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Human activities have accelerated the level of global biodiversity loss. As we cannot preserve all species and areas, we must prioritize what to protect. Therefore, one of the most urgent goals and crucial tasks in conservation biology is to prioritize areas. We could start by calculating ecological measures as richness or endemicity, but they do not reflect the evolutionary diversity and distinctness of the species in a given area. The conservation of biodiversity must be linked to the understanding of the history of the taxa and the areas, and phylogeny give us the core for such understanding. In such phylogenetic context, evolutionary distinctiveness (ED) is a feasible way for defining a ranking of areas that takes into account the evolutionary history of each taxon that inhabits the area. As our knowledge of the distribution or the phylogeny might be incomplete, I introduce Jack-knife re-sampling in evolutionary distinctiveness prioritization analysis, as a way to evaluate the support of the ranking of the areas to modifications in the data used. In this way, some questions could be evaluated quantitatively as we could measure the confidence of the results, since deleting at random part of the information (phylogenies and/or distributions), would help to quantify the persistence of a given area in the ranking.

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.

Systematic conservation planning deals with cost-effective allocation of conservation funds. There are diverse ways in which evolutionary history could be included in prioritization, but here we considered it at the local scale, valuing higher the locations where the local community has high phylogenetic diversity, while still aiming at maximizing overall species representation. We conducted the prioritization with the Zonation software for spatial conservation planning.

We prioritized areas for conservation in Europe using distribution data and phylogenies for 275 mammal species. We prioritized areas in Europe for conserving hotspots of evolutionary history. For comparison we made analyses with species occurrences alone. Analyses were done for the whole region and for each country separately. We explored the impacts of tree uncertainty, and analyzed how well existing protected areas performed with respect to Zonation priorities.

Our findings indicate that some hotspots of evolutionary history are missed by species-based prioritization, unless specifically accounted for. Uncertainty in spatial priorities caused by variation in phylogenetic tree structure was a minor concern for prioritization. Protected areas did not perform well when assessed against the Zonation priorities for species or for phylogenetic diversity, although highest national scale priorities had almost twice as much area protected as the overall average.

We emphasize that the chosen goals and analysis setups have strong impacts on spatial priorities and therefore care must be taken in defining them appropriately. But regardless of setups, the gap between the current conservation efforts and spatial prioritization outcomes is typically greater than the difference between including and excluding phylogenetic diversity. Therefore the focus should be on increasing the role of spatial analyses in practical conservation, but whenever feasible, also including evolutionary history in the analyses, because evolutionary history is not always well represented by targeting species for conservation.

Population declines and species extinction can be abated through the establishment of effective conservation policies. Actions and policies towards biodiversity conservation must be well planned and priorities must be set. Besides the widely recognized principles of systematic conservation planning, it is also important to consider species attributes, such as their evolutionary distinctiveness (ED) and distribution pattern. In this study we did a gap analysis to evaluate protection status of anuran species endemic to the Brazilian Cerrado. We then selected priority areas for conservation in this biome based on a systematic conservation planning framework, also including species attributes as prioritization criteria. We found 65 gap species, for which less than 20 % of their conservation targets are met by the current network of protected areas, and 39 of them are not protected at all. Priority areas are located in the central portion of the Cerrado, and include river valleys and mountaintops. Mountains in southeastern and central Cerrado are especially rich in endemic and range-restricted species, resulting in higher priority values for these areas. Priority areas selected here are also the richest regions and have greater Total Evolutionary Distinctiveness than the rest of the biome, demonstrating their high potential for conserving evolutionary history of anuran lineages in the Cerrado. Despite their great importance for biodiversity, areas that have higher richness of endemic species are also those that suffered from more severe loss of habitat, which reinforces the urgency for effective actions towards species conservation.

Several studies have shown how current climate change and human threats to aquatic environments are significantly impacting aquatic mammals worldwide. In response to these threats it is important to prioritize conservation efforts. A recent approach to evaluate conservation priorities is to combine information on species status from the International Union for Conservation of Nature (IUCN) Red List with information on the evolutionary history of the species from phylogenetic trees. This new approach provides a measure of biodiversity that complements estimates of species richness, adding evolutionary distinctiveness of species. Using near-complete species level phylogenies for the mammal groups with aquatic species (Carnivora, Cetacea, Sirenia) we calculated two measures (EDGE and HEDGE) of conservation priorities for 127 aquatic mammals under two scenarios of projected extinctions: a “pessimistic” approach, which represents a ‘worst case scenario’ for each species; and the “IUCN 50” a projected extinction risk over the next 50 years (Table 1 Then we analyzed the information to identify conservation priority areas (CPA) for aquatic mammals. We identified 22 CPAs distributed primarily along coastal waters in both northern and southern hemispheres. While thousands of marine protected areas (MPA) have been established in recent years, only 11.5 % of CPAs overlap with existing MPAs. Nevertheless, all phylogenetic CPAs identified in this study have also been proposed to be important by other independent studies using different prioritization criteria, highlighting the importance of focusing conservation efforts in these areas.

Many species have declined or already gone extinct due to the human activities across the world causing what is termed the current sixth mass extinction event. The biggest determinant of species survival is the availability of a network of suitable habitat, affecting population size and eventual extinction risk. Considering that modern technology allows us to efficiently quantify habitat loss, species distribution data can inform us of the required minimum connectivity of habitats. Evolutionary distinctiveness (ED) is already part of conservation schemes to prioritize rare traits and unique phylogenetic history. However, so far none of these prioritisations quantifies the spatial constraints of a species to estimate long-term persistence based on the fragmentation of the landscape. Metapopulation capacity (λ) is one such measurement for quantifying fragmentation. Here we propose a combination of metapopulation capacity and phylogenetic distinctiveness to prioritize important specific habitat patches for evolutionary distinct species. We applied the new framework to prioritize island mammals and found Data Deficient and Least Concern species with a high combined value in ED and λ. Balancing between the extinction risks of solitary islands and the potential loss of unique evolutionary history of rare species on these islands can be a worthwhile exercise in prioritization schemes.

The Neotropical region comprises six of the major biodiversity hotspots of the planet, including the Andean foothills, which harbour the most diverse terrestrial ecosystems. It is also one of those most threatened by habitat destruction and climatic changes, which cause species extirpation and sometimes extinction, resulting in community disassembly and loss of interspecific interactions. The effects of community disassembly can be particularly strong in highly coevolved mutualistic species assemblages, such as Müllerian mimetic species. Conservation strategies should therefore aim at preserving not only evolutionary diversity, but also species interactions. Here we use mimetic ithomiine butterflies (Nymphalidae: Danainae, Ithomiini) as a model to identify areas of both evolutionary and ecological importance, and hence conservation significance. Ithomiine butterflies form a tribe of ca. 380 species that inhabit lowland and montane Neotropical forests. All species engage in Müllerian mimicry, and drive mimicry in other, distantly related, Lepidoptera. We analyse phylogenetic, distribution and mimicry data for three diverse ithomiine genera, , and . We use different metrics to study geographical patterns of diversity. Patterns of species richness, phylogenetic diversity and mimicry diversity are highly congruent within genera but slightly different among genera. Mountainous regions contain the greatest taxonomic and mimetic diversity in ithomiines, with the Andean foothill region being the area of highest diversity, but other regions, such as Central America and the upper Amazon, are also important. Finally, a measure of vulnerability related to mimicry indicates that mutualistic interactions are not distributed evenly across space and genera. We argue that mutualistic interactions should be taken into account in conservation strategies.

Madagascar is renowned for its impressive species richness and high level of endemism, which led to the island being recognized as one of the world’s most important biodiversity hotspots. As in many other regions, Madagascar’s biodiversity is highly threatened by unsustainable anthropogenic disturbance, leading to widespread habitat loss and degradation. Although the country has significantly expanded its network of protected areas (PAs), current protocols for identifying priority areas are based on traditional measures that could fail to ensure maximal inclusion of the country’s biodiversity. In this study, we use Madagascar’s largest endemic plant family, Sarcolaenaceae, as a model to identify areas with high diversity and to explore the potential conservation importance of these areas. Using phylogenetic information and species distribution data, we employ three metrics to study geographic patterns of diversity: species richness, Phylogenetic Diversity (PD) and Mean Phylogenetic Diversity (MPD). The distributions of species richness and PD show considerable spatial congruence, with the highest values found in a narrow localized region in the central-northern portion of the eastern humid forest. MPD is comparatively uniform spatially, suggesting that the balanced nature of the phylogenetic tree plays a role in the observed congruence between PD and species richness. The current network of PAs includes a large part of the family’s biodiversity, and three PAs (Ankeniheny Zahamena Forest Corridor, the Bongolava Forest Corridor and the Itremo Massif) together contain almost 85 % of the PD. Our results suggest that PD could be a valuable source of complementary information for determining the contribution of Madagascar’s existing network of PAs toward protecting the country’s biodiversity and for identifying priority areas for the establishment of new parks and reserves.

Phylogenetic diversity has become invaluable for conservation biology in the last decades, reflecting its link to option values and to evolutionary potential. We argue that its use will continue to grow rapidly in the next decades because of the transformation of systematics with new molecular techniques and especially metagenomics. In a near future, phylogenetic diversity typically will be the very first result at hand, and the great challenge of biodiversity sciences will be to preserve its link with natural history and the remainder of biological knowledge through species vouchers and names. The phylogeny availability and the very wide sampling allowed will facilitate obtaining detailed biodiversity information at local scale and considering the transition across scales – a fundamental need well highlighted in international conservation guidelines, and historically so difficult to achieve. All this suggests that phylogenetic diversity might be at the center of more explicit identification of conservation priorities and options. For concluding, we explore an emerging local-to-regional-to-global challenge: the possibility of defining “planetary boundaries” for biodiversity on the basis of phylogenetic diversity.