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116 Cards in this Set
- Front
- Back
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C
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Group A is sister taxon to Group I
True or False |
False
group I no longer exists: its genetic lineage is now divided between taxa B and C So Group A is sister taxon to Groups B and C |
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List the sister taxon (or taxa) for:
a) B b) G and H c) E, F, G, and H d) E |
a) C
b) E, F c) D d) F |
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a) Which taxon or taxa share characters 6 and 7?
b) Which taxon or taxa share characters 6 and 5? c) Which of the numbered features is present in taxon E? d) Which of the numbered features is present in taxon H? |
a) E, F, G, H
b) D c) 6,7,9 d) 6,7 |
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a) How many evolutionary steps were needed for Tree 2?
b) How many evolutionary steps were needed for Tree 3? |
a) 2
b) 2 |
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a) List the number of changes found for each tree
b) Which tree is most likely to represent the pathway of evolution according to the Principle of Parsimony? c) How did you decide which tree was most parsimonious? |
b) Tree 1
c) Set outgroup to be arbitrarily zero. Then look at how many evolutionary steps to change into a non-zero number for each character state. The most parsimonious totaled to be the least number of steps. |
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a) Ingroup is L,M,N. Fill in Tree 3, there's only 1 correct construction. Find the total number of changes for each tree.
b) Which character(s) could be used to identify members of group L,M,N? c) Which character provides no useful information about the relationships among taxa L.M.N? d) Most likely sister group to taxon L? e) Ancestral state for character 1? f) Which state(s) are derived for character 1? |
a) Tree 3 (from left to right): XMLN
b) 1,4,6 c) 2,3,5 d) M e) 1 f) 0, 2 |
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Why would character(s) on a data matrix not be considered phylogenetically informative?
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No variation--no change
One taxon different, all others same--only 1 evolutionary step |
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If the wolf-like morphology occurs in the animals that share it because this body form produces a very efficient predator, the morphology is an example of _____________ evolution.
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Convergent
-two dissimilar species come to look like each other |
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Is a group containing grass, bees, and Formica a monophyletic group? Explain
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No
one of the descendants of the most recent common ancestor of this group (Myrmica) has been left out. |
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Assuming the tree is correct, does the term "prokaryote" describe a monophyletic group?
Note: Prokaryote = Bacteria & Archaea |
No
A monoplyletic group is a group that contains ALL descendants of a single recent common ancestor |
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In which of the trees do prokaryotic taxa form a monophyletic group?
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Tress 1 & 2
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Use clues obtained from the names of organisms, and from your general knowledge, to match the scientific names at left below with the correct description at right
Hints: Holger Jannasch was a microbiologist who explored deep ocean habitats. The Greek root "halos" refers to sea or salt. The Latin root "lactis" means milk. |
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Is the organism whose fundamental metabolism is shown in Figure 4 aerobic or anaerobic?
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Aerobic
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The curve for Escherichia coli is in red. What do you notice about its optimum temperature in relation to where it occurs in nature?
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Its optimum temperature (30-40 C) is also the same as the normal human body temperature. E. Coli is commonly found in the intestines.
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What problems do you foresee if a laterally transferred gene were used in a phylogenetic analysis?
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Introduced genes are highly variable
Genetic material is able to be transferred amongst many organisms, even those who are extremely distant Lots of polytomies |
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How might a cell protect itself from foreign DNA in light of transformations, conjugations, and transductions?
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The cell can produce its own foreign body fighters like interferons or have its host's phagocytes help, or become unfavored by natural selection so that the genes can be lost
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When might invasion with novel DNA from other organisms in the same habitat provide an advantage to the new host?
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Increase favor of natural selection, like antibiotic resistance, ability to tolerate new things, etc.
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Explain in your own words, why molecular sequence techniques revolutionize environmental microbiology.
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You can make a list of many different organisms from any location in the world because all organisms have the ss-RNA gene. It makes it easier to draw a tree and figure out extinctions, branches, MRCA. Information like this would be useful to figure out new ideas, plans, drugs, etc.
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A cladogram is a hypothesis about evolutionary relationships. Explain how hypotheses about evolutionary relationships can be tested.
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It can be tested with more evidence from fossils, dispersal and geological events, DNA, and comparing sister taxa. It'll either help accept or refute the hypothesis and make better cladograms.
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Taxon
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a group of organisms at an unspecified level of classification scheme
Species, a phylum, any other group of organism New taxa result from the splitting of a common ancestral taxon into descendants Taxa can rotate around the node |
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Tree
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a diagram depicting a pattern of lineage splitting – aka evolutionary tree
Branching pattern on a tree represents ancestor descendant relationships To construct a tree, need evidence and to determine parsimony (least number of steps) Ancestral character states and outgroup comparisons – needed in order to determine the most likely tree When constructing trees must eliminate useless data – aaag or aaaa Recognize that trees able to freely rotate, need morphology to characterize tree (subjective- behavioral data, DNA – molecular data) |
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Cladogram
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tree depicts only the sequence of splitting events
Each cladogram is a hypothesis about evolutionary relationships among taxa |
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Phylogram
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the length of each branch in a tree intended to be proportional to the amount of evolution that has occurred after the lineage splitting event
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Sister Taxa
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form by lineage splitting
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extant
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living species
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MRCA
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most recent common ancestor – all cladograms have one -
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Characters
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features or traits of organisms – can be morphological, molecular, and behavioral
Indicating a character means that it originated there and passed to all descendants of lineages from that point on Map characters one at a time |
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Principle of Parsimony
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biologist accept the most likely tree as the one with the least/ simplest steps that explains all the evidence
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Ingroup
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taxa of interest that are derived from a MRCA
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Outgroup Method
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based on the assumptions that the character state shared between the ingroup and the outgroup is ancestral
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Derived Trait
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character states that evolve beyond the MRCA and are novel for the ingroup taxa
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Why is knowing Ancestral Traits helpful?
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Knowledge of the ancestral states is useful because it tells which of the character states was present before in the ingroup before it actually evolved within the group and which evolved before the ingroup formed.
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Polarity
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can determine by knowing which character state is ancestral and which is derived
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Reversal of State
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way in which the character state starts at 0 changes to 1 and returns back to 0, causes extra steps – typically unparsimonious . when a character evolves independently evolves twice
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Why are morphological, molecular and behavioral characters are all useful for phylogenetic data?
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need some variation such that they come in different character states
need to be derived from a common ancestral form – homology (common ancestry) |
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homologous characters
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present in organisms because they were inherited from a common ancestor
example – mammals share hair, mammary glands, four chambered heart |
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If 2 structures look the same but did NOT come from a common ancestor must have evolved ___
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independently
Example: fish fin and dolphin fin – though appear similar evolved independently because don’t not have the same funtion. Dolphins are part of the mammalia family and classified under mammary glands etc. |
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Homoplasious/ analogous
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two structures with the same morphology but the morphology was not inherited from a common ancestor
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Convergent
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if the structures were shaped by NATURAL SELECTION for the same function (one way to form homoplasious structures
EX: Dolphins and fish fins |
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Traditional Classification
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italicized and binomial
genus then species (often descriptive) Kinky prostitutes can offer feel good sex (kingdom, phyla, class, order, family, genus, species) – point of hierarchy is to indicate different degrees of relationship |
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Cladistics
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construction of cladograms
critical that each part of the cladogram represents a monophyletic group (group contains all the descendants of a single common ancestor) |
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Polytomy
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undefined branching pattern
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How many trees possible when there are 4 taxa with 1 outgroup?
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3
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Paraphyletic
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MRCA but not all descendants
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Polyphyletic
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NO MRCA – least informative
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Congruent
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when characters support the hypothesized tree
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3 domains of life
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Bacteria, eukarya, and archaea
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Eukarya
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house genetic info within a membrane bound nucleus, large organisms
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Prokaryotes
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archaea and bacteria – the overwhelming majority of organisms
Prokaryotes are non-monophyletic missing eukarya thus it is paraphyletic |
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Body Forms
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Coccus – sphere
Bacillus – rod shapped Helical – spiral/ twisted Some have flagellum - not a homologous trait between the two groups, if seen will be singular post anterior |
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Phospholipid membrane
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surrounded by cell wall
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Asexual reproduction
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binary fission, either disperse or form multicellular colonies where some cells have specialized functions
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Energy
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To gather energy – captured by light (phototrophy) or taken by chemical reactions (chemotrophy)
Captured energy must be converted into ATP using an electron source Electron donors – inorganic substances (H2S and ammonia NH4) or organic substances (lactate or CH4 methane) |
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Lithotrophs
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use inorganic electron donors
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Organotrophs
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use organic electron donors
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Carbon Source
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atmosphere CO2 or from organic compounds
Autotrophs carbon source is from inorganic carbons Heterotrophs – carbon source taken from sugar (glucose) Other growth requirements – S, P, M, N |
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Vertical Transmission
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When the cell divides, chromosome copied so each daughter cell is genetically identical to the original cell.
Passing of genes from haploid parents to daughter or ancestor to descendant |
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Plasmids
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small circular DNA, accessory genes – not essential for the normal cell function allow to be pathogen etc.
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Housekeeping genes
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the large circular chromosomes required for critical function
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Lateral gene transfer
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plasmids able to be genetically transferred among microorganisms – among distantly related forms
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transformation
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DNA fragments from cells are moved into intact cells, fragments incorporated into the genome by CROSSING OVER (recombination), portion of the hosts DNA replaced with new sequence from outside cell. If can transform = “competent”
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conjugation
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: form of mating. Can occur between distantly related cells. A Pilus (tube) forms between cells (sex tube). Plasmid in donor cell replicates and passes through the sex tube to the other cell, pilus then breaks
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Transduction
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use viral phage particles, can move genetic material over large evolutionary distances – cause death to the cell
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Problems with Lateral Gene Transfer
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causes very messy and complex evolutionary history harder to phylogentically analyze
Can analyze RNA/DNA using genetic analysis – use PCR to replicate the sequence – align and determine relationships |
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LAST UNIVERSAL COMMON ANCESTOR – LUCA
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MRCA for all life (3 domains: bacteria, eukarya, archaea)
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Characters specific (synampomorphies) to Archaea:
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Occasional plasmids
methanogens No photosynthesis via chlorophyll Polymerase 2 No operons Linear |
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Synampomorphies for bacteria
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NONE all shared with either archaea or eukarya
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Synapmorphies for eukarya
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No nitrogen fixation,
rare plasmids, membrane bound lipids, mitosis, RNA polymerase I, II,III, ribosome size 80s, no operons, nucleotides usually linear |
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LUCA synapomorphies:
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DNA with ACTG
3 letter codon lipoprotein membrane |
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How to determine if a gene is ancestral
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Compare base pair sequence for a particular gene, if related organisms then expect genes to have similar transmissions
If gene inherited from a common ancestor then expect it to be shared widely/ distributed among descendants All genes inherited from a single common ancestor should produce same tree – if transferred gene then have very different trees Low number of GC = unstable = more likely for LGT |
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2 ways unique proteins arise in a genome
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LGT
Mutation |
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Most likely to transfer by LGT
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pathogens then antibiotic synthesis then energy metabolism
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mutualistic interactions of archaea and bacteria
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Symbiotic interactions – long term associations between 2 organisms
mutualism +/+ predation/ parasitism +/- bacteria = both mutualism and predation archaeons never parasitic only +/+ extreme forms of multulasim in eukaryotes – cyanobacteria --> chloroplasts; alpha-proteobacteria --> mitochondria bacteria example – fix nitrogen for plants – legumes and rhizods – rhizobium bacteria in soil invade root tissue and attach to plant in form of nodules. Inside nodules able to fix nitrogen use nitrogenases (enzyme). Inside nodule appear RED due to leghemoglobin cyanobacteria example – algae and fungi form LICHENS thermal vent tube worms – completely depend on internal pockets of chemoautotrophic bacteria – no light reaches use H2S bacteria and archaea help in cellulose digestion – TERMITES have protozoa help digest wood |
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Microbes save the earth
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bioremediation uses chemical processes to solve human pollution problems
most are bacteria ex. Gas storage, oil refining paper production fire retarding by products – carcinogenic three kinds -natural attenuation: microbes, substrates and necessary nutrients already present together -biostimulation – naturally occurring bacteria and archae – but pop artificially enhanced -bioaugmentation – needed organisms introduced into the environment methanogenic – archaea, extreme environment, product methanotophic- metabolize, soil, marshes, reduce methane gas |
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Microbial eukaryotes
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protists (unicellular or colonial eukarya)
very speciallzed organs for photosynthesis respire have genetic info in nucleus |
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Body Forms of Microbial Eukaryotes
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amoeboid – organic shape
- move by extension of the cytoplasm outward – PSEUDOPODIA! flagellate – have tail -similar to bacteria ciliate – short cilia in a row have cytoskeleton for cell wall allow to move, adhesion to surfaces |
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Microbial Eukaryote Reproduction
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unicellular (gametes) can fuse to form diplontic bodies – or asexually
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Euglena
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move: flagellum
photosynthetic evident by color, MIXOTROPH can also be heterotrophic |
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Stentor
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ciliate
photosynthetic autotroph – green color |
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Blepharisima
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2 morphs – rod and cannibal double rod , ciliate
HETEROTROPHIC pink color |
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Paramecium
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heterotrophic
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Amoeba
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pseudopodia, heterotroph
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Chlamydomonas
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2 FLAGELLAS! Photosynthetic (green)
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Naegleria gruberi
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amoeba
move by pseudopodia, over time the amoeba will FLAGELLATE – need more mobility so able to feed – able to SHAPE SHIFT need to adapt to food environment |
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origins of eukaryotic cell
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phagocytis – result of primary and secondary endosymbiosis
primary – bacterium (alpha proteobacteria) engulfed by heterotrophic eukarya secondary – when the primary eukarya is eaten by another eukarya (with organs) can determine by number of layers in cell |
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Strobilus
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when sporophylls that bear sporangia are clustered along an axis
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Pine life cycle
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Megasporangium (nucleus) produce 4 megaspores, 3 degenerate, remaining = egg
Microsporangium – sperm – develop into pollen grain with pollen tube nucleus and 2 sperm buclei |
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Gymnosperm
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3 generations in seed while angiosperm has 2 generations (due to double fertilizaiton) but has 3n endosperm
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Aggregate fruits
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multiple independent ovaries in a single flower – blackberry
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Thallus
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body of fungus
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Hyphae
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filaments make up body of fungi
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mycelium
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Mass of hyphae
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Septa
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hyphae may be divided by cross walls – to create individual cells
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Unicellular Fungi
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yeasts, dimorphic (change between mycelium and yeast form – heat activated like in body temp)
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Ascomycota
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45,000 species
have tiny sacs monophyletic unicellular filamentous have septae fungi internal fruiting body |
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Basidiomycota
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the club fungi
terresterial filamentous no flagella multicellular long lived dikaryotic stage tends to be external fruiting body \, 4 nucei exposed jelly like |
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aquatic animals have suspension feeding
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can be filtered with sieve element, phyranx- mouth with suctions
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Intracellular Digestion
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– if small can be taken straight into cells – sponges – no GUT CAVITY
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Extracellular Digestion
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need internal cavity, where enzymes concentrate- sac like, tube etc.
sac guts called one-way or two-way |
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monoecious
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no sex- hermaphrodite – similar to homospory – have both male and female sex cells (they will tend to be the same size)
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dieocious
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have 2 sexes – male and female – female tend to be larger
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Mosaic Cleavage
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distribution of mRNA determine fate, if cell LOST early then can NOT be replaced,
SPIRAl |
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Regulative Cleavage
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cell NOT determined by distribution of mRNA but by CHEMICAL GRADIENT , if cell lost then another can compensate for it
RADIAL |
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Sponges
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No true tissue, cells together to form skeletal structure
Body made of channels – special flagellated cells- choanocytes – move H20 and capture food Large pores – exits for chambers Radial symmetry No cephalization Absent gut |
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Cnidaria – sea anemones, jellies
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Sting bearing
2 body forms -polyp -medusa sexual and asexual reproduction polyp – asexual – budding or fission - can form clone, if stay together physically then colony radial symmetry one way gut stinging due to nematocyst (hooks) polyp – anemone medusa – jellies yes – cephalization |
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Mollusca – chitons and bivalves
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Shell, mantle, foot, and radula (inside mouth)
Radula – feeding part – scrape algal with mouth to get tissue to eat Lots of habitats – free living ( squids) or sediments (clams) Sessile bivalves – suspension feeders Molluscs example of protostomes Spiral, mosaic cleavage – blastospore becomes mouth BLASTOSPORE – TWO MAJOR CLADES – -Lophotrochozoans – by presence of a trocophore larval stage -Ecdysozoa – contains animals that grow by molting cuticle Bilateral – chitons an mollusks Incomplete chiton gut Cephalization?? |
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Mollusca – gastropods and cephalopods –snails
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Bilateral body
Squid – bilateral Yes cephalization Complete 1 way gut Tentacles |
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Annelida
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Earthworms and leeches
Segmented body – can tell bu outer and inner ring Each segmented is a repeated body unit – contain both respiratory Gut NOT segmented – runs from mouth to anus Terrestrial annelids have a limited range of body types – marine worms very extremely diverse Protostomes Spiral mosaic cleavage Bilateral symmetry Blind gut No cephalization Clitellum - fat band allows for worms to reproduce |
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Arthropoda - trilobites, chelicerates, myriapoda
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Segmented body
External and internal Curtain of tissue – septum, separates segment Each segment repeated body Contains respiratory and reproductive organs Runs from mouth to anus Exoskeleton – arthropods have a hardened cuticle – forms a protective covering the body Evolutionary trend – fusion of segments into discrete body regions – tagmata (singula tagma) Protostomes – different cleavage – changes spiral cleavage Blastospore – become the mouth Cuticle must be molded Appendages – joints 3 body parts to tagamtized body – cephalon, thorax, pygdium yes – arthropods cephalized complete gut |
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Arthropoda – hexapods
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6 legs, attached at joints
hemimetabolous - small increase |
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What does the barnacle use to extract particles from the water?
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Specialized appendages called cirri (modified legs) to comb through the water and trap particles
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How do snails, limpets, and chitons stay attached to rocks in the intertidal zone?
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It pushes down on the rock surface at the edges and is lifted in the center to create suction. Muscus is also used to increase the suction-cup effect
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Are polyps the products of sexual or asexual reproduction, or both? Are new medusae the products of sexual or asexual reproduction? In what stage are gametes produced?
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The 1st polyp, from planula, is the product of sexual reproduction, but all later polyps of the same genotype are the result of asexual reproduction
All medusae are the products of asexual reproduction, but they themselves make the gametes (they reproduce sexually) |
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Is the gut in the sea anemone complete (mouth and anus) or incomplete (mouth only)?
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Incomplete
There's a mouth, but no anus The gut just ends blindly in the middle half of the body |
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In molluscs, slow-moving animals have open circulatory systems, but rapid swimmers, like the squid, have closed circulatory systems. How can a flying insect with a large demand for oxygen get away with an open circulatory system?
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Insects are not using the circulatory system to supply oxygen to all the tissues. They use a separate system, the trachea, to supply oxygen directly to each cell without involving respiratory pigments in the blood. The roles of lungs or gills (oxygen pick-up) and blood (oxygen distribution) are both taken over by the trachea
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