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In the midst of a major extinction crisis, the scientific community is called to provide criteria, variables and standards for defining strategies of biodiversity conservation and monitoring their results. Phylogenetic diversity is one of the variables taken in account. Its consideration in biodiversity conservation stemmed from the idea that species are not equal in terms of evolutionary history and opened a completely new line of investigation. It has turned the focus to the need of protecting the Tree of Life, i.e. the diversity of features resulting from the evolution of Life on Earth. This approach is now recognized as a strategy for increasing options for future needs and values as well as for increasing the potential of biodiversity diversification in a future environment. Since its introduction in biodiversity conservation thinking much has been developed in order to compose our conceptual understanding of the importance of protecting the Tree of Life. The aim of this book is to contribute to the ongoing international construction of strategies for reducing biodiversity losses by exploring several approaches for the conservation of phylogenetic diversity. We hope that this concentrated effort will contribute to the emergence of new solutions and attitudes towards a more effective preservation of our evolutionary heritage. The chapters of this book are organized around three main themes: questions, methods and applications, providing a condensed updated picture of the state of the art and showing that either conceptually or methodologically phylogenetic diversity has everything to be on the global agenda of biodiversity conservation.

This chapter explores the idea that phylogenetic diversity plays a unique role in underpinning conservation endeavour. The conservation of biodiversity is suffering from a rapid, unguided proliferation of metrics. Confusion is caused by the wide variety of contexts in which we make use of the idea of biodiversity. Characterisations of biodiversity range from all-variety-at-all-levels down to variety with respect to single variables relevant to very specific conservation contexts. Accepting biodiversity as the sum of a large number of individual measures results in an empirically intractable framework. However, large-scale decisions cannot be based on biodiversity variables inferred from local conservation imperatives because the variables relevant to the many systems being compared would be incommensurate with one another. We therefore need some general conception of biodiversity that would make tractable such large-scale environmental decision-marking. We categorise the large array of strategies for the measurement of biodiversity into four broad groups for consideration as general measures of biodiversity. We compare common moral justifications for the conservation of biodiversity and conclude that some form of instrumental value is the most plausible justification for biodiversity conservation. Although this is often interpreted as a reliance on option value, we opt for a broadly consequentialist characterisation of biodiversity conservation. We conclude that the best justified general measure of biodiversity will be some form of phylogenetic diversity.

Feature diversity refers to the relative number of different features represented among species or other taxa. As a storehouse of possible future benefits to people, it is an important focus for biodiversity conservation. The PD phylogenetic diversity measure provides a way to measure biodiversity at the level of features. PD assumes an evolutionary model in which shared features are explained by shared ancestry. This avoids philosophical and practical weaknesses of the conventional interpretation of biodiversity as based on some measure of pair-wise differences among taxa. The link to features also provides a family of PD-based calculations that can be interpreted as if we are counting-up features of taxa. The range of feature diversity calculations assists comparisons of methods, and helps overcome the current lack of review and synthesis of the variety of proposed methods for integrating evolutionary history into biodiversity conservation. One family of popular indices is based on the evolutionary distinctiveness (ED) measure. These indices all have the limitation that complementarity, reflecting degree of phylogenetic overlap among taxa, is not properly taken into account. Related indices provide priorities or other scores for geographic areas, but do not effectively combine complementarity, probabilities of extinction, and measures of restricted-range. PD-based measures can overcome these problems. Applications include the identification of key biodiversity sites of global significance for biodiversity conservation.

Analysing extinction within a phylogenetic framework may seem counter-intuitive because extinction is a non-heritable trait. However, extinction risk is correlated with other traits, such as body size, that show a strong phylogenetic signal. Further, there has been much effort in identifying key traits important for diversification, and recent evidence has demonstrated that the processes of speciation and extinction may be inextricably linked. A phylogenetic approach also allows us to quantify the impact of extinction, for example, as the loss of branches from the tree-of-life. Early work suggested that extinctions might result in little loss of evolutionary history, but subsequent studies indicated that non-random extinctions might prune more of the evolutionary tree. Loss of phylogenetic diversity might have ecosystem consequences because functional differences between species tend to be correlated with the evolutionary distances between them. Here we explore how extinction prunes the tree-of-life. Our review indicates that the loss of evolutionary history under non-random extinction (the emerging pattern in extinction biology) might be less pronounced than some previous studies have suggested. However, the loss of functional diversity might still be large, depending on the evolutionary model of trait change. Under a punctuated model of evolution, in which trait differences accrue in bursts at speciation, the number of branches lost is more important than their summed lengths. We suggest that evolutionary models need to be incorporated more explicitly into measures of phylogenetic diversity if we are to use phylogeny as a proxy for functional diversity.

Phylogenetic trees represent the evolutionary relationships of taxa at the branch tips. Although long branches in a tree can arise because a taxon has no close relatives, they can also result from other processes; care is needed when inferences are made from the shape of a phylogeny. New Zealand has many endangered species and some biologists infer high evolutionary distinctiveness of these endemics. Although there is evidence that some New Zealand birds are phylogenetically distinct using them as a calibration of continental drift vicariance has been misleading. In reptiles, extensive conservation resources have been devoted to management of tuatara, in part due to their phylogenetic distinctiveness as sister to all lizards and snakes. The lack of extant diversity in the tuatara lineage could indicate that this line will contribute little to biodiversity in the future, in contrast to New Zealand squamates that have radiated to occupy diverse habitats. All life on earth has a common ancestor so phylogenetic distinctiveness of any organism must be viewed in the context of the whole. A logical extension of building conservation strategy this way is a focus on microscopic life because microbes encompass far more diversity than do eukaryotes. Furthermore, this diversity can be captured in microbiomes such as soils and marine sponges that include many species and many phyla. To achieve true phylogenetic representation of life on earth requires conservation of ecosystems. Although large animals and plants are traditionally chosen as flagship species, a more impartial approach might focus on microbes that underpin ecosystem function.

A relict is a species that remains from a group largely extinct. It can be identified according both to a phylogenetic analysis and to a fossil record of extinction. Conserving a relict species will amount to conserve the unique representative of a particular phylogenetic group and its combination of potentially original characters, thus lots of phylogenetic diversity. However, the focus on these original characters, often seen as archaic or primitive, commonly brought erroneous ideas. Actually, relict species are not necessarily old within their group and they can show as much genetic diversity as any species. A phylogenetic relict species can be geographically or climatically restricted or not. Empirical studies have often shown that relicts are at particular risks of extinction. The term relict should not be used for putting a misleading emphasis on remnant or isolated populations. In conclusion, relict species are extreme cases of phylogenetic diversity, often endangered and with high symbolic value, of important value for conservation.

The PD phylogenetic diversity measure provides a measure of biodiversity that reflects variety at the level of features, among species or other taxa. PD is based on a simple model which assumes that shared ancestry explains shared features. PD provides a family of calculations that operate as if we were directly counting up features of taxa. PD-dissimilarity or phylogenetic beta diversity compares the branches/features represented by two different areas. We also can consider a companion model, which shifts the focus to shared habitat/environment among taxa as the explanation of shared features, including those features not explained by shared ancestry and PD. That model means that PD-dissimilarities, among sampled and unsampled sites, can be predicted using a regression method applied to distances in an environmental-gradients space. However, PD-based conservation planning requires more than the dissimilarities among all sites, in order to make decisions informed by gains and losses of branches/features. The companion model also suggests how to transform dissimilarities to provide these needed estimates. This (“”) method out-performs other suggested strategies for analysis of dissimilarities, including the Ferrier et al. method and the Arponen et al. method. The global biodiversity observation network (GEO BON) can use the method for inferences of biodiversity change that include loss of phylogenetic diversity.

Conservation biologists need robust, intuitive mathematical tools to quantify and assess patterns and changes in biodiversity. Here we review some commonly used abundance-based species diversity measures and their phylogenetic generalizations. Most of the previous abundance-sensitive measures and their phylogenetic generalizations lack an essential property, the replication principle or doubling property. This often leads to inconsistent or counter-intuitive interpretations, especially in conservation applications. Hill numbers or the “effective number of species” obey the replication principle and thus resolve many of the interpretational problems. Hill numbers were recently extended to incorporate phylogeny; the resulting measures take into account phylogenetic differences between species while still satisfying the replication principle. We review the framework of phylogenetic diversity measures based on Hill numbers and their decomposition into independent alpha and beta components. Both additive and multiplicative decompositions lead to the same classes of normalized phylogenetic similarity or differentiation measures. These classes include multiple-assemblage phylogenetic generalizations of the Jaccard, Sørensen, Horn and Morisita-Horn measures. For two assemblages, these classes also include the commonly used and indices as special cases. Our approach provides a mathematically rigorous, self-consistent, ecologically meaningful set of tools for conservationists who must assess the phylogenetic diversity and complementarity of potential protected areas. Our framework is applied to a real dataset to illustrate (i) how to use phylogenetic diversity profiles to completely convey species abundances and phylogenetic information among species in an assemblage; and (ii) how to use phylogenetic similarity (or differentiation) profiles to assess phylogenetic resemblance or difference among multiple assemblages.

About 20 years ago the concepts of phylogenetic diversity and phylogenetic split networks were separately introduced in conservation biology and evolutionary biology, respectively. While it has been widely recognized that biodiversity assessment should better take into account the phylogenetic tree of life, it has also been widely acknowledged that phylogenetic networks are more appropriate for phylogenetic analysis in the presence of hybridization, horizontal gene transfer, or contradicting trees among genomic loci. Here, we aim to combine phylogenetic diversity and networks into one concept, split diversity (SD), which properly measures biodiversity for conflicting phylogenetic signals. Moreover, we reformulate well-known conservation questions under the SD framework and present computational methods to solve these, in general, computationally intractable questions. Notably, integer programming, a technique widely used to solve many real-life problems, serves as a general and efficient strategy that delivers optimal solutions to many biodiversity optimization problems. We finally discuss future directions for the new concept.

Like other measures of diversity, Phylogenetic Diversity (PD) increases monotonically and asymptotically with increasing sample size. This relationship can be described by a rarefaction curve tracing the expected PD for a given number of accumulation units. Accumulation units represent individual organisms, collections of organisms (e.g. sites), or even species (or equivalent), giving individual-based, sample-based and species-based curves respectively. The formulation for the exact analytical solution for the rarefaction of PD is given in an expanded form to demonstrate congruence with the classic formulation for the rarefaction of species richness. Rarefaction is commonly applied as a standardisation for diversity values derived from differing numbers of sampling units. However, the solution can be simply extended to create measures of phylogenetic evenness, phylogenetic beta-diversity and phylogenetic dispersion, derived from individual-based, sample-based and species-based curves respectively. This extension, termed ∆PD, is simply the initial slope of the rarefaction curve and is related to entropy measures such as PIE (Probability of Interspecific Encounter) and Gini-Simpson entropy. The application of rarefaction of PD to sample standardisation and measurement of phylogenetic evenness, phylogenetic beta-diversity and phylogenetic dispersion is demonstrated. Future prospects for PD rarefaction include the recognition of evolutionary hotspots (independent of species richness), the basis for ecological theory such as phylogeny-area relationships, and the prediction of unseen biodiversity.