Reproduction

Megafaunal Extinction

There were a relatively large number of extinctions of mammalian species roughly 10,000 years ago. To help understand why these extinctions happened scientists are interested in understanding if there were differences in the size of the species that went extinct and those that did not. You are going to reproduce the three main figures from one of the major papers on this topic Lyons et al. 2004.

You will do this using a large dataset of mammalian body sizes that has data on the mass of recently extinct mammals as well as extant mammals (i.e., those that are still alive today). Take a look at the metadata to understand the structure of the data.

1. Import the data into R. As with most real world data there are a number of issues with this dataset. Try to spot and clean them up during the import process, but understand that it is common to not discover some data issues until you start analyzing the data. Data cleaning is often an iterative process. Print out the structure of the resulting data frame.
2. Create a plot showing histograms of masses for extant mammals and those that went extinct during the pleistocene (extant and extinct in the status column). There should be one sub-plot for each continent and that sub-plot should show the histograms for both groups. Don’t include islands (Insular and Oceanic in the `continent column) and only include continents with species that went extinct in the pleistocene. Scale the x-axis logarithmically and stack the sub-plots vertically like in the original paper (but don’t worry about the order of the subplots being the same). Use good axis labels.
3. The 2nd figure in the original paper looks in more detail at two orders, Xenarthra and Carnivora, which showed extinctions in North and South America. Create a figure similar to the one in Part 2, but that shows 4 sub-plots, one for each order on each of the two continents.
4. The 3rd figure in the original paper explores Australia as a case study. Australia is interesting because there is good data on both Pleistocene extinctions (extinct in the status column) and more modern extinctions occuring over the last 300 years (historical in the status column). Make a plot similar to the previous plots that compares these three different categories extinct, extant, and historical). Has the size pattern in exinctions changed for more modern extinctions?

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