Lecture Notes: Environmental Biology

Wednesday, October 10, 2024 Chapter Four: Biodiversity of Life Natural selection is the differential survival due to differences in phenotype to match the environment. Classification-Diversity of Species Taxon: any named group of organisms that is sufficiently d...

Wednesday, October 10, 2024 Chapter Four: Biodiversity of Life Natural selection is the differential survival due to differences in phenotype to match the environment. Classification-Diversity of Species Taxon: any named group of organisms that is sufficiently distinct to be assigned a specific category Phylogenetics: the study of evolutionary related among groups of organisms Phylogenetic tree: Why determine evolutionary relationships? Facilitate discussions about different organism - scientists can talk accurately about a group of organisms Evolutionary relationships - Evolutionary relationship of all life - Mother nature is a very conservative lady! - Human exploitation What is a species? Biological Species Concept - Species are members of populations that actually or potentially interbreed in nature - Populations of organism that have a high level of genetic similarity Evolutionary Species Concept - A sexual species where the largest single lineage in which there is integration through gene flow - A lineage is a single line of direct ancestry and descent, or a single branch of a phylogenetic tree. Ecological species: set of organisms adapted to a particular set of resources, called a niche Reproductive species is naturally to produce fertile offspring of both sexes Isolation species: actually of potentially interbreeding populations Genetic species: similarity of DNA of individuals or populations Evolutionarily Significant Unit: population considered distinct for purposes of conservation - No less than 14 definitions depending on who is communicating - Only applicable to sexually reproducing eukaryotes 1. Asexual eukaryotes and prokaryotes share some characteristics with “species” but not all Biodiversity is the degree of variation of life forms within a given species, ecosystems, biome, or an entire plant. The totality of genes, species, and ecostemes of a region - Species diversity: the number of different kinds of organisms in an ecosystem - Ecological diversity: the richness and complexity of a biological community - Genetic diversity: variety of different versions of the same genes within a species Diversity indices account for the number of individuals and the number of species. Species Richness- count of species. But does not account for abundance One must account for both abundance and richness Numerous diversity indices - Dominance abundance of common species 1. Abundance of common species - Information statistics 1. Take in account rare species Ecosystem diversity: the richness of complexity of a biological community incorporating both the habitat(s) and the community(s) of organisms. Ecosystem diversity: Variety of ecosystems present in a biosphere, the variety of species and ecological processes that occur in different physical settings. Genetic diversity- variety of different versions of the same genes within a species Genetic diversity plays a very important role in survival and adaptability of a species because when a species’s variations are necessary to produce changes in the organisms’ anatomy that enables it to adapt and survive. Species ~ 1.7 million Estimates ~ 10-13 million Endemism: unique to a particular geographic location such as a specific island, habitat, nation or other defined zone Indigenous: originating or naturally occurring in a particular place, but not only in that location place. Introduced: brought to a particular place by human activity. Monday, October 14, 2024 What did David Attenborough give as an answer? Evolution is the process by which the biodiversity of life has arisen. Evolution: The change in the inherited characteristics of biological populations over successive generations. Descent with modification Evolutionary processes give rise to diversity at every level of biological organizations: - Species - Individual Organisms - Molecules Three tenets of natural selections/ Evolution by natural selection is based on three facts: - More offsprings are produced than can possibly survive - Traits vary among individuals - Trait differences are heritable Evolution occurs through changes in heritable traits Inherited traits are controlled by genes and the complete set of genes within an organism’s genome The complete set of observable traits that … Genotype: your genes Phenotype: what you look like Heredity and Variation Variation arises from genetic diversity Genetic diversity:the total number of genetic characteristics in the genetic makeup of a species - Variation comes from: 1. Mutations in genetic makeup 2. Sexual reproduction 3. Migration between populations Mutation Mutation changes in the genetic sequence of genomic material (DNA or RNA) Caused by - Radiation - Viruses - Mutagenic chemicals - Errors during meiosis Spontaneous mutation Induced mutation Deep homology is used to describe cases where growth and differentiation processes are governed by genetic mechanisms that are homologous and deeply conserved across a wide range of species Sexual Reproduction Sexual reproduction: the offspring of sexual organisms contain a random mixture of… Natural Selection An organism's physiology and behavior allow it to survive only in certain environments. Environmental factors have both minimum and maximum levels, called tolerance limits, beyond which a particular species cannot survive or is unable to reproduce. These factors determine an organism’s habitat or ecological niche. Organisms that are better adapted to coping with difficulties experienced during their life are more likely to be “successful” Success is indicated by “fitness” Less-fit individuals have lower or no success in reproduction Fitter individuals are disproportionately represented in future generations Categorized into three different types: - Directional selection - Stabilizing selection  - Disruptive Wednesday, October 16, 2024 Natural Selection Sexual Selection - Intersexual selection- between sexes - Intrasexual selection- same sex Adaptation No two species can occupy the same niche in the same environment for a long time Competitive exclusion principle - Competition causes resource partitioning and niche specialization - Over time traits diverge leading to 1. Specialization 2. Narrower niche width 3. Less competition Ecological niches Outcomes of Evolution Adaptation the process that makes organisms better suited to its habitat Speciation is the process where a species diverges into two or more descendant species Extinction is the disappearance of an entire species Game Changer: Farming Antibiotic resistance is a type of drug resistance where a microorganism is able to survive exposure to an antibiotic - Mutation followed by natural selection Adaptation of vertebrae forearm bones for different ecological niches - Mutation followed by natural selection Speciation Speciation is the evolutionary process by which new biological species arise Adaptive radiation- organisms diversify rapidly from an ancestral species into a multitude of new forms Human Evolution Biodiversity Why should we care? - how does it benefit us? Ecological service - Soil formation - Waste disposal - Air and water purification - Nutrient cycling - Solar energy absorption  Food - Bionics: the application of biological methods and systems found in nature to the study and design of engineering systems and modern technology. Drugs and Medicine Cultural and Aesthetic - Guam 1. $1.6 Billion 2. 20.300 jobs (33% of total employment) Monday, October 21, 2024 Chapter Five: Populations and Communities What is the most expensive fish ever sold? $1.8 million US- 222kg Bluefin Tuna $8108/kg _$3685/lb Bluefin Tuna 20 years- 8 years before 1st spawn Produce 30,000,000 eggs Top predators- 3m 1960- sushi market developed 70-90% depleted stocks Population biology- the science of modeling changes in species abundance Population Control Mortality Reproductive Rates Resource Competition Disease Accident Populations All of the members of a species within a particular area The first level of biological organization beyond individual organisms How do species get to islands? Includes not just the travel, but also the successful establishment of a population Walking Flying Hitchhiking Rafting Ballooning  Continental islands may form larger land masses during glacial events - Biota may arrive overland 1. Sumatran rhinoceros and tigers 2. Orangutan 3. Paleolithic human migrations into ISland Southeast Asia (ISEA) Oceanic islands have no historical continental connection - Introduced species arrived by human activity - Indigenous species arrive by natural means - Endemic species arise through evolution in situations Population founders must exist on island’s resources Habitat must be available and suitable Mates present Food present Nursery habitats present Predators? Competitors? Diseases? All individuals alive today are part of a continuum of success since the dawn of life! What factors increase population size? Birth & Immigration What factors decrease population size? Death & Emigration N= Birth + Immigration - Death - Emigration Many basic models of population growth assume a “closed” population, meaning no immigration or emigration In those models, populations change under the following circumstances: - Birth rate > death rate, n increases - Birth rate < death rate, n decreases - Birth rate + death rate, n stays the same Population growth in three phases Many populations can be modeled by a sigmoid curve - Lag phase 1. Slow (but positive) growth at low N 2. B > D - Exponential phase 1. Population increases rapidly over short time steps as N gets larger 2. B > D - Stationary phase 1. Population reaches the carrying capacity 2. B = D Biotic potential- the maximum reproductive rate of an organism, given unlimited resources and ideal environmental conditions. We can describe growth using a few general factors N= number r= reproductive rate t= time Exponential growth rate- a population can only groat at an exponential rate this fast if nothing limits its growth. N= number r= reproductive rate t= time (d)= change K= Carrying capacity Carrying capacity and population growth rate K is the maximum number of individuals within a population Other Common Metrics of Population Growth Biotic potential: the ability for a species to increase its population size if all offspring survive to reproduce in their parents’ turn - Species that have high fecundity (i.e., high reproductive output) will have greater biotic potential thant species with low fecundity Doubling time: the time required for a population to double in number - Larger populations will have generally have shorter doubling times than smaller populations Wednesday, October 23, 2024 Is there a carrying capacity for the global human population? What factors would determine K? Food per capita Pollution Natural resources Industrial per capita Population Demography is important to predicting population growth Demography is the statistical study of populations For most sexually reproducing species: - Reproduction occurs after a period of maturation Dynamics of population growth changes with development Population age-structure of Guam over time - How have the distributions changed overtime?  - What do you think are the factors responsible for those changes? - What are the implications for future population growth rates for Guam? Changes in birth and death rates result in demographic transitions in population Shift from high birth rates to low birth rates But prolonged survivorship Factors? Significant drop in death - after 1950 Increase healthcare Birth rate declines If you can bring down the death rate, why does the birth rate naturally go down? Population growth We live in two demographic worlds: - One is rich, technologically advanced, and has an elderly population that is growing slowly - The other is poor, crowded, underdeveloped, and growing rapidly. 1. How do we end poverty? Why does the fertility rate drop in more developed countries? Women’s rights affect fertility Total fertility declines as women’s education increases Child survival also is crucial in stabilizing population Women’s education decreases infant mortality Better nutrition, improved health care, simple oral rehydration therapy, and immunization against infectious diseases Estimated that saving 5 million children each year from preventable communicab;e diseases would avoid 20 or 30 million extra births. How many individuals in a population? How do we measure a population? - Census - transects/quadrats/plots - Mark-recapture methods - Many more! Accurate population estimates require representative sampling Communities “All of the species populations in a habitat and their interactions Predator-prey interactions Food web Competition Symbiosis Succession Symbiosis Symbiosis: “Living together” Symbionts: Organisms in a symbiotic association Species 1 Species 2 Type of Symbiosis + + Mutualism + - Parasitism + N/A Commensalism Parasitology Epiphytes and their hosts Who benefits? What are the benefits? How would you test these associations? Monday, October 28, 2024 Trophic Pyramid 1. Top Consumers 2. Secondary Consumers 3. Primary Consumers 4. Primary Producers Rule of Square: 10% rule 1 10 100 1000 10000 The big problem- where are the primary producers? Big fish Reef fish Crabs, shrimps, starfish Seaweed & algae Post WW2 Nuclear Tests Inverted trophic pyramid problem - Two famous ecologists - Odum brothers - Searching for the green plants that must be in higher abundance than the animals that eat them Primary Producers  Found the base in two places 1. Fleshy encrusting algae - 4 x biomass of primary consumers - 40 x biomass of carnivores 2. Corals - What is a coral? 1. Coral is a predaceous animal- not a plant! 2. Related to jellyfish and anemones 3. Coral polyps feed a night-daily plankton migration Corals - Heterotrophic - Give nutrients and CO2 - Receive fixed C and O2 Zooxanthellae - Autotrophic - Receive nutrients and CO2 - Give fixed C and O2 Anemone-Clownfish-Zooxanthellae Symbiosis Classic commensal relationship in literature New evidence suggests this is a mutualism between three species: - Clownfish receive protection from anemone - Zooxanthellae (microalgae) receive nutrients from fish via anemone - Zoox’s give carbon to anemone How do biological communities grow? Succession Mud dauber wasps- what is inside their nests? Caterpillars, in which they use to lay their eggs in Ectoparasitoid Succession: Changes over time in the species present in a given place Primary succession - Succession on a previously uncolonized substrate Secondary succession - Succession on a previously colonized substrate How is succession different than zonation? Primary succession Fresh substrate is nutrient poor and undeveloped Initial colonists are pioneer species that grow quickly (eg vines) with low investment in hard structures (like wood or carbonate) Pioneer species may eventually modify the substrate (eg increasing nutrient and soil depth in terrestrial systems) for future colonists Over time competitively dominant species replate pioneer species, often in predictable sequence Secondary succession Substrate (eg soil) may be suitable for colonization  Composition is influenced by the composition of the surrounding community Pioneer species grow quickly on exposed surfaces but are eventually replaced by woodier, more erect growth forms Wednesday, October 30, 2024 Chapter Six: Ecosystems & Biomes Ecosystem Structure & Trophic Levels Species- organisms with a close degree of genetic relatedness through a shared ancestry Population- all members of a given species living “together” at the same time Biological community- all species living “together” at the same time Ecosystem- a biological community and its environment (abiotic & biotic factors) Productivity- the amount of energy (accumulated material) and other biomass in a given area over a given time - The “economy” of the biosphere (GDP- basically how much energy is produced) - Solar radiation is the principle source of energy - drives ecological productivity (via photosynthesis) Primary producers (autotrophs) are plants and photosynthetic bacteria- the lowest trophic level Secondary producers ( or primary consumers; herbivores) feed on plants Tertiary producers (or secondary consumers; carnivores)feed on herbivores Quartney produces (or tertiary consumers; top carnivores) feed at the apex of the food ed Omnivores feed on both carnivores and herbivores Energy for Life Solar energy: photosynthesis Cellular respiration Primary Production The term “production” is used to quantify the amount of carbon locked into biomass- the amount fixed by photosynthesis. 6CO2 + 6H2O -> C6H1206 + 6O2 Rate function - carbon/unit area (volume)/time Gross - total amount of fixed carbon Net primary production- Ecological Pyramids One of the most important trophic levels is occupied by the many kinds of organisms that remove and recycle the dead bodies and waste products of others - Parasites - Scavengers  - Decomposers 1. fungi decomposing plumeria leaves - Detritivores 1. sea cucumbers consume sediment and digest out the organic material from reef flats Ecological productivity is pyramid-shaped - 10% assimilation rule - Because of these inefficiencies, there is always a much larger productivity of primary producers than of primary consumers Food web complexity of a coral reef Numbers in boxes give biomass and productivity(kg/km^2) Consequently, only the most productive, or very extensive, ecosystems can support top predators Monday, November 4, 2024 Livestock & the Environment Rising demand for animal products - By 2050, it is predicted that the human population will come to 10 billion - Food demand, meat, egg, milk, vegetables, fruits and others - Agriculture byproducts: 1. Animal By-products: gelatin, leather, wool, feather, insulin, pet food, manure 2. Plant By-products - Land and Water 1. Agriculture 2. Human residency & others As an animal scientist, what is our responsibility? - Efficiency, Efficiency, & Efficiency 1. Food: nutritional value, sustainability with byproduct, eat more, digest better 2. Genetic: grow faster, size bigger, produce more 3. Livestock management: density increase, easier to manage, lesser land, waste management, fertilizer, green energy, pollution 4. Time Efficiency: better growth rate, conceive rate, litter size 5. Food processing technology: food safety, longer shelf life, lesser waste from production, tastier healthier food, cheaper 6. Sustainability - Can be broken down into three areas: financially, in terms of human resources, and environment Environment Impact Raising livestock for human consumption generates nearly 15% of total global greenhouse gas emissions, which is greater than all the transportation emissions combined. It also uses nearly 70% of agricultural land, contributing to deforestation, biodiversity loss and water pollution. Manure Differences Different species  Their diet How they are raised/managed Treatment, final products, application Different nutrients of C, K, P and N Different level of water/moisture Different types of fertilizer produced Traditionally manure has been directly spread to crops as fertilizer Loaded with N, K, P Accessible Nutrition unbalanced Overfertilization Odor Leaching off of minerals Runoff of toxic compounds Accumulation of heavy metals and macronutrients Diseases Environment Impact How does this affect the air? - Odor - Nitrogen How does it affect the land/surrounding environment? - Refer back to list above How does this affect the surrounding water? - Algae bloom What are the common forms of organic nitrogen? What is composting? The managed, aerobic biological decomposition of organic materials by microorganisms. (113 to 160 degrees) Benefits of Composting - Reduces odors - Kills disease-causing agents(pathogens) - Reduces bulk Deep Litter System compared to Traditional Composting - Lesser heat produced - Lesser water used - Health benefits - Animal welfare - Rotten bed? Wednesday, November 6, 2024 Homo sapiens = self killers Genetics tell us that interbreeding occurred Top-Down Control: less top consumers = less primary producers Bottom-Up Control: less primary producers = less consumers Where do we fit in? - Hunters- gatherers were omnivores and opportunistic predators 1. They had a limited resource base of food to exploit - During human socio-cultural evolution, a cumulative series of innovations allowed for improved growing and harvesting of foods - Today, people eat an astonishing variety of plants and animals foods - Does the 10% rule still apply to us? Natural experiments in simple ecosystems - Very long residence time of water in lakes (very slow exchange with surrounding sea water) - Only few organisms survive - Low mixing and high stratification - Jellyfish lake 1. Low mixing and high stratification 2. Environmental gradient 3. Chemocline - Symbiotic jellyfish 1. Zooxanthellae 2. Daily migration to follow the sun 3. Night migrate to middle of lake and dive into the chemocline Biome A Biome is … - A geographically extensive ecosystem, occurring wherever environmental conditions are suitable for its development. - A grouping of ecosystems that are similar in vegetation structure physiognomy, features of the environment and characteristics of their animal communities. - A broad, regional type of ecosystem characterized by distinctive climate and soil conditions and a distinctive kind of biological community adapted to those conditions. What determines biomes? - You go through more different biomes when you go vertically, rather than horizontally 1. Temperature (Equator) 2. Rainfall Major terrestrial biomes: - Tundra: vegetation of short stature, occurring at high latitude (arctic) and high altitude (alpine) - Boreal forest: northern subarctic forest, usually dominated by coniferous trees  - Montane forest: a subalpine analogue Freshwater biomes Lentic- lakes and ponds Lotic- rivers and streams Wetlands- shallow, continuously or seasonally wet habitats Marsh- highly productive and dominated by reed Swamp Bog Fen Marine biomes - The open ocean: deep waters and highly unproductive - a marine desert - Continental shelf waters: - Persistent upwellings - Estuaries - Seashores - Coral reefs What factors determine biomes? 1. Temperature 2. Rainfall (altitude) Vegetation changes with elevation because temperatures are low and precipitation is greater high on a mountainside. Guam vegetation map - Limestone forest (north) - Savannah complex and ravine forest (south) - Urban (red)