Descent with Modification PDF

1. **Overview** More than 150 years ago, Charles Darwin synthesized a scientific explanation for the origins of diversity in living organisms. He noted the remarkable ways organisms seemed to be well suited to their particular environments. He recognized that there were some feature...

1. **Overview** More than 150 years ago, Charles Darwin synthesized a scientific explanation for the origins of diversity in living organisms. He noted the remarkable ways organisms seemed to be well suited to their particular environments. He recognized that there were some features that were widely shared amongst organisms, and others that were quite different between organisms, creating this odd paradox of unity and diversity. His book, On The Origin of Species, brought together these concepts into a framework that explained the similarities and differences amongst organisms. The idea of descent with modification became synonymous with evolution, explaining how organisms alive now are the products of pressures on their ancestors, which allowed some to survive and caused others to disappear. In this lecture, we will explore some of the basic concepts in evolution that we will encounter throughout the course. 2. **Learning Objectives**. At the end of this lecture and the associated textbook readings, you should be able to describe how descent with modification accounts for both the unity and diversity of life. You will be able to come up with many lines of evidence that support the reality of evolution and explain the phrase *the theory of evolution*. Finally, you will learn about the different evolutionary patterns seen in comparing groups, both populations and species. 3. **Most Challenging Concepts**. The concept of evolution is probably familiar to you in a general sense, but it is often misapplied, which leads to confusion. It is both a *process* and a *pattern*. In other words, it is the means by which diversity and change arise, but it is also seen as the product of these processes. Evolution can be thought of as *descent with modification*, and intrinsic to the concept are the factors that drive the change. Natural selection is just one of several processes that cause the evolution of organisms and we will touch on some others. When looking at traits that are similar in different organisms, it is fair to ask how they got that way. In some cases, it is a result of different organisms using the same blueprint but in different ways, creating homologous structures. In other cases, the traits in two distantly related organisms converge on the same pattern. When structures are similar but of different origins they are considered *analogs*. When thinking about evolution, there is the ability to make connections between specific genetic differences and how these culminate in distinctions arising in development and seen in adults. Modern evolutionary biology spans all of the biological levels of organization., from molecules to ecosystems. 4. **The Darwinian Revolution**. Prior to more scientific ways of thinking, each culture had its own dominant creation myths. Some, like the The Hebrew Scriptures, talk about the origin of life in 7 days. In most, but not all cultural mythologies, the process of creation culminates in the arrival of humans, usually at the apex of the creative process. Various Indigenous cultures invoke interactions with the environment, emphasizing the roles of water, air, fire and earth in shaping these processes. Some creation stories involve the appearance of organisms that look much like they are now, explicitly denying the potential for change over time. Others, like Buddhism accept ongoing change as integral to life. The Australian creation story explains diversity arising from the Sun Mother. In an effort to end the bickering between her creations she tells them each to pick a trait they like best. This is one of the rare creation stories that addresses the origins of diversity. I tend to think of these stories as cultural metaphors for the origins of life and diversity, which are quite distinct from a scientific approach to understanding how life arose and how it has changed over time. Scientific approaches to the origin of life as we know tend to explicitly distinguish between how life first arose on Earth, and how it has changed over time. With these scientific perspectives, we are more focused on the answers to the "how" questions rather than the "why" questions, which are more philosophical. 5. **Scala naturae** was the concept promoted by Aristotle, who recognized the differences in complexity of organisms and conceptualized them as a linear hierarchy, with humans on top, of course. In this ladder, each was an established step in a continuum, with a position that was independent and structure that was unchanging. In the 1700's, Linnaeus recognized that some organisms were more closely related to each other, and created one of the earliest ways of clustering them into groups. The world was essentially subdivided into animal, vegetable and mineral groups. You probably find this grouping a bit odd, but our modern distinctions between biological and physical worlds were not always so clear. Although the nature of the groups has changed, we continue to use his taxonomic terms today -Kingdom, Phylum, Class, Order, Family, Genus, and Species. However, the membership in each taxonomic group is regularly changing as we learn more about the relationships between organisms, driven primarily by advances in genetics. The binomial approach to naming species remains in use almost 400 years after its inception. 6. **The Darwinian Revolution**. The textbook goes into some detail on Darwin's voyages. To better understand Darwin's contribution you have to put his studies into the context of the time. What you see in this history is a transition from the idea that organisms have always looked the same toward accepting that changes happen over time. James Hutton wrote about the idea that the physical world changed over time, and that what we see now is a product of slow but continuous change. It was intended to be about the physical world, but the concepts were also applied to the biological world. Thomas Malthus wrote about the impact of population growth on economics, recognizing that as populations grew resources became limited. Though developed for economics, it also was a concept that could be applied to biology, where the environment was a resource with limits, and that populations were affected by those relationships. The concept of change over time was embraced by scientists of the day. Lamarck catalogued how different organisms within populations differed from each other, and acknowledged that these changes happen over generations. He was rather misguided in thinking that changes experienced by an individual would be carried through to the next generation, but he did acknowledge the concept of a gradual evolutionary change in organisms over generations. Around the same time, geologists were discovering and publicizing fossils that were collected around the world, presenting images of organisms many of which had little similarity to existing organisms. In the mid-1800s, Darwin travelled the world cataloguing diversity in plants and animals. His contribution was to connect the dots to offer explanations of how organisms change over generations, which we now talk about as *descent with modification*. 7. **Darwin and the Focus on Adaptation**. The textbook focuses on Darwin's finches as an example of how he used his observations to comment on the process of evolution. Here are three of the birds that are found on Galapagos Islands. These birds are similar in many respects but differ in the shapes of their beaks, which coincides with their diet. What Darwin noted is that, in addition to the beaks being well suited to a particular diet, that the same birds on different islands had different beaks that also aligned with the food they were eating. He posited that each population of birds had individuals with diverse beaks, but only those individuals with the most useful beaks would tend to survive and pass those traits onto their offspring, a process known as natural selection. Some examples of natural selection explain how populations of an organism change over time. For example, on the lower left we have a curly-tailed lizard, and it feeds on other lizards, like the anole on the right. These lizards live on various islands in the Bahamas. On islands where the curly-tailed lizard is present, the anoles show evidence of natural selection in response to this predation pressure. Males with longer legs are selected benefiting from a superior ability to escape its predator. The females, however, have a different strategy. Larger females are favoured, growing to a size that is too big for the predator to swallow. When a curly-tailed lizard population is introduced onto an island that lacks them, the response in the anole population can be seen within 6 months. 8. **Descent with Modification**. It is not always easy to get an appreciation of natural selection by looking only at modern animals, and understanding evolutionary events greatly benefits from looking at the fossil record. This is the first of many phylogenetic trees that you will see that tells about the relationships between organisms. On the left is a collection of relatives of modern elephants, looking at animals that lived over the past 40 million years or so. All but a few are recognizable as elephant-like animals. We now know the evolutionary history of this lineage fairly well through a combination of paleontology and molecular genetics, including analysis of tissues from long-dead woolly mammoths. There are three species of elephants alive now, and 7 lineages that have gone extinct, including mastadons and mammoths. The modern elephants last shared a common ancestor about 6 million years ago. A node represents a time in their history where they shared a common ancestor. For you and your first cousins, your node was likely about 40 years ago when you shared grandparents as common ancestors. When talking about trees, you would never talk about how your cousin was once you. The key is that at a point in time, your shared the same ancestor, and that ancestor was equally related to both you and your cousin. The tree also shows the closest living relatives are from two groups that look nothing like elephants: manatees and hyrax. These are considered "out-groups"- organisms that may be closely related to the group but not part of the group. Elephants, manatees and hyraxes likely shared a common ancestor about 60 million years ago. The appearance of that ancestor would likely be a mixture of these modern and extinct family members. 9. **Artificial selection**. In any population under evolutionary selection, you will have members of the population that differ from each other. Any individuals that are better suited to the environment are more likely to survive and generate offspring, and these will share those favourable traits. For example, in humans, you have tall individuals and short individuals. Tall individuals might be favoured in one environment, and short individuals in another. Decent with modification recognizes that some individuals will leave more offspring than others, and that over generations, those traits will become more common in the population. **Artificial selection** is the process where humans identify those with favourable traits and given them an artificial reproductive advantage, allowing them to pass on their traits. In this figure, the ancestor to a wide range of what we lump together as cruciferous vegetables was a lowly weed called wild mustard. Plant geneticists and farmers started by picking those mustard plants with the best features and allowed them to reproduce. Over generations, they selected plants that have few obvious similarities as a result of this artificial selection. You can probably come up with your own examples of artificial selection, such as dogs and horses though the differences are not quite as stark as with Brassica diversity. 10. **Natural selection.** Unlike artificial selection, with natural selection the organisms that are successful in their natural environment are able to pass those traits onto the next generation. On the left is an example of an insect called a soapberry bug. These insects feed by piercing the protective covering of plants to eat the seeds inside. The textbook expands on this example, but the simple story is that those insects with the best beak length survive and reproduce, and over generations, the average beak length changes to reflect those selective pressures. In this example, the insects have evolved beaks of particular lengths. If you took a southern Florida soapberry bug and hatched it in central Florida, that bug will have a beak that is far too long for the food, and likely would not succeed. In this example, the individuals are hardwired such that they demonstrate their phenotype regardless of the conditions. However, many aspects of the phenotype can change in the lifetime of the organism in response to conditions. This is the concept of **polyphenism**, or phenotypic plasticity. On the right is an example of a rhinocerous beetle. The two individuals here could be brothers or even identical twins, but they obtained different resources in early life. The larger male on the left uses its large horn to guard its mate's nest. Both individuals had the ability to make big or small horns, but the strategy that emerged depended on conditions. So if you see differences between individuals of a population, recognized that they may be due to natural selection favouring one phenotype over another, or phenotypic plasticity, which alters developmental pathways to change a phenotype an individual expresses. You can probably also come up with experiments to distinguish between these options. 11. **Natural selection**: The beauty of natural selection is that beneficial traits can continue to evolve, and as a result generate intriguing phenotypes over generations. On the top, there is an insect that has evolved an appearance to look like the grass on which it lives. You can imagine that those individuals that appear too dark or the wrong shape could be seen and eaten by predators. On the bottom we have another example of how evolution can favour survival and alter traits in populations and species. The monarch butterfly on the right has the ability to eat and accumulate toxins, and its potential predators recognize that insects that look like this are toxic, leaving them alone so that they are not eaten. The viceroy butterfly on the left does not eat the toxic plants, but it has evolved a similarity in appearance to the monarch. Where they coexist, the ability of the viceroy to mimic the monarch offers it protection from insectivores. We will talk about mimicry later in the course. 12. **Homology**: One of the consequences of natural selection is that over generations, populations can evolve novel anatomy and physiology. But in most cases, they are repurposing existing structures to do something different. Here we have images of the forelimbs of 4 mammals that differ profoundly in their lifestyle. Each species has evolved peculiar patterns of development that permit it to use its forearm bones to make novel structures, from the wing of the bat, to the fin of the whale. These structures are considered **homologs** of each other because they all come from the same developmental origins. 13. **Analogy**: In contrast to homology, there are often situations where similar structures evolve in unrelated animals from completely different developmental origins. All of these animals can fly, but only a subset of them use homologous structures. The rest demonstrate what is called **convergent evolution**, where structures appear similar but have different developmental origins. Can you identify which of these are homologs of each other and which are analogs? 14. **Tree thinking.** As we move through these lectures, we will often talk about organisms that are related to each other in some manner. Knowing the nature of the relationships helps you understand the mechanisms that cause them to be similar or different. The best way to conceptualize these relationships is through the use of a phylogenetic tree. The length of each branch reflects how much time has passed since the last common ancestor. It's a mathematical prediction based on the relative similarity of something like a genetic sequence. The branches emerge from nodes, which identify a point in time where the branches last shared an ancestor. One way to understand the origins of traits is to identify the last common ancestor that possessed those traits. For example, at node 2, the common ancestor possessed limbs that had digits-fingers and toes. All of the animals that followed were constrained by the developmental processes that gave rise to the digits, although on occasion a lineage will experience mutations that result in a loss of the trait that is otherwise shared with the relatives. For example, snakes have lost the ability to make digits. In early embryonic stages snakes actually do start to form fingers and toes, but quickly lose them as the animal develops and before it hatches. We will encounter many trees as we move through the course, so having a familiarity with what they mean is an asset. 15. **Evolution is just a theory**: A theory is the best explanation for why things are the way that they are. There is abundant and incontrovertible evidence in support of evolution as the explanation for the patterns in diversity, as well as the process by which that diversity arises. Nonetheless, as with any scientific theory, the specifics change as we learn more. For example, in the earliest versions of evolutionary theory, it was presumed to be a very slow process. However, there are many examples of where evolution can change populations very quickly. As well, natural selection is the most common mode of evolution for generating diversity, but there other mechanisms that also play roles in evolution in the natural world. Why, for example, does this peacock have what is undoubtedly and absurd collection of tail feathers? 16. **Summary**. The point of this lecture was to introduce the main themes in evolution. We will revisit these summary points throughout all of the lectures in this course.