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34 Cards in this Set
- Front
- Back
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Archaeal Origin of Eukarya |
-From within TACK sister of lokiarchaeota |
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Methanogenesis & Archaea |
MOST in Euryarchaeota BUT also a group in TACK (Bathyarchaeota) -methanogenesis NOT in an island LGT unlikely BUT if it did happen then that is evidence that methanogenesis may have been in an island once |
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Highest Temp Tolerance (Archaea) |
Methanopyrus kandleri 84-122*C |
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Euryarchaeota & Methanogenesis |
- complex process found in numerous groups, remnants found in others - may be ancestral - good niche to fill -> few capable |
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Euryarchaeota Groups (5) |
1. Methanogens
2. ANME-1 : oxidation of methane with sulfate (mutualism with sulfur reducing bacteria - coupling of metabolism in consortium makes process thermodynamically possible) 3. Haloarchaea/Halobacteriales: salt lover, only aerobic euryarchaeota 4. Thermoplasma: thermophile, acidophile, environmental LGT 5. Altiarchaeles: commensal with sulfide oxidizing bacteria |
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Altiarchaeales |
-archaea commensal with sulfur oxidizing bacteria -hooked appendages -> attach to partner/surfaces => found on space probes, in nature |
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Haloarchaea Metabolism |
- only Euryarechaea that AEROBIC -> use of 02 as TEA required complete restructuring of ETC -> genes to do so linker to bacteria (LGT) -fermentor with sensory rhodopsin used to move toward sunlight (LGT -> also in bacteria, fungi, etc) |
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Haloquadratum walsbyi |
Euryarchaeaota->Haloarchaea (AEROBIC) -SQUARE, large cells, lots of vacuoles, 2 day doubling time -SYNTHROPIC: symbiosis with food sharing -> live in associaton with Salibobacter -> much larger when grown together |
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Gas Vesicle (Haloquadratum) |
Euryachaeota -> Haloarchaeota - used to regulate buoyancy -2 genes always in a genomic island - can be transferred between archaea/bacteria -> LGT likely origin of vaculoe |
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Environmentally Influence LGT |
-seen in Thermoplasma/Sulfolobus (Euryarchaeota/TACK) - shared genes between 2 spp in the same environment, based on said environment |
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First Canadian Genome |
Sulfolobus |
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Cannulae |
hollow tubes connecting colonies of Pyrodictium abyssii, used to exchange nutrient, possibly DNA |
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Sulfolobus DNA repair |
S = TACK/Crenarchaeota damage induces pili formation, used to exchange dna |
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Crenchaeota Shared Chars (3-for spp given) |
spp = Sulfolobus, Pyrodictium abyssii - sulfur oxidizers - thermophiles - capabe of forming connection (pilli/cannulae) with neightbors |
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Eukaryotic Traits of Lokiarchaeota (2) |
1. actin-like filaments 2. membrane trafficking |
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General DPANN Chars |
- small genome MOST parasitic/symbotic, but free living present as well |
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Nanoarchaeota Host |
Ignicoccus hospilatus - discovered via microscopy as small structure attached to host cell -> novel primers made dna amplification impossible -co-evolution -> hospilatus has evolved structures to connect with nano |
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Ichthyspora Stages |
1. Traphic: multinucleate with numerous vacuoles 2. Reproductive: spore, flagellated, lobose amoeboid |
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lobose vs filose |
Lobose: fat, wide extensions Filose: thin extensions |
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Steps to constructing Gene Phylogenies (4) |
1. Choose gene 2. Identify homologs 3. Align sequence 4. Calculate gene tree |
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OTU |
Operational taxonomic unit - terminal nose on phylogenic tree |
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BLAST |
compares your sequence to those in database to find homologs |
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Sequence Alignment |
-algorithm applied based on cost of gap vs benefit of match B>C then include gap ALIGNMENT = HYPOTHESIS FOR POTENTIAL HOMOLOG |
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Masking |
- comparison of multiple sequence alignment shows which remain the same (unambiguous) and which change (ambiguous) -mask = analysis to determine ambiguous vs unambiguous, ambiguous scored as 0 and should be removed |
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Substitution Matrix |
grid showing cost associated with mutating from one to another Nucleotide: costs symmetrical Amino Acids: not symmetrical, calculated via differences AND probability of effecting the protein |
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Distance Matrix vs Oarsimony |
Distance: table of evolutionary distance between OTUs, represents dissimilarity Parsimony = score of events needed to get target sequence both = exploring tree space |
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Neighbor Joining Vs Subtree Pruning/Regraphting |
NJ: moving close together neighbors, determine prob score, works for small changes SP/R: moving entire branch/subbranches around tree, probability score, allows for far away optima |
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Long Branch Attraction |
more evolutionary change = higher probability of homoplasy = grouping together when not closely realted |
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Homoplasy |
creation of identical character states by separate evolutionary events |
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Phylogenetic Congruence |
- matching trees tip to tip to see if relationships remain the same |
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Arbituary root |
Rooting a tree by including a species known to have diverged before the common ancestor of everyone else Arbituary bc it requires prior knowledge of the common ancestor |
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Concantenated Alignment |
- lining up multiple genes to use together - if same relationship will increase power of tree BUT difference genes tend to have different evolutionary histories leads to an "average" evolutionary history that would not be seen in any of the genes |
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Xenolog |
divergence of homologs after LGT |
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Positional homology |
specific amino acid/nucleotide position in different proteins/genes from a common ancestor |
