Environmental Science Handout PDF

How does the Earth’s life change over time? In the mid-nineteenth century, when Charles Darwin was writing On the Origin of Species, naturalists recognized several tens of thousands of different plant and animal species. By the middle of the twentieth century, biologists had paid more attent...

How does the Earth’s life change over time? In the mid-nineteenth century, when Charles Darwin was writing On the Origin of Species, naturalists recognized several tens of thousands of different plant and animal species. By the middle of the twentieth century, biologists had paid more attention to less conspicuous forms of life, from insects to microorganisms, and estimates were up to 1 or 2 million. Biodiversity has multiplied those estimates at least tenfold(National Academy of Sciences, 1998). What is Biological Evolution? The process in which organisms gradually develop a greater number of genes and a wider variety of cell types over time (Fath, 2004). This seeks to explain the diversity of life: the variety of organisms and their characteristics, and their changes over time. It also seeks to interpret and understand organismal adaptation to environmental conditions. From a long-term perspective, evolution is the descent with modification of different lineages from common ancestors. From a short-term perspective, evolution is the ongoing adaptation of organisms to environmental challenges and changes (Meagher, 1999). Mechanisms of Evolution 1. Mutation is a change in the DNA sequence of an organism. Mutations can result from errors in DNA replication during cell division, exposure to mutagens or a viral infection. Because mutation rates are low relative to population growth in most species, mutation alone does not have much of an effect on evolution. Mutation combined with one of the other mechanisms of evolution can result in meaningful changes in allele frequencies in a population(Andersen, 2012). 2. Genetic Drift is a change in the gene pool of a small population that takes place strictly by chance(Rogers, 2020). It occurs in very small populations, but its effects are strong. It occurs due to an error in selecting the alleles for the next generation from the gene pool of the current generation. It does not occur due to any environmental influences(Byjus, 2024). 3. Gene flow is any movement of individuals, and/or the genetic material they carry, from one population to another. Gene flow includes lots of different kinds of events, such as pollen being blown to a new destination or people moving to new cities or countries. If genetic variants are carried to a population where they previously did not exist, gene flow can be an important source of genetic variation(Berkley, 2020).  4. Non-random mating can occur when individuals prefer mates with particular superior physical characteristics or by the preference of individuals to mate with individuals similar to themselves. Phenotypes of individuals can also be influenced by the environment in which they live, such as temperature, terrain, or other factors(Openstax, 2013). 5. Natural selection is given an alternative name as “survival of the fittest” (Ruse, 2023). Adaptation is a key evolutionary process in which variation in the fitness of traits and species is adjusted by natural selection to become better suited for survival in specific ecological habitats(William, 2019). Importance of Biological Evolution Evolution also explains that life has been on Earth for billions of years. Biological evolution accounts for the relatedness among organisms. Learning evolution helps us understand why and how some species can change space with new environmental challenges is critical to the sustainability of human endeavor (Meagher, 1999). Natural Selection Process that results in the adaptation of an organism to its environment by means of selectively reproducing changes in its genotype, or genetic constitution. According to Darwin, the preservation of traits can stem from how organisms that have favorable traits within their current environments are more likely to survive to reproductive age, mate, reproduce, and consequently pass on these traits to their offspring. Darwin called them ‘survival of the fittest. Principle of Natural Selection Natural selection will occur when the following 4 conditions are fulfilled. Overproduction: An organism produces more offspring than can survive and reproduce.  Variation: Within any population, there are differences or variations in traits. These traits can be physical, like the size of a bird’s beak, or behavioral, like how a predator hunts. Adaptations: Those organisms that have more beneficial adaptations are more likely to survive and reproduce. Selection: Over time, the traits that offer a survival or reproductive advantage become more prevalent in the population. Some desirable characteristics like hair color, skin color, eye color, and height are selected and passed on to the next generation. This simulation increases the chances of survival in the individuals. Examples of Natural Selection The different-sized beaks in Galápagos finches. Variation: Within the population of Galápagos finches, there was variation in beak size and shape. Some finches had long, slender beaks, while others had short, strong beaks. This variation was partly due to genetic differences among individuals. Environmental Pressure: The Galápagos Islands have a diverse range of habitats, each with different types of food sources. For example, some islands had more seeds, while others had more insects or fruits. The availability of food created environmental pressure. Differential Survival and Reproduction: Finches with beak shapes that were better suited to the available food sources in their environment were more likely to survive and reproduce. This meant that these birds were more likely to pass on their beak traits to their offspring. Inheritance: The traits that helped finches survive were passed down to the next generation. Over time, this led to a population of finches that were better adapted to their specific environment. Speciation: Over many generations, these changes in beak size and shape could become so pronounced that the finches on different islands became distinct species, each adapted to their unique environmental conditions. Misconceptions About Natural Selection "Survival of the fittest". In Darwin's writings, he intended for the word "fittest" to mean those who were most suited to their immediate environment. However, in the modern use of language, "fittest" often means strongest or in best physical condition. The "fittest" individual may actually be much weaker or smaller than others in the population. The Limitations of Natural Selection Natural selection may not produce a “perfectly-engineered” trait. For example, you might imagine that cheetahs could catch more prey and produce more offspring if they could run just a little faster. Here are a few reasons why natural selection might not produce perfection or faster cheetahs:  Lack of necessary genetic variation Natural selection can only use the traits that are already present in a population. If there aren’t any traits for running faster, cheetahs can’t become faster just through selection. Constraints due to history Organisms are limited by their evolutionary history. For example, the basic body structure of cheetahs is set by their genes, making major changes to their speed difficult. Trade-offs Improving one trait might come with drawbacks. For instance, making cheetahs faster might require longer, more fragile legs, which could offset any benefits from increased speed. The ‘Bad’ Gene Natural selection works by weeding less fit variants out of a population. We would expect natural selection to remove alleles with negative effects from a population, and yet many populations include individuals carrying such alleles. 9 populations, for example, generally carry some disease-causing alleles that affect reproduction. Why are these deleterious alleles still around anyway? What keeps natural selection from getting rid of them? Heterozygote advantage When having one copy of a gene provides a benefit, even if two copies are harmful, the gene persists. For example, the sickle cell allele provides malaria resistance when present in one copy. Mutation New mutations that introduce deleterious alleles can keep appearing in the population. This ongoing influx of new mutations can prevent natural selection from fully removing these genes. Gene flow If individuals from populations where the gene is not harmful migrate into other populations, they can introduce or spread the deleterious allele. This gene flow makes it harder for natural selection to eradicate the gene. Late onset Some genetic disorders only impact individuals later in life, after they have already reproduced. Types of Natural Selection Stabilizing selection: when selective Disruptive selection: or diversifying pressures select against the two extremes selection. Favors individuals at both of a trait, the population experiences extremes of a trait, leading to increased stabilizing selection. This happens when variation within a population. This means that the middle traits are the most successful, both very high and very low values of a trait so the population tends to stay the same. are advantageous, while intermediate values are not. Directional selection: is one of the common Sexual selection: is a special mode of forms of natural selection. This occurs natural selection in which the mating when one extreme trait or phenotype is preferences of one sex determine the phenotype of the other sex within a species. favored over the other, causing the allele frequency to shift towards that phenotype, so the population shifts in that direction. Types of Sexual Selection Darwin found that sexual selection depends on the struggle between males to get access to their female partners. Two mechanisms of sexual selection: 1. Intrasexual selection Works when members of the same sex (typically males) compete for access to members of the opposite sex, the females. This type of competition can be physical combat, displaying strength, and vocalization. 2. Intersexual selection Occurs from interactions between the sexes, involving a mating choice for males or females. Individuals with the most appealing characteristics are likely to mate and reproduce successfully. Why Does Sexual Selection Occur 1. Good Genes Hypothesis Suggests that individuals with attractive traits may have better genes, leading to healthier offspring. By choosing a mate with these attractive traits, the selecting individual increases the chances of having healthy and genetically fit offspring. 2. Fisherian Runaway Selection Proposes that once a preference for a particular trait exists in a population, it can reinforce itself over time. In this scenario, individuals with the desired quality become preferred mates simply because they possess the trait. This creates a cycle where the trait keeps getting reinforced and spreads through the population just because it’s already popular. Artificial Selection/Selective Breeding Humans breed plants or animals for specific traits. Unlike natural selection, where traits are selected by environmental pressures, artificial selection involves humans choosing which individuals reproduce based on desired characteristics. Examples: Stabilizing selection Black mice are easier to spot and eat more during the day, while white mice stand out at night. Gray mice survive more After generations of selective pressure, the entire population could be gray, depending on the genetic makeup of the trait. Directional selection Giraffes with longer necks can reach more food, giving them an advantage in survival and reproduction. Over time, the population of giraffes has shifted toward longer necks because this trait helps them survive better in their environment. Disruptive selection light-colored moths are well-camouflaged on the light-colored trees, making them less visible to predators and thus more likely to survive and reproduce. Conversely, dark-colored moths blend in with the dark trunks, gaining the same advantage in those areas. Moths with intermediate colors, however, do not match either background well and are more easily spotted by predators. As a result, natural selection favors both light-colored and dark-colored moths. Sexual Selection Intrasexual Selection Lion’s Mane ]Male lions with impressive manes are often seen as more dominant and formidable by other males. They are more likely to be selected by females for mating. Deer Antlers During the mating season, male deer engage in physical combat to establish dominance. The males with the largest and most robust antlers often win these battles and gain access to females. Elephant Seal Male elephant seals engage in fierce physical battles with their fellow male members to establish their supremacy over others. The successful male gets access to mating with the females residing there. Intersexual Selection Peacock’s Tail Bird Songs By choosing mates with impressive tails, female Many male bird species engage in complex and peafowls indirectly select for good genetic quality, as melodic songs, particularly during the breeding only healthy and well-nourished males can afford to season. Female birds are attracted to males with the grow such extravagant plumage. most intricate and captivating melodies. These songs are a sign of physical fitness and indicate that the Savanna Baboons Genitals male can defend a territory and provide food for offspring. Female baboons exhibit conspicuous genital enlargements known as ‘sexual swellings.’ Male baboons prefer mating, with females displaying the most pronounced swellings, often seen as potential indicators of heightened fertility. Geological Processes, Climate Change, and Catastrophes Affect Natural Selection 1. Geological Processes - changes in the Earth's physical structure, like the movement of continents, the formation of mountains, and volcanic activity. These processes can create new environments, isolate populations, and change ecosystems, all of which can drive natural selection. Continental Drift: The slow movement of continents over millions of years can separate populations of the same species. For example, when the supercontinent Pangaea split apart, species that were once together became isolated on different continents. As they adapted to their new environments, they evolved into different species. 2. Climate Change - long-term changes in temperature, precipitation, and other atmospheric conditions. These changes can alter habitats and force species to adapt or face extinction. Temperature Changes: As the Earth's climate warms or cools, species must adapt to the new temperatures. For instance, during the Ice Ages, species that could survive in cold environments thrived, while those that couldn't either migrated to warmer areas or went extinct. Today, with global warming, species are again being pushed to adapt. 3. Natural Catastrophes - sudden, dramatic events that can have a huge impact on the environment, often leading to mass extinctions and opening up new opportunities for natural selection. Asteroid Impacts: One of the most famous examples of a natural catastrophe that caused the extinction of the dinosaurs about 66 million years ago. The impact threw up so much dust and debris into the atmosphere that it blocked sunlight, leading to a drastic drop in temperatures and the collapse of ecosystems that the dinosaurs depended on. With the dinosaurs gone, mammals, which had been small and relatively insignificant, were able to evolve and diversify, eventually leading to the rise of humans. How do Speciation, Extinction, and Human Activities Affect Biodiversity? A species is defined as a group of organisms that can interbreed with one another in nature, reproducing living and fertile offspring. However, this definition for species does not apply to all. There are asexual organisms, such as bacteria, that only reproduce by themselves. There are four major types for asexual reproduction. They are binary fission, budding, fragmentation, and parthenogenesis. Binary fission is when a single parent cell individual. The parent eventually regenerates doubles its DNA, dividing it into two a new piece from where it was broken off afterwards. This can usually be found in from. This takes place in many plants and bacteria. certain animals such as corals, sponges, and starfish. Budding is when a small, surface growth from the parent breaks off, then it results in the Parthenogenesis is where an embryo formation of two separate individuals. This develops from an unfertilized cell. This usually exists in yeast and some animals. usually occurs in invertebrates, some fish, amphibians, and reptiles. An example would Fragmentation is when organisms break into be a komodo dragon. two or more fragments, developing into a new Speciation is a process where organisms go through change to form new and distinct species during the course of evolution. This process involves the splitting of a lineage into two or more genetically independent species. These changes are possibly inherited by the succeeding generations. For eukaryotic species undergoing speciation, the two key processes that occur are genetic separation and phenotypic differentiation. Genetic separation is the splitting up one gene pool into two or more distinct gene pools, while phenotypic differentiation is the diversification of a range of noticeable physical traits. How the speciation process begins has various theories, mainly differing in the function of geographic isolation and the start of reproductive isolation. Example 1 - Speciation Example 2 - Speciation Modes of Speciation The key to speciation is the evolution of genetic differences between the developing species. For a lineage to split completely, the two developing species must have genetic differences that are expressed in a certain way that causes mating between them to be futile. It does not need to be a large genetic difference, but a small change in the timing, location, or methods of breeding could be enough. This change might eventually evolve through natural selection or genetic drift. In addition, reduced gene flow probably plays an important role in speciation. The four different modes of speciation are often grouped according to how much the geographic separation of developing species can contribute to reduced gene flow. They are as follow: Allopatric (allo = other, patric = place) - new species are formed from populations isolated at a new geographic location. Peripatric (peri = near, patric = place) - new species are formed from a small population that is isolated near the border of a bigger population. Parapatric (para = beside, patric = place) - new species are formed from and beside a continuous population.  Sympatric (sym = same, patric = place) - new species are formed from within the range of ancestral populations. Geographic Isolation & Reproductive Isolation Geographic isolation, also known as allopatric speciation, is the isolation of two populations from one ancestral population by a new geographic barrier. This external element to the organisms prevents two or more species from breeding with each other, which eventually causes that lineage to speciate. Allopatry may start the process off, but the evolution of internal barriers, such as genetically-based changes, to gene flow is needed for speciation to be complete. If internal barriers to gene flow do not evolve further, individuals from the two groups of the species will freely interbreed if they come back into contact. Reproductive isolation prevents two or more populations from interbreeding with one another. The environment in which these new developing species are exposed to may force external barriers to reproduction. Any genetic differences that may have developed will be gone the moment their genes are given the chance to mix back together. Genetically-based changes to these aspects of mating could complete the process of reproductive isolation and speciation. An example is the bowerbirds. They construct intricate bowers and decorate them with different colors in order to woo females. If two developing species evolved differences in this mating method, it might permanently isolate them and complete the process of speciation. Factors Contributing to Geographic Isolation Geographic isolation can happen when: Rivers change course Mountains rise Continents drift Migration of organisms The geographic barrier does not need to be a physical barrier that separates two or more groups of organisms, it might also be an unfavorable habitat between the two populations that keeps them from mating with one another. Speciation in the Philippines In Mindoro, four distinct species of earthworm mice, Apomys, were discovered. They got their name from eating earthworm, but they also eat fruits and seeds. These four species can only be found in the Philippines, with one of these four can also be found in Luzon. However, after their DNAs were analyzed, the remaining three showed that they are new and only live in Mindoro. The studies showed that these mice evolved from a small group of ancestral species that traveled over from Luzon between 1.5 and 2.4 million years ago. This could have happened when these mice were on some floating debris during a typhoon, moving the group from Luzon to Mindoro within a few days. Due to the abundance of resources, the group was able to grow rapidly. These descendants were scattered all over Mindoro with some going up the mountains of the island. It was in these mountains where the new species were discovered by researchers, which was an indication that they were isolated from the lowland populations, allowing them to evolve into new distinct species. One Species of an Apomys Another Species of Apomys What are Endemic Species? Species that are exclusively found in a specific geographic location, such as a single island or a particular region, and are not naturally found anywhere else in the world. How does a species become endemic? There are many biological factors for the production of endemic species, such as low rates of dispersal or returning to and staying within the area they were born in. This results in a particular group of organisms to have high speciation rates and therefore many endemic species. Types of Endemic Species  Paleoendemic species- ancient species that were once very common but are now found in smaller regions. The causes for paleoendemic species include habitat loss, pollution, climate change, new predators being introduced, and other environmental changes.  Neoendemic species - newly evolved species that came about due to reproductive isolation, which prevents them from spreading to other regions. Endemic Species in the Philippines The Philippines is home to more than 52,177 species, whereby half of them are endemic. In terms of land vertebrates, the Philippines is known to have 1,238 species of which 618 (50%) are endemic. In terms of fishes, the Philippines has at least 3,214 species, of which about 121 are endemic and 76 are endangered. What is Extinction? Extinction is the complete loss of a species from our planet. Species loss occurs naturally over millions of years and is a normal part of evolution(GenV, 2022). Extinctions occur periodically at what we would call the "background rate". It refers to the standard rate of extinction in Earth's geological and biological history. Background extinction rates are typically measured in order to give a specific classification to a species and this is obtained over a certain period of time.There are three different ways to calculate background extinction rate (Popedadmin, 2018). - The first is simply the number of species that normally go extinct over a given period of time. For example, at the background rate one species of bird will go extinct every estimated 400 years. - The extinction rate can be given in million species years (MSY). For example, there is approximately one extinction estimated per million species years. - The third way is in giving species survival rates over time. For example, given normal extinction rates species typically exist for 5–10 million years before going extinct (Pimm, 2007). Mass extinctions are periods with much higher extinction rates than normal (Ritchie, 2020). There are five major mass extinctions in Earth’s History. End Ordovician Age(mya): 444 Percentage of species lost: 86% Cause of extinction: Intense glacial and interglacial periods created large sea-level swings and moved shorelines dramatically. The tectonic uplift of the Appalachian mountains created lots of weathering, sequestration of CO2, and with it, changes in climate and ocean chemistry. Late Devonian Age(mya): 360 Percentage of species lost: 75% Cause of extinction: Rapid growth and diversification of land plants generated rapid and severe global cooling. End Permian Age(mya): 250 Percentage of species lost: 96% Cause of extinction: Intense volcanic activity in Siberia. This caused global warming. Elevated CO2 and sulfur (H2S) levels from volcanoes caused ocean acidification, acid rain, and other changes in ocean and land chemistry. End Triassic Age(mya): 200 Percentage of species lost: 80% Cause of extinction: Underwater volcanic activity in the Central Atlantic Magmatic Province (CAMP) caused global warming and a dramatic change in the chemical composition of the oceans. End Cretaceous Age(mya): 65 Percentage of species lost: 76% Cause of extinction: Asteroid impact in Yucatán, Mexico. This caused a global cataclysm and rapid cooling. Some changes may have already pre-dated this asteroid, with intense volcanic activity and tectonic uplift. What is the consequence of extinction? When one species disappears, it can have far-reaching effects and consequences. When biodiversity is lost, habitats are less resilient and more susceptible to threats. Consequences include losing one species that relies on them, losing pollinators, losing medication that came from plants or animals, and negative impact on communities and industries (Cho, 2019). What roles do species play in ecosystems? Ecological niche First introduced by American ecologist Joseph Grinnell in 1917, and he viewed it as largely equal to a species’ habitat. His concept stressed environmental conditions that governed where a species might thrive. Charles Sutherland Elton, an English ecologist in 1927, stated that a species’ place in a trophic web was similar to its niche. According to his definition, a species’ interactions with other species – specifically, its interaction with food and predators – determine its niche. The multidimensional space of resources that a species can access and employ was first described by an English ecologist George Evelyn Hutchinson in 1958, nearly 40 years later, under the term “niche”. He combined the two definitions by Grinnell and Elton. His theory considers every biotic and abiotic component that can be quantified as influencing a species. Components of Ecological Niche The environment that an organism lives in (habitat) The organism’s behavior patterns (active periods may be diurnal or nocturnal) The resources that the organisms draw from the environment (food) The interaction pattern with other species in the community (predator-prey, host-microbe relationships) Types of Ecological Niche ( According to George Evelyn Hutchinson in 1957) A. Fundamental Niches (Pre-competitive niche) a. It examines the full spectrum of conditions in which a certain species might be able to survive, grow and reproduce. b. It does not take into account biotic ecological interactions like competition. c. Its size is large. B. Realized Niches (Post-competitive niche) a. It outlines the species’ experiences and how it copes with certain circumstances. b. It takes competition into account along with all other biotic and abiotic ecological interactions. c. Its size is small. It is considered a subset of a fundamental niche. The Principle of Competitive Exclusion, first articulated by a Soviet and Russian biologist and evolutionist, Georgy Frantsevich Gause, in 1934, which states that two species or populations cannot inhabit the same niche: one will consistently out-compete the other. To test this theory in 1934, he employed two closely related Paramecium species to conduct the first experimental testing. Both species populations exhibited typical S- shaped development curves when developed individually. However, when grown jointly, one species was wiped off. Niche Construction In Erwin Schrödinger’s book “What is Life?” (1944) he pointed out that living organisms are far- from-equilibrium systems relative to their physical surroundings. To preserve their out-of-equilibrium status, while creating order (structure, organization) in their bodies and their immediate surroundings, Schrödinger emphasized that organisms must actively do work on their environment. In other words, living organisms can only survive by constantly engaging in niche construction. This activity cannot be random: organisms must change environments in systematic, directional ways. Developmental biologist Conrad Waddington FRS (1957, 1959) was also an early advocate of the idea and he believed that evolutionary theory was incomplete, and suggested that one factor whose significance had not been fully appreciated was niche construction. The niche construction perspective was brought to prominence through the writings of Harvard biologist Richard Lewontin, (1983) who pointed out that organisms do not passively adapt to conditions in their environment, but actively construct and modify environmental conditions that may influence other environmental sources of selection. Examples: Termites build mounds to protect their colony and internal nest, while providing responsive control over their microenvironment.  Weaver birds construct complex nests to protect their chicks, who have a slow development rate, from predators, snakes in particular. Humans build shelter, domesticate wild plants and animals, and disrupt natural water systems to survive and live comfortably. Niche Partitioning The process by which natural selection forces the competing species into various resource-use patterns or niches. Four types of niche partitioning ➔ Spatial niche partitioning occurs when a resource is utilized similarly but in a different physical space. ➔ Dietary niche partitioning is when organisms ingest the same general type of food yet depend on various variants of this food type. ➔ Niche partitioning by resource height is based on what kinds of plants the organisms can reach to eat based on their height and the plant's height. ➔ Temporal niche partitioning is the utilization of the same resource at various times of the day or year. Niche Overlap: It is the overlapping state where two species use the same resources or other environmental factors. Nonetheless, in many cases, niches only partially overlap because resources are shared. Vacant Niche: The term vacant itself defines the vacant nature of a niche that is not yet occupied. Environmental disturbances and evolutionary possibilities are thought to be the root cause of it. An example is if a species becomes extinct, it would leave behind a vacant niche that needs to be filled in to maintain a balanced ecosystem. Generalist species and specialist species Generalist species: Larger range of tolerance and broader ecological niche makes them less prone to extinction and more likely to be invasive. Live in a variety of environments Broad food requirements High adaptability Giant African Land Snail Pigeon Rat Specialist species: Smaller range of tolerance and narrower ecological niche makes them more prone to extinction. Requires a specific habitat (i.e., endemics) Specific food requirements Less ability to adapt to new conditions  Philippine Tarsier Luzon Bleeding-Heart Giant Golden-Crowned Flying Fox Native, nonnative, indicator, and keystone species Native species: a species that naturally exists at a given location or in a particular ecosystem – i.e., they have not been moved there by humans. Bangus Tamaraw Straight-edged Red Parasol Non-native species: a species that moved into an ecosystem as a result of humans having moved them at some point or having removed a natural barrier (e.g., the removal of a natural barrier to fish passage). Giant African Land Snail Mahogany Tree Water Hyacinth Indicator species: a species whose status provides information on the overall condition of the ecosystem or of other species in that ecosystem. Example: Gumamela varaint, H. rosa-sinensis var. ‘Gelia Castillo and Pink-bellied Imperial Pigeon Keystone species: a species that helps define an entire ecosystem. Without it, the ecosystem would be dramatically different or cease to exist altogether. In addition, they have low functional redundancy.The ecosystem would be forced to radically change, allowing new and possibly invasive species to populate the habitat. Example: Philippine Eagle and Mangroves