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Lecture 4

BIOLOGY 207 Lecture 4: bio 207 lecture 4
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Department
Biology
Course Code
BIOLOGY 207
Professor
Manos

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Bio 207 Lecture 4
1-20-17
- When building a phylogenetic matrix or tree, “anchor” it with an outgroup, in slide 28,
the example is a lamprey which is very different BUT is similar in some sense with some
of the organisms
o Would not use a sponge, for example, or a cyanobacteria; but a lamprey is
somewhat similar to a shark, which is an organism included in this example
Discussion questions
- Adding a frog to the matrixshares all the traits with a salamander, but does not have a
tail
o To place it in the tree, would it be related to humans and gorillas with a common
ancestor who lost its tail?
o OR, would it be related to the salamander and have branched off from the
salamander with tail loss occurring
- The second scenario is much more likely, as to have the frog share a common ancestor
with gorillas and humans would mean the frog would then have to retain the tail loss and
then have lost all mammalian traits to become a frogclearly a forced explanation
(Slide 31)
- “bootstrapping” values: essentially random sampling from the data and creating matricies
and trees, and the values represented next to the branches demonstrate the percent of the
time that clade was present in the same runs
o Essentially a “confidence” value
(Slide 32)
- Ribosomal DNA is highly conserved in the stem region; all across organisms the
secondary structure of folding is extremely similar
Archaeans
- Archae are the most recent orgnasms to be discovered; this is because they are extremists;
living in deep sea vents hot springs
- Anaerobic, lives on CO2 and H2
- Are these ancestral habitats? (most likely not, more like these survived while the rest
became aerobic)
Symbiosis
- Primary endosymbiosis is a eukaryotic with bacteria but they get together in all sorts of
capacities like with legumes
o Leguminous plants have nitrogen fixing bacteria in their roots that create these
nodes, providing a source of nitrogen for the plant
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Description
Bio 207 Lecture 4 1-20-17 - When building a phylogenetic matrix or tree, “anchor” it with an outgroup, in slide 28, the example is a lamprey which is very different BUT is similar in some sense with some of the organisms o Would not use a sponge, for example, or a cyanobacteria; but a lamprey is somewhat similar to a shark, which is an organism included in this example Discussion questions— - Adding a frog to the matrix—shares all the traits with a salamander, but does not have a tail o To place it in the tree, would it be related to humans and gorillas with a common ancestor who lost its tail? o OR, would it be related to the salamander and have branched off from the salamander with tail loss occurring - The second scenario is much more likely, as to have the frog share a common ancestor with gorillas and humans would mean the frog would then have to retain the tail loss and then have lost all mammalian traits to become a frog—clearly a forced explanation (Slide 31) - “bootstrapping” values: essentially random sampling from the data and creating matricies and trees, and
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