This first section is composed of chapters addressing some central questions concerning the links between biodiversity conservation and phylogenetic systematics. The first, and perhaps the most important of these questions, concerns the nature of the role of phylogenetic systematics in conservation efforts. How do we value the Tree of Life? Why to use aspects of phylogeny in preference to other biodiversity variables? These questions are explored by Lean and Maclaurin in chapter “The Value of Phylogenetic Diversity”. They develop the idea that phylogenetic diversity plays a unique role in underpinning conservation endeavor and represents the foundation of a general measure of biodiversity. In a synthesis about the reasons and the types of values that should guide biodiversity conservation and qualify a general biodiversity measure, they propose that phylogeny is the only basis for large-scale conservation prioritization. They justify this argument by showing that phylogeny is the only guide for maximizing feature diversity (sensu Faith 1992) across many different taxa, and also is the best way to hedge our bets against uncertainties related to environmental changes and to human's future needs and values.
PD or Faith's PD: is the measure of phylogenetic diversity created by Faith (1992). Specifically it is the sum of the lengths of all phylogenetic branches (from the root to the tip) spanned by a set of species. In this book, we refer to PD or Faith's PD to indicate this measure.
Phylogenetic diversity: all over this book we use this term in very large sense, independently of the measure, willing to express the differences between organisms due to their evolutionary history, and so captured by a phylogeny. It can be used to express the uniqueness of one species or the representativeness of a set of organisms, according to several different measures.
Evolutionary distinctiveness (Isaac et al. 2007) or Evolutionary distinctness: is here used to indicate measures destined to assess the phylogenetic diversity of each species, independently if it is based on topology or branch length. Contrarily to PD, where the contribution of a species may vary from one set to another depending on the other species occurring in it, with measures of evolutionary distinctiveness each species has an invariable value. Taxonomic distinctiveness (Vane-Wright et al. 1991): like in the case of Evolutionary distinctiveness, it is used to express measures designed to assess the phylogenetic diversity of species, but this definition is restricted to those measures based on tree topology.
If the way we value phylogenetic diversity is central for any justifications for including phylogeny in conservations efforts, an equally important consideration must be the choice of the measure that adequately captures the aspects of phylogenetic diversity that are important for conservation. Lean and MacLaurin propose that this measure should maximize feature diversity. However, there are very few studies comparing the performance of the measures under such criteria (Redding and Mooers 2006; Schweiger et al. 2008; Pio et al. 2011). Dan Faith (chapter “The PD Phylogenetic Diversity Framework: Linking Evolutionary History to Feature Diversity for Biodiversity Conservation”) addresses this question through the comparison of PD (Faith 1992), in relation to several measures of Evolutionary Distinctiveness (ED) in the context of priority setting for conservation. The core of Dan's analysis is complementarity (marginal gains and losses of PD or feature diversity), an attribute intrinsic to PD's algorithm, but lacking in ED measures. Here he shows that PD complementarity allows the identification of sets of species with maximum PD, whereas ED indices are unable to reliably identify such diverse sets. The next contribution deals with the loss of phylogenetic diversity with extinction. Are there phylogenetic signals in extinctions? What is the role of extrinsic and intrinsic factors in extinctions, and what is the role of phylogeny in data exploration and analysis (Grandcolas et al. 2010)? Are extinction drivers similar to different groups of organisms? What is the role of evolutionary models in the patterns observed? These questions are here explored by Yessoufou and Davies (chapter “Reconsidering the Loss of Evolutionary History: How Does Non-random Extinction Prune the Tree-of-Life?”). They first review the main extinction drivers, showing that the most relevant might be quite different among vertebrates, invertebrates and plants. By exploring how non-random extinction prunes the Tree of Life under different models of evolution, they call our attention to the fact that the model of evolution is likely to be a key explanatory of the loss of evolutionary history.
They also argue that more branches are likely to be lost from the Tree of Life under the speciational model of evolution.
Many of our considerations about the conservation of the Tree of Life are based on our knowledge of a micro-fraction of the living world, given that we often focus on organisms that are very close to human eyes, like vertebrates, vascular plants, and a few emblematic insects. Likewise, most of the phylogenies used to this purpose are based on molecular data, very often on very small sets of short gene sequences. An advantage of molecular data for phylogenetic inference is provision of a standardized set of characters, often reflecting the main patterns of relationship of the species in a group of organisms. However, the extent to which these genes portions evolve and reflect the evolution of other traits is seldom well studied. Such an issue is central to arguments that phylogenetic diversity links to general feature diversity. These problems are explored by Steve Trewick and Mary MorganRichards (chapter “Phylogenetics and Conservation in New Zealand: The Long and the Short of It”). With examples of the phylogenetic position (as assessed through molecular data) of some legendary organisms from New Zealand such as Kākāpō, takahē and tuatara, they shake some established views about the extent molecular branch length reflects other extraordinary ecological, morphological or behavioral traits. Going further, they turn our lenses to the microscopic life that is much more deeply branched in the Tree of Life. Taking the example of marine sponges, they show that a single sponge provides an environment that can host several distinct microbial communities (microbiomes) and so preserve organisms from more than 40 phyla all branched much deeper than vertebrates and plants. At reading this chapter, we are guided to a more inclusive perspective of biodiversity and we can find more reasons for protecting Kākāpō, takahē, tuatara, marine sponges and… microbes.
Relict species are often presented as examples of important species for the conservation of phylogenetic diversity. Everyone has heard about Coelacanth and Platypus as examples of unique evolutionary histories. In spite of this, the concept of relict species is still plagued with misleading ideas and uses, potentially causing misunderstandings for the use of phylogenetic diversity in general. Philippe Grandcolas and Steve Trewick (chapter “What Is the Meaning of Extreme Phylogenetic Diversity? The Case of Phylogenetic Relict Species”) aim at freeing the concept from these problems, and use the extreme case of relict species to explore the nature and the use of phylogenetic diversity. The study of relicts helps understanding that early-branching species that make high values of phylogenetic diversity (the “unique PD” of Forest et al. 2015) are not necessarily evolutionarily “frozen”. Their conservation is not only aimed at retaining Life's diversity but also at keeping evolutionary potential. It is also worth-mentioning that such species have often been empirically shown to have special extinction risks, highlighting again the important role of phylogenetic diversity in conservation biology.