Assessing Hotspots of Evolutionary History with Data from Multiple Phylogenies: An Analysis of Endemic Clades from New Caledonia

Abstract

The great bulk of the present knowledge of the Tree of Life comes from many phylogenies, each with relatively few tips, but with lots of diversity concerning taxa and characters sampled and methods of analysis used. For several biodiversity hotspots this is the kind of data available and ready to be used to have a better understanding on the evolutionary patterns and to identify areas with remarkable evolutionary history. But relying on data coming from independent studies raises some methodological challenges of standardization, comparability and assessments of bias to make the best use of the currently available information. To bring light to this subject here we analyzed the distribution of phylogenetic diversity in New Caledonia, a biodiversity hotspot characterized by strong rates of regional and internal endemicity. We used a dataset with 18 phylogenies distributed in 16 study sites, and based our analysis on the measure Ws sum. Our study comprises the analysis of (1) the role of the number of phylogenies on site’ scores and a strategy of standardization of the dataset by the number of phylogenies; (2) the influence of species richness on site scores and the design of the measure Ws ranks to focus on the most divergent species of each phylogeny; (3) an assessment of the influence of individual phylogenies; (4) a resampling strategy using multiple phylogenies to verify the results’ stability.