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Flashcards in Chapter 5 Deck (34):

The disadvantage of using distance methods to construct trees include the fact that

Distance methods lack any sort of underlying evolutionary model;
The assumption is made that similarity is a reflection of homology


Phylogenetic trees are used to

-construct hypotheses about common ancestors
-construct hypotheses about how various species are related to each other
-test hypotheses about the relationships between various species


The older the clade, the

more likely its members will show sequence divergence


The basic conceptual approach to phylogenetic tree building involves

-the process of collecting information about character states
-the process of selecting taxa for inclusion in the tree
-the logic that species with many character states in common are more closely related than those without


The basic conceptual approach to p-tree building assumes (part two):

That species with many character states are more closely related than those without;
That common characters are homologies


Phylogenetic methods developed by evolutionary biologists to find the best tree possible for the taxa being studied include:

Parsimony methods; Distance methods; Maximum Likelihood methods; Bayesian Inference methods


The fundamental idea behind parsimony is

That the best phylogeny is the one that both explains the observed character data and posits the fewest evolutionary changes


Parsimony analysis offers the advantage of

conceptual simplicity


Parsimony has the disadvantage of

Being an inconsistent estimator; Long-branch attraction


Long branch attraction is

The inferring of too close a relationship between a rapidly evolving species or populations


The Fitch algorithm is

Determines how many evolutionary changes are required for a given tree and character; Does not find the best tree


Which of the following statements regarding rooted trees is/ are true?

-Any two rooted trees corresponding to the same unrooted tree will require the same number of character changes;
-The most common approach to rooting a tree is to use an outgroup


Which of the following statements regarding rooted trees is/are true?

-We can form a rooted tree from an unrooted tree simply by picking a branch around to which to root the tree.
-Knowing the root of a tree, along with info about species ranges, can tell us about the PHYLOGEOGRAPHY of a group of species


Arrange the steps of constructing a phylogenetic tree using the distance method in the correct order

1. The distance between species is measured using a character state changes
2. A distance matrix is created
3. Trees are constructed by arranging segments or branches derived from pair-wise distance comparisons
4. Phylogenetic inference software is used to choose the best tree


How many different unrooted tree arrangements are possible for a phylogenetic tree relating 4 species?



The advantage of using distance methods to construct trees include the fact that

Distance methods are conceptually STRAIGHFORWARD; & computationally among the FASTEST techniques


How many unrooted trees are possible for 5 species?



Arrange bootstrap resampling in correct order

1. A tree is constructed for the estimated phylogeny, based on the original character mix
2. Resampling is done from original character mix to create a collection of bootstrap replicate data sets
3. The same tree-building methods used on the original character set are used to create a collection of bootstrap replicate phylogenies
4. To assess the support for any feature of the original tree, the percentage of replicate trees that also display that feature are calculated


Bootstrap resampling

-can be used with any technique for phylogenetic inference
- does not yield statistical significance levels


Once we have used character data to infer a tree, how can we be certain this tree is correct?

We can test statistical confidence certain features of the tree are correct


Computer programs for reconstructing large phylogenies

only check a very small fraction of possible trees


Which of the following statements concerning trees is true?

-Each unrooted tree corresponds to numerous rooted trees
-An unrooted tree with k species has 2k-3 branches
-An unrooted tree with k species has 2k-3 times as many rooted trees as unrooted trees


How many UNrooted trees are possible for 22-species tree

more than there are stars in the universe


How many Unrooted trees for a 6-species and 7-species tree, respectively?

105 and 945


For extinct taxa

the fossil record is the primary source of data for constructing phylogenetic trees


Odds ratio testing

-Can be used only with model-based frameworks of max-likelihood or Bayesian inference;
-Can determine how strongly our character data support a given feature of a phylogenetic tree


The role of organisms in impacting the external environment

-Is the process of niche construction
-Is evident when investigating fire ecology
-Can feed-back into evolutionary processes


The method of independent contrasts

allows evolutionary biologists to use comparative methods for studying adaptations


If two sister species on the p-tree differ from the other two in a single character state (say dark or light fur), how many character state changes (evolutionary events) are needed to explain this pattern?



In the figure of "The Libyan HIV Sequences", the HIV that infected more than 400 children in Benghazi hospital

-is closely related to strains from Cameroon and Ghana
-Suggests a single introduction was responsible for the outbreak


The maximum likelihood tree constructed for the mammals in the figures above supports which of the following competing hypotheses for the evolutionary relationships among mammalian groups?

The Theria hypothesis


Based on the figure about "Two Competing hypotheses for the evolutionary relationships among mammalian groups" which of the following statements about competing hypotheses is true?

The placentals and marsupials are sister groups under the Theria hypothesis, and the monotremes and marsupials are sister groups under the Marsupionta hypothesis


To determine how strongly the character data support clade A (the grouping of species A1, A2, A3) on the tree above, we can

-Use an odds ratio test, comparing the best possible tree overall with the best possible tree in which clade A is not monophyletic;
-Use a bootstrap analysis


What does the "90" on the figure indicate?

The monophyletic clade of species A1, A2, and A3 appears as a monophyletic clade in 90% of all bootstrap replicates