Size effect in historical biogeography analysis
This protocol is extracted from research article:
Multiple macroevolutionary routes to becoming a biodiversity hotspot
Sci Adv, Feb 6, 2019; DOI: 10.1126/sciadv.aau8067

We assessed whether the differences in size between hotspot and non-hotspot regions within realms could explain the differences in macroevolutionary patterns that we observed. We first fitted a cluster point process model to the point pattern of the hotspots in each realm using the R package spatstat (60). We used these models to simulate 50 sets of “control” hotspots with similar size and spatial structure to the real datasets (fig. S9). Last, we repeated the biogeographic inference and the BSMs as detailed above for each of the 50 control hotspots in each realm. We then compared whether the rate estimates obtained with the real datasets were significantly different from the distribution of rate estimates obtained with the simulated hotspots. We found differences between the real and the simulated datasets that suggested that size alone could not explain our results: (i) rates of in situ cladogenesis in the Palearctic and Nearctic hotspots were higher in the real than in the simulated datasets (fig. S4A); (ii) rates of in situ cladogenesis in the non-hotspot regions in the Australasia, Indo-Malay, and Neotropics were smaller in the real than in the simulated datasets (fig. S4B); and (iii) rates of dispersal from the hotspots into non-hotspot regions were consistently higher in the real than in the simulated datasets across all realms (fig. S5A).

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