If, in that universe, humans with some mutant allele had higher average reproductive rates than humans with ancestral alleles at the same locus, the human population would evolve to have more mutants in it. That would be an accurate representation of how evolution works. What's not accurate is the idea that humans (or any other species) are progressing towards any particular evolutionary "goal" or going through particular "evolutionary stages." Which traits are favored by natural selection depends on the environment in which a population occurs and the existing variation present in that population

Synapomorphies may be lost in some members of the groups they define

Presence of 4 limbs= synapomorphy for the tetrapods (all vertebrates except fish) We know that both whales and snakes descended from ancestors that had four limbs, so they're still tetrapods, even though they've lost one of the main synapomorphies for that group (the presence of four limbs).

Independent evolutionary processes in different groups have produced the diversity of life on Earth

All species, living and extinct, are related to all other species No such thing as two species that are "not related," just different degrees of relatedness This is a theme we'll continue to come back to. The pattern of evolutionary relatedness among species and higher taxa is something we also sometimes call "macroevolution," or evolution above the species level. People who study macroevolution try to understand how different species are related to one another as part of the (family) tree of life. The figure is from a website called Tree of Life Web (tolweb.org), which I highly recommend you explore. It's maintained by experts on the evolutionary relationships of many different groups of organisms, and lots of professional biologists use it as a resource to learn more about where on the tree of life a particular species falls.

To find out for sure, we need a phylogeny!

Conveniently for the authors' analysis, living in the forest appears to have originated multiple times independently within the species Peromyscus maniculatus. That means the authors have multiple independent data points. They used two different variations on the phylogenetically independent contrasts method to test their hypothesis here and found that, after correcting for relatedness among populations, there was still a difference in average tail/body ratio between forest and prairie populations. If you're super interested, the reason why the authors had to modify the usual method slightly is that populations of the same species may be exchanging alleles, whereas different species generally don't. That's a point that's way beyond the scope of this class, though, so don't worry about it unless you think you might want to do this kind of analysis someday.

Not all similarities are due to common ancestry

Convergent evolution: independent evolution of similar traits in distantly related lineages that live in similar environments Traits that evolve convergently are analogous Again, I want to emphasize here that whales and fish are related, so it's not that they "don't have a common ancestor." However, the forked tails present in whales and fish evolved independently of each other, rather than being inherited from the common ancestor of whales and fish. That's what makes forked tails in whales and fish analogous traits rather than homologous traits. Convergent evolution, the process by which analogous traits arise, usually happens when distantly related species live in similar environments

Ediacaran fauna

Dominated oceans from 575-535 mya, many hard to relate to modern species Many common fossils from the Ediacaran period appear to be animals, but it's difficult to place them into modern animal phyla. They may belong to lineages that died out completely and have no modern descendants.

#5: New traits arise because they are "needed"

Evolution starts with genetic variation, and all genetic variations start out as mutations Mutations occur randomly with respect to their effect on fitness (this does not mean there is a 50% probability of a mutation being helpful-harmful mutations vastly outnumber helpful mutations) By chance, some small fraction of mutations are a good match for their environment and help individuals who have them survive or reproduce. Over generations, these new alleles increase in frequency Some kinds of mutations are more likely than others to occur, but a particular mutation is no more likely to occur in an environment where it would be helpful than in an environment where it would be harmful.

#7: Natural selection acts for the "good of the species"

Evolutionary fitness is measured by how many offspring an individual has that survive to adulthood, not by how well the population that individual belongs to is surviving Adaptations that benefit the individuals carrying them may be harmful to their population or species as a whole The first example illustrated is the ability to develop into a cannibal morph in tiger salamander larvae. Some individuals have alleles allowing them to make this drastic developmental shift when the ponds where they live as juveniles are drying up. Other individuals do not have these alleles and remain omnivores (eating mostly rotting plant material) regardless of the environmental conditions. Cannibal morphs, as their name implies, eat other members of their species. This speeds up their development and makes it more likely they'll be mature before the pond is dry. The ability to become a cannibal morph is beneficial to the individuals that have it but clearly not ideal for the growth rate of the population as a whole, since many other individuals in the population will be devoured. The other example is a little less dramatic - gypsy moths are a well-known invasive species that goes through drastic boom and bust population cycles. These cycles are partly caused by the fact that the caterpillars eat so voraciously that they can defoliate entire forests, leaving nothing for the next cohort of caterpillars to eat. These later caterpillars often starve to death, causing the population to crash. If natural selection were operating for the benefit of the species as a whole, you would expect caterpillars to restrain their consumption of leaves in order to leave something for later generations, but that's not what we observe. Within any one generation of caterpillars, the ones that eat the most leaves grow fastest and are the most successful, so there's selection for the ability to eat as much as possible.

Meiosis generates reproductive cells (gamates)

When homologous chromosomes line up during meiosis, maternal and paternal chromosomes can be either side Independent assortment The next few slides deal with the consequences of chromosome behavior during meiosis for evolution. If you don't remember how meiosis works, I recommend looking back at your notes from a previous class or at an introductory biology textbook. As a reminder, the basic function of meiosis is to generate haploid gametes from diploid body cells, so only one chromosome from of each set of homologous chromosomes ends up in each gamete. I'm not going to ask you to memorize all the stages of meiosis or what events occur during each of them - that's important for a class in genetics, but our focus in this class is evolution. For evolutionary biologists, the most important steps of meiosis to understand are those that generate variation among offspring (independent assortment, covered on this slide and the next one; and recombination, covered on the two slides after that). Independent assortment generates variation because there are many different combinations of maternal and paternal chromosomes that can end up in gametes after meiosis. See the next slide for an explanation of the think-pair-share question.

Alleles may be dominant or recessive

Whether an allele is dominant or recessive is unrelated to how likely it is the be passed from parent to offspring Whether an allele is dominant or recessive is unrelated to how common it is in a population Interactions between alleles of the same gene occurring in the same individual are called dominance. Whether an allele for a trait is dominant or recessive has nothing to do with how big the trait is, how likely the allele is to be passed on, or how common the allele is in the population. It just results from the biochemical interaction between the gene products produced by the two alleles at the same locus. If one of them masks the presence of the other, in terms of its effects on phenotype, the masking allele is dominant to the masked allele. Dominance and recessiveness are also not absolute characteristics of alleles. If there are more than two alleles of a gene present in a population (let's call them alleles A, B, and C for this example), it's possible for allele A to be dominant to allele B but recessive to allele C. Whether a particular allele is dominant or recessive depends on the allele with which it's paired. Mechanistically, this depends on how the different gene products (usually proteins) produced from the genes interact with each other.

Darwin and the HMS Beagle

• Charles Darwin (1809-1882) was a "gentleman naturalist," had a divinity degree. • In 1831, asked to accompany captain of survey ship during voyage around the world. • Insights from his observations were crucial to developing theory of evolution by natural selection. Darwin's voyage on the Beagle allowed him to observe and document geographical patterns in biodiversity that were very important in his later thinking. For example, plants and animals in temperate South America were more similar to plants and animals in tropical South America than they were to plants and animals in temperate regions of Europe. That observation is confusing if you assume all organisms have been specifically created for the environment where they're found but makes more sense if you assume species descend from ancestral species that typically lived near where you currently find them.

Dominant alleles can be rare in a population and may code for larger or smaller trait values than recessive alleles

The allele for achondroplastic dwarfism in humans is dominant (anyone with the allele has the disease, regardless of whether they have two copies or one). However, the allele is quite rare; it only occurs in about 1/25,000 people. The two photos are of Peter Dinklage, a well-known actor with dwarfism, and Michael C. Ain, a surgeon and professor at Johns Hopkins who specializes in treating bone problems associated with dwarfism and also has the condition himself. This example also illustrates that a dominant allele can generate a smaller version of a trait (in this case, height) than a recessive allele.

Darwin realized that variation is crucial

The finches on the left are six species of what are now called "Darwin's Finches," which live on the Galápagos islands, far off the coast of Ecuador in S. America. As you can see, they vary quite a bit in the size and shape of their bodies and beaks, in ways that make sense for what they eat and what habitats they use. The dull-colored grassquit Tiaris obscurus is the current best candidate for the closest living relative of Darwin's Finches, and it lives in mainland South America. It has a large range and is a generalist when it comes to habitat use and diet. Darwin noticed that finch species on the Galápagos are more specialized and seem to represent variations on a type when compared to similar mainland species. This was one of his first clues that variation within a population could be important to understanding the origins of biological diversity.

A better representation of humans and our close relatives

The species here don't correspond to the species in the terrible human evolution figure from the last slide, but I like this tree because it does a good job showing humans in the context of our living relatives. It's a tree based on molecular data, so it only includes species from which we can get DNA (i.e., living or recently extinct species). The dates at the nodes (branch points) show estimates of when the common ancestor of the species descended from each node lived. None of the species at the tips of the phylogenies (the ones with the photos) evolved into any of the other species at the tips of the phylogeny. Instead, they evolved from the common ancestors represented by the nodes. Just as a matter of common custom, the Neanderthal is placed a little bit below the other species on this tree to indicate that it's extinct. A student from a previous semester asked a good question about why we consider Neanderthals to be a different species than humans, when recent evidence has suggested that our own species (Homo sapiens) interbred with Neanderthals when both species were present in Eurasia near the end of the last glacial period. The answer is mostly because, although we can detect evidence of a few Neanderthal alleles that have become common in some human populations, the two species don't appear to have merged into a single, interbreeding population during the time they overlapped. There are many examples of species pairs that can interbreed to some limited extent, including polar bears and grizzly or brown bears. Usually, if both species seem to retain their separate identities, we continue to consider them separate species. The question of exactly how much interbreeding means we should reclassify two species as a single species isn't really resolved, though. We'll discuss both the definition of a species and the evolution of humans and our relatives later in this class.

Phylogenies are based on analysis of characters with different possible states

The table shows a set of characters, or traits, you might use to investigate the evolutionary relationships among Carnivora, an order of mammals including many familiar species. As you can see, each character is assigned two possible states (in theory, there can be more, but here there are two for simplicity). The outgroup species used here is a lemur, which is a primate and thus a member of a different order, but the same class (Mammalia). Notice that the lemur, the outgroup, has values of zero for all the characters. The assumption underlying this method is that the character states shared with the outgroup are ancestral, and that other character states present in some of the carnivore species are "derived" and thus may reflect close evolutionary relatedness among the species that share them. These are the reasons why the choice of which outgroup to use, and which characters to analyze in constructing a tree, is so important.

Principle of maximum parsimony

The tree requiring the fewest evolutionary steps is most likely to represent the true relationship You can see more clearly here that the tree on the right implies multiple cases of convergent evolution, where the same version of a trait evolves more than once independently, and evolutionary reversals, where a trait changes from one state to another and then back to its original state. The principle of maximum parsimony assumes that it's more likely for a trait to just change once, in a single lineage, than to arise convergently or undergo evolutionary reversal. Thus, the tree with the fewest "evolutionary steps" is most likely to be correct.

Diploid organisms have two sets of momologous chromosomes that contain the same sets of genes

The word "homologous" here is not used in exactly the same way as evolutionary biologists use it, although it's sort of the same idea. Homologous traits share most of their evolutionary history, and homologous chromosomes share the same sets of genes. You can also talk about different alleles of the same gene (located on different chromosomes) being homologous in the evolutionary sense, because derived alleles originate from ancestral alleles via mutations.

Polytomy: an unresolved pattern of divergence

This figure is meant to show you how to get information from a phylogenetic tree about what evolutionary events have happened in the past and how closely related to each other living taxa are.

"Man can hardly select, or only with much difficulty, any deviation of structure excepting such as is externally visible. . .He can never act by selection, excepting on variations which are first given to him in some slight degree by nature." -Charles Darwin, On the Origin of Species

When he returned to England, Darwin applied some of the ideas he had started to develop while on the Beagle to breeding domestic pigeons. The pictures on the right show some of the varieties of domestic pigeons produced by Victorian pigeon breeders. It was through his work on breeding different varieties of pigeons that Darwin had the crucial insight that all these extreme types originated from some slight variation in a particular direction in the ancestral population (one modern descendant of which is shown on the left and can be found on city sidewalks everywhere). Darwin knew from experience how pigeon breeders started with slight variations and bred selectively to generate more extreme versions of those variations. Based on his observations in the Galápagos and elsewhere, he was able to extrapolate that something similar might happen in nature.

Taxa with long branches may or may not have ancestral characteristics

Ancestral Galapagos iguana probably similar to neotropical land iguanas in behavior & physiology Some "basal taxa" represent the descendants of lineages that don't really seem to have changed much for thousands or millions of years. One example from last week would be sponges, which most phylogenies suggest are the sister group to all other animals (although there have been some studies recently that have cast doubt on that relationship). In any case, many researchers think sponges may be fairly similar in morphology and physiology to the ancestor of all other animals, which would suggest they represent a basal taxon that is similar to an ancestral taxon. However, that's not necessarily always true when a lineage is basal relative to some other group of organisms, as the example of the Galápagos marine iguana shows. The Galápagos islands were colonized by a land iguana millions of years ago (probably one somewhat similar to the central American land iguana shown on the left, although it wasn't that exact species). The descendants of that colonizer diverged into two lineages, the land iguanas and the marine iguana. Galápagos land iguanas have undergone two subsequent speciation events (probably due to their isolation on different islands). The marine iguana remains one species (possibly due to greater genetic exchange between populations - they can swim, after all), so it's basal relative to the group containing land iguanas. However, the marine iguana is very different in many traits from the land iguanas and from other close relatives. The land iguanas are probably more similar to the ancestral, colonizing species in terms of their morphology, physiology, and ecology; they've just undergone more speciation events since they diverged from the lineage leading to the marine iguana.

Biological Evolution

Any change in the inherited traits of a population that occurs from one generation to the next Important- individual organisms do not evolve, populations do I want to point out that the schematic doesn't show a perfect, steady increase in the proportion of dark gray mice over time. The proportion of dark gray mice doesn't change between generations 2 and 3, and it actually decreases between generations 5 and 6. That's an accurate analogy for evolution in real, natural populations - over time, traits that allow their bearers to survive or reproduce at higher rates become more common in populations. That process is called natural selection. However, as we'll learn, there are other mechanisms for evolution that can generate changes in traits that are not adaptive (genetic drift and migration are two you might have learned about in previous classes). Also, it's important to remember that differences in survival and reproduction among individuals with different trait values are average differences, not absolute differences. In the example above, it's highly unlikely that every single dark grey mouse would have more babies than any light grey mouse. If dark grey fur is selectively favored, it means that the average number of offspring produced by a dark grey mouse over its life is higher than the average number of offspring produced by a light grey mouse over its life.

Gene expression is regulated

Changes in gene expression often the mechanism for environmental effects on traits Different genes "turned on" in different cells and at different developmental stages In most multicellular organisms, nearly all cells in the body except gametes contain exactly the same set of genes. What makes heart cells different from brain cells, for example, is which genes are actually being expressed (i.e., transcribed into RNA and then translated into protein). Differences in gene regulation are often also the mechanism by which the environment affects organisms' phenotypes - some genes are "turned on" or "turned off" in response to environmental stimuli. In most genes, the stretch of DNA that's actually transcribed is only part of the gene. There's a regulatory region to which various kinds of regulatory proteins attach. These proteins can increase or inhibit the rate of transcription of the gene. There are also other ways in which gene expression can be regulated, and we'll discuss some of them next time.

If more than one tree is equally parsimonious, we can construct a consensus tree

Consensus trees often contain polytomies, showing relationships are uncertain

Genes on the same chromosome are linked, but the links can be broken

During meiosis, homologous chromosomes exchange pieces of themselves in a process called crossing over, which results in recombination of sets of genes on each chromosome We'll talk about the consequences of this fact for evolution later in this class, but the first important thing to understand here is that there are many genes on each chromosome. Alleles at different loci on the same chromosome are not inherited completely independently, especially if they're physically close to each other. That is, let's say that an individual has the alleles A at one locus and B at another locus on its maternal chromosome, and the alleles a and b on its paternal chromosome at those same two loci. It's more likely that the individual will make gametes containing the alleles A and B, or the alleles a and b, than it is that the individual will make gametes containing the alleles A and b or a and B. However, it's possible for alleles for different genes that were originally on different chromosomes to end up on the same chromosome (and thus in the same gamete) after meiosis. This happens through recombination, a process through which homologous chromosomes exchange little pieces of themselves during meiosis. This is the other step of meiosis that it's crucial for evolutionary biologists to understand. The farther apart two loci are, the more likely a recombination event is to separate those loci. If two loci are far enough apart on a chromosome, alleles at those loci are inherited independently, just as if they were on different chromosomes. If two loci are very close to each other on a chromosome, alleles at those loci tend to be inherited as a unit (some combinations of alleles are much more common than others). If the physical linkage is tight enough, two different loci can be mistaken for a single, pleiotropic locus based on inheritance patterns.

In general, anwser to this question is 2N, where N= haploid number of the organism N sets of chromosomes, with 2 possible chromosomes that can go into each gamate

During meiosis, pairs of homologous chromosomes line up in the middle of the cell before it divides for the first time (this is when the cell goes from being diploid to being haploid). The maternal and paternal copies can be on either side of the dividing line, and this happens independently for each pair of homologous chromosomes. This independent assortment of maternal and paternal chromosomes increases the number of different combinations of maternal and paternal chromosomes in the resulting gametes and is one of the ways genetic variation among offspring of the same two parents is generated. As a rule, if you're making a choice between X options Y times, the number of possible combinations are XY . Here, each pair of chromosomes can be arranged 2 ways, and there are N pairs of chromosomes, so the number of possible combinations is 2N.

Algae represent some of the oldest multicellular eukaryotes

Earliest fossils of multicellular eukaryotes (algae) date to 1.6 bya Red algae: 1.2 bya Green algae: 750 mya The earliest identifiable organisms to evolve multicellularity in nature appear to have been algae.

The dawn of animals

Early animals resemble sponges Oldest fossils 650 myo Presence of compounds only produced by animal cells also demonstrates existence of sponges during this time

Many extant animal phyla first appear during the early Cambrian, aka "cambrian explosion"

Early cambrian: 542-511 mya New niches appear, such as predation origin of most extant animal phyla, including Chordata The increasing complexity of ecosystems during the Cambrian may have meant there were more available ecological niches, which would tend to increase the rate of species diversification. Another way of thinking about this is that the existence of more trophic levels leads to more species interactions and thus more coevolution, in which an evolutionary change in one species affects the evolution of another species with which the first species interacts.

Alleles at different genetic loci interact

Epistasis: genotype at one locus influences how/whether alleles at another locus are expressed One of the reason why new combinations of alleles at different loci on the same chromosome are important for evolution is because alleles at different loci interact with each other. These interactions are called epistasis. A classic example is from the genetics of Labrador retrievers, a common breed of dogs. There are three possible coat color phenotypes in Labrador retrievers, black, brown (or "chocolate"), and yellow. This variation results from two different genetic loci, the B/b locus and the E/e locus. At the B/b locus, the B allele generates black pigment and is dominant to the b allele, which generates brown pigment. The E/e gene, however is epistatic to the B/b gene. If a dog is homozygous recessive ee, no pigment will be deposited in the hair at all, no matter what the dog's genotype is at the B/b locus. This leads to the pale coat color characteristic of "yellow Labs."

#9: Evolution produces organisms that are perfectly adapted to their environment

Evolutionary history, existing genetic variation, and trade-offs constrain how likely traits are to evolve A particular trait variant doesn't need to be ideal to become common, just better than the other variants in its population Some evolutionary paths are "easier" than others, due to what preexisting structures are present and/or how drastic the changes required would be. For example, an engineer who was designing a flying vertebrate might add two new limbs sticking out of its back (as seen in imaginary creatures such as fairies or dragons). However, the vertebrate lineages that actually evolved powered flight did so through the modification of their forelimbs into wings. This is probably because the changes required to modify forelimbs were less dramatic, and thus more likely to occur, than the changes that would be required to generate two completely new, functional limbs originating from an organism's back. Similarly, many traits are the result of trade-offs between conflicting selection pressures. Bipedal locomotion selects for a particular size pelvis in humans, which is in conflict with selection pressures for longer gestation times (which would allow human infants to be born at a more advanced developmental stage). Both walking efficiently and giving birth to developmentally advanced babies, independently, are probably associated with increased fitness. However, the ideal pelvis widths for these two functions are different. The difficulty of childbirth in humans results from a balance between those two conflicting pressures.

Origin of multicellularity was a major transition in history of life

Evolved independently in different lineages (animals, fungi, plants) Earliest evidence ~2.1 bya, lineage unclear Extant organisms provide clues about origin of multicellularity In multicellular organisms, many different cells "cooperate" and share resources. This is different than the competitive relationship that would have existed between different cells (which would have been different individuals) prior to the evolution of multicellularity. It makes the most sense for cells to cooperate if they are genetically identical - otherwise, an individual could be helping to pass on alleles it didn't have, which doesn't make evolutionary sense. Some amoebas and bacteria have both single-celled and multicellular stages, so researchers study what factors lead to cells "cooperating" and what conditions must be met for them to do so.

When traits are similar for reasons other than common descent, building a phylogeny is challenging

Homoplasy: character state similarity not due to common descent Convergent evolution: independent evolution of similar trait Evolutionary reversals: reversion back to an ancestral character state One reason why the tree with the fewest evolutionary steps might not be the "true" tree is when many traits are homoplasious, or similar for reasons other than common ancestry. This can occur if similar-looking traits arise independently in distantly related lineages, such as forked tails in whales and fish. It can also happen if a lineage loses a trait its ancestors had. One example of this is Plasmodium, the parasite that causes the blood disease malaria. Its phylogenetic position was confusing until researchers realized that a structure inside Plasmodium cells called the apicoplast was actually a vestigial chloroplast (the structure plants and photosynthetic algae use to photosynthesize). Plasmodium can't photosynthesize, but they descend from algae that could. A more familiar evolutionary reversal that we already discussed in this class is the loss of limbs in snakes. We know based on other evidence that snakes descend from tetrapods that had four limbs, but a phylogenetic analysis of the vertebrates based only on limb number might group snakes with fish. The massive oversimplification of how you deal with homoplasious characters when building phylogenies is that you use as many characters as possible and go with the tree that most of the characters support. Which characters you use, exactly, and how you weight the evidence coming from different characters, are some of the complications we'll discuss in later classes.

Homologous traits are similar die to common descent

Human-dog: hair, milk, 4 legs, inner ear bones, arrangement of bones in forearm, lots of others Human-fish: spine, camera-type eye, intestines, bilateral symmetry Human-plant: use of DNA as genetic material, genetic code, presence of mitochondria in cells

The environment also affects organisms' phenotypes

Hydrangea flowers= pink in basic soil, blue-violet in acidic soil, bright blue when free aluminum present The environment an organism lives in can change the organism's phenotype without any change to the organism's DNA. That is, two individuals with identical genotypes might exhibit different versions of a trait if they live in different environments. Many (probably most) traits in living organisms are influenced both by genetic variation and by the environment. Height is a good example of such a trait in humans. That's actually the source of the positive correlation between human height and intelligence (at least as measured by IQ) that sometimes gets discussed in the popular press. As a fairly short person, I was motivated to investigate why that correlation shows up . I'm somewhat relieved to report it doesn't appear to result from pleiotropy (that is, there aren't alleles that generate both increased height and increased intelligence). Rather, an environmental factor, specifically malnutrition, tends to lead to humans both being shorter and having lower IQs than their genetic potential would otherwise allow. Unfortunately, malnutrition is still common enough in many parts of the world that some humans who have the genetic potential to be tall remain short due to insufficient calories or micronutrients. Malnutrition also affects brain development, so people who are short due to malnutrition may also face cognitive challenges as adults. However, if a human is short for genetic reasons, that doesn't tell you anything about what alleles he or she has that may affect his or her IQ.

DNA is packed into chromosomes inside living cells

If it were all stretched out to its maximum length, the DNA inside a single human cell would be about 2 meters long, much too long to fit inside the dell's nucleus. Instead, DNA in eukaryotes is packed into linear chromosomes, which replicate and condense into the familiar "X" shape before mitosis or meiosis Prokaryotes have one large, circular chromosome with most of their DNA, and then a few smaller, circular pieces of DNA called plasmids. Plasmids are important to understanding prokaryotic evolution because they are often exchanged between prokaryotes from very distant lineages. They also often contain genes coding for traits like antibiotic resistance.

Comparisons among species must take phylogeny into account to be statistically valid

If the phylogeny on the left (version A) is the true relationship between the species you're studying, you really do have 12 independent cases of large body size being associated with high cheese attraction or small body size being associated with low cheese attraction. However, if the phylogeny on the right (version B) is correct, you actually only have two independent data points. The common ancestor of species A, C, E, G, I, and K appears to have had large body size and high cheese attraction. The common ancestor of species B, D, F, H, J, and L appears to have had small body size and low cheese attraction. Those two data points, however, are not enough to conclude that body size and cheese attraction are correlated.

Evolution of amniotes

Mammals & reptiles (including birds) = amniotes Amniotic sac (ancestrally inside a shelled egg), not tied to water for reproduction Birds= last surviving dinosaur lineage Mammals evolved from within synapsids Dominant vertebrates ~280 myo First mammals emerged 150 mya

A global test for phylogentic signal in shifts in flowering time under climate change

Many plants have shown a change in flowering time in response to increasing average temperatures Are particular clades more likely to show this shift than others This is a fairly simple phylogenetic analysis (complicated in this case by the extremely large tree the authors used). As Earth's climate warms, many different researchers have observed that flowering plants tend to flower earlier in the year than they had in past decades. The question the paper asks is whether plant species that show these shifts are more closely related than we might expect them to be by chance. The technical term for this is "phylogenetic signal." Based on the phylogeny, you can see that the red lineages (the ones showing a shift in flowering time) tend to form clusters, although they are not all each other's closest relatives. This means that shifts in flowering time have occurred multiple times, but primarily in particular clades of plants. Follow-up research could ask what other characteristics these clades share, as a way of predicting where the effects of climate change are likely to be most pronounced. As a note, you may be wondering why the gymnosperms are on this tree, since they are not flowering plants. The answer is that they were used as the outgroup in the phylogenetic analysis.

Fossils of animals not found alive anywhere on Earth provided evidence of extinction

Mary Anning (1799-1847) discovered several species of extinct marine reptiles Initially, geologists and biologists who found fossils in Europe thought that those organisms must still be alive somewhere else in the world. As greater contact between people from different parts of the world and the exploration of uninhabited regions failed to reveal these species, however, some researchers began to suspect that many fossils might represent species that were no longer living. The finding that many species had become extinct during Earth's history cast doubt on the idea that all species had particular divine purposes, as well as contributing to our understanding of how drastically the Earth and its species have changed throughout their history. Mary Anning was a fossil collector working in England, at a time when very few women were involved in science. She was from a working-class family, so she often had to sell the fossils she found in order to earn money, but even so, she made major contributions to the science of the time. She found and reconstructed many fossils that clearly represented extinct species of reptiles; unfortunately, she often didn't get the credit she deserved for her work due to her sex.

The tree of life includes three domains: Bacteria, Archaea, and Eukarya

Mitochondria and chloroplasts results from ancient endosymbiosis between bacteria and eukaryotes Some evidence suggests that Eukarya and Archaea are more closely related to each other than either is to Bacteria, but divergence events from billions of years ago are very difficult to reconstruct. It's even possible that the eukaryotes form a group within the archeans, which would mean that some archeans are more closely related to eukaryotes than they are to other archeans. We'll learn more about why "deep time" phylogenies are so challenging to construct throughout this class.

DNA provides many more characters for constructing phylogenies than morphology does

Modern phylogeneticists usually use DNA sequences to construct phylogenies, instead of morphology Homologous traits in DNA sequences are identical nucleotides at the same position in a gene (or non-coding region). The first step in making a DNA phylogeny is just identifying enough homologous sites to align the sequences with each other (i.e., figure out which locations along the gene correspond to each other). This is easy for closely related species but becomes much harder for distantly related ones. Shared, derived traits in DNA sequence data would be mutations at a particular site in the DNA sequence that are shared among taxa due to common ancestry. For example, a synapomorphy defining the clade including species 2-5 above would be a mutation from A to T at the 8th nucleotide position in the sequence. One important point here is that only variable sites are helpful for phylogenetic analyses. For example, the first nucleotide position above is C in all the species, so it gives us no information about their evolutionary relationships. It's also possible for different DNA sequences to contain short, identical sequences of nucleotides totally by chance, which would be an example of an analogous trait in molecular data. Another type of analogous trait would be if more than one mutation occurred at a particular site. Especially in cases where the second mutation returns the site to its ancestral state, this can really muddy the waters when using DNA to construct phylogenies. If we found a species 6 with the sequence shown, it could have that sequence because it's closely related to species 3. However, it would only take one mutation (from G back to C at the final nucleotide position) to get the sequence in species 6 from the sequence present in species 4 and 5. If the sequence in species 6 arose through this kind of evolutionary reversal, using the principle of maximum parsimony would lead you to an incorrect conclusion about how species 6 fit into the phylogeny. That is, you would put it into a clade with species 3, when it was really more closely related to species 4 or species 5.

Mapping characters onto existing trees helps us understand how they evolved

Most amniotes have intromittent organs Missing in birds and tuataras Which is the ancestral state, presence, or absence of a phallus? The tree here shows several groups of amniotes (mammals and reptiles, where reptiles include birds), as well as whether males in those taxa have, or do not have, a phallus (yes, squamates, or lizards and snakes, have paired penises. They're called hemipenes, and I could tell you way more about them than you want to know). By looking at the tree, we can come to conclusions about how the evolution of the phallus most likely occurred. There are two ways the current distribution of presence or absence of a phallus could have arisen in the amniotes. 1) The ancestral state was absence of a phallus, and the phallus evolved independently in squamates, turtles, crocodilians, and mammals. 2) The ancestral state was presence of a phallus, and the phallus has been lost independently in Sphenodon and in birds. The second hypothesis is considered more likely, as it involves fewer changes, so you can see that the authors have concluded that the presence of a phallus was the ancestral state for amniotes. The important point here is that the researchers already had the tree before they performed the mapping analysis of phallus evolution. The fundamental question here was not, "How are different groups of amniotes related?" but rather, "How has the phallus evolved during the diversification of amniotes?"

The Great Chain of Being or Scala Naturae

Philosophical scheme that ranked species on a scale from most to least divine Not scientific, but represents an early attempt to understand how living things relate to one another Before the development of the scientific method and the modern conception of science as the testing of falsifiable hypotheses, science was not really distinct from philosophy or religion. An idea from this time, the Scala Naturae, is the source of the still-prevalent misconception that there are such things as "higher" and "lower" organisms. Early natural philosophers were interested in how humans related to other living things. Based on their religious beliefs, they developed a classification system that placed certain living things closer to the divine than others, with humans, of course, being the closest of all. Belief in a Scala Naturae organization of living and nonliving things was common in the Middle Ages both in (largely Christian) Europe and the (largely Islamic) Middle East. One prominent Islamic scholar who wrote about these ideas was Ibn Khaldoun, who lived in Tunisia in the 14th century.

Darwin's observations and inferences

Observation: All species of organisms have more offspring than the environment can support. Observation: Populations usually do not grow exponentially in nature. Inference: A "struggle for existence" occurs, in which not all individuals survive or reproduce. Observation: Individuals in natural populations of organisms vary in their traits. Observation: Offspring tend to resemble their parents. Inference: Some variants will survive and/or reproduce better in their environment than others (i.e., be "more fit"). Inference: Because the descendants of fitter individuals resemble their parents, those individuals' traits will become more common in the population over time. This is really the theory of evolution by natural selection in a nutshell. Obviously, it has huge implications for how we understand the world around us, and there are many consequences of this theory we're still working to understand, but the basis for all biology since Darwin is here. Given that not all offspring born in any generation of any population of organisms will survive or reproduce, there must be competition among those individuals. Members of all populations vary, and some of those variants are more successful in surviving and/or reproducing than others. Those individuals have more offspring, and because those offspring resemble their successful parents, the successful traits (a.k.a. adaptations) become more common in the population over time. The last inference is the one that's tied to the findings of geologists like Hutton & Lyell, because knowing how old the earth was meant you could propose explanations for biological diversity that would have taken huge amounts of time to play out. Most evolutionary changes are subtle on the scale of a few generations, but by extrapolating over billions of years of the history of life on earth, you can start to understand where all life's diversity came from.

DNA is also the molecule of inheritance

Often, offspring seem to represent a "blend" of their parents' trait During the first half of the 19th century, people had long been aware that offspring resembled their parents and seemed to represent a mix of their parents' traits. But the leading hypothesis of the time, "blending inheritance," had major problems. The idea that some material from the parents was mixed together in the offspring, leading to intermediate traits, didn't explain how parental traits could sometimes reappear in later generations. More generally, how was variation maintained at all? Wouldn't all of this hypothetical genetic material just get mixed together over the generations, leading to an entire population of individuals with intermediate traits? In the 1850's and 1860's, Gregor Mendel performed experiments with pea plants that helped lay the foundation for our modern understanding of genetics. Specifically, he discovered that discrete "factors" were inherited as units, affecting which variant of a particular trait an individual had.

The very first life forms probably did not leave fossils

Oldest evidence of life dates to 3.7 bya Carbon contained in rocks, enriched for lighter isotope carbon-12 Claim is controversial Oldest stromatolite (bacteria) fossils date to 3.45 bya Carbon exists as several isotopes, including carbon-12, carbon-13, and carbon-14. The metabolisms of living organisms preferentially use the lighter isotopes, especially carbon-12. That's why some researchers argue that deposits in rocks that contain a higher proportion of carbon-12 than is present in inorganic carbon represent the oldest evidence of life on Earth. Stromatolites are colonies of bacteria that you can still find in some places on Earth (most famously a location called Shark Bay in Australia). Fossils of very similar looking bacterial colonies date back 3.45 billion years and represent the oldest uncontroversial fossils of living organisms.

First terrestrial plants and fungi are linked

Oldest terrestrial plant fossils are 475 myo Large forest ecosystems within 100 million years fungi appear ~400 myo Associated with plants Fungi have both mutualistic and parasitic relationships with plants. For example, mycorrhizae are fungi that grow on the roots of plants and allow the plants to take up more water and nutrients, in exchange for sugars the plants produce by photosynthesis. Many other plants are parasites or pathogens of plants, which absorb the plants' nutrients without giving anything back.

First terrestrial vertebrates

Oldest trackways date to 390 mya Oldest fossils of true tetrapods date to 370 mya First tetrapods= amphibians, tied to water for reproduction Tiktaalik roseae is the best fossil found so far of an early tetrapod. Tetrapods evolved from a lineage of fish called the lobe-finned fish, which include coelocanths.

Eukaryotic genomes contain large stretches of non-coding DNA

Only 5-10% of most vertebrate genomes consist of genes or known functional elements (regulatory regions, etc) Even within a protein-coding gene, large stretches of DNA are not translated The figure shows the structure of a typical eukaryotic gene, with the regulatory region, the promoter (to which proteins involved in transcription initially attach), and the coding region of the gene. The "coding region" actually contains some sections that will be spliced out of the mRNA transcript before translation. These sections are called introns. The parts of the gene that will actually end up corresponding to protein sequence are just the exons (as a mnemonic for this, remember, "exons are expressed"). As you can see, the exons are far from representing the entirety of the gene. The importance of these findings to evolution is that mutations to different regions of a gene (regulatory regions, promoter, intron, exon, etc.) have very different effects on organisms' phenotypes and thus experience natural selection differently. Zooming out further, genes actually constitute only a small percentage of the genome in most large, complex eukaryotes. The rest is what we call "non-coding DNA." Researchers used to refer to it as "junk DNA," but that term has become less common, because we're finding that some of it does have a function, often a regulatory function. There are still large sections of most eukaryotic genomes whose function (if they have one) is unknown, however. For example, up to 2/3 of the human genome appears to consist of short, repeated DNA sequences with no clear role in our biology. It's thought they may represent traces of ancient viruses that incorporated themselves into the genome and replicated. Why selection hasn't acted to remove these repeats is a question evolutionary biologists are still working to answer.

DNA contains "blueprints" for most organisms

Order of nitrogenous bases adenine, thymine, cytosine, and guanine (A, T, C, and G) transcribed to mRNA, which is then translated to protein Codons containing 3 bases direct which amino acids added to protein Most amino acids specified by more than one codon Proteins perform many functions, including catalyzing reactions (enzymes) and making up many of the structural components of organisms' bodies.

Oxygenic photosynthesis drasically changed the nature of life on Earth

Oxygen was toxic to many ancient organisms There's evidence of structures similar to those used in photosynthesis even in stromatolites from 3.4-3.7 billion years ago, but based on what we know about oxygen levels at that time, early photosynthesis probably didn't generate oxygen. Atmospheric O2 levels were very low until around 2.4 billion years ago, when they started to rise in what's called the "Great Oxygenation Event." Current best estimates are that organisms similar to modern cyanobacteria may have evolved the ability to use H2O as an electron donor in photosynthesis around 2.7 billion years ago, which led to gradual increase in atmospheric oxygen levels over time. Although it's hard to make inferences about that time, given that all life was unicellular and left few traces, it's likely this increase in oxygen levels caused a global mass extinction of organisms that were poisoned by oxygen. Like mitochondria, chloroplasts result from an endosymbiosis event between an ancient, photosynthetic bacterium and an ancient eukaryote. That is, chloroplasts are the descendants of what were once free-living prokaryotes, which is why they have their own DNA. This endosymbiosis eventually led to the evolution of green plants, among other photosynthetic lineages. The spike in oxygen levels between 320-275 Mya may have resulted from the diversification of the land plants. The two lines on the graph show upper and lower estimates of oxygen levels, from a variety of geological sources. Geologists estimate oxygen levels by measuring the proportions of minerals that tend to form in the presence or absence of oxygen in different rock layers. Unsurprisingly, you might find anaerobic organisms (those whose metabolisms don't require oxygen) in environments with very little oxygen, such as deep ocean vents, mud flats, or even animal intestines.

Radiometric dating estimates the age of the earth at 4.6 billion years old

Radioactive isotopes of some elements gradually decay into other elements over time. Geologists can use the ratio of some radioactive elements relative to reference, non-radioactive elements to determine how long ago rocks hardened. Which radioactive element researchers use depends on the half life of the (the amount of time it takes for half the element to decay). The longer the half life of an element, the older the rocks it can be used to date. This technique has revealed that the very oldest rocks on Earth appear to be 4.6 billion years old.

#3: living species "evolve into" other living species

Species living today share common ancestors that existed in the past. "Closely related" species share a very recent common ancestor Sometimes, people who don't have a good understanding of evolution say things like, "Well, if humans evolved from chimpanzees, why are there still chimpanzees?" The answer to that confusion is that humans didn't evolve from chimpanzees. Instead, humans and chimpanzees shared a common ancestor a few million years ago. One lineage of that ancestor's descendants eventually became chimpanzees, and another lineage became humans. The common ancestor of humans and chimpanzees, however, is now extinct. So, if you hear anyone asking the question about humans and chimpanzees, the correct response is, "Humans didn't evolve from chimps. Humans and chimpanzees both evolved from another species of ape, which lived between 7 and 9 million years ago and no longer exists."

#10: Anyone who accepts evolution must also be an atheist

Science deals with hypotheses about the natural world that can be falsified (shown to be false) The existence of supernatural beings that can act outside the laws of nature cannot be falsified, because anything is possible for such beings Evolutionary biology, astronomy, geology, and other areas of science have shown that traditional stories from many faiths are not literally true. However, science cannot be used to prove or disprove the existence of supernatural powers I don't want to spend too much time this semester addressing misconceptions regarding whether evolution happens at all, because we have a great deal to learn about how it happens. However, I did want to mention this topic briefly, since it dominates a lot of popular discourse about evolutionary biology. This is a personal opinion, but I think far too many people are turned away from studying evolution by the false perception that evolutionary biologists are out to disprove the existence of God or other supernatural beings. It's impossible to gather evidence that would disprove the existence of a being or beings that could, in theory, modify whatever evidence you found. Ideas about the existence of the supernatural are not falsifiable hypotheses and are thus beyond the realm of science. Many faiths do have stories about where the Earth and the species living on it came from, and evolutionary biology is among the areas of science that have falsified those stories (or at least their literal interpretation). However, evolutionary biologists include members of virtually all the world's religions, and many religious evolutionary biologists have written about their perspectives on faith and science. The Dobzhansky essay I posted to Blackboard is a good place to start if any of you are interested in this issue

The outgroup roots a phylogeny and allows us to determine which character states are ancetral vs derived

Should be clearly outside group of interest but closely related enough that homologies are clear Remember that the "ancestral" version of a trait is the older one, and a "derived" version of the trait is the form that evolved from the ancestral version.

Insights from evolutionary biology explain why Zika Virus only recently began to cause microcephaly

Similar to the previous paper, the phylogenetic tree from Yuan et al. (2017) shows the relationships between viral strains from southeast Asia, where Zika virus has circulated for many years, and Pacific Islands/Latin America, where it emerged recently and has been linked to microcephaly. The authors also found out which mutations separated different lineages of the virus from each other and estimated when in time those mutations occurred. A mutation (S139N) occurred around 2013, causing an amino acid change from serine to asparagine in the protein prM, which is involved in viral maturation and secretion from host cells. This was just before an outbreak in French Polynesia in which the first cases of Zika virus causing neurological symptoms were recorded. Researchers knew what the function of the mutated protein was based on previous research in dengue virus, a close relative of Zika virus. To confirm that the S139N mutation was responsible for Zika virus causing microcephaly, the authors generated several mutant virus strains that each differed from the less harmful SE Asian strain by only one of the mutations that separated the SE Asian and Latin American strains. They showed that the S139N mutant strain was more virulent (i.e., killed a higher percentage of infected individuals) and also caused infected neonate mice to have smaller brains and thinner cerebral cortices, due largely to increased apoptosis of brain cells in that region, compared to the wild type 16 virus from SE Asia and the other mutant strains. We'll talk in much more detail about the techniques described here during this semester, so don't worry if this seems confusing now, but I wanted to use this example to start the class off, since it's a very timely one.

Genotype affects phenotype

Sometimes, there's a clear link between a single trait and a single gene Free vs. attached earlobes in humans, flower color in pea plants, and short vs. long hair in cats are all traits where variation results primarily from different alleles at a single genetic locus.

Why study evolution?

The central unifying theory of modern biology Not to imply that this is the only reason to study evolution, but the recent Zika outbreak provides a good example of how evolutionary biology research can impact human life and health. Zika is a mosquito-borne (and sexually transmitted) virus that causes serious birth defects in the babies of women who are infected while pregnant. Prior to 2016, it was known from Africa and parts of Asia, but it wasn't a topic of intense study. Since the beginning of 2016 or so, Zika has become a major human health threat, spreading from South America, through Central America and Mexico, and recently into Florida. A few studies did investigate the evolution of Zika virus strains before the virus broke out in South America. In one example, researchers identified sites in the protein coat that could be glycosylated, or have molecules added to them that affect how infectious the virus is. You'll notice, however, that this study came out in the journal PLOS Neglected Tropical Diseases, which is not the most widely read journal in the world. At the time, the people doing the research couldn't have known how important their research would later be.

Vertebrate phylogeny reflects the limitations of the Linnean system

The colored boxes show the traditional vertebrate classes as described by Linneaus. As we'll discuss in our next lecture, our modern understanding of phylogenetics has shown that this classification scheme has some problems.

Eukaryotic genomes contain large stretcges of non-coding DNA

The figure shows the structure of a typical eukaryotic gene, with the regulatory region, the promoter (to which proteins involved in transcription initially attach), and the coding region of the gene. The "coding region" actually contains some sections that will be spliced out of the mRNA transcript before translation. These sections are called introns. The parts of the gene that will actually end up corresponding to protein sequence are just the exons (as a mnemonic for this, remember, "exons are expressed"). As you can see, the exons are far from representing the entirety of the gene. The importance of these findings to evolution is that mutations to different regions of a gene (regulatory regions, promoter, intron, exon, etc.) have very different effects on organisms' phenotypes and thus experience natural selection differently. Zooming out further, genes actually constitute only a small percentage of the genome in most large, complex eukaryotes. The rest is what we call "non-coding DNA." Researchers used to refer to it as "junk DNA," but that term has become less common, because we're finding that some of it does have a function, often a regulatory function. There are still large sections of most eukaryotic genomes whose function (if they have one) is unknown, however. For example, up to 2/3 of the human genome appears to consist of short, repeated DNA sequences with no clear role in our biology. It's thought they may represent traces of ancient viruses that incorporated themselves into the genome and replicated. Why selection hasn't acted to remove these repeats is a question evolutionary biologists are still working to answer.

What phylogenies show and don't show remember- all living species are equally "evolved"

The first misconception here is the idea that a phylogeny shows species A transforming into species B, which then transforms into species C, which then transforms into species D. All the species at the tips of a phylogeny are currently alive, so none of them have transformed or will transform into any of the others. This is the response to the somewhat uninformed criticism people sometimes make of evolutionary theory: "If humans evolved from chimpanzees, why are there still chimpanzees?" The answer to that question is that humans didn't evolve from chimpanzees. Both humans and chimpanzees evolved from another, now extinct, species of ape that existed a few million years ago. One lineage of that ape's descendants evolved into chimpanzees, and another evolved into humans. Chimpanzees and humans are now each other's closest living relatives (although there are actually many extinct species that were more closely related to humans than chimpanzees are). The last pair of phylogenies is meant to illustrate that what matters for a phylogeny isn't the order in which the taxa at the tips are written, but rather how recent the different common ancestors are. Both those trees are identical, even though the extant species are listed in different orders. In both of them, the pattern of how closely different species are related is the same. In general, you can rotate the branches around any node without affecting the structure of a phylogeny. The misconception here is the idea that a phylogeny shows which species are more "advanced," "evolved," or otherwise "superior," All living species are equally evolved, because all of them descend from lineages that have been evolving since the origin of life on Earth. It's possible that species A in this pretend phylogeny might physically resemble the common ancestor of species A, B, C, and D more than the other species do. If that were so, we would say that A has the "ancestral phenotype," but we wouldn't say it was "less evolved," because it's been evolving for just as long since that ancestral species existed as any of the other species in the phylogeny. You could also imagine a situation where species A from this example was in a very different environment from species B, C, and D, however, which might mean that natural selection would have pushed it in a very different evolutionary direction

The fossil record is an incomplete but valuable record of ancient life forms

The fossil record is both extremely important and also extremely incomplete. It gives us a window into the history of life on Earth, but we know that only a tiny, tiny percentage of dead organisms actually fossilize. The organisms that fossilize also represent a very biased sample of all organisms that existed at a particular time, since most fossils represent hard bones or shells, which many organisms don't have. A few places on Earth preserve a record of organisms that died in an anaerobic environment, so that their tissues were not broken down as completely. This allows us to see soft-bodied organisms and makes those fossil beds extremely valuable. Possibly the most famous such place is the Burgess Shale in British Columbia, which preserves a record of the Cambrian Explosion of animal life (more on this later today). The organisms preserved in the Burgess Shale probably died in a sudden mudslide, which killed them instantly and prevented much oxygen from reaching their remains. That's why their soft tissues were preserved, rather than being eaten by scavengers or consumed by aerobic bacteria.

Codominance: Heterozygote phenotype is a mix of the phenotypes would be produced by each allele on its own

The goats are just dyed for comedic effect, but the chicken is real - the result of a cross between a white parent and a black parent. Both white and black are present in its phenotype, but they're not mixed (as they would be in incomplete dominance). Similarly, the lizards I did my PhD on show a pattern of codominance in the inheritance of blue and orange throat color alleles - heterozygotes have both blue and orange on their throats, rather than some sort of green color, as they would if incomplete dominance were occurring.

Most genes are pleiotropic, affecting multiple traits

The human genetic disorder cystic fibrosis is caused by a single mutation in a gene that codes for a protein in an ion channel. That ion channel is present in many different tissues, and the fact that water and chloride ions can't pass freely through cell membranes in those tissues has many negative health consequences. This means the gene exhibits pleiotropy, or affects many different phenotypic traits. Pleiotropy is probably more the rule than the exception. The definition of "trait" can be a little fuzzy, but it's rare to find genes that really, truly, do only one thing.

Do forest mice have longer tails than prairie mice?

The question this paper asks is whether deer mice that live in forest habitats tend to have longer tails, relative to their bodies, than deer mice that live in prairie habitats. To find out, the authors first sampled many different populations of the species Peromyscus maniculatus, both from the wild and from natural history museum collections. You can see their raw data in the figure on the left - it certainly appears there's a trend, but is there really? We need a phylogeny of these populations to find out

Joseph Felsenstein developed the first widely-accepted method to control for phylogeny in comparative analysis

The quote is from Felsenstein's paper and outlines the problem he was seeking to resolve. The name of the method he developed to resolve it is "phylogenetically independent contrasts," and it takes advantage of the fact that, although the actual values of particular phenotypic traits are not independent of each other in related species, the changes that occur to a trait after a speciation event are independent (since the new species are no longer exchanging alleles). I'm not going to get too deeply into the details of how to calculate phylogenetically independent contrasts. You don't do it by hand, in any case - you use a computer modelling program, because you generally have to estimate the phenotypes of extinct ancestors. What's extremely important for you to understand, however, is why this method is necessary - you can't treat species (or higher taxa) as independent data points, because some taxa are more closely related to each other than others are.

Phylogenetic trees show how species are related

Use many traits (morphology and DNA) to draw conclusions about evolutionary relatedness Placing "unusual" taxa within a phylogeny can tell us whether they have lost some of the synapomorphies that define a group they belong to Placing similar traits on a phylogeny can tell us whether those traits are homologies or analogies We'll talk a great deal about phylogenetic trees this semester, so don't worry if you don't understand them yet. Essentially, a phylogeny is a family tree showing how closely different species are related. To build a phylogeny, researchers can use morphological (body form) traits and/or genetic traits (usually DNA). Using many, many traits helps avoid false signals due to lost synapomorphies or convergent evolution. Deciding which morphological traits and which genes to use, however, is fairly complicated. Using DNA isn't some sort of "magic elixir" that makes phylogeny simple, however. It comes with its own substantial challenges Students often have the impression that researchers just compare entire genomes between different species and measure overall similarity when building DNA phylogenies. That's not accurate - we've learned a lot about how DNA evolves in the past 30 years or so, so we're able to use models to weight different kinds of changes relative to each other. That's another topic we'll discuss at length in this class. The figure above is from a paper published last year that built a phylogenetic tree showing the relationships between many different species of lizards and snakes. The authors included both living and fossil taxa in the tree, so they used a mix of morphological and genetic traits (morphological traits for all species, genetic traits for living species only).

Common misconceptions about evolution and science in general

Virtually everything we will talk about today is an incorrect idea many people have about evolutionary biology. Educational researchers have spent a lot of time trying to figure out how to combat misconceptions students come into classes with, and no one really has a good solution. It seems to be much harder for our brains to eliminate incorrect information that we already "know" than it is for them to absorb new information. Misconceptions are therefore very difficult to get rid of, but I really hope you'll all apply as much effort as you can to trying to correct any inaccurate ideas about evolution you might have picked up during your previous education or from the popular press. Having a misconception doesn't mean you're not smart or not educated, just that you picked up an inaccurate idea at some point in the past.

Synapomorphies define evolutionary groups

Whales share synapomorphies with other mammals -mammary glands & milk -three middle ear bones -hair (in developing embryos) Synapomorphy: a homologous trait used to define a taxonomic group Arose in common ancestor of group, inherited by its descendants You'll sometimes also see the term "synapomorphy" defined as a "shared, derived trait." A synapomorphy is derived because it evolved from whatever version of the trait existed before. The older version of the trait would then be called ancestral. The shared part of the definition is because a synapomorphy is shared among the members of the group it defines, due to their common descent from the ancestor in which the synapomorphy evolved.

Using independent data can alter conclusions about evolutionary relationships

You can't use a character to construct a phylogeny and then use the phylogeny to study that same character, because you would be biasing your conclusion. The example I gave in class was a silly one but illustrates the same principle. Imagine I had a hypothesis that male students prefer to sit on the right side of a room and female students prefer to sit on the left. If I walked into class and said, "OK, all the men should sit on the right today, and all the women on the left," I couldn't then use the fact I saw mostly men on the right and women on the left as evidence in support of my hypothesis. Instead, I would have to observe many classes, independently and without influencing how students distributed themselves. If I consistently saw a higher proportion of men on the right side of the room and women on the left side of the room, I might conclude my hypothesis was supported. In the same way, if you want to answer any questions about the evolutionary history of a trait, you can't use that trait to make the phylogeny you will use in your analysis. Using a trait to make a phylogeny means you make assumptions about how that trait evolved, so you'd just get your own assumptions back if you used a tree made using a trait (even if it wasn't only that trait), to analyze that trait's evolutionary history. This is a concept students have struggled with when I've taught this class before. Please spend some time thinking hard about it and come talk to me if you need to talk it through again. The phylogeny is from the paper in which fossils from the genus Arctotherium were first described. These fossils include large-bodied, short-faced bears from South America. Based on body size and skull morphology, they were initially placed in a clade with Arctodus, a genus of very similar looking bears from North America.

Early naturalists recognized that organisms could be classified into groups

• Linnean system still used in modified form, especially the genus and species names of organisms - e.g., Homo sapiens Linnaeus had no understanding of evolution, but he developed a system that classified living organisms based on how similar they were to each other, with nested groups containing more and more similar species. The main problem with using the Linnean system of classification today is that there are far more branch points in the tree of life than there are levels in the Linnean system. Therefore, it's not really clear where to draw the lines delineating genera, families, orders, etc. Within a genus, for example, some species are more closely related to each other than others are. Should we make a "sub-genus" to reflect these relationships? How about a "sub-sub-genus?" You certainly still do hear biologists refer to groups of organisms using the classifications of the Linnean system, however, even though we all recognize that it's not an adequate description of our current understanding of biological diversity. We especially still use the Linnean system of binomial Latin names to identify species across different languages and cultures. Scientific names are written in Latin because that was the common language of educated people in Europe, at the time when Linnaeus was working. A scientific name consists of the genus (capitalized) and species name (not capitalized) of a particular kind of organism. Scientific names are written in italics to emphasize that they come from a different language than whatever the rest of the text is written in. For example, Homo sapiens is the scientific name for modern humans, our own species.

Darwin's book was published in 1859

• On the Origin of Species by Means of Natural Selection, or the Preservation of Favored Races in the Struggle for Life • All species share common ancestry • Changes occur through natural selection The two major parts of Darwin's book correspond to the two levels at which we'll be studying evolution. Evolution helps us understand the interrelatedness of all Earth's organisms, as well as how the different traits those organisms possess arose over the generations.

The Population Problem

• Realized that among humans as among other organisms, population size has the potential to increase exponentially. • But there are never enough resources to support limitless population growth. Thomas Malthus wrote "An Essay on the Principle of Population" in 1798. He was a clergyman who worried about the fact that the poor were always most affected by the struggle for resources in overcrowded cities. He saw humans' potential for exponential population growth as a reason it would be impossible to ever eliminate poverty or war, because population would always increase faster than available resources like food or space. In terms of understanding evolution, Malthus's important insight was that even apparently slow-reproducing species like humans are capable of having many more offspring than the environment can possibly support (i.e., of exponential population growth). That's more obvious in the case of fast-reproducing organisms like bacteria or insects, but it's true of all organisms, given enough time.

Lamarck proposed a reasonable, but incorrect, mechanism for evolution

• Used series of fossils to document how species changed through time • Thought that somatic changes during an individual's life could be inherited • We now know that's (usually) not true, but it was a reasonable idea at the time One of the first researchers to propose that species change over time was JeanBaptiste Lamarck. Lamarck's hypothesis for how this occurred assumed the inheritance of acquired characteristics. He thought that changes occurring to an organism's body during its life (like the pruning that causes a tree to grow as a bonsai or a giraffe stretching its neck to reach higher leaves) could be passed on to offspring. We now know that's not the case. Bonsai trees have offspring of normal size, and if you spend hours in the gym developing enormous muscles, that will not cause you to have stronger children. We should note, though, that Lamarck died more than a quarter century before Gregor Mendel did his most important work on the mechanism of heredity, so there was no way he could have benefited from Mendel's findings about inheritance. Lamarck's hypothesis for the mechanism of evolution was reasonable and testable; it just turned out to be wrong. The "usually" in reference to the inheritance of somatic changes has to do with the developing field of epigenetics. Phenotypic changes that occur during an individual's life do not alter DNA sequences, so they don't represent evolutionary changes. However, some environmental changes can affect how loci within an individual's genome are expressed (whether a gene is "turned off" or "turned on"), and there's evidence those changes can sometimes be passed from one generation to the next. We'll talk more about this in a few weeks!