22. Evolutionary Genetics

Phylogenetic Trees

Open Question
When the human genome is examined, the chromosomes appear to have undergone only minimal rearrangement in the 100 million years since the last common ancestor of eutherian mammals. However, when individual humans are examined or when the human genome is compared with that of chimpanzees, a large number of small indels and SNPs can be detected. How are these observations reconciled?
Open Question
The mtDNA sequence of Neandertals is more similar to that of modern humans than to that of Denisovans. However, analyses of nuclear DNA clearly indicate that Neandertals and Denisovans share a more recent common ancestor than either of these hominins shares with modern humans. Propose a hypothesis to resolve the discrepancy between the mtDNA and the nuclear genome.
Open Question
If you were to compare your genome sequence with that of your parents, how would it differ? If you were to compare your genome sequence with another student's in the class, how would it differ? What additional difference might you see if your genome was compared with that of a sub-Saharan African, or if you are of sub-Saharan African descent, with that of a non-African?
Open Question
Using the following amino acid sequences obtained from different species of apes, construct a phylogenetic tree of the apes. <>
Open Question
Examine Figure 1.17 and answer the following questions.

What characteristics are shared by the mammalian clade and the primate clade? What characteristic distinguishes the primates from other members of the mammalian clade?
Open Question
Examine Figure 1.17 and answer the following questions.

What characteristic is shared by all clades in the figure?
Open Question
Examine Figure 1.17 and answer the following questions.

How many clades are shown in the figure?
Open Question
Considering the phylogenetic assignment of Plasmodium falciparum, the malarial parasite, to the phylum Apicomplexa (see Figure 17.17), what might you speculate as to whether the parasite is susceptible to aminoglycoside antibiotics?
Open Question
What is meant by the term homology? How is that different from the meaning of homoplasmy?
Open Question
If one is constructing a phylogeny of reptiles using DNA sequence data, which taxon (birds, mammals, amphibians, or fish) might be suitable to use as an outgroup?
Open Question
Recent reconstructions of evolutionary history are often dependent on assigning divergence in terms of changes in amino acid or nucleotide sequences. For example, a comparison of cytochrome c shows 10 amino acid differences between humans and dogs, 24 differences between humans and moths, and 38 differences between humans and yeast. Such data provide no information as to the absolute times of divergence for humans, dogs, moths, and yeast. How might one calibrate the molecular clock to an absolute time clock? What problems might one encounter in such a calibration?