1. The relationship between nucleotide differences and time determined for each data point was found by comparing the amino acid sequences of proteins in pairs of species that were known to share a common ancestor and diverge at some point in the past. Researchers sequences a few proteins from different species which resulted in the ability to plot the corresponding DNA sequence differences against the estimated time of divergence.
2. The approximate slope of the best-fit line for non-primate mammals in the figure is about 0.61. This slope represents that about every 0.61 million years one nucleotide difference emerges between the non-primates. The approximate slope of the best-fit line for primate mammals in the figure is about 1.3. By comparing these two slopes it can be seen that it has taken primates have diverged more slowly than other mammal groups.
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The maximum parsimony method does not always lead to the correct phylogeny. Even though this method constructs a tree using the fewest evolutionary changes, it does not confirm that this is how it actually took place. One scenario that lead to more complex phylogenies than predicted by parsimony is homoplasy. Homoplasy results from convergent evolution, parallel evolution, and evolutionary reversal. This causes problems with estimating phylogenies because the similarities between two species are not caused by a common ancestor. A second scenario that leads to more complex phylogenies is rapid diversification. This is where a lineage rapidly diversifies into new lineages that have evolved different adaptations. The third scenario that make redicting phylogenies difficult is introgression of genes between different species. Introgression has been cause by hybridization and gene transfer which has caused extensive genetic mixing causing many parts of the genome to have conflicting gene