Bio Notes week 6
Bio Notes week 6 BIO 121 - M001
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BIO 121 - M001
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This 9 page Class Notes was uploaded by Andrea Scota on Saturday October 10, 2015. The Class Notes belongs to BIO 121 - M001 at Syracuse University taught by Staff in Fall 2015. Since its upload, it has received 48 views. For similar materials see General Biology I in Biology at Syracuse University.
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Date Created: 10/10/15
Mentioned in class Bio Notes Week 6 TEXTBOOK CHAPTER 26 Phylogeny and the Tree of Life Phylogeny the evolutionary history of a species or group using systematics Phylogenies show evolutionary relationships 261 Taxonomy how organisms are named or classified 0 Latin scienti c names called binomials 1St part is the genus specifies species Hierarchial classi cation domain kingdom phylum class order family genus species Classifying is a way to structure the human view of the world Larger categories are often not comparable in lineages Evolutionary history shown in phylogenetic trees they represent hypotheses about the evolutionary relationships depicted as twoway branch points each point shows a common ancestor Because the Linnaean system fails to tell anything about different groups relationships to one another some systematics suggest trees based solely of evolution Sister taxa the closest shared branch pointthe closest relative it is called a polymata when there are two related A phylogenetic tree is rooted begins at one point Basal taxa lineage diverges early in history Phylogenetic trees show patterns of descent The sequence of branching does not indicate absolute ages of species Do not assume taxons on phylogenetic trees evolved from the one next to it Phylogenies are inferred from morphological and molecular data 262 Recall phenotypic and genetic similarities due to shared ancestry are called homologies 0 Example bone structure Anology is the similarity of organisms that is due to convergent evolution oftentimes confused with shared ancestry o Occurs when similar environmental pressuresnatural selection produces similar analogous adaptations on organisms from different evolutionary ancestry o Analogous structures that arose independently are homoplasies Analyzing DNA sequencing is a way to show how species derived from similar ancestor if they match up in mostly all places then they are closely related 0 See of bases of common ancestors align to take into account deletions and mutations Shared characters are used to construct phylogenetic trees 263 Cladistics method for inferring phylogeny from homologous characteristics Common ancestry is the main criteria for classifying 0 Species places in clades each includes ancestral species and all decedents nested in linear clades Taxon clade only if it is monophyletic consists of an ancestral species and all descendants vs paraphyletic consists of ancestral species and some descendants vs polyphyletic distantly related species not most recent common ancestor A shared ancestral character is a character originated in an ancestor of taxon A shared derived character is an evolutionary novelty unique to a clade 0 So we should be able to tell the clade that appeared at which branch when each shared derived characteristic rst appeared Outgroup species or group of species from evolutionary lineage known to have derived before lineage that include species studying the ingroup Some branches are long showing proportion to the amount of evolutionary change and times at which particular events occurred To narrow down systematics biologists apply principles of maximum parsimony and maximum likelihood Maximum parsimony rst investigate simple explanation that is consistent with facts for DNA the fewest base changes Maximum likelihood identi es species most likely to have produced a given set of DNA Well supported phylogenetic hypotheses are consistent with a wide range of data An organism s evolutionary history is documented in its genome 263 Genes evolve at different rates if change so molecular trees can represent short and long periods of time o rRNA evolves slowly useful in investigating relationships in taxa while mtDNA mitochondrial evolves rapidly useful in investigation recent changes orthologous genes the homology is the result of a speciation event and hence occurs between genes found in different species paralogous genes homology results from gene duplication hence multiple copies of these genes have diverges from one another within species Distantly related species have orthologous genes Genes are versatile and have many functions because little variation of them in so many species Molecular clocks help track evolutionary time 265 Molecular clock approach for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates 0 Assumption underlying is that the number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed sine the genes branched from their common ancestor divergence time o For paralogous genes the number of substitutions is proportional to the time since the ancestral gene was duplicated Calibrate by graphing the number of genetic differences 0 If the gene has a reliable average it determines the rate of evolution Studies suggest that the most common strain of HIV jumped from primates to humans in the early 1900 s Our understanding of the tree of life continues to change based on new data 266 Phylogenies have led to biologists adopting a three domain system Bacteria Archaea and Eukarya Bacteria mostly prokaryotes Archaea diverse group of prokaryotic organisms that inhibit a wide variety of environments Eukarya all organisms that have cells containing a true nucleus Eukarya and protists are more closely related than either are to bacteria Genes yield different results due to movements of genes between organisms of different domains Horizontal gene transfer process in which genes are transferred from one genome to another through mechanisms such as exchange of transposable elements and plasmids viral infection and perhaps fusion of organisms TEXTBOOK CHAPTER 27 Bacteria and Archaea Structural and functional adaptations contribute to prokaryotic success 271 Bacteria include the vast majority of prokaryotes of which most people are aware Diverse nutritional types are scattered among the major groups of bacteria F Has cell wall containing peptidoglycan a polymer composed of modi ed sugars crosslinked by short polypeptides Categorize many bacteria by cell wall composition through a o simpler walls with lots of peptidoglycan appear dark after gram stain more structurally complex less peptidoglycan in their cell walls instead have 2 membranes appear light after gram stain these bacteria are more resistant to antibiotics o Gram stains are valuable in medicine for guring out kinds of infections O F 0 To stick to things or other cells Bacteria lack compartmentalization have some membranes that perform metabolic functions their membranes infold sometimes and they have less DNA Endospores develop within the cell under hash conditions The original cell produces a copy of it s chromosomes surrounded by the endospore Fimbriae hair like appendages on the outside of the cell used to attach to things 12 of prokaryotes are capable of taxis the directed movement away from or towards a stimulus with their agella 0 Their agellum evolved through exadaptation existing structures take on new functions through descent with modi cation 0 Reproduce with binary ssion they split Rapid reproduction mutation and genetic recombination promote genetic diversity in prokaryotes 272 0 Mutations and genetic recombination cell has 2 different sets of DNA increase gene diversity quickly in species with short generation times and large populations 0 Transformation transduction and conjugation bring together prokaryotic DNA from different individuals 0 genotype and possibly phenotype are altered One cell donates their DNA and the other receives it Due to a cells F factor for quotfertilityquot that can exist wither as an Fplasmid of as a segment of DNA A cell with Ffactor built in is called Hfr cells Some are resistant to antibiotics called Rplasmids quotresistantquot Diverse nutritional and metabolic adaptations have evolved in prokaryotes 273 Obligate aerobes must use oxygen for cellular respiration and cannot grow without it Obligate anaerobes poisoned by oxygen they extract their chemical energy by anaerobic respiration Facultative anaerobes use oxygen if present but carry out fermentation or anaerobic respiration Nitrogen xation convert nitrogen in the atmosphere to ammonia Prokaryotes cooperate with one another to use environmental resources they couldn t alone can t metabolize and do other at the same time 0 Most cells in lament carry out photosynthesis some are heterocyst s and carry out only nitrogen xation 0 Metabolic cooperation occurs in cells bio lms Prokaryotes have radiated into a diverse set of lineages 274 I Increase in technology and research has revealed diverse genomes of prokaryotes Horizontal gene transfer played a key role in their evolutions I Major Protobacteria gram negative bacteria photoautotrophs chemoautotrophs and heterotrophs and gram positive bacteria 0 Archaea o Extremophiles quotloversquot of extreme conditions I Extreme halophiles live in highly saline environments I Extreme thermophiles thrive in very hot environments I Methanogens live in moderate environments Prokaryotes play crucial roles in the biosphere 275 I Decomposers heterotrophs break down dead organisms and material and synthetic activities of autotrophsnitrogen Fixing prokaryotes recycle elements in ecosystems Many prokaryotes have symbiotic two species live in close contact relationships with other organisms hosts 0 Mutualism both organisms bene t 0 Commensalism one organism bene ts other is not affected or harmed o Parasitism host is harmed by parasite parasite eats hosts tissues blood etc Prokaryotes have both bene cial and harmful impacts on humans 276 I Humans depend on mutualistic prokaryotes in intestines to break down food I Pathogenic bacteria cause diseases almost 12 of all 0 Cause illness by 0 Exotoxins proteins are secreted by certain bacteria and other organisms o Endotoxins liposaccharide components of gram negative bacteria Only released with a cell dies or the cell wall breaks down 0 Horizontal gene transfer spreads genes associated with virulence to harmless speciesstrains I Prokaryotes can be used in bioremediation the production of biodegradable plastics synthesis of vitamins antibiotics etc TEXTBOOK CHAPTER 28 Protists Protists very small eukaryotes 52 micrometers Most eukaryotes are singlecelled organisms 281 0 Protists are in domain eukarya they have a nucleus and other membrane enclosed organelles a cytoskeleton and most are unicellular 0 Some protists rely on organelles not in eukaryotes contractile vacuole Can be autotrophs heterotrophs or mixotrophs do both Some produce sexually some asexually 4 super groups 0 Excavata excavated groove on one side of body mainly parasites o quotSAR clade stramenopila alveolatea rhizaria o Archaeplastida red algae green algae land plants 0 Unikonta amoebas animals fungi closely related to animals and fungi 0 Endosymbiosis how diversity arose relationship between two species in which one organism lives inside another cellcells of another organism o Mitochondrion arose from alpha proteobacterium which also gave rise to two photosynthetic protists algae 0 On several occasions redgreen algae went through secondary endosymbiosis Excavates include protists with modi ed mitochondria and protists with unique agella 282 0 Excavata diplomonads parabasalides both lack plastids and have highly modi ed mitochondria and are anaerobic and euglenozoans All are monophyletic o Dimplomonads reduced mitochondria s quotmitosomesquot lack electron transport chains so they can t use oxygen many are parasites 2 nuclei agella o Parabasalids reduced mitochondria called quothydrogensomesquot o Euglenozoans predatory heterotrophs photosynthetic autotrophs mixotrophs parasites rod shaped with spiralcrystalline structure inside agella kintoplastids and euglenids I Kinetoplastids large mitochondrion DNA quotkintoplastquot I Euglenids pocket at one end where 1 out of the 2 agella occur some mixotrophs some heterotrophs and some autotrophs The quotSAR clade is a highly diverse group of protists de ned by DNA similarities 283 quotSAR clade straneopiles aveolates and rhizarians monophyletic o Straneopiles most important photosynthetic organisms on the planet agellum with hair like projections and other smaller smooth one Diatoms unicellular algae glass like walls in organism s matrix made of silica provides protection against pressures most abundant in lakes and oceans their photosynthetic activity affects the global carbon dioxide levels Golden algae yellowbrown due to carotenoids bi agellate photosyntheticmixotrophic Brown algae largest and most complex algae multicellular have holdfast stipe and blades photosynthetic Alteration of generations alteration of multicellular haploid and diploid forms most complex life cycles gametuphytes aka 3 female a i 39 39 zygizute spnmphyte MITOSIS Adapted 39EITI Biological Eatenre by Freeman E 29 Pearson Educatinn Inc 0 Alevolates membrane enclosed sacs Dino agallets reinforces by cellulose plates 12 are heterotrophic some are phytoplankton sometimes cause quotred tides Apicomplecans parasites of animals intricate life cycle both sexual and asexual stages Ciliates use cilia to move and feed mostly predators 2 nuclei micro nuclei and a macro nuclei 0 Rhizarians amoebas protists move and feed by means of pseudopodia Radiolarians delicate symmetrical internal skeletons made of silica Forams quotforamina ferans pourous shells called tests live in oceans and fresh water attach to rocks and algae Cercozoans amoeba agellated protists use threadlike pseudopodia marine freshwater soil heterotrophs parasites predators Red algae and green algae are the closest relatives of land plants 284 0 Make up the third super group Archaeplastida 0 Red algae red due to photosynthetic pigment prycoerythim live in warm costal waters mostly unicellular reproduce sexually 0 Green algae charophyteschlorophytes produce color most live in freshwater Unikonts include protists that are closely related to fungi and animals 285 Unikonta extremely diverse includes animals fungi other protists amoebozoans opisthokonts o Amoebozoans lobe of tubelike pseudopodia slime molds tubulins eantamoebas Slime moles plasmoldial or cellular plasmoldial are bright colored form plasmodium unicellular and cellular solitary cells that function individually form fruiting asexual body Tublins lobe or tube like pseudopodia soil freshwater marine most heterotrophs Eantamoebas parasites affect invertebrate and vertebrate animals 0 Opistnikonts nuclearrids fungi choano agallets animals Protists plat key roles in ecological communities 286 0 Form wide range of mutualisticparasitic relationships that affect partners and many other members of communities Photosynthetic among most important producers in aquatic communities 0 Base of food wed factors that affect protists affect the communities Producers organisms that use energy from light to convert carbon dioxide into organic compounds
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