This last section is composed by contributions exploring the application of phylogenetic diversity methods in study cases. These studies are deliberately diverse in approaches of the use and applications of phylogenetic diversity, and of measures, spatial scales, geographic locations and taxonomic groups as well. It starts with two analyses integrating the conservation of evolutionary history in systematic conservation planning, a field of conservation biology that deals with conservation prioritization taking in account multiple factors, and in which we can define and revise pre-established criteria and goals (Margules and Pressey 2000; Ball et al. 2009; Moilanen et al. 2009; Kukkala and Moilanen 2013).

In chapter “Representing Hotspots of Evolutionary History in Systematic Conservation Planning for European Mammals” Arponen and Zupan use the Zonation software for spatial prioritization to prioritize areas for conservation of the evolutionary history of mammals in Europe. With an analysis at continental and at the scale of each European country, they show that: (a) a strategy focusing only on species richness would miss some areas with important levels of evolutionary history, mainly in regions with medium or low values of species richness; (b) the present system of protected areas performs worse than random selections for protecting the evolutionary history of mammals; and (c) a strategy to protect mammals at the continental scale would be much more effective than separated strategies for each country, although from a political point of view this last one is likely to be more feasible.

In the following contribution, Silvano et al. (chapter “Priorities for Conservation of the Evolutionary History of Amphibians in the Cerrado”) use a Gap Analysis to evaluate the protection status of 82 anuran species endemic from Brazilian Cerrado and to define priority areas for their conservation. Their results indicate an alarming situation in which 39 (48 %) endemic and restricted range species are completely unprotected, among them species with very high ED values, and other 43 (52 %) are gap species with less than 20 % of their targets met. The priority areas for the conservation of these species mostly occupy the central portion of the biome, a region that already suffered major habitat destruction, and are forecast to undergo important habitat loss if economic scenario remains unchanged.

The following triad of studies explores the integration of species threat and phylogenetic diversity. It starts with the research of May-Collado, Zambrana-Torrelio and Agnarsson (chapter “Global Spatial Analyses of Phylogenetic Conservation Priorities for Aquatic Mammals”) dealing with the prioritization of areas for conservation of 127 marine mammals worldwide. Here they use the EDGE (Isaac et al. 2007) and HEDGE (Steel et al. 2007) measures to provide the first spatial analysis for phylogenetic conservation priorities incorporating threat information at global scale. By assessing conservation under “pessimistic” and “optimistic” IUCN extinction scenarios they show how fragile is the world system of protected areas to conserve the evolutionary distinctiveness of marine mammals. They identified 22 Conservation PriorityAreas all over the world and showed that only 11.5 % of them overlap with existing marine protected areas. Their results complete prior findings on conservation prioritization for marine mammals, providing a helpful tool for the Conservation of Biological Diversity plan to protect 10 % of world's marine and coastal regions by 2020.

In the next contribution, Jessica Schnell and Kamran Safi (chapter “Metapopulation Capacity Meets Evolutionary Distinctness: Spatial Fragmentation Complements Phylogenetic Rarity in Prioritization”) design a framework to predict threat status of Data Deficient and Least Concern species. They propose to combine evolutionary distinctiveness with metapopulation capacity derived from habitat isolation. Here they apply this framework to terrestrial mammals endemic of oceanic islands worldwide, and show that balancing between extinction risks associated to island's isolation and potential loss of evolutionarily unique species can be very useful to characterize conservation status of island endemic species. Based on it they show that islands such as Guadalcanal, Isle of Pines, Madagascar and Nggela Sule are very representative for reducing the extinction of mammals with high ED values.

In chapter “Patterns of Species, Phylogenetic and Mimicry Diversity of Clearwing Butterflies in the Neotropics”, Chazot et al. explore the patterns of distribution of several features of diversity of three genera of ithomiine butterflies in Neotropical Region. Ithomiine display Müllerian mimetism and numerically dominate many butterfly assemblages across the Neotropics, probably conditioning the distribution of other species that interact with them in positive or negative way. So, the loss of ithomiine species in local assemblages may strongly influence the vulnerability of butterfly assemblages. Here they show that, on the one hand, the pattern of distribution of phylogenetic diversity, species richness, and mimicry diversity are highly congruent within genera, and, in a lesser extent, across genera. On the other hand, the potential loss of species due to disruption of mimicry rings, as captured by a measure of vulnerability designed in this study, are not evenly distributed across genera presenting peaks in areas completely distinct of those observed to the other features. This is a good example of the “agony of choice” of Vane-Wright et al. (1991) illustrating the difficulty of finding an optimal solution in situations in which several parameters account for the existing biodiversity.

We close this section with a note of optimism. The analysis of Soulebeau et al. (chapter “Conservation of Phylogenetic Diversity in Madagascar's Largest Endemic Plant Family, Sarcolaenaceae”) shows that the system of protected areas of Madagascar is likely to protect all lineages and 97 % of the phylogenetic diversity of Sarcolaenaceae, the largest endemic plant family of this island. This result is particularly important because neither Sarcolaenaceae nor phylogenetic diversity were specifically considered in the conception or in the recent expansion of Madagascar's network of protected area (Kremen et al. 2008), showing that a large system of protected area may capture much more biodiversity components and features than originally expected.

For concluding, in the last chapter we – Roseli Pellens, Dan Faith and Philippe Grandcolas – describe the recent transformations of phylogenetic systematics in the light of new facilities of molecular sequencing and data analysis, and discuss its impacts in biological conservation. We finish by exploring the possibility of defining “planetary boundaries” for biodiversity on the basis of phylogenetic diversity, and its important role in linking biodiversity into broader societal perspectives and needs.

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