Phylogenies and Genetics
Phylogenies and Genetics BIO 121
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Date Created: 10/19/14
Phvlogenies Evolutionary Relationships Linnaeus s binomial classification system gives organisms two part names a genus and a specific epithet Species are grouped into Taxa Taxa Related genera FamilyOrderClassPhyluKingdomDomain Systematics depict evolutionary relationships and branching phylogenetic trees Many Systematists want to base classification on evolutionary relationships Phylogenetic trees indicate patterns of descent Much information can be learned about a species from its phylogenetic history Shared characteristics are used to construct Phylogenetic Trees a clade is a monophyletic grouping that includes an ancestral species and all of its descendants Monophyletic Group an ancestor and all its descendants Paraphyletic Group Common ancestor and some but not all of its descendants Phylogenies are inferred from morphological and molecular data Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with very different structures and genetic sequences Homology similarity due to shared ancestry Analogy similarity due to convergent evolution Evolutionary History documented in Genome Orthologous Genes homologous genes found in different species as a result of speciation Paralogous Genes homologous genes within a species that result in gene duplication such genes can diverge and potentially take on new functions Distantly related species often have many orthologous genes The small variation in gene number in organisms of varying complexity suggests that genes are versatile and may have multiple functions Molecular Clocks Help Track Evolutionarv Time Some regions of DNA change at a rate consistent enough to serve as a molecular clock In which the amount of genetic change is used to estimate the date of past evolutionary events Other DNA regions change in a less predictable way Molecular Clocks analysis suggests that the most common strain of HI V jumped from primates to humans in the early I900 s Tree of Life Classication system Domain BacteriaArchaeaEukarya Phylogenies based in part on rRNA genes suggest that eukaryotes are most closely related to Archaea While some data suggests a closer relationship to bacteria Genetic analysis indicates that extensive horizontal gene transfer has occurred throughout the evolutionary history of ly e Prokaryotes StructureFunction of Prokaryotic Success F imbriae hair like appendages that help cells adhere to other cells or substrate CapsuleSticky layer of polysaccharide or protein that can help cell adherence andor evasion of a host s immune system Internal Organization no nucleus or other membraneenclosed organelles usually complex compartmentalization Fla gella structures used by most motile bacteria for propulsion many species can move toward or away from stimuli Cell Wall found in nearly all prokaryotes structure differs in gram positive and gram negative bacteria Circular Chromosome often accompanied by smaller rings of DNA called plasmids Not surrounded by a membrane located in nucleoid region Sex Pillus appendage that facilitates conjugation pass on resistance to bacteria Many prokaryotic species can reproduce quickly by binary fission leading to the formation of populations containing enormous numbers of individuals Rapid reDroduction mutation and genetic recombination promotes genetic diversity Because prokaryotes multiply rapidly mutations can spread equally as fast Prokaryote populations can evolve in short periods of time in response to changing conditions Recombination in DNA between two cells Prokaryotic Diversity transfer of advantageous alleles genetic combination can promote adaptive evolution Diverse nutritional and metabolic adaptations have evolved in Prokarvotes Nutritional diversity is much greater in prokaryotes than in eukaryotes As a group prokaryotes perform all of the modes of nutrition PhotoautotrophyChemoautotrophyPhotoheterotrophyChemoheterotrophy Among prokaryotes obligate aerobes require oxygen Obligate anaerobes are poisoned by oxygen Facultative Anaerobes can survive with or without oxygen Prokaryotes can metabolize nitrogen in many dyferent forms Eukaryotes cannot Some prokaryotes can convert atmospheric nitrogen to ammonia Nitro2en Fixation Anabaena photosynthetic cells and nitrogen fixing cells exchange metabolic products Biotilms surface coaters metabolic cooperation happens here Prokarvotesgt Diverse set ofLineages Molecular Systematics is helping biologists classyy prokaryotes and ident39y new clades Diverse nutritional types scattered among the major groups of bacteria ProteobacteriaGram Positive Bacteria Prokarvotic Role in the Biosphere Decomposition synthetic activities of autotrophic prokaryotes nitrogen fixation Leads to recvcling of elements in ecosvstem Some carry out photosynthesis Manv Drokarvotes have a svmbiotic relationship Mutualism Commensalism Parasitism Prokarvotes have beneficialharmful effects on humans humans depend on mutualistic prokaryotes for digestion Pathogenic bacteria can cause disease by releasing exotoxins or endotoxins Prokaryotes can be used in bioremediation production of biodegradable plastics and the synthesis of vitamins antibiotics and other products Gram Positive Bacteria VS Gram Negative Bacteria GramPositive Thick Peptidoglycan layer Alcohol rinse does not remove crystal violet dye Appear Dark Purple after gram staining Less resistant to antibiotics Gram Negative Thin Peptidoglycan layer Outer membrane structure Appear pink after gram staining Resistant to antibiotics Nutritional Modes of Bacteria Autotrophs require energy only from inorganic sources Heterotrophs require energy from at least one organic nutrient Autotrophs Chemoautotrophs use chemicals as energy source Photoautotrophs use light as energy source Both require energy only from inorganic sources Heterotrophs Photoheterotrophs use light as energy source Chemoheterotrophs use chemicals as energy source Both require energy from at least one organic nutrient PhotoautotrophsPhotoheterotrophs classified as Phototrophs Chemoautotrophs Chemoheterotrophs classified as Chemotrophs Transformation bacteria cell brings in DNA fragments released by another cell Cell DNA is picked up by bacteria cells to transform it Viruses could infect this DNA infect the bacteria Bacteria Virus Bacteria Phage Transduction phage carries bacterial cell DNA from one bacterium to another Coniugationtwo cells of different mating types exchange genetic material Archaea Certain bacterial traits Certain eukaryote traits Archaea that live in extreme environments ThermophilesExtreme Halophiles Other Archaea tend t live in places with moderate temperatures soillakes Extreme Halophiles live in highly saline environments Extreme Thermophiles live in very hot environments Methano gens swamps and marshes produce methane as a waste product Anaerobes poisoned by oxygen Genetic ProsDecting finding more and more Archaea Providing info about early l e Eukarva Protists Most Eukaryotes are single celled organisms Domain Eukarya includes many groups of protists along with plants animals and fungi Unlike prokaryotes protists and other eukaryotes have a nucleolus and other membrane enclosed organelles as well as a cytoskeleton that enables them to have asvmmetric forms allow change in shape for growthmovementabsorption of nutrients Most Protists are unicellular and live in aquatic environments Photoautotrophsheterotrophs mixotrphs Evidence indicates that eukaryotes emerged through endosymbiosis when an archaeal host engulfed a alpha proteobacterium that would evolve into an organelle found n all eukaryotes the mitochondrion Plastids are thought to be descendants of cyanobacteria that were engulfed by early eukaryotic cells The plastid bearing lineage eventually developed into Red Algae and Green Algae Other groups of protists evolved from secondary endosymbiosis events in which Red Algae and Green Algae were themselves engulfed Tvpes of Protists Excovates protists with modified mitochondria Protists with unique agella Spiral or Crystalline quotMajor Groups Diplomonads Parabasalids Euglenozoans K inetoplastidsE uglenids Stramenonhiles HarrySmooth agella quotMajor Groups DiatomsGolden AlgaeBrown Algae Alveolates Membrane enclosed sacs alveoli beneath plasma membrane quotMajor Groups DinoflagellatesApicomplexans C iliates Rhizarians Amoeba with threadlike pseudopodia quotMajor Groups Radiolarians Forams Cercozoans Red Algael Green Algae Major Groups Red Algaephycoerythrin photosynthetic pigment Green Algae plant type chloroplasts Land Plants mossesfernscony ers lowering plants UnikontsProtists closely related to fungianimals lobetube shape pseudopodia Amoebozoans slime moldsTubulinidsEntamoebas Ogisthokonts Protists Roles I Ecological Communities Protists form a wide range of mutualistic and parasitic relationships that effect their svmbiotic partner and many other members of the community Photosynthetic protists are among the most important producers in aquatic communities They are the base of the food web Factors that effect photosynthetic protists affect many other species in the community Unicellular Organisms microscopic Colonies loosely connected group of cells Coenocytes multicellular masses of cytoplasm wo cellular division between them Multicellular 0rganisms composed of many different cells Most protists obtain their nutrients autotrophically or heterotrophically Interactions Free living or symbiotic Symbiotic relationships range from mutualismparasitism Reproduction SexuallyAsexually Relationships among Protists Protist Kingdom not really recognized anymore Paraphyletic group Determined by ultrastructure electron microscopy Comparative molecular data Protists to be familiar with Disicristates Choano agellate C iliates Dinoflagellates Diatoms Brown Algae Foramin erans Actinopods Red Algae Green Algae Plants Monophyletic group including Red Algae Green Algae Land Plants based on molecular data presence of chloroplasts bounded on outer and inner membranes AnimalsFungiPlants evolved from protist ancestors