Phylogenetic Diversity and Conservation Evaluation: Perspectives on Multiple Values, Indices, and Scales of Application

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Chapter One Phylogenetic Diversity and Conservation Evaluation: Perspectives on Multiple Values, Indices, and Scales of Application

Abstract "Phylogenetic diversity" and its abbreviation "PD" have now become popular terms describing a fundamental aspect of biodiversity based on phylogeny. After more than twenty-five years of work on PD, methods and applications have explored a wide range of taxonomic groups and geographic scales. PD provides a way to address biodiversity at the level of features or characteristics of species, based on its well-corroborated model linking phylogeny and feature variation. The quantification of feature diversity justifies PD as a measure of option value - the value of living variation in keeping options open for society. This justification for PD in biodiversity conservation gives attention to often-neglected arguments for the value to society of biotic diversity. These largely global option values are complemented by the "insurance" value of PD at the local ecosystem scale. Microbial applications of PD, particularly in human health studies, have successfully implemented a range of PD calculations, including PD dissimilarities among samples. Reduced microbial PD in the human body may indicate reduced resilience, and it is now associated with many human diseases. "Macrobial" ecology has been less successful in integrating PD into a consistent coherent approach. Here, the traditional recognition of many "diversity" indices has been extended to phylogeny. PD as a "biodiversity" measure is confounded with the multitude of phylogeny-based diversity indices describing various ecological factors. Greater integration among the different areas of PD application could better establish PD as a core biodiversity measure, with a shared toolbox providing a range of PD-related calculations.

Background

My title echoes the title of the paper, "Conservation evaluation and phylogenetic diversity" which proposed "phylogenetic diversity" ("PD") as a natural phylogeny-based measure of biodiversity. The definition of PD provided in that paper was deceptively simple: the PD of a subset of species (or other taxa) from a phylogenetic tree is the total length of the branches spanning that subset on the tree. I say "deceptively" for two reasons. First, that simple definition corresponded to a not-so-simple framework to quantify the relative "feature diversity" of subsets of taxa, equating features with the units of biodiversity that we would like to count up. Second, feature counting meant that the simple definition of PD did not just define one simple "index." Instead, it established a basis for a whole family of associated calculations (the PD "calculus") that could be used for practical decision-making in biodiversity conservation. As I will discuss in this perspectives paper, these not-so-simple aspects of PD continue to be debated in the many studies that now apply, critique, and extend this popular approach.

As my title also indicates, the many published PD studies now range widely across taxonomic groups and scales of application. Prior to nineteen ninety-two, a handful of papers had used the term "phylogenetic diversity," largely descriptively. Following the Faith nineteen ninety-two paper, there have been about five thousand papers in Web of Science with the key term "phylogenetic diversity." At the time of this writing, the nineteen ninety-two paper is the most-cited paper ever in Biological Conservation from the more than seven thousand papers in that journal spanning more than forty years. While there are some partial reviews of this work, for example, by Porter and Hajibabaei in the genomics context, in a recent book, and in Faith, there appears to be no single review covering the full range of PD studies.

Some exciting areas of PD application have departed from organismal phylogeny. As examples, PD is now applied to conservation of "phylogenetic language diversity," and PD is used as an analogous biodiversity measure for hierarchies other than phylogenies (environmental hierarchies, and functional trait hierarchies). As I will discuss below, more communication is needed among all these different areas of PD application. This need includes better integration of the PD work in microbial and macrobial ecology.

As preparation for discussion in this chapter of the ongoing applications of PD, it is useful first to look back at PD's "prehistory" (the history of a term before it was invented). This reveals how PD naturally emerged from some important precursors, including early discussions about biodiversity's value, about "taxonomic distinctiveness," and about how phylogeny informs us about characters or features.

It is commonly thought that the development of methods for using taxonomy and phylogeny in biodiversity conservation was an "explosive radiation," given that several notable papers appeared at about the same time

Vane-Wright, Faith, Weitzman, and Crozier. The reality is that there was significant foundational thinking on this topic over the decade prior to the appearance of those papers. Foremost among this work was the "World Conservation Strategy" report by IUCN. This single report foreshadowed later thinking on biodiversity option values, on ecological integrity, and on taxonomic distinctiveness (all relevant to this chapter) and also on the integration of distinctiveness and extinction threat. These early IUCN influences complemented other foundations for PD, including early influential work in systematic that explored the links from phylogeny to features.

As part of this Background section, I will discuss these precursors below, under the headings "Taxonomic Distinctiveness," "The Link from Phylogeny to Feature Diversity," "Option Values," and "Insurance Value/Ecological Integrity." With these in mind, the main body of this chapter then will explore some current challenges in applications of PD. Here, my discussion of microbial and "macrobial" ecology applications will complement the discussion of PD at the regional/global conservation scale, found in other chapters in this book.