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Material and Methods

European Mammal Distributions We used data on the spatial distribution of european terrestrial mammals described in Maiorano et al. (2013). The primary data were extents of occurrence (EOOs) of the species occurring in Europe and Turkey obtained from the Global Mammal Assessment ( tives/mammals; accessed 15 August 2013 (IUCN 2012)). To refine EOOs and remove potential false presences, habitat requirements were used in an expert-based modelling approach. More specifically, for each species, habitat requirement was defined by experts (G. Amori, D. Russo and L. Boitani) and published literature (see Maiorano et al. 2013 for the full list of references) based on three environmental variables: land cover, elevation and distance to water. For each species, data collected were used to assign a suitability score (0, unsuitable; 1, secondary habitat and 2, primary habitat) to each of the 46 GlobCover land-use/land-cover classes. Elevation and distance to water were then combined to the habitat suitability score to refine the available EOOs and obtain current distribution with a cell size of 300 m resolution. The models were validated with help of field data (see Maiorano et al. 2013 for more details). From these 288 species we used 275 for which phylogenies were available.

As running the phylogenetic analyses and Zonation prioritization at 300 m resolution would have been too demanding for the equipment available at the time, we scaled up the species distributions following a regular grid of 10′. As a value for each 10′ cell, we kept the percentage of 300 m cells considered as either 1 (primary habitat) or 2 (secondary habitat), and we refer to this value as “the proportion of suitable area” hereafter. For aesthetic reasons, all the maps presented hereafter have been projected using the Lambert conformal conic projection (UTM zone 34).

Mammal Phylogenies Phylogenetic data for mammals were based on the supertree of Bininda-Emonds et al. (2007) updated by Fritz et al. (2009). We used 100 fully resolved phylogenetic trees, where polytomies were randomly resolved applying a birth-death model to simulate branch lengths (Kuhn et al. 2011).

Protected Areas We used the WDPA dataset on protected areas (UNEP 2010) categories I-IV (I: Strict nature reserve or wilderness area, II: National park, III: Natural monument or feature and IV: Habitat/Species management area) excluding the categories that are generally considered less beneficial for biodiversity conservation (categories V and VI), and areas where the category was either 'not reported' or 'not applicable'. We used the proportions of area protected in each cell for our analyses of overlap of Zonation priorities with protected areas. WDPA data are polygons. As Zonation operates with raster data, we transformed the polygons into a raster, following the same grid as the species distribution data (10′ cells regular grid). To do so, we overlapped the polygons on the grid and retained the proportion of area protected in each grid cell.

Measuring Phylogenetic Diversity To measure the phylogenetic diversity at each cell, we used the Rao's quadratic entropy (Rao 1982), an index of alpha-diversity, which is extended to account for the pair-wise dissimilarities of species:

dij is derived from the ultrametric phylogenetic tree (Pavoine et al. 2005b) and corresponds to the phylogenetic dissimilarity between each pair of species i and j. pi and pj are the respective proportions of suitable habitat for the species i and j available in the 10′ pixel c. It is now recognized in the literature that the values of most of diversity measures (like the Rao's quadratic entropy) do not behave intuitively because they do not satisfy the “replication principle” (Jost 2007; de Bello et al. 2010; Chao et al. 2010; Leinster and Cobbold 2012; Chao et al. chapter “Phylogenetic Diversity Measures and Their Decomposition: A Framework Based on Hill Numbers”). The replication principle (or “doubling property”) states that if we pool two equally diverse and equally large groups with no shared species, the total diversity should be two times the diversity of a single group (Chao et al. 2010; Chao et al. see their Fig. 2 in chapter “Phylogenetic Diversity Measures and Their Decomposition: A Framework Based on Hill Numbers”). To make the Rao's quadratic entropy behave this way, we need to transform it into an equivalent number through a simple algebra step (1/(1-QE), Jost 2007). The outcome is a raster layer with the value of QE in equivalent number for each of the 10′ pixels with the same spatial extent and resolution as the mammal distribution data.

The Zonation Approach Zonation is a spatial prioritization software meant to be used as a decision support tool (Moilanen et al. 2009). While other approaches typically select a fraction of the landscape according to a pre-determined target, e.g. 10 % of species distributions, or maximize what is achieved with a pre-determined budget, Zonation instead ranks all cells in the entire landscape in the order of conservation value. A Zonation solution can be used to identify any best (or worst) fraction of the landscape.

The ranking is based on the evaluation of range size normalized richness of biodiversity features in each cell (Moilanen et al. 2005, 2011). In plain words, this means that features (e.g. species) with broad distributions contribute very little to the conservation value of a single cell, whereas narrowly distributed species substantially increase the conservation value of the cells they occupy. At every iteration (removal of one cell) Zonation recalculates the conservation value for the remaining cells based on the remaining feature distributions, which become smaller with each iteration. Thus, Zonation removes first cells with few, broadly distributed features, and during the ranking these features become rarer and rarer in the remaining landscape. As an outcome, the remaining highest priority fraction of the landscape will contain the cells with high species richness and narrow endemics.

Zonation provides two options as cell-removal rules that determine how the marginal value of a cell is calculated (Moilanen et al. 2005; Moilanen 2007). The additive benefit function approach allows for more flexible trade-offs to occur between features, because it considers cell value as the sum over benefit functions of representation of the features in the cell. This means that narrowly distributed species in species poor (or expensive) cells may be traded off against species rich cells. We chose to use the Core-area cell removal rule, which defines the cell value based on the most valuable occurrence over all species in the cell. This means that if a cell contains a large fraction of the range even for only one species, it will get high value, regardless of the species richness in the cell. This way the core areas of all species' ranges are retained in the highest priority fraction of the landscape. As species distribution data, we used the raster layers of proportion of suitable habitat per cell for each species, as described above in the section “European mammal distributions”.

Even though Zonation does not consider phylogenetic data by default, it offers also options for accounting for evolutionary history in the prioritization. For example, species could be weighted based on their evolutionary distinctiveness either globally, or with different region-specific weights (Moilanen and Arponen 2011). Alternatively, locations can be weighted based on the phylogenetic diversity of the local community. In this case study we focus on the latter approach. Technically this happens through defining a “cost layer” as inversely proportional to the diversity. This way a cell with one-fifth of the phylogenetic diversity of another cell is considered five times as costly to protect, lowering its position in the Zonation ranking. The cost layer can be scaled differently according to how much importance is given to phylogenetic diversity. The equivalent numbers of Rao's quadratic entropy values went from ca. 1 to 7, and the direct inverse was used in our “medium weighting” (that is, cost goes from 0.14 to 1), and this scale was halved (“low weights”, 0.28–1) and doubled (“high weights”, 0.07–1) to test for sensitivity to this parameter (see Fig. 1 for analysis setups).

The latitudinal gradients in species richness and range sizes cause the spatial priorities in analyses at any scale to be concentrated in the more species rich lower latitude areas (Eklund et al. 2011; Moilanen et al. 2013). Even though cost-effective from the perspective of species conservation, focusing conservation efforts into these regions only would be very difficult for many reasons (see section “Discussion and Conclusions”). Therefore we also performed an analysis where countries were considered as independent administrative units, each aiming to conserve the diversity within their borders. This is implemented through the Administrative units analysis in Zonation (Moilanen and Arponen 2011). The analysis would allow for a compromise solution between purely European-scale and purely national-scale analyses, but for our analytical purposes, we chose the extreme cases only. A national-scale prioritization provides an interesting reference for comparison to protected areas. We did this for one tree only. Thus, we ended up with four main Zonation solutions to assess protected area performance regarding the representation of species and phylogenetic diversity at both European and national scales (Fig. 1).

Case Study Setup

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