BIS 2C Lab Practical
1. Lab 1: Tree Thinking: ur a tree u 8==D
2. Basic anatomy of a phylogeny and data matrix: nodes: Node: the most
recent common ancestor of specified descendant organisms and/or species
3. Basic anatomy of a phylogeny and data matrix: roots: Root: root node =
most recent common ancestry (MRCA)
4. Basic anatomy of a phylogeny and data matrix: taxa: Taxa: any organism,
or species, or group of species that we designate or name
5. Basic anatomy of a phylogeny and data matrix: sister taxa: Sister group:
two clades or species that are each other's closest relatives (the two
descendant taxa of a single node)
6. Basic anatomy of a phylogeny and data matrix: characters: Character: an
observable feature/trait of an organism, either acquired or inherited
7. Basic anatomy of a phylogeny and data matrix: character states: Character
state: versions of a characters- ex. Character = horns, character states =
straight, curly, ...
8. Basic anatomy of a phylogeny and data matrix: polytomies: Polytomy: a
section of a phylogeny in which the relationships cannot be fully resolved to
dichotomies, thus presenting an unlikely picture of many apparently
simultaneous temporally based branches.
9. Monophyly vs. paraphyly: Monophyly: monophyletic group = a group of
organisms consisting of their most recent common ancestor (MRCA) and all its
descendants
We try to make sure that when we name groups of species there are
monophyletic...why?
1. Non-monophyletic groups are artificial groups
2. Non-monophyletic groups cannot be delimited by features that arose in a
unique common ancestor
Paraphyly: paraphyletic group = a group of organisms consisting of their MRCA
but excluding some of its descendants
10. Homology vs. homoplasy: Homology: traits that are inherited from a
common ancestor
Homoplasy: traits that are a result of convergent evolution
11. What is a phylogeny?: a hypothesis of relationships among a set of taxa
, BIS 2C Lab Practical
12. How can relationships be tested in a phylogeny?: phylogenetic
relationships= inferred from the similarities that are observed among species or
populations (terminal taxa)
1. Apply codes to character states
2. Record character states for each terminal taxa with data matrix
3. Evaluate similarity between taxa and create a tree
4. Apply principle of parsimony for least amount of character changes
13. How to construct a simple data matrix?: 1. Choose the taxa. You decide to
study the major clades of vertebrates shown in the leftmost column of the table.
2. Determine the characters. After studying the vertebrates, you select a set of
traits, which seem to be homologies, and build a data table to record your
observations.
14. How to generate trees?: Build your tree following these rules:
1. All taxa go on the endpoints of the tree, never at nodes.
2. All nodes must have a list of synapomorphies, which are common to all taxa
above the node (unless the character is later modified).
3. All synapomorphies appear on the tree only once unless the character state
was derived separately by evolutionary parallelism.
15. How to decide among trees using parsimony?: Basic procedure for finding
the most parsimonious trees:
1. Ignore parsimony-uninformative characters (for the moment).
2. Consider possible trees.
3. For each informative character count the minimum number of steps required on
each tree.
, BIS 2C Lab Practical
4. Sum over all characters to get the "score" (number of steps) for each tree. Add
the count for the parsimony-uninformative characters (which is the same for all
trees).
5. The most parsimonious tree(s) is/are the one(s) with lowest score.
16. How to read, interpret, and root unrooted trees?: Unrooted tree: a tree in
which the root has been removed and relationships among taxa are more
ambiguous ; remove root & straighten branch; shows branch splitting events
but says nothing about the temporal sequence of these events ; no direction
17. How to evaluate character conflict and congruence on a phylogeny?:
Congruence - synapomorphy coupled with weight of evidence from other
character data.
--true synamorphies
Conflict - similarities which are not true synapomorphies may be due homoplasy
(convergence, parallel evolution, or reversal) or symplesiomorphy (shared,
ancestral similarity).
18. What are the causes of homoplasy? Provide examples from lab.:
Homoplasy = traits inherited from convergent evolution
19. What is the difference between cladograms, phylograms, and
chronograms?: Cladogram - only relative branching order shown, no
meaning to branch lengths
Phylogram - branch length proportional to amount of character change; units of
character divergence
Chronogram - branch length proportional to time; units of time
20. Lab 2: Bacteria/Archaea: u bac to bac arc-a-licious
21. What is the difference between rooted and unrooted trees?: Unrooted tree
with root removed and relationships among taxa are ambiguous; remove the
root and straighten the branch; does not show temporal sequence or direction
22. How does rooting a tree affect our interpretations?: Unrooted trees do not
imply a known ancestral root- shows relationships among taxa due to
character traits
, BIS 2C Lab Practical
23. Distinguish among the three domains of life; what is LUCA? What are the
major characteristics of each of the domains?: LUCA: last universal common
ancestor
Archaea:
Unicellular-Consists of only one cell. Prokaryotic-Cells which contain no nulcleus
and lack internal complexity. (Hint: this domain is closest to bacteria)
Bacteria:
Unicellular-Consists of only one cell. Prokaryotic-Cells which have no nucleus and
lack internal complexity.
Eukarya:
Unicellular and Multicellular-May consist of one or more cells. Eukaryotic-Cells
which contain a nucleus and internal complexity.
24. What is LGT and why is it problematic for phylogeny reconstruction?:
LGT = lateral gene transfer
LGT: the transmission of genes between individual cells.
These mechanisms not only generate new gene assortments, they also help move
genes throughout populations and from species to species.
There is no obvious line of descent and it interferes with the task of identifying
earlier ancestors based on existing traits.
25. What are symbioses? Use examples from lab.: interaction between two
different organisms living in close physical association, typically to the
advantage of both--mutualism!
26. What does it mean to be a ruminant?: Chordates have a couple of diff
chambers in their guts with symbionts to help them process and break down
their food
27. Recognize these examples from lab: Rhizobium: Rhizobia and legume
symbiosis - bacteria take N2 from the atmosphere and convert it into
Nitrate/Nitrite, which the plant can take up into its proteins sugar from plant
1. Lab 1: Tree Thinking: ur a tree u 8==D
2. Basic anatomy of a phylogeny and data matrix: nodes: Node: the most
recent common ancestor of specified descendant organisms and/or species
3. Basic anatomy of a phylogeny and data matrix: roots: Root: root node =
most recent common ancestry (MRCA)
4. Basic anatomy of a phylogeny and data matrix: taxa: Taxa: any organism,
or species, or group of species that we designate or name
5. Basic anatomy of a phylogeny and data matrix: sister taxa: Sister group:
two clades or species that are each other's closest relatives (the two
descendant taxa of a single node)
6. Basic anatomy of a phylogeny and data matrix: characters: Character: an
observable feature/trait of an organism, either acquired or inherited
7. Basic anatomy of a phylogeny and data matrix: character states: Character
state: versions of a characters- ex. Character = horns, character states =
straight, curly, ...
8. Basic anatomy of a phylogeny and data matrix: polytomies: Polytomy: a
section of a phylogeny in which the relationships cannot be fully resolved to
dichotomies, thus presenting an unlikely picture of many apparently
simultaneous temporally based branches.
9. Monophyly vs. paraphyly: Monophyly: monophyletic group = a group of
organisms consisting of their most recent common ancestor (MRCA) and all its
descendants
We try to make sure that when we name groups of species there are
monophyletic...why?
1. Non-monophyletic groups are artificial groups
2. Non-monophyletic groups cannot be delimited by features that arose in a
unique common ancestor
Paraphyly: paraphyletic group = a group of organisms consisting of their MRCA
but excluding some of its descendants
10. Homology vs. homoplasy: Homology: traits that are inherited from a
common ancestor
Homoplasy: traits that are a result of convergent evolution
11. What is a phylogeny?: a hypothesis of relationships among a set of taxa
, BIS 2C Lab Practical
12. How can relationships be tested in a phylogeny?: phylogenetic
relationships= inferred from the similarities that are observed among species or
populations (terminal taxa)
1. Apply codes to character states
2. Record character states for each terminal taxa with data matrix
3. Evaluate similarity between taxa and create a tree
4. Apply principle of parsimony for least amount of character changes
13. How to construct a simple data matrix?: 1. Choose the taxa. You decide to
study the major clades of vertebrates shown in the leftmost column of the table.
2. Determine the characters. After studying the vertebrates, you select a set of
traits, which seem to be homologies, and build a data table to record your
observations.
14. How to generate trees?: Build your tree following these rules:
1. All taxa go on the endpoints of the tree, never at nodes.
2. All nodes must have a list of synapomorphies, which are common to all taxa
above the node (unless the character is later modified).
3. All synapomorphies appear on the tree only once unless the character state
was derived separately by evolutionary parallelism.
15. How to decide among trees using parsimony?: Basic procedure for finding
the most parsimonious trees:
1. Ignore parsimony-uninformative characters (for the moment).
2. Consider possible trees.
3. For each informative character count the minimum number of steps required on
each tree.
, BIS 2C Lab Practical
4. Sum over all characters to get the "score" (number of steps) for each tree. Add
the count for the parsimony-uninformative characters (which is the same for all
trees).
5. The most parsimonious tree(s) is/are the one(s) with lowest score.
16. How to read, interpret, and root unrooted trees?: Unrooted tree: a tree in
which the root has been removed and relationships among taxa are more
ambiguous ; remove root & straighten branch; shows branch splitting events
but says nothing about the temporal sequence of these events ; no direction
17. How to evaluate character conflict and congruence on a phylogeny?:
Congruence - synapomorphy coupled with weight of evidence from other
character data.
--true synamorphies
Conflict - similarities which are not true synapomorphies may be due homoplasy
(convergence, parallel evolution, or reversal) or symplesiomorphy (shared,
ancestral similarity).
18. What are the causes of homoplasy? Provide examples from lab.:
Homoplasy = traits inherited from convergent evolution
19. What is the difference between cladograms, phylograms, and
chronograms?: Cladogram - only relative branching order shown, no
meaning to branch lengths
Phylogram - branch length proportional to amount of character change; units of
character divergence
Chronogram - branch length proportional to time; units of time
20. Lab 2: Bacteria/Archaea: u bac to bac arc-a-licious
21. What is the difference between rooted and unrooted trees?: Unrooted tree
with root removed and relationships among taxa are ambiguous; remove the
root and straighten the branch; does not show temporal sequence or direction
22. How does rooting a tree affect our interpretations?: Unrooted trees do not
imply a known ancestral root- shows relationships among taxa due to
character traits
, BIS 2C Lab Practical
23. Distinguish among the three domains of life; what is LUCA? What are the
major characteristics of each of the domains?: LUCA: last universal common
ancestor
Archaea:
Unicellular-Consists of only one cell. Prokaryotic-Cells which contain no nulcleus
and lack internal complexity. (Hint: this domain is closest to bacteria)
Bacteria:
Unicellular-Consists of only one cell. Prokaryotic-Cells which have no nucleus and
lack internal complexity.
Eukarya:
Unicellular and Multicellular-May consist of one or more cells. Eukaryotic-Cells
which contain a nucleus and internal complexity.
24. What is LGT and why is it problematic for phylogeny reconstruction?:
LGT = lateral gene transfer
LGT: the transmission of genes between individual cells.
These mechanisms not only generate new gene assortments, they also help move
genes throughout populations and from species to species.
There is no obvious line of descent and it interferes with the task of identifying
earlier ancestors based on existing traits.
25. What are symbioses? Use examples from lab.: interaction between two
different organisms living in close physical association, typically to the
advantage of both--mutualism!
26. What does it mean to be a ruminant?: Chordates have a couple of diff
chambers in their guts with symbionts to help them process and break down
their food
27. Recognize these examples from lab: Rhizobium: Rhizobia and legume
symbiosis - bacteria take N2 from the atmosphere and convert it into
Nitrate/Nitrite, which the plant can take up into its proteins sugar from plant
