1A & 1C - Bio 10B Assessment PDF

Assessment 1 1c. Explain basic concepts associated with microevolution, speciation, and macroevolution. Evolution Review These are the evolution concepts you should understand from Bio 10A: ○ Populations evolve, not individuals. ○ Natural selection and sexual selection ar...

Assessment 1 1c. Explain basic concepts associated with microevolution, speciation, and macroevolution. Evolution Review These are the evolution concepts you should understand from Bio 10A: ○ Populations evolve, not individuals. ○ Natural selection and sexual selection are non-random forms of microevolution. ○ Selection pressures are the environmental (biotic and abiotic) that cause differential survival. ○ Selection can increase the frequency of phenotypes that promote survival and reproduction (positive selection) or it may weed out phenotypes that decrease survival and reproduction (negative selection). ○ Genetic drift, gene flow, and mutation are random forms of microevolution. ○ Natural selection deals with the evolution of traits that increase survival while sexual selection deals with traits that increase reproduction. ○ Fitness is the relative proportion of genes an individual contributes to the next generation. It requires survival AND reproduction. ○ Genetic variation is the caused by mutation and is the raw material on which selection acts. ○ Genetics is more complex than ever! Phenotypes are often produced by many genes and involve epigenetic effects. ○ Inheritance is not limited to simple Mendelian genetics. Inheritance can take the form of epigenetics, learned behavior, and language. ○ Selection acts on whole organisms so we shouldn't expect them to be perfectly adapted to their environments in every way. Humans prove this point in many ways. ○ Speciation is not a necessary consequence of allopatry. ○ Speciation requires reproductive barriers in sexually reproducing species. These barriers evolve just like any other phenotype. ○ Sympatric speciation usually involves ecological niche partitioning (ecotypes) and assortative mating. The proximity of ecotypes reinforces reproductive barriers. ○ Macroevolution is evolutionary change above the species level. It is the formation of new genera, families, orders, classes, phyla, kingdoms, and domains. Descent with Modification ○ Darwin Theory of natural selection Aka descent with modification by natural selection a theory is an hypothesis that is supported by multiple lines of independent evidence The Origin of Species published Since then, many lines of evidence have emerged to support evolution.  ○ Descent with modification by natural selection requires: phenotypic variation within a population, petal color or wing length, can be physiological and behavioral. differential survival among phenotypes, and trait enables individuals to survive better than individuals without the trait, (positive selection) trait can increase an individual's chance of dying (negative selection). genetic variation that is heritable. genes act in complex ways to produce phenotypes. Very few traits are determined by one gene Descent with Modification (Microevolution) Lecture ○ Concepts to understand Populations evolve, not individuals Mutations result from DNA copying errors and create variation in genotypes Selection pressures are the environmental (biotic and abiotic) factors that cause differential survival. Natural selection and sexual selection are non-random forms of microevolution. Traits are associated with increasing survival and reproduction, respectively. Genetic drift, gene flow, and mutation are random forms of microevolution Fitness requires survival AND reproduction. Genetics is more complex than ever! Phenotypes are often produced by many genes and involves epigenetic effects Selection acts on whole organisms so we shouldn’t expect them to be perfectly adapted to their environments in every way. Humans prove this point in many ways. ○ Evolution: change over time Biological Usually millions of year of change Focused on populations throughout generations rather than individuals Microevolution: change in allele frequency of a population You can have two different population in two different ares for example in norcal vs socal, evolution is usually happening in one population ○ Allele frequency: is the relative proportions of the alleles that exist for a particular phenotype Speciation: formation of a new species Macroevolution: formation of a new taxonomic group above the species level  New phylum or class ○ Descent with Modification via Natural Selection Darwin (and a little bit: Wallus) Descent with modification by natural selection requires: 1) phenotypic variation within a population, ○ petal color or wing length, ○ can be physiological and behavioral. 2) differential survival among phenotypes, and ○ Selection pressure: environmental factor that imposes selection on the population Ex: predators ○ Position selection: trait enables individuals to survive better than individuals without the trait Promotes phenotypes in the population Ex: fast and strong legs to run away from predators ○ negative selection: trait can increase an individual's chance of dying Removes phenotypes from the population 3) genetic variation that is heritable ○ genes act in complex ways to produce phenotypes. Very few traits are determined by one gene ○ Epigenetics Environmental factors that affect expression of genes, phenotypically ○ Heritability: measure of how much of that phenotype is determined by the genotype/the genetic variation and not the environment Also predicts how responsive or how much change there will be over time  Ex: if a certain gene is highly heritable, then more likely that offspring will have that gene/trait as well; not much “watering down” of the gene by environmental factors ○ Ex: ○ ○ Useful in agriculture and animal breeding Beef for example ○ 3 Outcomes of Natural Selection Directional selection Diversifying selection Stabilizing selection  ○ Other mechanisms of evolution Sexual selection Trait of focus is focused on the reproduction part of life and not the survival part of life Genetic drift (bottleneck effect and founder effect) Change in allele over time by chance or accident random change in a small populations Bottleneck effect ○ changes the population because some environmental factor only allows a small proportion of an existing population to survive ○ individuals who survive do so because they are lucky and not because they possessed traits to help them survive ○ the few individuals that get through the "bottleneck" are proportionately different than the original population and eventually the population evolves. Founder effect ○ a few individuals migrate away from the original population ○ new population may have a different genetic composition than the original population by chance depending on who the founding population happened to be. Migration (immigration and emigration) Gene flow ○ With random mating and genetic recombination, new phenotypes may spread through the population. ○ Mutation  an error that happens in the genetic code during its duplication and it is the mechanism that introduces new genetic variation to a population A mutation can kill an organism, lead to a new beneficial trait, or not have any effect on the organism for a mutation to matter to evolution it must happen in a gametic cell (egg or sperm) because those are the genes that make it into the next generation Although mutations may happen in somatic cells (e.g. skin cells), those mutations will die with the individual. ○ Fitness The relative proportion of genes an individual puts into the next generation Depends on the ability to survive and reproduce Can help scientists predict how quickly an new phenotype will spread throughout the population ○ Evolutionary Fallacies There are constraints on the evolution of traits “Anything is possible” Ex: dumbo, elephant’s with big ears that allow them to fly ○ Impossible, bc elephants are mammals and their dense bones structures in terms of evolution have led them to not be able to fly ‘Survival of the fittest’ does not mean that only the strongest organisms survive Ex: bacteria aren’t the strongest living organisms in the physical sense but are the most dominant in the planet and some are very dangerous and can take down some of the strongest organisms down on the planet Organisms are not always perfectly adapted to their environment If you think about our skeletons, we’ve evolved to be bipedal ○ We’ve had to work with skeleton, there have been a few changes, the hip has widened, stronger femur bones and knee joints to support the weight of bipedal walking ○ But the spinal column itself evolved to be a suspension bridge type structure. When you’re walking on all fours it just holds all the tissue together but when you’re bipedal, now it needs to support the entire weight of your body and that’s why humans have a lot of lower back problems. Dodo bird ○ Didn’t have traits to learn to run away from predators because there were no predators ○ When explorers came, the birds did not run away and people started to consider them as easy food  ○ Dodo didn’t learn or change to run away - there was also too short of a time period to evolve - and slowly went extinct Humans are not the “goal” of evolution Because we evolved last, humans think that we’re the pinnacle of evolution, but we don’t want to think that all things on the planet as evolving toward human-like form Some are very simple organisms and they reproduce and survive and have evolved over time just like us There is no preconceived goal Other mechanisms of microevolution ○ natural selection is the most commonly known mechanism ○ Sexual selection, similar to natural selection, leads to the evolution of traits directly associated with reproduction ○ Sexual selection operates based on traits associated with reproduction, while natural selection focuses on traits related to survival. ○ Random mechanisms: mutation, gene flow, and genetic drift, also contribute to genetic variation in populations ○ Mutations introduce new genetic variation, but only those occurring in gametic cells affect evolution ○ Gene flow occurs when new individuals immigrate or emigrate, causing changes in genetic variation Gene flow can change genetic variation in populations through immigration or emigration of individuals. ○ Genetic drift involves random changes in a small population, either through a bottleneck effect or a founder effect The bottleneck effect changes the population because some environmental factor only allows a small proportion of an existing population to survive. The individuals who survive do so because they are lucky and not because they possessed traits to help them survive. The founder effect also involves a small subset of the population. However, in this example a few individuals migrate away from the original population. The new population may have a different genetic composition than the original population by chance depending on who the founding population happened to be. ○ Evolutionary biologists aim to determine which mechanism is responsible for a trait’s evolution, based on its impact on survival or reproduction. Sexual Selection ○ the concept of sexual selection: a mechanism for explaining the evolution of traits that increase reproductive success  ○ Darwin’s theory of natural selection alone cannot explain the existence of certain traits such as the elaborate tails of peacocks, which actually decrease the survival of males ○ Sexual selection, which involves mate choice and male-male competition, is proposed as a complementary theory to explain the evolution of these traits ○ Sexual selection operates through differential reproductive success, where individuals with certain traits have higher chances of reproducing. ○ examples of sexual selection in various species: Geladas, elephant seals, marsh harriers, and bowerbirds. Strategies: “sneaker” male strategy Intrasexual selection involves competition among members of the same sex for access to mates intersexual selection involves traits that make individuals attractive to the opposite sex. ○ importance of sexual selection in shaping the evolution of traits related to mating and reproduction. Speciation and Macroevolution Lecture ○ Biological species concept: Defines a species as a group of individuals living in one or more populations that can potentially interbreed to produce healthy, fertile offspring ○ Other species concepts Ex: Recognition species concept: species are groups of individuals that share a common fertilization system ○ Modes of speciation Allopatric speciation geographic isolation Sympatric speciation reproductive isolation ○ Does a geographical barrier guarantee speciation DOES NOT GUARANTEE SPECIATION May separate a population for a long amount of time, they do have to accumulate enough genetic differences, such that they are reproductively isolated when you bring them back together ○ Process of speciation  rFr frfrrr rffefFrrrffrfrTrFrrrrfIn fretrr trrrr trfrrrfrf trRefr ○ Parapatric: new species arises on the periphery of that original population A part of the population that’s exposed to a slightly different environment, but they’re not geographically separated; exposure to diffsyserent environment is significant enough that it causes selection on that population and changes them through time, such that a reproductive isolation mechanism has evolved Patri- means homeland Alo -means different Sym - means same Para - means close to or adjacent to ○ Speciation over time We look at patterns over time Can have gradually or very quickly Biologists have to use a lot of evidence and different types of clues to figure out what happened because obviously no one was about when these evolutionary processes are taking place Lots of times fossil records are also biased Tend to save bone structure and not color or behavior Often use inferences based on living species ○ Macroevolution Effect of many many many generations of speciation Defines the big differences in the other taxonomic levels Different kingdoms or classes 1a. Identify overarching patterns associated with the history of life on earth and explain how they provide evidence for evolution. History of Life on Earth Introduction Earth is over 4 billion years old, and scientists think there has been life on our planet almost since the beginning—for at least 3.5 billion years. For most of that long history microbial life was the only life present, and in many respects microbial processes still dominate many ecosystems today. A key development in Earth’s history that made larger, more complex, multicellular life possible was a dramatic increase in oceanic and atmospheric oxygen. Scientists have constructed the timeline of life on Earth from two main types of evidence: geological evidence and genetic evidence. Fossils are the most familiar type of geological evidence and provide beautifully detailed glimpses of ancient life, at least for larger, more recent organisms. However, soft-bodied microscopic organisms fossilize only under rare circumstances and the process of plate tectonics has destroyed and buried most fossils. Fortunately, scientists can turn to other types of geological evidence to study ancient life. These include molecular traces, like cholesterol and other chemical signatures; isotope ratios resulting from living processes; features in limestone that reflect microbial interactions with sediments; and markers of environmental conditions, like banded iron formations. This record of life found in rocks is further enriched by analysis of the genomes of animals, plants, and microbes living today—the descendants of the first organisms that populated our planet.  Earth formation ○ Earth formed from the accretion of interstellar dust and debris. During accretion, the growing mass, called proto-Earth, was compressed by gravity, causing an increase in temperature. This rise in temperature, along with additional heat supplied by radioactive decay, caused the proto-Earth to become a hot molten mass. As the proto-Earth cooled, it stratified according to density leading to a layered composition. ○ 4567 million years ago Chemical evidence for life ○ The earliest evidence of life consists of rock samples containing organic compounds with an isotopic signature low in carbon-13. (inorganic vs organic different in 25 parts per thousand) ○ 3800 million years ago ○ Visible evidence for life ○ Modern stromatolites are layered mounds composed of mineral sediments and organic compounds formed by successive generations of microbial communities. Geologists have found comparable mounds dating as far back as 3.4 billion years  ago that appear to be formed by similar processes. These fossil stromatolites provide the oldest physical evidence for life on Earth. ○ 3500 million years ago ○ Biomarkers ○ Lipids, such as cholesterol, are well preserved in rocks and represent the oldest direct products of living organisms. ○ 2700 million years ago Great oxygenation event ○ Oxygen gas produced by cyanobacteria began to accumulate in the atmosphere. ○ 2400–1400 million years ago Origin of eukaryotes ○ A hallmark of eukaryotes is the presence of internal organelles, such as a nucleus and mitochondria, which are not found in prokaryotes. Genetic evidence has revealed that mitochondria in fact arose from a symbiotic relationship in which a bacterium was engulfed by another cell, perhaps an archaea. The origin of eukaryotes triggered a biological revolution, which set the stage for multicellularity and increased size and complexity. Today nearly all visible forms of life are the product of this amazing symbiotic association. ○ 2400–2000 million years ago Grypania spiralis ○ The oldest eukaryotic fossils are from this organism that has the appearance of a type of algae. ○ 1800 million years ago ○ Origin of chloroplasts ○ Analogous to mitochondria, chloroplasts resulted from a symbiotic event in which a photosynthetic bacterium (likely a cyanobacterium) was engulfed by a host eukaryote. Over time, the engulfed organism evolved to become a specialized photosynthetic organelle. ○ 1600–1400 million years ago Bangiomorpha pubescens  ○ This fossil of a type of red algae is the oldest example of an organism belonging to an extant phylum. The fossil includes differentiated reproductive cells that are the oldest evidence of sexual reproduction. Sexual reproduction increased genetic variation, which led to an increased rate of evolution and the diversification of eukaryotes. ○ 1200 million years ago Origin of animals ○ The precursors of multicellular animals were likely single-celled protozoans. They evolved predatory feeding by ingestion, enabling rapid cycling of organic matter and higher energy production, which led to increased size and multicellular complexity. Animals begin to appear in the fossil record 635 million years ago, but genetic estimates suggest they evolved as early as 800 million years ago. ○ 635 million years ago First vertebrates ○ Early in the Cambrian period, a new group of animals appeared in the fossil record: tiny jawless fish, 2 to 3 cm long, with primitive vertebrae and a brain protected in a cranium. ○ 530 million years ago Trilobites ○ Trilobites are a large group of extinct arthropods that were numerous during the Cambrian explosion. They roamed the seas for approximately 250 million years before disappearing during the Permian-Triassic mass extinction. ○ 525 million years ago Early land plants ○ The earliest evidence of land plants consists of fossilized spores and pollen grains dating back 470 million years. Vascular plants evolved about 50 million years later. Cooksonia is a notable fossil that represents the transition to vascular plants. By the end of the Silurian Period, 420 million years ago, there was an increased diversity of plants and ecosystems on land. ○ 425 million years ago Tetrapods invade the land ○ The Devonian Period is known as the “Age of Fish” because the oceans teemed with life. But the first examples of four-legged animals adapted to life on land also appeared during this period. The more well-known transitional fossils of animals with features common to fish and tetrapods include Tiktaalik, Acanthostega, and Ichthyostega. ○ 365 million years ago Diversification of land plants ○ During the Carboniferous Period (approximately 360 million to 300 million years ago), terrestrial plants increased in diversity, leading to more complex ecosystems. The vast amounts of organic matter buried during this period are the principal source of fossil fuels that humans use today. ○ 340 million years ago Early mammal-like reptiles  ○ Among the most successful predators of their time, Dimetrodons are often featured in dinosaur books. However, they are reptiles, more closely related to mammals than dinosaurs, with a hallmark feature being a particular arrangement of ear bones. Dimetrodons were prevalent during the early Permian Period (approximately 300 million to 252 million years ago) and preceded the first dinosaurs by about 40 million years. ○ 280 million years ago Permian-Triassic Extinction ○ Sometimes referred to as the “Great Dying,” the Permian-Triassic was the largest extinction event in Earth’s history, with a loss of about 56% of genera and 96% of species. The exact cause is still being debated, but evidence points to massive volcanism, in what is now Siberia, that caused catastrophic climate change, ocean acidification, and widespread depletion of oxygen in the oceans. The fossil record shows that mammal-like reptiles declined, clearing the way for new life forms to dominate, leading to the “Age of Dinosaurs.” ○ 252 million years ago Age of Dinosaurs ○ Dinosaurs first appeared during the Triassic Period about 230 million years ago and were the most prevalent large animals in the mid- to late Mesozoic Era (200 million to 66 million years ago). Over this time, they developed an incredible diversity of body shapes and sizes. They ranged in size from less than half a meter in length to over 23 meters. Some dinosaurs took to the air and their descendants became modern birds. ○ 155 million years ago Cretaceous-Paleogene Extinction ○ The most well-known of the five mass extinctions marked the end of the dinosaurs. The world lost about 40% of genera and 76% of species. Multiple lines of evidence support the conclusion that a 10-km-diameter asteroid struck Earth. The impact caused massive climate change and ecological disruption, leading to mass extinction. The extinction of the dinosaurs opened new ecological niches for mammals to exploit. ○ 66 million years ago Last common ancestor among humans and chimpanzees ○ Chimpanzees are the closest genetic relatives of humans. The two lineages diverged about 6 million years ago from a common ancestor that was neither a chimpanzee nor a human but rather some species that does not exist today. ○ 6 million years ago Modern Humans ○ Humans are the dominant form of life on Earth in terms of our effect on ecosystems. However, we have only been around for a tiny sliver of Earth’s history, and the world we live in was—and continues to be—shaped by all the life that preceded us. For example, carbon, oxygen, nitrogen, and sulfur are essential elements for all life on Earth, including human life, and the processes responsible for cycling these elements are at least in part driven by microbes.  ○ 0.2 million years ago Metabolisms on early Earth An essential part of life is to generate energy using chemical reactions that join electron donors and acceptors. Electron donors include hydrogen, hydrogen sulfide, sulfur, ferrous iron, and methane. Electron acceptors include carbon dioxide, carbon monoxide, sulfur, sulfate, nitrate, and nitrite. Early in Earth’s history, microorganisms evolved different metabolic pathways that could make use of all of these naturally available electron donors and acceptors. These ancient metabolic pathways made early life on Earth possible and continue to be used by microorganisms today; without them, the richness of life on Earth would be severely limited. Mass Extinction ○ Mass extinctions are events in Earth’s history where a significantly larger number of species go extinct compared to the number of new species emerging ○ Mass extinctions disrupt the balance between species loss and new species emergence. ○ There have been five mass extinctions recorded the current era potentially being the sixth, known as the Anthropocene extinction caused by human activities  The Ordivician-Silurian extinction occurred around 444 million years ago due to glaciation and a significant drop in sea levels, affecting species such as trilobites and corals. Glaciation, drop in sea levels, and global cooling were factors in the Ordivician-Silurian extinction. The Late Devonian extinction, approximately 359 million years ago, was caused by increased rock weathering and the spread of trees, leading to dead zones in the oceans and global cooling. The Permian-Triassic extinction, 252 million years ago, was the most severe, triggered by massive volcanic eruptions and a subsequent rise in carbon levels. The Triassic-Jurassic extinction, around 201 million years ago, resulted from increased CO2 levels, acidifying the oceans and affecting amphibians and reptiles. Lastly, the Cretaceous-Tertiary extinction, 66 million years ago, was caused by an asteroid impact, leading to global cooling and the extinction of dinosaurs.