WorksheetsOrganic Evolution Test #1 D
Total questions: 93
Worksheet time: 52mins
What is the main idea behind grouping taxa together in phylogenetic inference?
The idea is to group taxa together based on shared evolutionary history (closely related taxa should have more similar features).
The idea is to group taxa together based on their geographic location only.
The idea is to group taxa together based on their size and color.
The idea is to group taxa together randomly without any criteria.
Fill in the blank: Only certain types of characters (features or traits) are useful in phylogenetic inference. These characters must be ________ (similarity due to descent from a common ancestor).
homologous
analogous
convergent
random
What are synapomorphies?
Synapomorphies are the only homologies that are useful in estimating phylogenies.
Synapomorphies are characteristics unique to a single species.
Synapomorphies are traits that arise independently in unrelated groups.
Synapomorphies are features shared by all living organisms.
What does the term 'derived' mean in evolutionary biology?
Different (changed) from a common ancestor due to mutation.
Unchanged from a common ancestor.
A trait that is always harmful.
A feature that is present in all living organisms.
What is a synapomorphy?
A derived character shared within a clade (monophyletic group) and present in the clade’s common ancestor ('shared & derived').
A character unique to a single species and not found in any relatives.
A trait that is ancestral and found in all descendants of a distant common ancestor.
A random mutation that does not affect evolutionary relationships.
According to the diagram, what is a synapomorphy in species 1 and 2?
Dark coloration is a synapomorphy in species 1 and 2.
Light coloration is a synapomorphy in species 1 and 2.
Both species 1 and 2 lack synapomorphies.
Species 1 and 2 share no common traits.
In this tree, dark coloration is an analogous trait in species 1 and 2 because it evolved twice in parallel, once along each branch. What is this type of trait called?
Homoplasy
Symplesiomorphy
Synapomorphy
Autapomorphy
If a derived trait (here, light coloration in species 3) has arisen recently and appears in only one of the two most closely related species, the two more distantly related species (species 1 and 2) share an ancestral trait (dark coloration). What is this shared ancestral trait called?
Homoplasy
Symplesiomorphy
Synapomorphy
Autapomorphy
Fill in the blank: A homoplasy is a trait that _________
evolved twice in parallel, once along each branch (is an analogous trait that evolved independently in different lineages)
is inherited from a common ancestor (is a homologous trait)
is always beneficial to the organism
is only found in extinct species
Symplesiomorphy refers to an ancestral character that is ancestral but is not shared by the two most closely related taxa.
True
False
According to the diagram, which trait is identified as a synapomorphy?
White tail
Masked face
Long beak
Webbed feet
According to the diagram, which trait is identified as a sympleisomorphy?
Masked face
White tail
Short wings
Orange legs
Fill in the blank: One way to avoid sympleisomorphies is to select characters that are prone to changing ______ over time (works best with phenotypic characters).
slowly
rapidly
randomly
frequently
Fill in the blank: To avoid sympleisomorphies, use a large number of characters so ______ are more common than homoplasy or sympleiosmorphies.
synapomorphies
autapomorphies
analogies
plesiomorphies
Fill in the blank: Another method to avoid sympleisomorphies is to use an ______.
outgroup
ingroup
cladogram
synapomorphy
Refer to the diagram labeled 'Rooting a Phylogeny: An Example'. Which species is at the root of the first phylogenetic tree (leftmost tree)?
Elephant
Armadillo
Whale
Which species is at the root of the second phylogenetic tree (middle tree)?
Elephant
Armadillo
Whale
Which species is at the root of the third phylogenetic tree (rightmost tree)?
Elephant
Armadillo
Whale
What is an outgroup in a phylogenetic analysis?
A taxon that diverged after the last common ancestor of all other taxa
A taxon that diverged prior to the last common ancestor of all other taxa
A taxon within the ingroup
A taxon unrelated to the phylogeny
Refer to the diagram showing a phylogenetic tree with labels 'ingroup' (A, B, C, D) and 'outgroup' (O). Which taxon is the outgroup?
O
A
B
C
When must the outgroup be chosen in phylogenetic analyses?
After the analysis
During the analysis
Before the analysis
It does not matter
Choosing an outgroup requires prior knowledge of the outgroup status.
True
False
Fill in the blank: The outgroup should be close enough to the ingroup so that the characters are comparable, but clearly ______ of the ingroup.
outside
inside
part
member
Refer to the diagram titled 'Rooting a Phylogeny: An Example'. Which animal is shown as the outgroup in the phylogenetic tree?
Elephant
Whale
Armadillo
Kangaroo
List the order of animals from the root to the most derived in the rooted phylogenetic tree.
Kangaroo, Armadillo, Whale, Elephant
Elephant, Whale, Armadillo, Kangaroo
Whale, Kangaroo, Elephant, Armadillo
Armadillo, Kangaroo, Elephant, Whale
Refer to the diagram titled 'Rooting a Phylogeny: An Example'. Which two animals are most closely related according to the rooted tree?
A) Elephant and Whale
B) Armadillo and Kangaroo
C) Elephant and Armadillo
D) Whale and Kangaroo
Refer to the diagram labeled 'O1 and O2 are outgroups.' Which of the following statements is correct?
O1 and O2 are part of the main clade of interest
O1 and O2 are outgroups used to infer ancestral traits
O1 and O2 are the most derived members of the clade
O1 and O2 do not provide any information about trait polarity
Fill in the blank: Using multiple outgroups can allow us to estimate the order of appearance of traits and may help us identify _________
symplesiomorphies
autapomorphies
homoplasies
cladistics
According to Figure 5.5, what do outgroups O1 and O2 provide information about?
The order of appearance of derived traits
The polarity of a trait
The evolutionary relationships within the main clade only
The number of species in the clade
Which tree (A, B, or C) represents the scenario where only one evolutionary event is needed to explain the observed traits?
Tree A
Tree B
Tree C
In which tree(s) do we require two evolutionary events to explain the observed traits?
Only Tree B
Only Tree C
Both Tree B and Tree C
Tree A
Fill in the blank: Red arrows in the diagrams indicate ________ changes in the trait.
evolutionary
seasonal
random
temporary
Resolving the polytomy helps us identify symplesiomorphies.
True
False
What is the first step in the gene analysis method shown in the table?
Choose gene(s) of interest
Analyze protein structure
Sequence the entire genome
Perform PCR amplification
What is the second step in the gene analysis method shown in the table?
Identify homologs
Sequence the gene
Isolate proteins
Analyze gene expression
What is the third step in the gene analysis method shown in the table?
Align sequences
Extract DNA
Amplify gene
Sequence gene
What is the fourth step in the gene analysis method shown in the table, as illustrated by the gene tree diagram?
Calculate gene tree
Extract DNA samples
Sequence alignment
Collect environmental data
What may a character correspond to? Fill in the blank: It may correspond to an entire gene, part of a gene, an intron, transposable element, entire genome, etc. (or ________ features).
morphological
chemical
behavioral
environmental
For closely related species, which type of sequences should be chosen?
Fast evolving sequences
Slowly evolving sequences
Both
Neither
Which of the following is a factor that choice depends on when choosing characters (sequence)?
Ease of acquisition
Color of the sample
Size of the laboratory
None of the above
Which type of data is better?
Depends on the question.
Quantitative data is always better.
Qualitative data is always better.
Numerical data is always better.
Categorical data is always better.
What is the evolutionary relationship between dinosaurs and birds?
Morphological data - DNA is difficult to obtain from extinct organisms.
Fossilized feathers are only found in mammals.
Birds evolved directly from modern reptiles, not dinosaurs.
There is no scientific evidence linking birds and dinosaurs.
What is the evolutionary relationships among algae?
DNA data - many algae have few morphological characters.
Fossil records - algae are well preserved in fossils.
Leaf structure - algae have complex leaves.
Root systems - algae have extensive root networks.
Fill in the blank: To generate new sequences using specific primers to amplify sequence of interest, the process used is called _______.
Sequencing
Transcription
Translation
Ligation
Fill in the blank: The process of using a sequence of interest to search through databases for similar sequences (in an automated process such as BLAST) is called _______.
Database search for previously sequenced genes
Gene cloning
PCR amplification
DNA sequencing
Fill in the blank: To classify organisms based on their physical traits, the method used is called _______.
Classify organisms based on morphological characters
Classify organisms based on genetic code
Classify organisms based on habitat
Classify organisms based on diet
What does the data matrix in Table 27.1 represent?
A) A list of species and their habitats
B) A character matrix showing character states for nine traits (A-I) in eight OTUs (1-8)
C) A table of gene sequences
D) A chart of amino acid frequencies
In the data matrix, what could the OTUs (rows) represent? Fill in the blank: OTUs could represent ________ or ________.
species, genes
colors, shapes
numbers, letters
cells, tissues
Which of the following could be examples of character traits (columns) in the data matrix?
Number of teeth
Presence of fur
Nucleotides
All of the above
What is the organism mentioned in the first sequence entry from the GenBank Database?
Homo sapiens
Norma chrysophthalma
Norma chrysophthalma isolate Gaya 06_1
Archaea
What type of genetic sequence is provided for Norma chrysophthalma isolate Gaya 06_1?
16S rRNA gene
18S small subunit ribosomal RNA gene, partial sequence
Mitochondrial DNA
Protein-coding gene
Fill in the blank: The sequence identifier for the Norma chrysophthalma isolate Gaya 06_1 entry is _________.
JQ301629.1
AB123456.1
MN908947.3
AY789012.2
Fill in the blank: The sequence identifier for the consensus sequence entry is _________.
Ar_001_consensus
Ar_002_variant
Seq_123_main
Consensus_Ar001
What does it mean when residues in one column are different states of a homologous character? (i.e., they are hypothesized to derive from a common ancestor.)
They are random mutations
They are unrelated sequences
They are hypothesized to derive from a common ancestor
They are errors in sequencing
Fill in the blank: Residues in one column are different states of a ________ character (i.e., they are hypothesized to derive from a common ancestor.)
homologous
analogous
random
unique
Based on the aligned sequences shown, which OTU has the most gaps at the beginning of the sequence?
OTU 1
OTU 2
OTU 3
OTU 4
The image above visualizes which type of data?
Categorical data
Numerical data
Textual data
Geographical data
Name one of the consensus sequences shown in the alignment visualization.
TxA consensus
GCT consensus
ATG consensus
CGA consensus
Fill in the blank: One method to calculate a gene tree is (a) .
Maximum Parsimony
Distance
Maximum Likelihood
Bayesian Inference
Fill in the blank: One method to calculate a gene tree is (a) .
Maximum Parsimony
Distance
Maximum Likelihood
Bayesian Inference
Fill in the blank: One method to calculate a gene tree is (a) .
Maximum Parsimony
Distance
Maximum Likelihood
Bayesian Inference
Fill in the blank: One method to calculate a gene tree is (a) .
Maximum Parsimony
Distance
Maximum Likelihood
Bayesian Inference
Fill in the blank: In most methods to calculate gene trees, the steps used to construct tree(s) are called the __________.
algorithm
sequence
matrix
domain
Fill in the blank: In most methods to calculate gene trees, the objective measure used to decide how good the tree is called the __________.
optimality criterion
phylogenetic signal
bootstrap value
consensus index
Fill in the blank: An ________ is the set of steps used to find a winter coat, such as constructing tree(s).
algorithm
jacket
season
pattern
Which of the following is an example of an optimality criterion when choosing a coat?
The store location
Warmest
The brand name
The salesperson's name
According to the Principle of Maximum Parsimony, what is the best phylogeny?
The one with the most evolutionary changes
The one that explains the data with the fewest evolutionary changes
The one that is the most complex
The one that is the oldest
The Principle of Maximum Parsimony is based on the premise that the _______ explanation is often the best one (Occam’s razor).
simplest
complex
elaborate
ambiguous
Based on the diagram comparing Hypothesis I and Hypothesis II, which hypothesis is more parsimonious (requires fewer evolutionary changes)?
Hypothesis I
Hypothesis II
The evolutionary relationship of taxa (species) b, c, d, e is:
They share a common ancestor and form a monophyletic group.
They are unrelated and do not share a common ancestor.
They evolved independently from different ancestors.
They are all more closely related to species a than to each other.
Which tree requires the least amount of change? 4 taxa = 3 possible unrooted trees. Select the correct tree from the diagrams shown.
Refer to the table of DNA sequences for taxa b, c, d, and e. What is the DNA sequence for taxon b?
GCAAAC TTT
GCAAGC TTT
GCAAAT TTT
GCAAAC TTA
Refer to the table of DNA sequences for taxa b, c, d, and e. Which taxon has the sequence ACAAGAAAT?
Based on the diagrams labeled 'Character 1', which taxa are grouped together with nucleotide G at the first position?
A) b and c
B) d and e
C) b and d
D) c and e
Refer to the table of DNA sequences for taxa b, c, d, and e. What is the DNA sequence for taxon d?
ACAAGAAAT
ACGAGAAAT
ACAAGGAAT
ACAAGAAAC
Refer to the table of DNA sequences for taxa b, c, d, and e. Which character position (1-9) is different in all four taxa?
Character 1
Character 2
Character 5
Character 7
Look at the phylogenetic trees labeled 'Character 2'. Which taxa are grouped together in the top tree?
b and d, c and e
a and b, d and e
a and c, b and e
a and d, b and c
Not all characters in the DNA sequence table are informative.
True
False
What are informative characters?
Informative characters are characters that allow distinction between alternate trees.
Informative characters are characters that have no impact on tree distinction.
Informative characters are characters that are always identical in all trees.
Informative characters are characters that are not used in tree analysis.
Columns represented by at least two different character states in at least two different taxa are considered informative characters.
True
False
Based on the table of taxa and characters, which character columns (1-9) are represented by at least two different character states in at least two different taxa?
Columns 3, 7, 8, and 9 are represented by at least two different character states in at least two different taxa.
Columns 1, 2, 4, and 5 are represented by at least two different character states in at least two different taxa.
Columns 2, 5, 6, and 9 are represented by at least two different character states in at least two different taxa.
Columns 1, 3, 6, and 8 are represented by at least two different character states in at least two different taxa.
Fill in the blank: __________ are the only useful characters for constructing phylogenies.
Synapomorphies
Autapomorphies
Homoplasies
Analogies
Which of the following is NOT one of the four basic steps necessary to conduct a phylogenetic study?
Choose characters
Collect data
Align sequences
Publish results
Analysis
Multiple methods exist to construct phylogenetic trees, and many of these consist of an algorithm and optimality criterion.
True
False
What principle does maximum parsimony operate under in phylogenetic tree construction?
The tree requiring the smallest number of changes is the best one.
The tree with the most branches is the best one.
The tree that matches the fossil record is the best one.
The tree with the longest branches is the best one.
Why is it important to assess the robustness of trees with the use of multiple methods and bootstraps?
To ensure the reliability and robustness of the phylogenetic trees.
To increase the number of branches in the tree.
To make the tree look more complex.
To reduce the computational time required for analysis.
Bootstrap values are a way to evaluate how consistent the data is. If there is a large amount of ______ (conflicting characters), support values will be low.
homoplasy
parsimony
synapomorphy
monophyly
Internal nodes with greater than what percentage of bootstrap support are generally considered strongly supported?
50%
70%
90%
100%
Often nodes below a certain threshold will be ______ to indicate uncertainty.
collapsed
highlighted
expanded
removed
The pattern of evolution in aphids follows that of their symbiotic bacteria, as shown in the evolutionary trees for both groups in the diagram.
Yes, the evolutionary patterns are similar.
No, the evolutionary patterns are completely different.
The evolutionary patterns are unrelated.
There is not enough information to determine.
What is a heuristic search?
An algorithm that uses a short-cut to reduce the amount of time needed to construct a tree.
An algorithm that guarantees the optimal solution every time.
A method that increases the time needed to construct a tree.
A process that ignores tree construction.
Fill in the blank: A heuristic search is an algorithm that uses a _______ to reduce the amount of time needed to construct a tree.
short-cut
loop
database
randomizer
What does the vertical axis labeled 'tree score ("best" tree)' represent in the context of heuristic search?
The vertical axis represents the score or quality of different trees, with the highest point indicating the 'best' tree according to the scoring method used.
The vertical axis represents the number of trees evaluated during the search process.
The vertical axis represents the time taken to find the best tree.
The vertical axis represents the number of branches in each tree.
