I highly recommend that you read Chapter 2 before attempting to answer these questions. In general, you do not need to focus on the details of the Materials and Methods regarding phylogenetic analyses and dating estimates to understand the main points of these papers. You do not need to view the Supplementary Materials noted in the Monkey paper. Gecko Footprints Paper:
1. In Figure 1, what does the author mean by a plesiomorphic condition, and how does this relate to the toepad morphology seen in burrowing geckos like Palmatogecko? Hint: it is not just climbing.
2. Answer the question in the last sentence of the introduction.
3. Explain why the transition from ancestral climbing lineages to rupicolous and terrestrial lineages makes sense with the climatic and habitat changes that occurred in Southern Africa during the Miocene and Pleistocene.
4. Why is it adaptive to have reduced toe pads and spinose digital scales in a sandy environment?
New World Monkey Paper:
1. Using your Evolution book to help (see pgs. 465–66), can you explain why orthologous sequences are necessary to construct a phylogeny of these monkeys (or any other group for that matter)? Why wouldn’t paralogous sequences be useful for this?
2. How does your answer to Question #1 relate to the inconsistent relationships of the six different genes that are explained in the first paragraph of the discussion?
3. Can you explain what the authors mean when they say there is 100% support (in Maximum Parsimony, Likelihood, and Bayesian analyses) for the families Atelidae, Cebidae and Pitheciidae?
4. Based on Figures 4 & 5, how far back in time must one go to find the common ancestor of all New World monkeys? Knowing that South America split away from Africa during continental drift approximately 95–100 million years ago, is it possible the ancestor to New World monkeys was present in South America during the split, or more likely that the ancestor somehow crossed the ocean from Africa to South America after this split?