BIO1202: Genetics and Evolution Lecture 12 PDF

BIO1202: Genetics and Evolution Lecture 12: Experimental evolution and Evolutionary applications Lecturer: Dr. Arianne-Elise Harris What is Experimental Evolution? It is the use of laboratory or controlled field manipulation to investigate evolutionary processes. It usually makes use of organisms wi...

BIO1202: Genetics and Evolution Lecture 12: Experimental evolution and Evolutionary applications Lecturer: Dr. Arianne-Elise Harris What is Experimental Evolution? It is the use of laboratory or controlled field manipulation to investigate evolutionary processes. It usually makes use of organisms with rapid generation times and small physical size, often microbes, to observe phenomenon that in large multicellular organisms occur too slowly. Experimental Evolution Garland and Rose (2009) defined experimental evolution as research in which populations are studied across multiple generations under defined and reproducible conditions, whether in the laboratory or in nature. This definition allows for various types of experiments that involve evolutionary changes i.e crossgenerational, genetically based etc. Experimental evolution – Field evolution studies At one end of the continuum, the study of evolutionary responses to naturally occurring events (e.g., droughts,fires, invasions, epidemics) may constitute a kind of adventitious experimental evolution, especially if these events occur repeatedly and predictably enough that the study can be replicated, either simultaneously or in subsequent years. Next we have intentional "field introductions," in which a population is placed in a new habitat in the wild, or a population’s habitat is altered by adding a predator, a pesticide, a food source, fertilizer, etc. The experimental population is then monitored across generations and compared with an unmanipulated control population. Experimental evolution – Laboratory natural selection This type denotes experiments in which the environment of a laboratory-maintained population is altered (eg. change of temp., culture medium etc.) as compared with an unaltered control population. “Laboratory culling” involves exposing an experimental population to a stress that is lethal (or sublethal) and then allowing the survivors to become the parents of the next generation. In all forgoing experiments, the investigator does not specifically measure and select individuals based on a specific phenotypic trait or combination of traits. Rather, selection is imposed generally – the population has great freedom to respond across multiple levels of biological organization (eg. behaviour, morphology, physiology) Experimental evolution Artificial selection This refers to the intentional reproduction of individuals in a population that have desirable traits. In sexually reproducing organism, two adults that possess a desired trait are bred together or “selective breeding” experiments. These experiments are the process by which humans used animal breeding to select and develop particular phenotypic traits by choosing which animal males and females will have offspring together. Organisms are “scored” for one or more specific traits, then breeders are chosen based on their score. Depending on the level of biological organization at which selection is imposed – the precision with which the phenotype is defined in practice- multiple solutions may again be common. Experimental Evolution Domestication This is an interesting (and ancient) type of experimental evolution that involves some amount of intentional selective breeding. The process has been replicated enough times that the general principle might be discerned. Whenever organisms are brought from the wild to the laboratory or agricultural setting some amount of adaptation to the new conditions will occur, and this can be studied. Once domesticated, organisms may be subject to additional selective breeding programs, with varying degrees of control and replication, leading to multiple breed or lines. From Wolves to pugs – the history of domestication of Canine sp. Dogs are man’s best friend – and one of man’s most famous examples of experimental evolution. It’s suggested that wolf domestication was by accident ! – A result of wolves being fed and sheltered in small tribes/villages. The timing and causes of the domestication of dogs are both uncertain. Genetic evidence suggests that dogs split from their wolf ancestors between 27,000 and 40,000 years ago. The oldest known dog burial is from 14,200 years ago, suggesting dogs were firmly installed as pets by then (taken from newscientist.com) Dog breeds from 100 years ago look nothing like their modern day relatives – This is due to selective breeding of species for specific, profitable, traits i.e shorter legs or stockier builds. Image: Sled dog Society of Wales.com Evolutionary experiments More recently, the unintentional effects of various actions by human beings have been studied from the perspective that they constitute selective factors whose consequences may be predictable. Examples of this include changes to commercial fisheries and various ungulates that are hunted. To qualify as experimental evolution, we require most if not all of the following fundamental design elements: Maintenance of control population Simultaneous replication Real-time observation over multiple generations Prospect of detailed genetic analysis Evolutionary Applications Evolutionary Applications Evolution is the unifying principle of all biology. It helps us understand phenomena in fields as diverse as genetics, ecology, and physiology. The application of evolutionary biology addresses a wide range of practical problems in medicine, agriculture, the environment, and society. Such cutting-edge applications are emerging due to recent advances in DNA sequencing, new gene editing tools, and computational methods. Evolutionary Applications The history of life on Earth traces the processes by which living and fossil organisms evolved, from the earliest emergence of life to present day. Evolutionary Applications Relevance of evolution: agriculture It would seem that with the advent of fertilizers, pesticides and biotechnology, our ability to produce crops should be limitless. But biological systems evolve. Insects and diseases evolve as new technologies are introduced. Variables change, because evolution is change over time through descent with modification. So in the fields of agriculture and economics, just as in medical science and conservation, history matters. Evolutionary Applications Relevance of evolution: agriculture Artificial selection and Breeding and Genetic Engineering A major technological application of evolution is artificial selection, which is the intentional selection of certain traits in a population of organisms. Humans have used artificial selection for thousands of years in the domestication of plants and animals. More recently, such selection has become a vital part of genetic engineering, with selectable markers such as antibiotic resistance genes being used to manipulate DNA in molecular biology. It is also possible to use repeated rounds of mutation and selection to evolve proteins with particular properties, such as modified enzymes or new antibodies, in a process called directed evolution. Evolutionary Applications Relevance of evolution: agriculture During infection, pathogens secrete many molecules, collectively called effectors. Some of these effectors can be recognized directly or indirectly by resistance (R) proteins from the plant and are then called avirulence (AVR) proteins. This recognition usually triggers defense responses including the hypersensitive response and results in resistance of the plant. R—AVR gene interactions are frequently exploited in the field to control diseases. Evolutionary Applications Relevance of evolution: agriculture Artificial Selection and Breeding Corn and its untamed cousins: wild genes in domestic crops The small ears of the teosinte plant might not seem to be of much economic value. But, in fact, they may contain a genetic goldmine for the domestic corn market. Scientists have discovered that domestic corn and wild teosinte are evolutionary cousins — research suggests that native Americans domesticated maize from wild teosinte stocks using artificial selection — and so genes found in teosinte may also be useful in corn. Evolutionary Applications Relevance of evolution: agriculture Artificial Selection and Breeding In addition to agricultural crops we also artificially select or breed for specific traits in animals e.g. increased muscle mass in meat birds. Evolutionary Applications Relevance of evolution: agriculture Pesticide resistance Pests evolve resistance to our pesticides at an alarming rate. Evolutionary Applications Relevance of evolution: agriculture Refuges of genetic variation: controlling crop pest evolution Evolutionary theory tells us how we can slow the rate at which genes for pesticide resistance spread: by providing refuges where non-resistant insects thrive. Evolutionary Applications Relevance of evolution: agriculture Knowledge of genetic variation and evolutionary relationships helps farmers improve the ability of crops to resist disease. Pesticide resistance evolves can provide strategies to minimize pest damage. In these ways, a knowledge of evolution can secure the world's food supply and improve the quality of human life. Evolutionary Applications Relevance of evolution: Species preservation and population size According to evolutionary theory, very small populations face two dangers — inbreeding depression and low genetic variation — that might keep them from recovering, despite our best efforts to preserve them. Evolutionary Applications Relevance of evolution: Species preservation and population size In a small population, matings between relatives are common. This inbreeding may lower the population's ability to survive and reproduce, a phenomenon called inbreeding depression. For example, a population of 40 adders (Vipera berus) experienced inbreeding depression when farming activities in Sweden isolated them from other adder populations. Higher proportions of stillborn and deformed offspring were born in the isolated population than in the larger populations. Evolutionary Applications Relevance of evolution: Species preservation and population size The explanation for inbreeding depression lies in the evolutionary history of the population. Over time, natural selection weeds deleterious alleles out of a population — when the dominant deleterious alleles are expressed, they lower the carrier's fitness, and fewer copies wind up in the next generation. Evolutionary Applications Relevance of evolution: Species preservation and population size Low genetic variation Genetic variation is the raw material of evolution. Without genetic variation, a population cannot evolve in response to changing environmental variables and, as a result, may face an increased risk of extinction. For example, if a population is exposed to a new disease, selection will act on genes for resistance to the disease if they exist in the population. But if they do not exist —i.e. if the right genetic variation is not present — the population will not evolve and could be wiped out by the disease. Evolutionary Applications Relevance of evolution: Medicine Because bacteria and viruses reproduce rapidly (and some mutate quickly), they evolve rapidly. These short generation times — some bacteria have a generation time of just 15 minutes — mean that natural selection acts quickly. In each pathogen generation, new mutations and gene combinations are generated that then pass through the selective filter of our drugs and immune response. Over the course of many pathogen generations (a small fraction of a single human lifetime), they adapt to our defenses, evolving right out from under our attempts to rid ourselves of them. For example the common flu has a mutation rate of almost 50 mutations per year and as such it is difficult to develop one permanent vaccine to fight this disease. Evolutionary Applications Relevance of evolution: Medicine Vaccines Vaccines exploit the efficiency of our own immune system to recognize and eliminate microbial threats that have been previously introduced into our bodies. Because these threats evolve, vaccines must change too. Evolution makes sense of the need for a new vaccine, and point the way toward developing it. Evolutionary Applications Relevance of evolution: Medicine Evolutionary Applications Relevance of evolution: Medicine Antibiotic Resistance Penicillin was once a “miracle” drug, but today medical professionals find a host of diseases— from staph infections to tuberculosis—evolving resistance to antibiotics. The origin of antibioticresistant organisms is a textbook example of natural selection. Evolutionary Applications Genome editing and CRISPR Genome editing (also called gene editing) is a group of technologies that give scientists the ability to change an organism's DNA. These technologies allow genetic material to be added, removed, or altered at particular locations in the genome. Several approaches to genome editing have been developed. A recent one is known as CRISPR-Cas9, which is short for clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9. CRISPR-Cas9 was adapted from a naturally occurring genome editing system in bacteria. The bacteria capture snippets of DNA from invading viruses and use them to create DNA segments known as CRISPR arrays. The CRISPR arrays allow the bacteria to "remember" the viruses (or closely related ones). If the viruses attack again, the bacteria produce RNA segments from the CRISPR arrays to target the viruses' DNA. The bacteria then use Cas9 or a similar enzyme to cut the DNA apart, which disables the virus. Genome editing is of great interest in the prevention and treatment of human diseases. Currently, most research on genome editing is done to understand diseases using cells and animal models. It is being explored in research on a wide variety of diseases, including single-gene disorders such as cystic fibrosis, hemophilia, and sickle cell disease. It also holds promise for the treatment and prevention of more complex diseases, such as cancer, heart disease, mental illness, and human immunodeficiency virus (HIV) infection. Evolutionary Applications Relevance of evolution: Medicine Emerging Diseases The outbreak of the H1N1 “swine flu” in 2009 reminds us of our vulnerability to emerging diseases. Like SARS in 2002, H1N1’s abrupt appearance emphasizes the fact that viruses evolve, producing new and potentially pandemic- causing contagions. Rapid evolution combined with rapid travel means that emerging diseases threaten human health and therefore, understanding how these diseases evolve is vital. More recently, between the years 2019-2023, we faced a new threat in the form of COVID 19/SARS-CoV-2. Scientists have used evolutionary theory and techniques such as a phylogenetic tree and haplotypes to make inferences about the origin and spread of the virus over time and around the world, and what type of vaccine may be most effective. Evolutionary Applications Relevance of evolution: Medicine HIV: the ultimate evolver The human immunodeficiency virus (HIV) is one of the fastest evolving entities known. It reproduces sloppily, accumulating lots of mutations when it copies its genetic material. It also reproduces at a lightning-fast rate — a single virus can spawn billions of copies in just one day. To fight HIV, we must understand its evolution within the human body and then ultimately find a way to control its evolution. https://www.nigms.nih.gov/education/Inside-Life-Science/Pages/everyday-evolution.aspx Evolutionary Applications Scientists studying the evolutionary history of HIV found that it is closely related to other viruses. Those viruses include SIVs (simian immunodeficiency viruses), which infect primates, and the more distantly related FIVs (the feline strains), which infect cats. Evolutionary Applications Relevance of evolution: Medicine When a patient begins taking an HIV drug, the drug keeps many of the viruses from reproducing, but some survive because they happen to have a certain level of resistance. Because of HIV's speedy evolution, it responds to selection pressures quickly: viruses that happen to survive the drug are favored, and resistant virus strains evolve within the patient, sometimes in just a few weeks. However, basic evolutionary theory points out a way that this evolution of resistant viral strains can be delayed. Patients are prescribed "drug cocktails" — several different HIV drugs taken together. Evolutionary Applications Relevance of evolution: Medicine If a patient is already infected with a drug-resistant HIV strain, basic evolutionary theory has also pointed out a way to make the drug useful again. Studies of the evolution of resistance often show that you don't get something for nothing. Specifically, it "costs" a pest or pathogen to be resistant to a pesticide or drug. If you place resistant and non-resistant organisms in head-to-head competition in the absence of the pesticide or drug, the non-resistant organisms generally win. Evolutionary Applications Other applications of evolution The evolutionary principles of natural selection, variation, and recombination are the basis for genetic algorithms. This engineering technique has many practical applications, including aerospace engineering, architecture, astrophysics, data mining, drug discovery and design, electrical engineering, finance, geophysics, materials engineering, military strategy, pattern recognition, robotics, scheduling, and systems engineering. Moreover, tools developed for evolutionary science have been put to other uses. End of Lecture 12