Exam 5: Inferring Phylogeny

The maximum likelihood tree (the tree with the clades numbered) constructed for the mammals in the figures shown supports which of the following hypotheses for the evolutionary relationships among mammalian groups?

Long-branch attraction is

The phylogenetic tree shown was constructed using a nucleotide distance matrix of Ebola isolates from Guinea in March 2014 ("G"), Sierra Leone ("S"), and Mali ("M") in October/November 2014. Describe what the phylogeny revealed regarding the three Ebola outbreaks.

Evolutionary biologists have developed a number of different phylogenetic methods to find a tree that best corresponds to a number of character states for a given group of taxa. Describe the fundamental idea behind parsimony, and explain the strengths and weaknesses of this method.

Which of the following statements regarding rooted trees is FALSE?

From the DNA sequence data for the eight species (A through H) shown below, what is the genetic distance between Species B and Species G?

Why do some evolutionary biologists have philosophical concerns about using distance methods to construct evolutionary trees?

Why is phylogenetic inference a difficult and computationally intensive problem? What solution(s) do evolutionary biologists use to address this problem?

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

If two nonsister species (any pair of species other than Species 2 and 3) on the phylogenetic tree in the figure below differ from the other two in a single character state (e.g., the nonsister species have light fur, whereas the sister species have dark fur), where would the likely evolutionary change(s) be? Indicate change(s) by drawing an X-or Xs-on the tree. Be sure to label each X as a loss or gain. In this case, assume that the ancestral state was "dark fur."

The method of independent contrasts

In the spring of 1999, six medics were accused of purposely infecting over 400 Libyan children with HIV in a Benghazi hospital. Explain how a team of researchers were able to construct and use the phylogeny in the figure below to convince the Libyan Court to lift its death sentence for the "Benghazi six."

What is the fundamental idea behind parsimony?

Which of the following is a DISADVANTAGE of parsimony analysis?

The figure shown is a phylogeny created with DNA sequence data and has high bootstrap support values. The tree also includes observed phenotypes (in varying shades of gray) for the five taxa. The character states are indicated by "B" or "b," "G" or "g," and "P" or "p." Evaluate the hypothetical phylogenetic tree using a parsimony approach. What is the minimum total number of state changes necessary to describe the observed distribution of characters in the taxa?

The older a clade is, the

Does the Fitch algorithm indicate the most likely character states for the ancestral node? Explain your answer.

The figure shown is a phylogeny created with DNA sequence data, but it is NOT well-supported with bootstrap analysis; in other words, all clades of the tree have very low (<50%) bootstrap values. The tree also includes observed phenotypes (in varying shades of gray) for the five taxa. The character states are indicated by "B" or "b," "G" or "g," and "P" or "p." Evaluate the hypothetical phylogenetic tree using a parsimony approach. If a more parsimonious tree were to be drawn based only on phenotypes (excluding the DNA data), which of the following would be grouped as sister taxa on the new tree?

Most computer programs for reconstructing large phylogenies

Which of the following is an advantage of parsimony analysis?