Biological Diversity PDF
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Summary
These notes cover various aspects of biological diversity, encompassing ecosystem services, different types of organisms, and evolutionary theories. They include insights into ecological processes and the valuation of biodiversity, which is important context for environmental considerations.
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iological Diversity - B Bio diversity creates exotic species on islands Creates different versions of forests and ocean habitats The variety of life forms in a habitat Variety of biological system, typically conceived as number of species, but also in relation to biochemistry,...
iological Diversity - B Bio diversity creates exotic species on islands Creates different versions of forests and ocean habitats The variety of life forms in a habitat Variety of biological system, typically conceived as number of species, but also in relation to biochemistry, genes and ecosystems Ecosystem services - Biodiversity services in relation to humans angroves: M Carbon Food Protection for endangered species Prevent coastal drift ervices: S Fruit, Wood, CO2, prevent environmental change, cosystem services are the functions of natural systems that provide value to humans “free of E charge” 3 Categories - Provisioning (physical goods), regulating (Ecological processes), Cultural (Tourism/idea value) aluation of Biodiversity V Pros: - Money is easy to understand and communicate - Makes hidden value visible - Easy to misuse things that are free - Useful for conservation Cons: - ime consuming and challenging T - Ethical values that cannot be quantified with money - Impossible to measure all values - Makes biodiversity easier to sell by making it a commodity lpha Diversity = Measuring one community’s biodiversity A Multiple Alpha Diversity Compared = Beta Diversity Gamma Diversity = Using Alpha and Beta to figure out theoretical larger scale diversity iversity Metric: D Species Richness - Number of different species in a certain area. Species Evenness = Community based on how evenly distributed each species is. Relative Abundance = How abundant a species is compared to other species Phylogenetic Diversity = Evolutionary diversity Species Diversity = EX: Shannon Diversity Index - Numerical based on richness and evenness igh Evenness = Highly equal representation among species H Low = Low representation equality Relative Abundance is used for evenness per species and combine to get fully evenness value lato - Each organism = Perfect organisms created by divinity, diversity within species = copy P error - Typological Thinking ristotle - Also in typological thinking, helped introduce scale of nature, as well as words A species and genus Ideas Before Darwin - Species are unchanging, Species are independent. Lamarck - Change over time through lifetime changes Darwin - Species change over time, common ancestry among species, Populations evolve, not singularly organisms. Natural selection occurs to individuals. Evolution by Natural Selection: 1.) Species are not unchanging 2.) Not typological, but population thinking 3.) Testable, scientific mechanism Modern Summary of Evolution by Natural Selection: 1.) Variation among individuals 2.) At least some variation inherited 3.) Some variants survive and reproduce at higher rates than others Fitness = Ability to produce viable offspring Adaptation = Heritable trait that increases fitness in an environment volution = Change in allele frequency in a population over time E Allele = A variant form of a given gene volution Forces: E Natural selection, genetic drift, gene flow, mutation, non-random mating (sexual selection), and environmental variances (usually related to natural selection) atural vs Artificial Selection - N Artificial: Deliberate manipulation of fitness by humans through selective breeding odes of Natural Selection - M Stabilizing: Reduces variation, favors the average value, phenotype that is higher/lower than average has lower fitness Directional selection: Favors an extremity, high fitness of one extreme, Diversifying Selection: Both extremes are selected for creating more diversity and variation. onvergence = Similarity in form/function of distantly related organisms C Divergence = Variety in form/function among closely related groups of organisms ossil Record: F Steno’s law of superposition - Gives a sequential record based on depth of fossil Earth is old Vast museum of life Incomplete fossil record means preservation bias Erosion can also cause incomplete fossil record ossil record challenge: F Biased record Incomplete preservation Never exposed Destruction by geologic process Destroyed before discovery Relative ages omology = A similarity that exists due to common ancestry H Analogous = Convergent evolution Embryonic Homology = Study of homology based on embryos Vestigial Trait = Trait only kept due to common ancestry, not very useful iogeography: B Galapagos tortoises Tectonic Shift olecular Biology in Evolution: M Phylogenetic trees volution’s Internal Consistency: E Fossil phylogeny Hippos are whales nearest relatives Vestigial bones Fossil record Phylogeny of living whales and dolphins Relative Dating Absolute Dating We can absolutely study evolution in a lab ig 4 B Natural selection Genetic drift Gene flow Mutation (Sexual selection) (Environmental variances) enetic drift: G Can increase or decrease fitness Most important in small populations, can also occur in big populations Over time can lead to loss or fixation of alleles auses of Genetic Drift: C Bottleneck, founder effect, sexual reproduction ottleneck = Reduction in population size B Founder effect = population moving and creating new population ene Flow: G Can increase or decrease fitness, Equalizes allele frequencies between populations utation: M Many not heritable Ultimate source of genetic variation DNA mutation = Can produce novel AA sequences RNA mutation = Can change gene regulation of expression Chromosome level mutations = Gene duplication, loss of function, new alleles, Horizontal/Lateral gene transfer on-Random Mating: N Physical location Mate choice ating choice questions: M How choosy am I? What traits do I care about? How much do I invest into gaining access to mates? How much do I invest in offspring initially? Do I stay or do I go? exual reproduction = Reproduction involving meiosis, giving rise to offspring that have S genetically unique combination of genes Anisogamy = Gamete-producing sexually-reproducing species have gametes of different sizes Sexual dimorphism = Strong phenotypic differences between egg and sperm individuals in anisogamous species. ale = Exclusively produce smaller gamete, sperm M Female = Exclusively produce larger gamete, eggs Pattern: Sexual selection usually acts more on males over females Process: Fundamental asymmetry of sex - Females generally invest more resources in offspring, female reproduction is often limited by resources whereas male reproduction is limited by access to mate otential Reproductive Rate = Reproductive rate with unlimited access to mates P Operational Sex Ratio = Ratio of males and females ready to mate OSR leads to mating competition Many factors underlie sexual selection Mate choice can lead to higher reproductive sex Inbreeding = Mating between relatives Inbreeding influences evolution indirectly because increases rate at which natural selection eliminates deleterious alleles nvironmental variances in evolution - E TSD - Temperature dependent sex determination Cline in pine tree height up a mountain Assortative mating is a mating pattern where people with similar traits are more likely to mate with each other than expected by random chance eterozygote advantage: Sickle cell for example (mix of dominant and recessive gives H resistance to both) Hardy Weinberg = Null hypothesis (negative hypothesis, ie, if correct, evolution is not occurring) Hardy Weinberg Assumptions: No selection, no mutation, no gene flow, No genetic drift, random mating If assumptions are met, allele frequencies don’t change Reproductive Isolation: If fertile offspring are produced, they are reproductively compatible (same species) Species - Produce fertile offspring in nature rezygotic reproductive isolation - P Temporal: Time for breeding Habitat: Breed in different habitats (geography) Behavioral: Courtship displays differ and do not interbreed. Genetic: Eggs and sperms are incompatible Mechanical: Reproductive structures are physically incompatible ostzygotic: P Hybrid viability: Hybrids do not develop and die as embryos Hybrid Sterility: Sterile as adults Morphospecies concept: Morphology similarity leads to connections between species olymorphic species = Single species with multiple morphologies P Cryptic species = Multiple species look like one species hylogenetic species concept: Phylogenetic species groups and descendants are used for P speciation Biological Species: - Criteria: Reproductive isolation between populations - Advantages: Able to study living organisms and contemporary behavior - Disadvantages: Not applicable to fossils/asexual, and hard to use without geological overlap Morphological: - Criteria: Morphologically distinct populations - Advantages: Fossil record is vast and can be used to link for common ancestor - Disadvantages: Polymorphic species are one of the ways that this falls apart, because they look different but are from one species Phylogenetic: - Criteria: Using phylogeny and DNA similarities to create speciation borders (Smallest monophyletic group on a phylogenetic tree) - Advantages: Can help distinguish between very similar species based on DNA structure - Disadvantages: Can classify multiple species with similar DNA structure as the same How do species form: Allopatric: Geographic separation between populations Sympatric: Forms within same physical range Patric = Place, allo = other, sym = same llopatric - Vicariance: Physical barrier emerges and separates populations A Allopatric - Dispersal: Species moves to new area and separates from original population, and evolves on its own ympatric - Diversifying Selection: Original fruit tree with own set of flies, and new fruit tree S comes and flies switch to other fruit tree and come into process of speciation because some are using one tree as habitat while other flies are using other tree, based on preference for tree. Sympatric - Polyploidization: Diploid = 2 copies of each chromosome (1 from mom 1 from dad) also referred to as 2N (N = Chromosome #) Gamete of Diploid would be haploid (1N) utopolyploidy - Diploid with daughter cell that is triploid (3N) or tetraploid (4N) - “Mistakes” in A replications leading to polyploidy can create a new species with different ploidy than original species llopolyploidy - 2 Diploids create a daughter with more genetic information to create a tetraploid A offspring that is now a new species due to difference in ploidy Polyploidy can also be used for artificial selection Speciation Process: How fast it happens: 1.) Gradualism a.) Speciation happens by slow accumulation of gradual changes 2.) Punctuated equilibrium a.) A sudden burst of evolutionary change ene flow in terms of Speciation - G Complete speciation = No recognition as potential mates Population fusion = Random mating produces fit hybrids Hybrid zone = Geographic area where inbreeding occurs and hybrid offspring are common What happens to hybrid zone during secondary contact? einforcement - Hybrids are less fit than either purebred species. The species continue to R diverge until hybridization can no longer occur Fusion - Reproductive barriers weaken until the 2 species become 1 Stability - Fit hybrids continue to be produced Hybrid Fitness Likely Result Selection Pressure Low Reinforcement of divergence Traits that prevent inbreeding Medium Hybrid Zones High ybridization into new H Traits of hybrid offspring species In mating, if allele drifts and concentrates on a certain genotype, without selection pressure, it is genetic drift. Sexual selection - Individuals in population selecting for certain traits in sexual reproduction hile both terms are related to mate choice,"sexualselection" specifically W refers to the evolutionary process where individuals with certain traits are more likely to be chosen as mates due to their advantageous characteristics, while "non-random mating" is a broader term encompassing any situation where mate selection is not completely random, whichcan include sexual selection but also other factors like geographic proximity or phenotypic similarity (assortative mating) Fragmentation = Physical divide in a population causing a divide in species —-----------------------------—-----------------------------—-----------------------------—---------------------------- Part 2:Tree Thinking axon = Single level of taxonomic classification T Taxonomy/Systematics = Science of classifying organisms Phylogeny = Evolutionary history Cladistics = System to organize homologous traits to describe phylogenies Carl Linnaeus = Father of Taxonomy Shifting consensus to hierarchical monophyletic groups identified by synapomorphies , 2, 3, 6 1 4, 5, 7, 8 olytomy - Unresolved relationship among branches (multiple branches to one node) P Branch that ends before others means extinct Branch length is arbitrary unless otherwise stated Data matrix - 1 = yes, 0 = no icrobial planet: M Oxygen production Nitrogen Fixation Metal cycling Decomposition Extreme environments: Acid river, salt pond, hydrothermal vents lien Physiologies: Extraterrestrial analogues A Europa Taq polymerase Bioprospecting I am a microbial world Microbe: Microscopic organisms rokaryotes = Archaea and Bacteria = Unicellular organisms lacking membrane bound P organelles and nucleus iffusion limits cell size in most bacteria D 100nm to 100um orizontal gene transfer - Swapping of genetic material across branches of the tree H A.) Bacterial transformation - Donor cell releases DNA into a recipient cell B.) Bacterial Transduction - Phage takes a bit of DNA and brings it to another organism C.) Bacterial Conjugation - Bacteria of same type, 2 cells physically connected and a plasmid moves between them. Less tree of life, more web of life with HGT orphological diversity - Diversity of shape, size, behavior, color, movement, M Swarming - Multiple microbes move their flagella to move together Swimming - Microbe Swimming with flagellum Twitching - Extend structures and pull towards a direction Gliding - Attach self to a surface and roll Sliding - Spreading by growth acterial multicellularity - Microbes are capable of coordinated complex behavior B Bacteria are the dominant life forms on Earth Teaspoon of seawater = ~5 million microbacteria icrobiomes: Biodiversity inside of us M Bacterial and Archaeal phylogeny is a work in progress Traditional microbiology - Culture-based methods in a lab Great plate count anomaly - Discrepancy between microbes we can see versus ones we can culture/grow Mesocosm/Microcosm experiments simulate ecosystems Microscopy can identify signature activity enomic sequencing + Bioinformatics: G DNA Extraction Amplicon sequencing - Multiple copies of fragments from1 target gene Metagenomics sequencing - short sequence fragments from ‘all’ DNA Whole genome sequencing is also an option Use LUCA (Last universal common ancestor) Three Domains: acteria - Generally unicellular, generally single circular chromosome (some with plasmids), B Cell walls with peptidoglycan rchaea - All known unicellular, All known single circular chromosome (some with plasmids), A cell membranes phospholipids with unique structural features ukarya - Cells with extensive, complex cytoskeleton, cells with array of organelles, linear E chromosomes -> DNA + Histone proteins = chromatin, double membrane bound nucleus, mitochondria Information processing is shared with Archaea and Eukarya Convergent evolution of cellular motility Shared traits of all organisms - Cells, Central Dogma, ATP, C-C organic compounds acteria - Peptidoglycan, translation not started with methionine B Archaea + Eukarya - Translation started with methionine, histone proteins Archaea - Ether-linked membrane lipids with branched tails Eukarya - acteria/Archaea/Eukarya typically distinguished genetically based ribosomal RNA gene B sequences acteria include organisms that cure and cause disease B Antibiotic resistance is a major problem in medicine Probiotics have been shown to have positive effects on irritable bowel syndrome and chronic digestive disease, respiratory infections, infection, cardiovascular health, obesity, mental health. Beneficial prokaryotes play major roles in - Human health, global biogeochemical cycles, food systems, bioremediation Nitrogen gas - fixation -> ammonia - biosynthesis -> organic n in proteins OR ammonia - nitrification -> nitrite - nitrification -> nitrate - biological reduction -> organic n in proteins OR nitrate - denitrification -> n2 gas Bioremediation Fungi and Protists Synapomorphies of Eukaryotes - ndergoing meiosis U Having a nucleus Having a mitochondria Larger Cells Different type of cellular reproduction ynn Margulis proposed endosymbiosis L DNA confirmed theory of endosymbiosis Archaeal host cell and an alphaproteobacteria endosymbiont merged together, resulting in first eukaryotic cell. rotists - All eukaryotes except land plants, fungi, and animals P Protists have diversity in number/types of nuclei, ingestive feeding strategies, movement strategies, nutritional habits, life cycles, lternation of generations - Many multicellular protists alternate between haploid and diploid A generations - Type A -> Type B -> Type A - Sporophytes produce spores by meiosis, gametophytes produce gametes by mitosis Importance of protists - Human Health, environmental health, fossil record. Some protists are primary producers, consumers or decomposers roups of Protists - G SAR Clade - Stramenopiles - Two unequal flagella, one with bristles, group with diatoms, kelp in this as well, Alveolates - Sac-like alveoli under membrane, dinoflagellates, apicomplexan, ciliates, Rhizarians - Lack cell walls, cells move with threadlike extensions, important roles in marine carbon and nitrogen cycling rchaeplastida - Land plants (not protists) and algae (protists) A Archaeplastida Plantae = Chloroplasts with double membrane Archaeplastida - Red algae - Red from phycoerythrin, enables algae to do photosynthesis at deeper depths, Green algae + Green plants - Cellulose and chlorophyll a+b, morphea - Fungi, animals + some protists (Amoebozoa and Opisthokonta) A Amoebozoa - Lack cell walls, engulf food, amoeboid movement, include lobose amoeba and slime models Opisthokonta - Reproductive cells with single flagella at base, contains fungi and animals xcavata - Protists - Feeding groove, lack typical mitochondria, includes metamonads and the E discobids etazoa = Animals M Animals = Multicellular, heterotrophic, movement under their own power, neurons and muscle cells (except sponges), ingest food before eating, Porifera are sister taxa for metazoans for now rotostomes and Deuterostomes are separate in development and create different changes in P body nimal Key Innovations - Created Embryonic tissue layers A Diploblastic = Specialization, 2 layers Triploblastic = 3 Layers of developing cells for specialization Cephalization = Animal with head with nerves and central nervous system Coelom = Body cavity to hold organs Segmentation = Bodies that have distinct segments Cambrian explosion - Explosion of new developments under the surface, - More atmospheric oxygen-> increased aerobic respiration -> larger, more active bodies (environmental) - Emergence of bilateral symmetry -> evolution of eyes (developmental) - Vision -> Predation -> New selection pressure -> arms race -> skeletons (ecological) - Movement off sea floor -> Newly available niches (ecological) - New genes (developmental) -> Hox genes determine body plan in most animals - Duplications and diversification of hox genes led to larger more complex bodies ot-Bilaterian phyla -> Porifera, ctenophora, Cnidaria. N Porifera = Sponges -> Marine, benthic, mostly asymmetrical, no germ layers, uses silica or CaCO3 for structural support, suspension feeders, larvae swim, asexual via fragmentation, self fertilization or cross-fertilization -Unique fromchoanocytes and spicules tenophora - Comb jellies, marine, planktonic, mostly asymmetrical, transparent, ciliated, C gelatinous, diploblasts, float in water, predators, adults are mobile, most self fertilize, usually external fertilization -synapomorphies = ctenes (comb-likebands of cilia) nidaria - jellies/corals/sea anemones - diploblastic, neurons, muscles, have cnidocytes, C radially symmetrical, mostly marine, some triploblast some diploblast, hydrostatic skeleton, sessile polyp, polyps reproduce asexually, sexual reproduction with external fertilization Diploblast means - Body is built at initial developmental stage from 2 layers of cells rotostome - Mouth first development P Deuterostomes - Mouth second development Difference is based on if mouth forms first or anus forms first Coelom - Body cavity Protosomes -> Ecdysozoa (nematoda) and Most animals are protostomes (specifically insects) Multiple water to land transitions for animals ophotrochozoan - 2 distinct morphologies, spiral cleavage, L Annelids - Group of Lophotrochozoan - Segmented worms, coelomate, bristles Mollusca - Open circulatory system, all have mantle, radula, visceral mass, and foot. Foot is a muscular hydrostat hy plants? (Ecosystem services) W Oxygen production, soil (prevent erosion), moderate temperature/climate, primary production, resources Archaeplastida - Green algae and land plants reen algae outgroup G Bryophytes Vascular plants = All have lignin Land plants 475 million years ago and plants -> SIlurian Explosion -> Carboniferous club mosses -> gymnosperms -> L angiosperms ll land plants have: A Cell walls with cellulose Chlorophyll a and b Land plants are monophyletic quatic plants are beneficial because dissolved nutrients and abundance of water, structural A support, ll land plants have: A Cuticle - Watertight seal that prevents water loss Stomata - Pores that can open/close to do gas exchange Flavonoids - UV Absorbing pigments to prevent DNA Damage Alternation of generations onvascular plants - Smaller, lower lying. Usually in damper areas, size limited by diffusion, lack N true roots, gametophyte dominated alternation of generations Vascular Tissue - elongated cells organized into water collecting tube All vascular plants have lignin for vascular tissue eedless vascular plants - Polypodiopsida S Many are tropical epiphytes Large leaves (fronds) coiled with young fiddleheads Sporophyte-dominated alternating generations One type of spore (homospory) ametophyte - Multicellular, haploid, produce gametes by mitosis G If haploid dominates, gametophyte dominates eterospory - Different sized gametophytes H Seed plants are heterosporous, which allows diversification eed plants: S Seeds, true leaves, wood, pollen, and heterospory Gymnosperms - Ovules not enclosed Fertilization produces seed & embryo surrounded by nutrients Angiosperms - Encased seed Success driven by evolution of flower as a reproductive organ, and coevolution with pollinators Metabolism - Requires energy, carbon, macronutrients, micronutrients. Primary productivity = Synthesis of organic products from inorganic carbon —---------—---------—---------—---------—---------—---------—---------—---------—---------—---------—---- Ecology: Population Growth - ambda = Finite rate of increase, Lamba = n1/n0 L If pop size is same, lambda = 1, lambda > 1 then increasing, lambda < 1 then decreasing n(t) = n0 times lambda^t ittle r = instantaneous growth rate L Lambda = e^r, n(t) = n0 times e^rt If pop stays same, r = 0, increase r > 0, decrease r < 0 ROTIST = EUKARYOTE THAT ISNT ANIMAL PLANT OR FUNGI P 2 Main Branches of Bacgteria - Gracilicutes and Terrabacteria Important Groups of Bacteria: 5 Gacilicutes = Bacteroidota and Proteobacteria, Terrabacteria = Cyanobacteria, actinobacteria, firmicutes roteobacteria = Heterotroph and chemoautotroph, some important pathogens (ie cholera, food P poisoning, plague, dysentary), Bacteriodota = Some pathogens, common in probiotics Cyanobacteria = Endoysymbiosis, aquatic photoautotrophs, Actinobacteria = Branched filaments, found in soil and freshwater, chemoheteroautotroph, some pathogens Firmicutes = Low GC gram positives main archaea groups = 4 Euryarchaeota = Methane producers, heat lovers, acid lovers, hydrocarbon degradation, S/N/Fe cycling, decomposition of organic matter DPANN = Obligate symbionts with reduced genomes, biofilms with many infecting viruses, TACK = Crenarchaeota - Similar to old archaeans, sulfur cycling, anaerobic heterotrophs, Thaumarchaeota, some methanogens in this group Asgard Archaea = Relevance to eukarya, have pathways for bacteria/eukarya-like ester-linked membrane lipids, 4 Clades of Eukarya = Excavates, SAR, Archaeaplastida, amorphea SAR = Stramenopila (unequal flagella, brown algae/kelp), Alveolata (Sac-like alveoli under membrane), Rhizaria (lack cell wall, move with threadlike extension, important in marine C/N cycles) Archaeaplastida = Land plants (not protists) and algae (protists), chloroplasts = double membrane morphea = Amoebozoa - Lack cell walls, engulf food, amoeboid movement, include lobose A amoeba and slime molds, Opisthokonta - Reproductive cells with single flagella at base (contains fungi, plants and animals) Gametophyte = Squishy green, sporophytes = white Seed plants
