Week 3 Ch.

28 + 29
Chapter 28: Phylogenies and the History of Life

1/18/2014 9:03:00 PM

Phylogeny: Evolutionary history all placed onto a Phylogenetic Tree Estimated from the best data possible Character: any trait to be studied (genetic, physiological) Out-group: closely related species o Ancestral trait and derived trait (mutations, selections) Cladistics: make tree from shared traits, aka synapomorphy Used to make monophyletic groups, aka clades of common ancestor and all the descendants How to pick the best tree? Parsimony Pick the tree with the least change since independent evolutions are rare Focus on branch pattern not length unless indicated Homology traits shared due to common ancestor Homoplasy similar traits due to factors other than common ancestor Convergent Evolution Hox Genes: similar in fruit flies and vertebrates Clustered in the same way, similar homeobox seq., and similar functions Three types of trees to determine phylogeny Morphological traits, DNA Sequence Data, and Transposable o Transposable: SINEs rare for SINE to be inserted in the same exact location Fossil Records: provide the direct evidence After sedimentation: what can occur after is: decomposition, compression of the fossil into stone, cast made after decomposition, or petrification Limitations of Fossils Habitat Bias: needs to be mudflats, swamps, beaches Taxonomic and Tissue Bias: need slow decay and hard parts fossilize best Temporal Bias: recent fossil are more evident, older ones are more likely to be decomposed Abundance bias: more abundant species are easier to find

Previously used fossil layers to make time intervals, now radiometric dating is used to assign absolute dates Precambrian (Between 4.6 bya earth formation and first animal) Unicellular life Oxygen absent. Later created by photosynthetic bacteria Phanerozoic Eon (Between Precambrian to present) Paleozoic era: origin and diversification, first land animals Mesozoic era: gymnosperms and dinosaurs Cenozoic era: angiosperms and mammals o Cenozoic era broken up into epochs Fundamental idea of timeline CONSTANT CHANGE Adaptive Radiation: rapid diversification in a lineage Caused by: (ecological opportunity) new resources and new ways to exploit resources + morphological innovations Ecological opportunity hypothesis no competitors Mini-radiation to use new resources Evolution of key morphological traits diversification, rapid speciation Flowers (reproductive mechanisms) Feathers/Wings (insulations and flight) Cambrian explosion: adaptive radiation in Cambrian Period Unicellular to multicellular Three major fossil assemblages (fauna = distinct collection of species) o Doushantuo = tiny sponges/corals o Ediacaran = sponges, jellyfish o Cambrian Fauna: wormlike creatures, increase in size and complexity Major diversification What triggered the Cambrian Explosion? Increased oxygen levels to support larger bodies Evolution of predator = prey evolve to avoid predator o Selection pressure in niches by predators drive more niche creation New genes = new bodies (Hox genes for diversification)

Mass extinction vs. Background extinction Mass extinction: more than 60 percent died within 1 million years o Sudden, extraordinary reductions in populations Background extinctions: normal environmental change, disease, and competition and such What caused the End-Premian Extinction, Mother of Mass Extinction? All these are hypothesis Flood basalts of molten rock created heat, CO2 High CO2 levels trapped heat, causing global warming Oceans became axonic, lacking oxygen Drop in sea levels and less land habitat as well Impact Hypothesis: extinction of dinosaurs by meteor Evidence: o Sediment contrained iridium, found in meteors o Shocked quartz and Microtektites found in meteors o HUGE crater in Mexicos Yucatan peninsula What could the impact have done? o Fireball of hot gas for wildfires o Large tsunami o Impact created SO4, reacting with water to make acid rain o Massive dust to block out sun Was the extinction selective? o No, clear data yet unavailable o Possible some organisms may have hibernated Process: Diversification then extinction then mammals diversified more Mammals diversified because no predators Sixth Mass Extinction? Possible, due to our own faults o Pollution, overfishing, invasive species o o o BIG PICTURE PAGE 527 Chapter 29: Bacteria and Archaea Three major branches to life: Bacteria, Archaea, Eukaraya

 Bacteria: peptidoglycan in cell walls Archaea: unique phospholipids in plasma membrane Why do we study bacteria and archaea? Ancient and abundant for studies show evolution history Most total volume of living material on the planet They live in virtually ALL environments Why are extremophiles being studied? (organisms living in extremes) First form of life lived in extreme conditions (low oxygen/high Temp) Possible to find extremophile outer planet organisms!? Use extreme enzymes for industrial use Taq polymerase kind Medical importance of studying Archaea/Bacteria Many bacteria, but only few are disease causing pathogenics o Bacteria have diverse lineages o Pathogenics affect through open wounds Kochs postulates First to establish link between bacteria and disease Studied Anthrax blood poisoning in Cattle Four requirements to finalize causative links: Microbe found in only diseased individuals not healthy Grow pathnogenic on its own If healthy organisms are injected, diseased Isolate organisms from diseased population and compare to pure disease culture Germ theory of disease States that diseases are infectious can pass around Infectious due to transmission of bacteria/virus Virulence: ability to cause disease heritable traits o o o o Such as toxin producing virulent genes Antibiotics kill bacteria to reduce competition for resources Problem: antibiotic resistance Biofilms: dense bacterial colonies that grow Bioremediation: reduce pollution accidents using bacteria to degrade toxins Add nitrogen fertilizer to induce bacteria growth Seeding: adding certain bacteria/archaea to contaminated areas How do we study bacteria/archaea?

Enrichment culture: place colonies into specific conditions and analyze the prosperous healthy organisms to survive the conditions o Helped discover thermophiles heat lovers Metagenomics (environmental sequencing): rapidly identify and characterize DNA of organisms extracted from anss environment o Collect organisms and extract DNA o Generate small fragments and sequence as many as possible o Overlap sequences and compare with known genes Direct sequencing: isolate and sequence specific genes o Metagenomics requires an accurate phylogenetic tree to

analyze the sequences Once thought to be only Eukarya and Prokarya But ribosomal RNA moecules show Bacteria, Archaea, and Eukaraya What themes occur in the diversification of Bacteria and Archaea? Two themes of diversification: morphology and metabolism Morphology diversification: Size, Shape, Motility (Motility is movement) Cell-Wall Composition identified by Gram stain analysis o Gram-Positive cell wall with peptidoglycan o Gram-Negative: cell wall with peptidoglycan and outer phospholipid bilayer Metabolic Diversity need chemical energy to make ATP and Carbon-carbon bonds as building blocks for protein, DNA, RNA Produce ATP by: o Phototrophs: light energy to excite electrons for phosphorylation o Chemoorganotrophs: use organics as electron donor o Cehmolithotrophs: use inorganics as electron donor How to make own building blocks: o Autotrophs: make own building blocks from simple material like CO2 and CH4 o Heterotrophs: Use ready-to-use compounds from environment o Eukaryotes are simple in terms of metabolic processes compared with bacteria/archaea

Bacteria/Archaea use variations of these processes to diversify to occupy diverse habitats ATP via Cellular Respiration: Variation in electron donors/acceptors Most are Chemoorganotophs o Use organic molecules for electrons transport high energy electrons to electron transport chain produce proton gradient ATP synthase o Cellular Respiration: high energy acts as electron donor and is oxidized and low potential energy serves as final electron acceptor and is reduced Common glucose as starter and O2 as final acceptor Fermentation (No electron transport) various substrates Not as efficient, used as alternative (Some use as main source for ATP) Some others use different substrates (Charts of Electron Donors and Acceptors) Photosynthesis: variation in electron sources and pigments Three different Photosynthesis: o Light activate bacteriorhodopsin to transport protons across membranes flow induces ATP synthesis o Some use the deep sea vents for geothermal radiation instead of light energy o Pigments raise electrons to high energy with light and use transport chain to release energy for more ATP o Oxygenic: split water for electrons and release O2 o Anoxygenic: use other sources and produce elemental sulfur and ferric ions Building Blocks via different pathways Autotrophs or heterotrophs Calvin cycle: fixes CO2 into organic molecules Some archaea/bacteria do not use Calvin cycle to making building blocks o Some are methanotrophs: use methane as starter o Some use CO or methanol as starter o

ATP via ATP via

Archaea/Bacteria are abundant and diverse so they are potent forces for global change throughout Earths history Oxygen Revolution o NO oxygen in beginning: no possible source early on and old earth rocks show formation without oxygen o Cyanobacteria: first oxygenic photosynthesis organism (crucial) o With enough oxygen aerobic respiration could occur Oxygen is so EN, it can allow more energy release during the transport chain MORE ATP Nitrogen Fixation and the Nitrogen Cycle o Nitrogen levels regulate growth of grasslands o Archaea/Bacteria: nitrogen fixation by nitrogenase makes Nitrogen into ammonia for fixation use o Archaea/bacteria all use the nitrogen and the by-products in a nitrogen cycle Nitrate Pollution o Good as fertilizer, but nitrate is a by-product that can be washed into the ocean as pollutions

Bacteria Firmicutes: Gram positives with GC nucleotides o Rods and Sphericals some can rest as spores o Fix nitrogen, anoxygenic photosynthesis, fermentation o Common in human gut Cyanobacteria: Blue-Green Algae o Form filaments and form ball shaped clusters o All perform oxygenic photosynthesis o Responsible for origin of oxygen Actinobacteria: high GC Gram Positive (peptidoglycan cell wall) o Shapes vary from rods to filaments o Form filaments called mycelia o Heterotrophs o Mycobacterium cause tuberculosis and leprosy Spirochetes: Smaller bacteria o Corkscrew shape and flagella o Make ATP via fermentation

Chlamydiae: Gram-negative o Spherical o Live as endosymbionts: live inside as parasites o Cause blindness Proteobacteria: many shapes o Rods, spheres, spirals o Moves as colonies known as fruiting body o Perform most feats except oxygenic photosynthesis

Archaea Thaumarchaeota: monophyletic archaea, mesophilic (grow at moderate temperatures) o Rod shaped and abundant o Ammonia oxidizers Crenarchaeota: Oldest Archaeans o Shaped like filaments, rods, discs, or spheres o Cellular respiration through different organic compounds Eukarychaeota: broad meaning found in almost all habitats o Spherical, falimentous, rod, disc shapes, or spiral o Methanogens: produce methane as by-produce of cellular respiration (Cause pollution)

1/18/2014 9:03:00 PM

1/18/2014 9:03:00 PM