A1simon Veron
email: sveron@edu.mnhn.fr

A1victor Saito
email: victor.saito@gmail.com

A1nélida Padilla-García

A1yves Bertheau
email: yves.bertheau@mnhn.fr

*H1THE USE OF PHYLOGENETIC DIVERSITY IN CONSERVATION BIOLOGY AND COMMUNITY ECOLOGY: A COMMON BASE BUT DIFFERENT APPROACHES

Keywords: phylogenetic diversity, ecosystem services, evolutionary potential, feature variation, option values, spatial planning

AB2The use of phylogenetic tools and studies has strongly increased in the last two decades especially in conservation biology and community ecology. Phylogenetic trees have been essential to understand the processes of community or network assembly, to identify centers of diversification, and to help protect Earth's evolutionary heritage. Despite two decades of research and syntheses, there are still many discussions on how phylogenetic diversity (PD) methods should be effectively applied to those fields. In particular, conservation approaches based on PD have become similar to these used in community ecology. Thus, the main benefit of using PD calculations in conservation biology may have been ignored or misinterpreted. Our goal is to discuss and provide guidelines to the use of PD in biodiversity conservation so that its benefits are not hidden or lost in the approaches employed. We also aim that benefits and uses are better recognized and more easily understood by researchers or practitioners who would like to include PD in their studies and conservation planning.

*T1The development of humanity has impacted Earth, causing damage to ecosystems, species extinction, and habitat loss that-among the many potential impacts-may in turn threaten human societies. It has become urgent to establish appropriate actions that could mitigate this "crisis" affecting humankind. However, conserving representative populations of all species is generally perceived to be unrealistic due to limited resources and, therefore, effective decisions are needed to best protect biodiversity. Conservation strategies based on species richness and abundance (which aim to preserve species and habitats at a broad scale) have been the rule rather than the exception. For example, the influential "hotspots" of biodiversity have been identified based on endemic and threatened species [START_REF] Myers | Biodiversity hotspots for conservation priorities[END_REF]. Moreover, these approaches were easier to implement than those based on functions or phylogenies (e.g., no need to collect timeconsuming and expensive traits or molecular data nor to estimate functional/phylogenetic relationships between species). However, approaches that consider all species as equal are limited when conservation priorities have to be defined because they fail to recognize their distinctiveness [START_REF] Avise | A role for molecular genetics in the recognition and conservation of endangered species[END_REF][START_REF] Vane-Wright | What to protect?-systematics and the agency of choice[END_REF][START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF]). On the contrary, progress in phylogenetic inference has enabled the prioritization of conservation efforts based on the evolutionary history of species [START_REF] Mace | Preserving the tree of life[END_REF]. Similarly, in community ecology and biogeography, considering all species ecologically equal is inherent to neutral hypotheses [START_REF] Hubbell | The Unified Neutral Theory of Biodiversity and Biogeography[END_REF], whereas other methodologies, such as phylogenetic approaches, consider that species assemblage may be guided by species niches [START_REF] Webb | Phylogenies and community ecology[END_REF].

In the 1980s, the International Union for the Conservation of Nature (IUCN) emphasized the interest of taxonomic distinctiveness for conservation by stating that "the greater the gap between the nearest related family (or genus) . . . and therefore the more distinct" (IUCN 1980:22;Faith 2016aFaith , 2018a)). From this, "taxonomic hierarchy provides the only convenient rule of thumb for determining the relative size of a potential loss of genetic material" because "different positions in this hierarchy reflect great or lesser degrees of genetic difference" (IUCN 1980:22). The significance of the taxonomic distinctiveness concept prompted its use by several state agencies in Australia at the end of the 1980s and through research in systematics and conservation biology [START_REF] Avise | A role for molecular genetics in the recognition and conservation of endangered species[END_REF][START_REF] Faith | Genetic diversity and taxonomic priorities for conservation[END_REF]Faith , 2018a)). Quantitative measures of taxonomic distinctiveness for conservation originated in the 1990s with studies from [START_REF] May | Taxonomy as destiny[END_REF] and [START_REF] Vane-Wright | What to protect?-systematics and the agency of choice[END_REF]. [START_REF] Vane-Wright | What to protect?-systematics and the agency of choice[END_REF] introduced a measure of taxonomic distinctness that ranks species according to the number of cladistic groups they belong to, a perspective that was later refined by other authors (e.g., [START_REF] Erwin | An evolutionary basis for conservation strategies[END_REF][START_REF] Brooks | Phylogeny and biodiversity: conserving our evolutionary legacy[END_REF][START_REF] Crozier | Genetic diversity and the agony of choice[END_REF][START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF][START_REF] Faith | Genetic diversity and taxonomic priorities for conservation[END_REF][START_REF] Weitzman | On diversity[END_REF]; [START_REF] Crozier | Genetic distances and the setting of conservation priorities[END_REF][START_REF] Williams | Biodiversity, taxonomic relatedness, and endemism in conservation[END_REF][START_REF] Witting | The optimization of biodiversity conservation[END_REF]. However, taxonomic distinctiveness did not allow for the ability to measure the diversity of a set of species [START_REF] Vane-Wright | What to protect?-systematics and the agency of choice[END_REF]. [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF] proposed to link diversity and distinctiveness by introducing the notion of phylogenetic diversity (PD) as the sum of the branch lengths of the minimum spanning path joining a set of taxa on a tree. Phylogenetic diversity is assumed to represent the relative feature diversity of organisms so that maximizing PD may be a sound strategy for conservation because it would, on average, maximize the protection of feature diversity (a "feature" is a particular trait characteristic of a taxa). Due to their high number and because many are unknown, all taxon features cannot usually be accounted for [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF][START_REF] Faith | Genetic diversity and taxonomic priorities for conservation[END_REF](Faith , 2016a;;[START_REF] Pavoine | Is the originality of a species measurable?[END_REF]. This relation was based on an evolutionary model in which shared features are inherited from shared ancestry [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF], which was later shown to have important implications not only in conservation, but also in community ecology and biogeography (e.g., [START_REF] Webb | Phylogenies and community ecology[END_REF][START_REF] Gerhold | Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better)[END_REF][START_REF] Saito | Ecological versatility and the assembly of multiple competitors: cautionary notes for assembly inferences[END_REF]. Indeed, this assumption resulted in the use of phylogenetic information to unravel the process at the origin of diversity patterns and community assembly [START_REF] Webb | Phylogenies and community ecology[END_REF][START_REF] Davies | Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals[END_REF]. For example, it was hypothesized that the occurrence of distantly related species in a given area might indicate potential competition exclusions of evolutionary close species with similar niches. On the other hand, communities composed of closely related species may indicate possible environmental filtering of species adapted to a similar environment [START_REF] Webb | Phylogenies and community ecology[END_REF]. From this, the use of phylogenetic information in conservation biology and community ecology became on occasion indistinguishable, whereas the purposes of each domain highly differ in general. This resulted in the absence of consideration of one of the main goals of the use of phylogenetic information in conservation for many studies: the preservation of features' variations that may allow to maintain future options for humanity [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF].

This review aims to reinforce the rationale for the use of phylogenetic metrics in biodiversity conservation and their direct link with practical strategies while identifying some limitations and areas requiring further development in the existing methods. A parallel will be drawn with the use of phylogenetic information in community ecology to highlight how different assumptions and objectives, which are discussed for both biodiversity conservation and community ecology, may result in different uses of phylogenetic information. Finally, limitations for those uses in both fields are discussed in detail and we highlight how they may be alleviated. *S1Basic Principles For the Use of PD in Conservation Biology *T1The reason to use PD in conservation relies heavily on its link with feature diversity [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF]). Here we present the principles at the basis of this relationship and some of the resulting implications for conservation biology. We focus on the main arguments that justify the use of PD, although some others can be found elsewhere (e.g., [START_REF] Maclaurin | What is Biodiversity?[END_REF][START_REF] Tribot | Taxonomic and functional diversity increase the aesthetic value of coralligenous reefs[END_REF]Faith 2017Faith 2016b). The aim here is to guide readers to understand the value of PD in regard to practical applications such as the ones proposed in the following sections. We also referred to studies that have investigated the mechanisms at stake to explain the relationships between phylogenetic and functional diversity in macro-organisms, but also in micro-organisms (e.g., [START_REF] Goberna | Predicting microbial traits with phylogenies[END_REF]Faith 2018a). *S2Phylogenetic Diversity and Feature Diversity: A Relationship Based on Evolutionary Principles *T1Darwin observed that "species of the same genus have usually, though by no means invariably, some similarity in habits and constitution" (Darwin 1859:76). This observation has been one of the main justifications behind the use of phylogenies in conservation biology, but is also a matter of debate (Faith 2018a,b;[START_REF] Mazel | Is phylogenetic diversity a surrogate for functional diversity across clades and space? bioRxiv[END_REF]. Many phylogenetic metrics used in conservation were assumed to capture the variability or the scarcity of morphological or functional traits (e.g., [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF][START_REF] Redding | Incorporating evolutionary measures into conservation prioritization[END_REF][START_REF] Davies | Deconstructing the relationships between phylogenetic diversity and ecology: a case study on ecosystem functioning[END_REF]). This assumption is inherent to Darwin's theory that introduced the principle of filiation with modification in which shared characters can be explained by shared ancestry. This principle on which PD (among other measures) relies, have several implications: first, closely related species may share more characters than distantly related species; second, species descending from long branches are more likely to capture more ancient characters than species descending from shorter branches; and, third, summing the branch lengths that join species on a tree (a calculus from which the set of PD-based indices originates) captures, on average, their feature variation. Yet, some approaches missed this pattern-process model, which led to some misinterpretations [START_REF] Kelly | Phylogenetic trees do not reliably predict feature diversity[END_REF]. *S2Can Evolutionary History Reveal Future Benefits to Societies? *T1Biodiversity provides multiple services to humanity [START_REF] Gascon | The importance and benefits of species[END_REF] that have been classified under the notion of "ecosystem services." These services include regulation, production, habitat, and information functions (Millennium Ecosystem Assessment 2005). Going further, [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF][START_REF] Faith | Genetic diversity and taxonomic priorities for conservation[END_REF] introduced the primary goal of PD for conservation: by measuring feature diversity, PD maintains unanticipated and future benefits of biodiversity to human wellbeing, i.e., option values. Although ecosystem services are useful at focusing on current rapidly sensible benefits, option values consider long-term, human well-being that may depend on overall and more complex biodiversity sets [START_REF] Faith | Common ground for biodiversity and ecosystem services: the "partial protection" challenge[END_REF]. The concept of option values dates back to the 1970s: at this time it was already predicted that high rates of species extinction may cause the loss of options to humanity [START_REF] Iltis | Shepherds leading sheep to slaughter: the extinction of species and the destruction of ecosystems[END_REF]; see Faith 2018a for a review). For Bishop, "[t]he loss of any species irreversibly reduces the reservoir of future resources" (Bishop 1978:17) where resources "are not, they become" (Bishop 1978:11), depending on human tastes, preferences, and needs, among others. [START_REF] Bishop | Endangered species and uncertainty: the economics of a safe minimum standard[END_REF] showed that resources are uncertain and may irreversibly be lost with species extinctions. Today, preserving those unexpected future benefits appears crucial in the face of the many threats accelerating species extinctions and population loss such as climate change [START_REF] Faith | Climate change impacts on the tree of life: changes in phylogenetic diversity illustrated for Acropora corals[END_REF]. Indeed, it is almost given that uncertainties linked to the consequences of biodiversity losses will always persist, but the best conservation decisions have to be taken in spite of those uncertainties [START_REF] Forest | Phylogeny, extinction and conservation: embracing uncertainties in a time of urgency[END_REF][START_REF] Oliver | How much biodiversity loss is too much?[END_REF].

The unanticipated services of biodiversity may be provided by species evolutionary history and potential and, thus, captured by a measure such as PD that may help to maximize a variety of features on which future services depend [START_REF] Mouillot | Global marine protected areas do not secure the evolutionary history of tropical corals and fishes[END_REF]. Biodiversity conservation strategies based on PD are a "form of risk analysis that involves estimating patterns of variation, and then trying to conserve as much of that estimated variation as possible-as a way to retain 'options' (possible values) for the future" (Faith and Baker 2006:121). A well-known example of option values and PD was presented by [START_REF] Forest | Preserving the evolutionary potential of floras in biodiversity hotspots[END_REF] who found through experimentation that maximizing PD is the best way to conserve the medicinal and economic uses of the Cape flora, whereas a strategy based on species richness alone was less efficient. [START_REF] Oka | Phylogenetic clustering in beneficial attributes of tree species directly linked to provisioning, regulating and cultural ecosystem services[END_REF] found that phylogenetic distant tree species in Japan tended to provide different provisioning, regulating, and cultural services and, therefore, it may be expected that PD could capture the variation of these services. In a similar logic, Faith (2018a) highlighted the insurance value of PD at the scale of ecosystems. The identification of species allowing for the preservation of ecosystem resilience is uncertain, but PD may help to maintain a variety of features that may permit ecosystem to respond to the disturbance. Another striking example is the emerging positive contribution of PD to human health. Indeed, maintaining bacterial phylogenetic diversity could have important consequences on the resilience of those bacterial communities and their metabolic potential [START_REF] Blaut | Metabolic diversity of the intestinal microbiota: implications for health and disease[END_REF][START_REF] Lozupone | Diversity, stability and resilience of the human gut microbiota[END_REF]; see also Faith 2018a for some other examples). Although most of this review is built from studies on macro-organisms, PD has also huge implications in the field of microbiology, especially because phenotypes of microorganisms are largely unknown, but their variation may be predicted through phylogenetic information [START_REF] Goberna | Predicting microbial traits with phylogenies[END_REF].

The potential surrogacy of PD for option values has encouraged its use for regional and global conservation programs (Millennium Ecosystem Assessment 2005;[START_REF] Ipbes | Nature's contributions to people and quality of life. Page 41[END_REF]. In particular, it may support the definition of a global measure of biodiversity based on a PD metric, which would guide conservation efforts in the long term in the context of uncertainties regarding environmental change [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF](Faith , 2016b;;[START_REF] Forest | Phylogeny, extinction and conservation: embracing uncertainties in a time of urgency[END_REF]. Indeed, conservation based on PDbased measures should on average provide more goods to societies than those based on other measures of biodiversity [START_REF] Forest | Preserving the evolutionary potential of floras in biodiversity hotspots[END_REF][START_REF] Lean | The value of phylogenetic diversity[END_REF]. Measures based on phylogenies were also proposed as planetary boundaries in order to maintain a safe operating system in which biodiversity benefits to societies would be preserved [START_REF] Faith | Evosystem services: an evolutionary perspective on the links between biodiversity and human well-being[END_REF][START_REF] Mace | Approaches to defining a planetary boundary for biodiversity[END_REF]. The rationale for using phylogenetic information as a planetary boundary is that it may provide long-term ecological and evolutionary potential (but see below) and, as previously stated, future benefits for societies. Last but not least, the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) called to maintain the options provided by nature to humankind facing future needs [START_REF] Díaz | The IPBES Conceptual Framework-connecting nature and people[END_REF]. From this, IPBES drew a framework based on PD to estimate those "option values" and their threats [START_REF] Faith | Indicators for the expected loss of phylogenetic diversity[END_REF][START_REF] Ipbes | Nature's contributions to people and quality of life. Page 41[END_REF]. All of these proposals based on "option values" make PD a powerful approach for conservation goals that aim to maintain human well-being.

Although conserving PD may allow an increase in the probability that features providing unexpected benefits to humankind are maintained, the relationship between PD and option values would be even stronger if phylogenetic trees could reveal the evolutionary potential of species [START_REF] Mouquet | Ecophylogenetics: advances and perspectives[END_REF]. Indeed, this would help predict which set of species would best adapt or diversify in the face of ecological changes and would be more likely to provide or preserve future ecosystem functions and services [START_REF] Sarrazin | Evolution in the Anthropocene[END_REF]. *S2Do Phylogenetic Trees Reflect Opportunities For Future Evolution? *T1Past and current human activities, besides species domestication, have imposed a strong selection on species, their genetic diversity, and on their number [START_REF] Hendry | Evolutionary principles and their practical application[END_REF].

Estimating and preserving the possibilities for species to evolve, as a single unit and in communities, appears crucial for the maintenance of biodiversity, especially in the face of impending global environmental changes. Conserving species with high evolutionary potential would contribute to maintaining biodiversity into the future and would help to preserve the functions and associated services it provides to humans [START_REF] Sarrazin | Evolution in the Anthropocene[END_REF].

How can phylogenies help identify the evolutionary potential of species? First, using PD to maximize feature variation would in principle increase the probability that feature diversity, which is vital for species to be able to adapt to future environmental changes, will be maintained, consequently providing evolutionary potential. This assumption has been introduced by Faith who noted that PD ensures "that one or more members of the subset can adapt to changing conditions" (Faith 1992:2). Later, Forest et al. stated that features useful for the adaptation of species to change are not known such that "maximizing PD will in turn maximize the options for future diversification" (Forest et al. 2007:759). Yet, the relationship between PD and evolutionary potential require further investigation.

Evolutionary history of species influences their phenotype and genotype, which then may impact on the direction and speed of contemporary evolution [START_REF] Hendry | Evolutionary principles and their practical application[END_REF]). In the absence of specific selection pressures, species with a long history of evolutionary independence are more likely to harbor unique genetic variation that, in turn, may allow them to adapt to change in different ways from other species. Indeed, due to random mutations they may become either more vulnerable or more resistant than other species [START_REF] Hendry | Evolutionary principles and their practical application[END_REF]. In contrast, young lineages may evolve more rapidly and have a greater capacity to diversify or adapt and could serve as the source of long-term evolution [START_REF] Hendry | Evolutionary principles and their practical application[END_REF][START_REF] Mouquet | Ecophylogenetics: advances and perspectives[END_REF]). However, whether long or short branches best represent the possibilities of future evolution is still poorly understood and further research on this topic is needed to guide conservation practices [START_REF] Rolland | Using phylogenies in conservation: new perspectives[END_REF]. Some authors suggested that estimating past diversification rates across current lineages might indicate which lineages would be more prone to diversify in the future [START_REF] Rolland | Using phylogenies in conservation: new perspectives[END_REF]). The potential for future evolution of a species might also be assessed by combining information on rates of trait evolution and diversification [START_REF] Morlon | Inferring the dynamics of diversification: a coalescent approach[END_REF]. However, several researchers do not support the idea of using phylogenies for estimating the future possibilities of evolution in particular because empirical proofs are lacking, which paves the way for new research [START_REF] Rolland | Using phylogenies in conservation: new perspectives[END_REF][START_REF] Winter | Phylogenetic diversity and nature conservation: where are we?[END_REF]. Thus, in spite of some authors arguing that PD is related to evolutionary potential (e.g., [START_REF] Voskamp | Global patterns in the divergence between phylogenetic diversity and species richness in terrestrial birds[END_REF], there are no stringent proofs, to our knowledge, that it is actually the case. *S2Can Phylogenetic Information Reveal Ecosystem Processes? *T1Although the primary goal of using PD for conservation is the maintenance of feature variation and "option values," some authors have been interested in the relationship between PD and the diversity of some functional traits (e.g., [START_REF] Loreau | Biodiversity and ecosystem functioning: current knowledge and future challenges[END_REF][START_REF] Hooper | Effects of biodiversity on ecosystem functioning: a consensus of current knowledge[END_REF]. Given that phylogenetic variation may represent variation in species traits, based on the principle of "filiation with modification," it has been argued that PD could be a good surrogate of functional diversity (Faith called this the proxy value of PD; Faith 2018a) and capture ecosystem functions [START_REF] Srivastava | Phylogenetic diversity and the functioning of ecosystems[END_REF][START_REF] Davies | Deconstructing the relationships between phylogenetic diversity and ecology: a case study on ecosystem functioning[END_REF]. The main idea follows the community ecology framework [START_REF] Webb | Phylogenies and community ecology[END_REF]: communities with high mean phylogenetic distance among species (i.e., communities composed of distantly related species) should comprise species with high niche complementarity owing to the evolution of different traits, implying high niche differentiation among distantly related species [START_REF] Srivastava | Phylogenetic diversity and the functioning of ecosystems[END_REF]. Given this higher niche difference, and consequently higher complementarity, the resources in the environment would be more efficiently used, providing higher yields of given processes such as productivity in plants [START_REF] Srivastava | Phylogenetic diversity and the functioning of ecosystems[END_REF].

Moreover, communities composed of distantly related species should have lower levels of exploitative competition due to niche differentiation and, thus, would be more buffered against competitive exclusions [START_REF] Webb | Phylogenies and community ecology[END_REF]. Second, as phylogenetic difference may relate to feature difference and ecological functions are generally provided by interrelated multiple traits, a community of distantly related species may be functionally highly diverse, and this was shown to increase the ecosystem functions provided [START_REF] Cadotte | Phylogenetic diversity and productivity: gauging interpretations from experiments that do not manipulate phylogenetic diversity[END_REF][START_REF] Cadotte | Phylogenies in Ecology: A Guide to Concepts and Methods[END_REF]. Contrary to the rationale for the use of PD to conserve option values, the relationship between PD and ecosystem functions is thus not based on the preservation of biodiversity units but rather on the maintenance of ecological integrity (Faith 2018a). However, the relationship between PD, functional diversity, and ecosystem functions is not always well supported, a topic we discuss further (see the section titled When Phylogenetic and Feature Variation Are Not Congruent:

Limitations and Solutions).

A conclusion that can be drawn from this section is that the surrogacy between PD and feature diversity is well founded: it relies on basic evolutionary principles that tend to make closely related species more similar in traits than distantly related ones. Many assumptions that use PD in conservation depend on this relationship. The conservation logics presented here comprises the proxy value (PD may reveal ecosystem processes), the option value (PD may capture unexpected future benefits to humanity), and the insurance value (PD may preserve the resilience of an ecosystem; Faith 2018a). The option value argument is certainly the bestsupported reason for the use of PD in conservation. Further, we will discuss appropriate conservation practices that correctly consider the relationship between PD and feature diversity, and others that fail to account for this surrogacy, leading to the loss of benefits linked to the use of PD. In particular, we will emphasize approaches based on evolutionary distinctiveness that, although they may not allow to maximize feature variation, have a high practical interest. *S1Practical Use of Phylogenetic Information in Conservation *S2Conserving PD and Feature Variation *S3The PD Calculus *T1As stated above, the main benefits linked to the use of measures based on phylogenies in conservation is to capture feature variations, which is beneficial to society faced with unpredictable change and may help for the adaptation of biodiversity to change [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF].

Justified by the rationale that shared features are due to a shared ancestry, optimizing the conservation of feature variation may be achieved by securing the species that capture the highest proportion of a phylogenetic tree. This aim is reached by maximizing the sum of branch lengths of a phylogenetic tree that is protected, i.e., maximizing the PD calculus (the PD of a set of species is equal to the sum of the lengths of all the branches from the corresponding minimum spanning path; Faith 1992), whereas measures that preserve some branch lengths several times do not maximize feature variation [START_REF] Faith | Integrating phylogenetic diversity, complementarity, and endemism for conservation assessment[END_REF][START_REF] Faith | Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges[END_REF]. A direct consequence is that in a scenario where only a limited number of species can be rescued, those capturing the most PD should be prioritized. On the contrary many metrics based on phylogenetic trees may not be suitable to achieve this goal (see for example "*T1Another strategy is to give priority to the threatened diversity of a region. Several PD-based measures have been developed with this specific aim in mind (e.g., Faith 2008;[START_REF] Rosauer | Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history[END_REF]. A crucial aspect to consider is that the risk of losing a deep branch depends on the risk of losing all of the species it supports (i.e., the phylogenetic complementarity of extinction risks). If this complementarity is not accounted for, the risk of losing deep branches will be incorrectly assessed and, consequently, so is the risk of losing PD [START_REF] Steel | Hedging our bets: the expected contribution of species to future phylogenetic diversity[END_REF]Faith 2008;[START_REF] Veron | Loss and conservation of evolutionary history in the Mediterranean Basin[END_REF][START_REF] Veron | Predicting loss of evolutionary history: where are we?[END_REF]. Extinction risks are generally based on probabilities of extinctions (Faith 2008) or on the restricted range of species [START_REF] Rosauer | Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history[END_REF]. Estimating PD on a phylogenetic tree where branches are weighted by those extinction risks may represent how much feature diversity is threatened. In spatial planning, those measures can be included in a PD gain strategy as described above. One would prioritize the sites that would secure the maximum threatened PD of a region while considering its phylogenetic complementarity [START_REF] Veron | Priority areas for phylogenetic diversity: maximising gains in the Mediterranean basin[END_REF]. This may result in very different conservation strategies than when extinction risks are not accounted for. Finally, information about land use, probability of strategy success, or conservation costs could also be used together with a PD gain approach to comply with the requisites for conservation planning assessments (e.g., [START_REF] Billionnet | Solution of the generalized Noah's Ark problem[END_REF].

In conclusion, the approaches described above are not exhaustive and several strategies may be adopted to conserve PD in spatial planning or in species prioritization strategies (other measures are described by Faith 2008). However, assuming that shared traits are due to shared ancestry, the rationale to preserve feature variation and potential option values should rely on the phylogenetic complementarity of sites and/or species. This may help to clarify the use of PD in conservation [START_REF] Winter | Phylogenetic diversity and nature conservation: where are we?[END_REF]) and to consider the criteria of evolutionary history in the implementation of practical conservation actions.

Figure 1. THREE PRIORITIZATION STRATEGIES BASED ON PD. PD is measured as the sum of branch lengths on the spanning path joining taxa on a tree to the root. In all scenarios we assume that only three sites out of four can be protected due to limited resources. Protected sites are represented by red squares and safe branches are shown in black. 1) The conservation value of a site is represented by its total PD. The first site to be chosen includes species A, B, and D (PD = 26 Ma). The second site selected comprises species A and B with PD = 20 Ma, although no additional branch length is protected. Finally, the third site to protect harbors species C and D (PD = 13 Ma). 2) Sites are selected in function of their local PD gain: branch lengths are weighted by the proportion of their range that is safe following the protection of a site. The order of selection of sites is 1, 4, and 2. 3) Sites are prioritized following a global PD gain strategy: the protection of one occurrence of a species conduct to the gain of all branches supporting that species. Only two sites, those numbered 3 and 2, are needed to protect the entire tree. *S2THE ED FRAMEWORK"). Going further, and by considering reasonable that phylogenetic variation is a good surrogate of feature variation, PD, and PD-like measures (e.g. [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF]Faith 2008;[START_REF] Rosauer | Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history[END_REF][START_REF] Veron | Predicting loss of evolutionary history: where are we?[END_REF], are likely to be the only existing measures based on phylogenetic trees that may help to preserve feature diversity of conservation interest [START_REF] Faith | Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges[END_REF][START_REF] Faith | Integrating phylogenetic diversity, complementarity, and endemism for conservation assessment[END_REF]). *S3PD Gain *T1Various measures have been proposed to extend the PD framework (Faith 2008). In particular, we highlight here a method that allows the preservation of feature variation based on PD gain [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF]Faith et al. 2018a). Phylogenetic diversity gain is defined as the amount of branch length a species adds to the PD already represented by a given set of species, also known as PD complementarity or PD endemism value, when the set of species is all other species [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF][START_REF] Faith | Integrating phylogenetic diversity, complementarity, and endemism for conservation assessment[END_REF]). In a conservation strategy, PD gain is the additional branch length that is secured after the protection of species and/or sites. Consequently, PD gain is of great interest for conservation planning because it helps to unravel how sites complement each other in order to represent the overall diversity of a region. However, several regional studies have used the total PD of a given site (often a grid cell) as its conservation value and thus did not consider that branches can be shared among sites. This departure from the basic framework of conservation planning based on the complementarity of sites [START_REF] Margules | Systematic conservation planning[END_REF] may originate from the community ecology framework where the total PD of a site is of interest (e.g., [START_REF] Gómez-Ortiz | Spatial variation of mammal richness, functional and phylogenetic diversity in the Mexican transition zone[END_REF]; see the section titled Why Approaches in Community Ecology and Conservation Biology Should Be Different). Yet, in conservation biology, the purpose to maximize the protection of a region's diversity is not achieved with this method because sites with the highest total PD will most likely share branches and thus redundant information (Figure 1; [START_REF] Pollock | Large conservation gains possible for global biodiversity facets[END_REF]Faith et al. 2018a). This could lead to the prioritization of sites that add little branch length (i.e., little PD gain) and, consequently, little feature diversity to a set of already protected sites.

Considering phylogenetic complementarity of sites and species is thus more appropriate to capture feature variation. A recent set of works have incorporated PD gain as a strategy to protect biodiversity (e.g., [START_REF] Pollock | Large conservation gains possible for global biodiversity facets[END_REF][START_REF] Rosauer | Phylogenetically informed spatial planning is required to conserve the mammalian tree of life[END_REF][START_REF] Veron | Priority areas for phylogenetic diversity: maximising gains in the Mediterranean basin[END_REF]. Interestingly, [START_REF] Pollock | Large conservation gains possible for global biodiversity facets[END_REF] showed how PD gain could be used for conservation objectives at both global and local scales. At global scale, securing one occurrence of a given species results in a gain equivalent to the full length of the branches supporting that species (Figure 1). On the other hand, when the aim is to emphasize local assemblages, the PD gained at a local site is measured on a phylogenetic tree where each branch is weighted by the proportion of its protected range (Figure 1; Pollock et al. 2007). Thus, a strategy to spatially protect PD would be to prioritize the minimum number of sites that maximize the gain in PD (Figure 1; see also [START_REF] Faith | Indicators for the expected loss of phylogenetic diversity[END_REF] to define an order of priority among these sites). Whether conservation objectives are local or global may cause the identification of priority sites to differ (Figure 1).

One drawback of this PD gain approach is that it defines an effective set of protected sites yet, in practice, protected areas are rarely implemented as a set. Thus, it remains essential to identify sites that are likely to be important to include over many possible sets even though they do not optimize the overall PD of a region. Those sites could be based on a hotspot approach as proposed by [START_REF] Veron | Priority areas for phylogenetic diversity: maximising gains in the Mediterranean basin[END_REF]. Moreover, the PD gain approach for macro-organisms has mainly been used at global or regional scales with the view of preserving "option values" (e.g., [START_REF] Mouillot | Global marine protected areas do not secure the evolutionary history of tropical corals and fishes[END_REF]. This approach could be extended at the scale of ecosystems where PD may provide an "insurance value" (Faith 2018a). Species in the ecosystem that may be useful for its resilience are unknown, but maximizing their PD and feature diversity may maximize its chance to resist and/or recover from perturbations. *S3PD At Risk *T1Another strategy is to give priority to the threatened diversity of a region. Several PDbased measures have been developed with this specific aim in mind (e.g., Faith 2008;[START_REF] Rosauer | Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history[END_REF]. A crucial aspect to consider is that the risk of losing a deep branch depends on the risk of losing all of the species it supports (i.e., the phylogenetic complementarity of extinction risks).

If this complementarity is not accounted for, the risk of losing deep branches will be incorrectly assessed and, consequently, so is the risk of losing PD [START_REF] Steel | Hedging our bets: the expected contribution of species to future phylogenetic diversity[END_REF]Faith 2008;[START_REF] Veron | Loss and conservation of evolutionary history in the Mediterranean Basin[END_REF][START_REF] Veron | Predicting loss of evolutionary history: where are we?[END_REF]. Extinction risks are generally based on probabilities of extinctions (Faith 2008) or on the restricted range of species [START_REF] Rosauer | Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history[END_REF]. Estimating PD on a phylogenetic tree where branches are weighted by those extinction risks may represent how much feature diversity is threatened. In spatial planning, those measures can be included in a PD gain strategy as described above. One would prioritize the sites that would secure the maximum threatened PD of a region while considering its phylogenetic complementarity [START_REF] Veron | Priority areas for phylogenetic diversity: maximising gains in the Mediterranean basin[END_REF]. This may result in very different conservation strategies than when extinction risks are not accounted for. Finally, information about land use, probability of strategy success, or conservation costs could also be used together with a PD gain approach to comply with the requisites for conservation planning assessments (e.g., [START_REF] Billionnet | Solution of the generalized Noah's Ark problem[END_REF].

In conclusion, the approaches described above are not exhaustive and several strategies may be adopted to conserve PD in spatial planning or in species prioritization strategies (other measures are described by Faith 2008). However, assuming that shared traits are due to shared ancestry, the rationale to preserve feature variation and potential option values should rely on the phylogenetic complementarity of sites and/or species. This may help to clarify the use of PD in conservation [START_REF] Winter | Phylogenetic diversity and nature conservation: where are we?[END_REF]) and to consider the criteria of evolutionary history in the implementation of practical conservation actions. in the phylogenetic tree. For example, the widely used fair proportion index partitions the branch lengths of a phylogenetic tree (i.e., PD) among all of the species it supports [START_REF] Isaac | Mammals on the EDGE: conservation priorities based on threat and phylogeny[END_REF]).

Species are then prioritized according to their ED value. This also implies that the sum of all ED scores measured on a phylogeny is equal to the total PD of all taxa comprised in this tree.

The ED order of prioritization is, however, not as efficient as the PD calculus at capturing the variations of features (Figure 2). This is mainly because ED measures do not account for the phylogenetic complementarity among species (i.e., by conserving species with the highest ED, some deep branches are likely to be represented several times whereas others may not be represented at all; Figure 2). Feature variation is therefore not properly captured. For example, [START_REF] Isaac | Mammals on the EDGE: conservation priorities based on threat and phylogeny[END_REF] argued that the species with the highest ED scores, and thus the highest priority, would be two closely related species. However, the choice of those two species does not look to be the best strategy to maximize feature variation as it does not represent the highest protected proportion of the tree of life (see the section titled *S2Conserving PD and Feature VARIATION). In a PD-based strategy, two distantly related species would have been selected to protect most feature variation.

Similarly, some spatial planning research has focused on preserving sites with the highest ED values, especially by summing/averaging ED scores of the species occurring in each site and prioritizing sites with the highest cumulative ED (e.g., [START_REF] Daru | A global trend towards the loss of evolutionarily unique species in mangrove ecosystems[END_REF][START_REF] Safi | Global patterns of evolutionary distinct and globally endangered amphibians and mammals[END_REF][START_REF] Jetz | Global distribution and conservation of evolutionary distinctness in birds[END_REF]. This method should also not be viewed as a conservation planning strategy that maximizes feature variation because phylogenetic complementarity is not taken into consideration. These arguments related to spatial planning can be applied to all types of ED measures even those that include extinction risks or endemicity such as Evolutionary Distinctiveness and Global Endangerment (EDGE; [START_REF] Isaac | Mammals on the EDGE: conservation priorities based on threat and phylogeny[END_REF] *S3Evolutionary Distinctiveness Remains a Useful Measure For Practical Conservation *T1Although an approach based on preserving species with high ED may not be the best strategy to capture feature variation, this measure is still valuable for conservation biology. First, the rationale of protecting species with high ED values is linked to their isolation from all other species and to the fact that they may represent long branches capturing old features shared by very few species [START_REF] Magnuson-Ford | Rockfish (Sebastes) that are evolutionarily isolated are also large, morphologically distinctive and vulnerable to overfishing[END_REF][START_REF] Redding | Evolutionary distinctiveness, threat status, and ecological oddity in primates[END_REF][START_REF] Turvey | Investing in evolutionary history: implementing a phylogenetic approach for mammal conservation[END_REF][START_REF] Stein | Global priorities for conserving the evolutionary history of sharks, rays and chimaeras[END_REF]; but see [START_REF] Grandcolas | What is the meaning of extreme phylogenetic diversity? The case of phylogenetic relict species[END_REF]. From this, conservation of species with a high ED generally would be able to capture a lot of PD (although it is not the maximum PD) and would contribute to the maintenance (but not the maximization) of feature variation [START_REF] Faith | Indicators for the expected loss of phylogenetic diversity[END_REF].

Other arguments to preserve highly evolutionary distinct species are essentially practical (e.g., [START_REF] Faith | Phylogenetic diversity, functional trait diversity and extinction: avoiding tipping points and worst-case losses[END_REF][START_REF] Forest | Gymnosperms on the EDGE[END_REF][START_REF] Stein | Global priorities for conserving the evolutionary history of sharks, rays and chimaeras[END_REF][START_REF] Thévenin | Reintroductions of birds and mammals involve evolutionarily distinct species at the regional scale[END_REF]. Isaac et al. justified the protection of species with the highest ED values, despite the fact that they are closely related, because "the extinction of either would leave a single descendant of the oldest and most unusual lineage in the phylogeny" (Isaac et al. 2007:2). For [START_REF] Redding | Incorporating evolutionary measures into conservation prioritization[END_REF], real-world conservation practice is based on lists of threatened species, and PD does not offer an order of conservation prioritization, especially because there will be as many possible rankings of species as there are PD maximizing solutions in a set of species. A species list based on PD may be difficult to implement at the management level [START_REF] Redding | Incorporating evolutionary measures into conservation prioritization[END_REF]. Moreover, strategies based on maximizing PD are based on a set of species (or sites). Consequently, the conservation of a species outside this set may lead to the identification of a new and very distinct set to preserve PD, and management actions are rarely implemented on a set of species or sites (e.g., [START_REF] Thévenin | Reintroductions of birds and mammals involve evolutionarily distinct species at the regional scale[END_REF]). Thus, it remains important to identify species that may capture large amounts of PD independently of a given set. To this aim, because they may be evolutionarily isolated and descending from long branches, species with high ED may capture more branch lengths and more PD than species with low ED as showed by [START_REF] Redding | Evolutionarily distinctive species often capture more phylogenetic diversity than expected[END_REF].

Regarding extinctions, [START_REF] Chaudhary | Projecting global land use-driven evolutionary history loss[END_REF] showed that summing the ED scores of extinct species was strongly correlated to PD loss. By looking at the calculus of ED and expected loss of PD, [START_REF] Faith | Indicators for the expected loss of phylogenetic diversity[END_REF] showed that the sum of ED scores of threatened species was approximately the total expected loss of PD, assuming that the probabilities of extinctions of threatened species were close to 1.

To summarize, the ED approach has many advantages, but future research based on this measure should be aware that it does not maximize feature variation and option values. High ED species may capture rare features and have practical interest to capture more PD than expected when the protection of a set of species maximizing PD cannot be set up in real-world conservation actions. The rationale to preserve feature variation and related conservation benefits may be reached by a PD calculus that maximizes the proportion of the Tree of Life protected. However, some PD approaches were erroneously thought to protect feature variation whereas they may be more informative in the field of community ecology. In the next section we will underline what these approaches are and how different goals in conservation biology and community ecology require different uses of PD. *S1Why Approaches in Community Ecology and Conservation Biology Should Be Different *T1Some approaches using PD in conservation biology have likely been influenced by those applied in community ecology (or at least they became similar on occasions) resulting in wrong interpretations and practices. Although we previously discussed what phylogenies can tell us about feature variation and its potential for conservation, in this section we discuss what PD can tell us about species interactions influencing community and network assembly. By doing so we will show why and when approaches in conservation biology and community ecology should differ.

*S2Some Phylogenetic Information of Interest in Community Ecology: Niche Conservatism and

Community Assembly *T1As previously mentioned, the idea that phylogenetic distance should be related to species interaction can be traced back to Darwin (1859). He hypothesized that, because of their common ancestry, congeners should have many similar characters, increasing the chances of exploiting the environment in a similar fashion-what would be later known as the competitionrelatedness hypothesis (Cahill et al. 2008). [START_REF] Gause | Experimental analysis of Vito Volterra's mathematical theory of the struggle for existence[END_REF], inspired by Darwin's ideas and by [START_REF] Lotka | Elements of Physical Biology[END_REF] and [START_REF] Volterra | Fluctuations in the abundance of a species considered mathematically[END_REF], established the foundations for the theory of competitive exclusion. This theory proposes that two species occupying the same ecological niche cannot coexist in a stable manner. It was later complemented by the limiting similarity modelintroduced by MacArthur and Levins (1967) and revised by [START_REF] Abrams | The theory of limiting similarity[END_REF]-that demonstrates mathematically how species coexistence could be limited by their degree of niche overlap. Works by [START_REF] Felsenstein | Phylogenies and the comparative method[END_REF] and [START_REF] Harvey | The Comparative Method in Evolutionary Biology[END_REF] introduced the first formal discussions surrounding the concept of niche conservatism. Because a species is expected to not easily adapt to conditions outside its fundamental niche, evolutionary changes are likely to be an inherently conservative process [START_REF] Holt | Analysis of adaptation in heterogeneous landscapes: implications for the evolution of fundamental niches[END_REF][START_REF] Wiens | Niche conservatism: integrating evolution, ecology, and conservation biology[END_REF]. Thus, closely related species should fundamentally overlap in their niches.

Based on the concepts of niche conservatism and limiting similarity, [START_REF] Webb | Phylogenies and community ecology[END_REF] proposed the use of phylogenetic relatedness as a surrogate for niche overlap, which allowed for the understanding of community assembly through the analysis of patterns of phylogenetic structure. According to their logic, when closely related species co-occur more often than expected by chance (i.e., phylogenetic clustering), one could infer the predominance of environmental filtering, whereas when closely related species co-occur less than expected by chance (i.e., phylogenetic overdispersion), one could infer the predominance of competitive exclusion due to the limited similarity among closely related species. This concept has been widely used due to the straightforward way that observed patterns can be interpreted and the increasing availability of comprehensive data sets [START_REF] Cavender-Bares | Phylogenetic overdispersion in Floridian oak communities[END_REF][START_REF] Vamosi | Body size, rarity, and phylogenetic community structure: insights from diving beetle assemblages of Alberta[END_REF][START_REF] Emerson | Phylogenetic analysis of community assembly and structure over space and time[END_REF].

Although environmental filtering and competitive exclusion are only a part of the story explaining how species could coexist [START_REF] Gerhold | Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better)[END_REF][START_REF] Saito | Ecological versatility and the assembly of multiple competitors: cautionary notes for assembly inferences[END_REF], these assumptions foster the use of PD in community ecology that, therefore, relies on very different logic than in conservation biology. *S2Phylogenetic Diversity in Community Ecology-A Generalization *T1From the logic described above, several metrics based on phylogenetic trees have been developed in community ecology that are related to divergence, diversity, and evenness [START_REF] Tucker | A guide to phylogenetic metrics for conservation, community ecology and macroecology[END_REF]). We will here focus on the use of PD to show how it differs from its use in conservation biology; reviews on other measures are available elsewhere (e.g., [START_REF] Pavoine | Measuring biodiversity to explain community assembly: a unified approach[END_REF][START_REF] Tucker | A guide to phylogenetic metrics for conservation, community ecology and macroecology[END_REF].

The PD value [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF]) of a set of species found at a given site has been employed as a measure of phylogenetic alpha diversity (e.g., [START_REF] Chai | Patterns of taxonomic, phylogenetic diversity during a long-term succession of forest on the Loess Plateau, China: insights into assembly process[END_REF] to assess the coexistence or functional differences among species (Cadotte et al. 2010). One particular approach has been to compare the PD and species richness (SR) at a given site. High PD compared to SR would relate to the occurrence of distantly related species and indicate potential competitive exclusions, while low PD over SR may reveal communities composed of closely related species and possible environmental filtering (overdispersion versus clustering; see above). For example, [START_REF] Chai | Patterns of taxonomic, phylogenetic diversity during a long-term succession of forest on the Loess Plateau, China: insights into assembly process[END_REF] used this approach to reveal the deterministic and stochastic process at the origin of diversity patterns in a long-term study of forest succession. Moreover, relative PD might provide insights into evolutionary processes, including the balance between speciation and extinction that affect community assembly [START_REF] Pavoine | Measuring biodiversity to explain community assembly: a unified approach[END_REF]. [START_REF] Davies | Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals[END_REF] measured the mammal relative PD in individual sites to disentangle areas where speciation has been rapid and immigration rare (low PD relative to species richness) and areas where diversification has been slow and long-distance immigrations frequent (high PD relative to species richness). This is, of course, a very general view of the use of PD in community ecology that is often employed in combination with other measures (Cadotte et al. 2010;[START_REF] Pavoine | Correlations between phylogenetic and functional diversity: mathematical artefacts or true ecological and evolutionary processes?[END_REF]).

However, this shows that PD is used for different purposes in community ecology and conservation biology and should not be confused. Although the PD of a given site may be of interest to understand community assembly, it may be less important in conservation biology where, to preserve feature variation, the phylogenetic complementarity of sites and species is considered. There are cases when community ecology and conservation ecology meet, for example, to predict the effect of invasions [START_REF] Yguel | Phytophagy on phylogenetically isolated trees: why hosts should escape their relatives[END_REF][START_REF] Yguel | Insect herbivores should follow plants escaping their relatives[END_REF] or ecosystem functioning, as discussed above. Yet, we prefer to highlight the main differences and avoid sources of confusion in both fields of ecology. *S1When Phylogenetic and Feature Variation Are Not Congruent: Limitations and Solutions *T1A common point in conservation biology and community ecology frameworks is the use of PD under the assumption that large evolutionary distances among species indicate more feature differences among them. All of the benefits that can result from this relationship make it likely that many studies based on PD will be conducted in the future. Yet, existing limitations and misinterpretations to this assumption have fuelled the ongoing debate on the use of phylogenetic information in both conservation biology and community ecology (e.g., [START_REF] Cadotte | Why phylogenies do not always predict ecological differences[END_REF][START_REF] Mazel | Is phylogenetic diversity a surrogate for functional diversity across clades and space? bioRxiv[END_REF]. As stated by Faith and from what is clear in the original PD paper [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF]) "PD should not be expected to magically make inferences about every favorite character or feature" (Faith 2018a:6). This implies that, despite clear benefits, some conclusions from PD investigations should be drawn with care. We present some of the most common sources of limitations in the PD and feature diversity relationship, their consequences, and how they may be alleviated. Some limitations have also been treated in depth by other authors, so the general overview we present here may be complementary to previous work (e.g., [START_REF] Cadotte | Why phylogenies do not always predict ecological differences[END_REF]Box 1). We focus our attention on how these limitations may (or may not) weaken the conclusions drawn from PD analyses in conservation and community ecology presented in the section above. *S2A General Overview of Existing Limitations *S3Phylogenetic Reconstruction *T1Modern phylogenetic trees originated from cladistics, a set of methods used to reconstruct relationships between organisms established by Hennig [START_REF] Hennig | Grundzüge einer Theorie der Phylogenetischen Systematik[END_REF][START_REF] Hennig | Phylogenetic systematics[END_REF].

Phylogenetic trees enable the grouping of species/organisms based on the analysis of homologous characters (i.e., characters inherited from a common ancestor). Currently, this method is the preferred principle to classify organisms and numerous statistical and computational tools have been developed (Box 1; e.g., maximum parsimony, maximum likelihood, and Bayesian methods) in the quest to find the most accurate phylogenetic trees [START_REF] Huelsenbeck | Bayesian inference of phylogeny and its impact on evolutionary biology[END_REF][START_REF] Tamura | MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods[END_REF].

All of the tools available for phylogenetic tree reconstruction have advantages, drawbacks, and limitations that should be carefully considered. In Box 1 we relate sources of uncertainties in some of the most employed methods for phylogenetic reconstruction. This shows that the relationship between phylogenetic variation and feature variation may already be blurred by these reconstruction methods.

BOX 1

Phylogenetic tree reconstruction methods as source of uncertainties

The construction of phylogenetic trees is a difficult task since there is no methodology that guarantees the recovery of the "true" tree. Methods for inferring phylogenetic trees are classified into two categories according to the type of data used: distance-based and characterbased. *S1Distance-Based Methods *T1Distance matrix methods start by converting molecular data into a pairwise distance matrix, which is then used for inferring a phylogenetic tree. There are mathematical models to calculate distances between each pair of operational taxonomic units (OTUs), based on different models of molecular evolution that result in different genetic or evolutionary distances. Most distance methods use clustering algorithms to construct a single phylogenetic tree. These methods are suitable for the rapid analysis of large datasets as they are not computationally demanding. *S2Unweighted Pair Group Method with Arithmetic Means (UPGMA) *T1UPGMA is one of the simplest methods for tree reconstruction. The clustering works by searching for the smallest pairwise distance value between OTUs in the matrix that will form a new cluster. Then a new distance matrix is calculated between the newly formed cluster and the remaining OTUs. The process continues until all OTUs are clustered. The tree is formerly additive and thus all nodes are equally distant from the root. UPGMA assumes that evolutionary rates in all branches are similar, which is generally not the case [START_REF] Nei | Relative efficiencies of different tree-making methods for molecular data[END_REF]. *S2Neighbor Joining (NJ) *T1This method differs from UPGMA in that there is no assumption about the distance between OTUs. The NJ algorithm does not construct clusters, but minimizes the length of all internal branches [START_REF] Saitou | The neighbor-joining method: a new method for reconstructing phylogenetic trees[END_REF]. The process begins with an estimation of evolutionary distances correcting for multiple substitution events at the same site. In a second step, the minimal distance is used to introduce a new node that groups a pair of OTUs for which evolutionary distance is minimal. Then a new matrix is calculated from the new node to each other's terminal node. The process is repeated until an unrooted tree is constructed. A distantly related taxon (outgroup) can be chosen to root the tree.

A serious weakness for distance methods such as NJ and UPGMA is that the observed differences between sequences are not accurate reflections of the evolutionary distances between them, especially due to non-constant evolutionary rates. In that case, corrections must be applied, but there is no consensus on what correction could be the best. NJ and UPGMA appear as suitable methods when sequences have diverged recently, but could be particularly misleading when estimating old relationships [START_REF] Holder | Phylogeny estimation: traditional and Bayesian approaches[END_REF]. Other distance-based methods are Fitch-Margoliash, minimum evolution, or least-squares algorithms. *S1Character-Based Models *T1Character-state methods use variation in a set of discrete characters (e.g., sequence data) to construct phylogenetic trees. In contrast to distance-matrix methods, they can be used to reconstruct ancestral character states because they retain the original character status of the taxa. *S2Maximum Parsimony (MP) *T1Under the maximum parsimony criterion, the best tree is one that requires the minimum number of character changes (e.g., nucleotide substitutions) to produce the data (e.g., a set of homologous sequences). However, there are many plausible scenarios that could have produced a group of sequences and considering a single mutational path, as MP does, may be misleading [START_REF] Holder | Phylogeny estimation: traditional and Bayesian approaches[END_REF]. MP assumes that common characteristics are inherited from a common ancestor, but when homoplasy (parallelisms, convergences, and reversal events) is present, the most parsimonious method may underestimate the actual evolutionary divergences. The MP algorithm usually finds more than one tree with the same parsimonious length. A consensus approach is then built up to combine all of the most parsimonious trees. The MP method does not consider the fact that the number of character changes may vary on each branch of the tree. Longbranch attraction occurs when rapidly evolving taxa are placed together on a tree because they have many mutations [START_REF] Rizzo | Review of phylogenetic tree construction[END_REF]). Yet, parsimony performs relatively well if the amount of convergence is rare compared with the number of mutations that are conveying useful information [START_REF] Holder | Phylogeny estimation: traditional and Bayesian approaches[END_REF]. There are other different parsimony algorithms such as weighted, transversion, or Dollo parsimony. *S2Maximum Likelihood (ML) *T1This method allows for the correction of multiple mutational events at the same location.

Likelihood methods measure the probability of the data given the hypothesis (i.e., it prefers the tree with the highest probability to fit the observed sequences). ML optimizes the likelihood of observing data given a tree topology and a model of nucleotide evolution [START_REF] Egan | Theory of phylogenetic estimation[END_REF]. ML assumes a model of evolution and the tree returning the highest likelihood is considered the best tree. An advantage of ML is that it accounts for the possibility of unseen events such as back mutations or complex pathways [START_REF] Holder | Phylogeny estimation: traditional and Bayesian approaches[END_REF]. As for MP, it examines different tree topologies. This method is very robust for reconstructing old relationships and fast evolutionary events, but is one of the most computationally demanding and may be inappropriate for relatively large data sets. To tackle those computer load issues, more recent methods based on ML have been developed, in particular PhyML [START_REF] Guindon | New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0[END_REF], RAxML [START_REF] Stamatakis | RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models[END_REF], and IQ-TREE [START_REF] Nguyen | IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies[END_REF], among others. All of the methods described above require a form of confidence assessment for the relationships inferred in the tree. The most common tool to establish this confidence is called "bootstrapping," which consists of creating pseudo-replicate data matrices by randomly resampling the original data set (with replacement) and reconstructing phylogenetic trees for each [START_REF] Lemey | The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing[END_REF]. Bootstrap values provide a measure of support for the monophyly of clades and the relationships among studied taxa. *S2Bayesian Methods *T1Bayesian methods simultaneously estimate trees and measures of support for every branch. This approach searches for a set of trees representing the data by using a prior probability for the distribution of each parameter of the model (or equal probabilities if we do not have prior information). The optimal tree is the one that maximizes the posterior probability that is proportional to the likelihood multiplied by the prior probability. The posterior probabilities specify the probability of each tree given a model, a prior, and the data. A technique called Markov chain Monte Carlo (MCMC) is used to explore tree space. An advantage of Bayesian techniques is that they allow the implementation of complex models of sequence evolution.

Moreover, contrary to ML, Bayesian approaches may be reliable even when the ratio of data points over the number of parameters is low. Unfortunately, Bayesian methods are very computationally demanding and selecting an uninformative prior may result in serious issues. *S3Different Rates of Feature Evolution and Convergences Can Blur Phylogenetic Signals *T1Evolutionary rate variation among features may influence how similar closely related species are in a phylogenetic tree. Fast evolving features may tend to be very different between closely related species and reveal little about evolutionary history [START_REF] Losos | Seeing the forest for the trees: the limitations of phylogenies in comparative biology (American Society of Naturalists Address)[END_REF]. Phylogenetic signals in features can thus be revealed only when the rates of character evolution are low relative to rates of clade evolution [START_REF] Losos | Seeing the forest for the trees: the limitations of phylogenies in comparative biology (American Society of Naturalists Address)[END_REF].

Another reason why phylogenetic similarity may not reflect feature similarity is because of convergent evolution [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF]. This is the process by which evolutionarily unrelated organisms show similar features as a result of natural selection and adaptation. Because of convergences, several features in different clades do not show any phylogenetic signal (Mazel et al. 2017). As stated by [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF], the PD index does not capture convergent features because they depart from the assumption that shared traits are due to a common evolutionary history.

Although this principle is inherent in the evolutionary model on which PD is based, it has been missed in some studies (e.g., [START_REF] Kelly | Phylogenetic trees do not reliably predict feature diversity[END_REF]. Therefore, convergent features should be considered through other metrics, such as shared habitats as suggested by [START_REF] Faith | Environmental diversity: on the best-possible use of surrogate data for assessing the relative biodiversity of sets of areas[END_REF]. *S3Species Descending From Long Branches Do Not Always Retain Old Features *T1Species descending from deep nodes do not always exhibit features older than species found in shallower nodes [START_REF] Grandcolas | What is the meaning of extreme phylogenetic diversity? The case of phylogenetic relict species[END_REF]). There are two potential reasons for this situation. First, all characters of a species that have been in an evolutionary stasis are not in a primary state. [START_REF] Grandcolas | What is the meaning of extreme phylogenetic diversity? The case of phylogenetic relict species[END_REF] showed that species found on long branches may also have features considered more modern. Second, isolated species on long branches can be remnants from a lineage formerly much more diverse that was decimated by subsequent extinction events. Thus, the species that are remnants from an ancient group previously comprising more species represent a combination of features of this group, but not always the character states present in its ancestor [START_REF] Grandcolas | Relict species: a relict concept?[END_REF][START_REF] Grandcolas | What is the meaning of extreme phylogenetic diversity? The case of phylogenetic relict species[END_REF].

The conservation interest of evolutionary distinct species and long branches, capturing large amounts of PD, may not always rely on their unique features and possible related functions in an ecosystem, but also to their level of endangerment and symbolic value [START_REF] Isaac | Mammals on the EDGE: conservation priorities based on threat and phylogeny[END_REF][START_REF] Grandcolas | What is the meaning of extreme phylogenetic diversity? The case of phylogenetic relict species[END_REF][START_REF] Trewick | Phylogenetics and conservation in New Zealand: the long and the short of it[END_REF]. *S3Uncertainties Due to the Model of Feature Evolution *T1The expectation that greater evolutionary distances indicate that species have accumulated more ecological differences assumes a very particular evolutionary model (i.e., the Brownian motion model). Phylogenies are often built following a Brownian motion model [START_REF] Diniz-Filho | Darwinian shortfalls in biodiversity conservation[END_REF]. This model assumes that features continue to diverge linearly over time and that convergence is rare. This supports the rationale to use PD in conservation and community ecology (i.e., that shared features may be explained by shared ancestry; [START_REF] Cadotte | Why phylogenies do not always predict ecological differences[END_REF]. [START_REF] Cadotte | Why phylogenies do not always predict ecological differences[END_REF] showed that under the Brownian motion model the relationship between ecological and phylogenetic distance was linear only when multiple features (or ecological traits) were considered, whereas this was not true for a single feature. PD may be a good surrogate for variation of multiple features, but this surrogacy may weaken when the number of features decrease [START_REF] Diniz-Filho | Darwinian shortfalls in biodiversity conservation[END_REF][START_REF] Cadotte | Why phylogenies do not always predict ecological differences[END_REF][START_REF] Tucker | On the relationship between phylogenetic diversity and trait diversity[END_REF], as stated in the original paper introducing PD [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF]). Yet, evolutionary, physiological, or ecological constraints tend to make evolution models more complex than a Brownian motion model. Many studies show that only a small proportion of features (or ecological traits) followed a linear model of evolution and a model of bounded evolution was generally favored [START_REF] Davies | Losing history: how extinctions prune features from the tree of life[END_REF]. From this, the relationship between phylogenetic distance and ecological distance and between the sum of branch lengths joining species and their feature variation can take many forms [START_REF] Cadotte | Why phylogenies do not always predict ecological differences[END_REF][START_REF] Tucker | On the relationship between phylogenetic diversity and trait diversity[END_REF]. For example, if evolution slows down over time, phylogenetic diversity may capture little feature variation, whereas if evolution occurs in bursts, much feature variation may be captured [START_REF] Davies | Losing history: how extinctions prune features from the tree of life[END_REF]. A useful review of the issues related to the model of evolution can be found in [START_REF] Cadotte | Why phylogenies do not always predict ecological differences[END_REF], and some practical solutions have been proposed by [START_REF] Pagel | Inferring the historical patterns of biological evolution[END_REF][START_REF] Diniz-Filho | On the selection of phylogenetic eigenvectors for ecological analyses[END_REF], [START_REF] Letten | Trees, branches and (square) roots: why evolutionary relatedness is not linearly related to functional distance[END_REF], [START_REF] Davies | Losing history: how extinctions prune features from the tree of life[END_REF], and [START_REF] Mazel | Improving phylogenetic regression under complex evolutionary models[END_REF].

Yet, despite numerous possible evolutionary models, if "large numbers of species [are examined] and combine multiple traits, which have been subject to different selection regimes, then the pattern of evolution is likely to be indistinguishable from BM [Brownian motion model]" (Cadotte et al. 2017:537-538). When this condition is met, PD may then still be a good predictor of feature (or ecological traits) diversity, independent of the evolutionary model of features [START_REF] Cadotte | Why phylogenies do not always predict ecological differences[END_REF]. *S2Consequences For the Use of Phylogenetic Information in Conservation Biology… *T1One main benefit for the preservation of PD highlighted in this review is its relationship with ecosystem processes and option values [START_REF] Kraft | Trait evolution, community assembly, and the phylogenetic structure of ecological communities[END_REF]. Up until now, some studies have found that ecosystem processes were related to species richness, with a small fraction of increase due purely to higher phylogenetic diversity [START_REF] Venail | Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re-examination of 16 grassland biodiversity studies[END_REF]; but see [START_REF] Cadotte | Phylogenetic diversity and productivity: gauging interpretations from experiments that do not manipulate phylogenetic diversity[END_REF]. From the discussion above, it is clear that there are many reasons why phylogenetic diversity itself may not be able to forecast functional diversity or the value of ecosystem services [START_REF] Venail | Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re-examination of 16 grassland biodiversity studies[END_REF]. First, traits that control ecological functions are not phylogenetically conserved, so that maximizing PD may not maximize feature variation.

Moreover, this implies that closely related species do not have similar ecological functions and distantly related species do not complement each other's function. Second, closely related species do not compete more strongly than distantly related ones, given all of the reasons discussed above (see [START_REF] Mayfield | Opposing effects of competitive exclusion on the phylogenetic structure of communities[END_REF]. Thus, communities composed by distantly related species do not have more niche complementarity and better productivity than communities formed by closely related species. Third, closely related species commonly experience facilitative interactions [START_REF] Cianciaruso | Including intraspecific variability in functional diversity[END_REF]). Thus, communities composed by closely related species can have higher productivity when these species facilitate each other, in comparison with communities of distantly related species that face competitive interactions. In spite of all these possible imitations, PD was shown to be a strong predictor of ecosystem functioning [START_REF] Cadotte | Phylogenetic diversity and productivity: gauging interpretations from experiments that do not manipulate phylogenetic diversity[END_REF]. This is likely because by summing the phylogenetic distances of species in a community, PD represents the variation (and not the difference) in species traits (i.e., the total niche space occupied; Cadotte et al. 2017). Moreover, when the additional benefits of using PD over other measures to capture ecosystem processes are not clear, phylogenetic information may still be valuable [START_REF] Cadotte | Phylogenetic diversity and productivity: gauging interpretations from experiments that do not manipulate phylogenetic diversity[END_REF].

For instance, [START_REF] Yguel | The evolutionary legacy of diversification predicts ecosystem function[END_REF] argued that, even if PD remained useful for predictions related to ecosystem processes, it may be too simple to depict differences in the phylogenetic structure of communities. These authors then proposed a measure called Evolutionary Legacy of Diversification, which describes branching patterns and may better predict ecosystem processes than other commonly used metrics such as PD. Besides, ecological functions may not always be provided by feature diversity but rather by key innovations [START_REF] Davies | Deconstructing the relationships between phylogenetic diversity and ecology: a case study on ecosystem functioning[END_REF]. In that case phylogenetic placement, for example, measured by metrics that describe the connectedness or centrality of nodes and edges within a network, may better represent those functions than PD does [START_REF] Davies | Deconstructing the relationships between phylogenetic diversity and ecology: a case study on ecosystem functioning[END_REF]).

In addition, many studies showed that PD was not a good proxy for functional diversity and that spatial patterns were incongruent most of the time [START_REF] Devictor | Spatial mismatch and congruence between taxonomic, phylogenetic and functional diversity: the need for integrative conservation strategies in a changing world[END_REF][START_REF] Pavoine | Correlations between phylogenetic and functional diversity: mathematical artefacts or true ecological and evolutionary processes?[END_REF][START_REF] Pollock | Large conservation gains possible for global biodiversity facets[END_REF][START_REF] Cadotte | Difficult decisions: strategies for conservation prioritization when taxonomic, phylogenetic and functional diversity are not spatially congruent[END_REF][START_REF] Mazel | Is phylogenetic diversity a surrogate for functional diversity across clades and space? bioRxiv[END_REF]. Again, these results were expected because only a few traits were considered, convergence may occur or models were not convenient (see discussion in Faith 2018b). Appropriate measures to estimate functional diversity and spatial priorities, which separately consider functional and phylogenetic diversity, are therefore necessary (e.g., [START_REF] Cadotte | Difficult decisions: strategies for conservation prioritization when taxonomic, phylogenetic and functional diversity are not spatially congruent[END_REF].

Although some limitations and improvements can be found regarding the relationship between PD and ecosystem processes and that some features do not show any phylogenetic signals [START_REF] Faith | Conservation evaluation and phylogenetic diversity[END_REF], PD remains an important calculus to maintain option and insurance values. PD may on average capture feature diversity that may be the best way to maintain unexpected benefits to humanity and for the resilience of ecosystems. As shown above, this relationship does not rely on only a few existing traits, but on the overall features of species with unknown variation and unknown future values. Analyses based on a few traits have sometimes led to the wrong interpretation that PD does not capture option values (Faith 2018b). On the contrary, "option values" is the primary argument for the use of PD calculus in conservation such that "maximizing the retention of phylogenetic diversity (PD) should also maximize option value" [START_REF] Larsen | Conserving critical sites for biodiversity provides disproportionate benefits to people[END_REF].

In conclusion, despite the fact that niche conservatism provides the foundation for the PD ecosystem services agenda, it has some limitations that should be acknowledged. Although PD has been shown to be a strong predictor of ecosystem functioning, the key to understanding the processes that explain this prediction is to go deeper into the phylogenetic signature of species interactions that may result in the definition of new metrics based on phylogenies. Studies investigating the relationship of PD and ecosystem functions and services will be more fruitful if we acknowledge the underlying premises of phylogenetic signals and niche complementarity, otherwise studies will have strong contingency and with low generalization for conservation purposes. *S2…and in Community Ecology *T1From the limitations described above (see the section titled *S1When Phylogenetic and Feature Variation Are Not Congruent: Limitations and SOLUTIONS), assuming that niche conservatism indicates the maintenance of the fundamental niche over time a priori and to link it directly to competition between closely related species may sometimes be flawed [START_REF] Kraft | Trait evolution, community assembly, and the phylogenetic structure of ecological communities[END_REF]. Although many features are more conserved through evolutionary history than expected, in cases of convergent or divergent evolution, the interpretation of phylogenetic patterns in the face of assembly processes becomes confused [START_REF] Losos | Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species[END_REF][START_REF] Losos | Seeing the forest for the trees: the limitations of phylogenies in comparative biology (American Society of Naturalists Address)[END_REF]. For example, species from distinct lineages where trait evolution is predominantly convergent can be assembled in communities driven by environmental filters and yet their phylogenetic pattern can be overdispersed. In this case, if we assume niche conservatism, phylogenetic patterns, such as the relationship between PD and SR, would be erroneously interpreted as competition between closely related species. Moreover, when species are assembled by asymmetric competition-i.e., species have different competitive abilities-communities can have phylogenetically clustered structures due to the competitive exclusion of distantly related species with inferior competitive abilities [START_REF] Mayfield | Opposing effects of competitive exclusion on the phylogenetic structure of communities[END_REF][START_REF] Gerhold | Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better)[END_REF][START_REF] Saito | Phylogenetic clustering among aggressive competitors: evidence from odonate assemblages along a riverine gradient[END_REF][START_REF] Saito | Ecological versatility and the assembly of multiple competitors: cautionary notes for assembly inferences[END_REF]. From this, relationships between phylogenetic overdispersion/clustering and competition/environmental filtering is also not uniform across clades [START_REF] Pearse | The interaction of phylogeny and community structure: linking clades' ecological structures and trait evolution[END_REF]. [START_REF] Cadotte | Why phylogenies do not always predict ecological differences[END_REF] provides a review on how to interpret the lack of phylogenetic signals in community assembly. Other points for the weakness and strengths of inferring assembly processes from phylogenetic information, such as understanding how coexistence leads to the macroevolutionary diversification of habitat lineage pools or, on the contrary, how macroevolutionary contingency of habitat lineage pools affects present-day species coexistence [START_REF] Gerhold | Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better)[END_REF] were explored by others [START_REF] Mayfield | Opposing effects of competitive exclusion on the phylogenetic structure of communities[END_REF][START_REF] Mason | Does trait conservatism guarantee that indicators of phylogenetic community structure will reveal niche-based assembly processes along stress gradients?[END_REF][START_REF] Gerhold | Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better)[END_REF][START_REF] De Bello | Decoupling phylogenetic and functional diversity to reveal hidden signals in community assembly[END_REF].

The use of PD in conservation biology and community ecology relies on a strong theoretical background. Limitations exist that may blur or nullify the relationship between phylogenetic variation and variation in some traits (e.g., [START_REF] Cadotte | Difficult decisions: strategies for conservation prioritization when taxonomic, phylogenetic and functional diversity are not spatially congruent[END_REF], potentially influencing the conclusions that can be drawn from PD approaches. In particular, this may influence the predictions of species interactions so that niche complementarity, species assemblage, and ecosystem functioning can sometimes be difficult to interpret through PD. As stated above, this situation could be improved by a clearer understanding of the phylogenetic signature of species interactions. Finally, the relationship between genotypes and phenotypes and how it affects the use of PD has received, to our knowledge, nearly no attention. Still, the limitations regarding the use of PD in conservation and community ecology are better understood (e.g., [START_REF] Cadotte | Why phylogenies do not always predict ecological differences[END_REF]) and incorrect interpretations occasionally arise from unfit analyses or inaccurate understanding of the rationale of PD usage (e.g., [START_REF] Kelly | Phylogenetic trees do not reliably predict feature diversity[END_REF][START_REF] Venail | Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re-examination of 16 grassland biodiversity studies[END_REF].

Several corrections, but also additional applications, have been proposed (e.g., [START_REF] Cadotte | Phylogenetic diversity and productivity: gauging interpretations from experiments that do not manipulate phylogenetic diversity[END_REF][START_REF] Gerhold | Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better)[END_REF][START_REF] Yguel | The evolutionary legacy of diversification predicts ecosystem function[END_REF]. Although conclusions about the use of PD should sometimes be mitigated, we believe that such improvements and good practices will allow the appropriate use of phylogenetic information as a powerful tool for the future of conservation biology and community ecology.

*S1Conclusions

*T2

1. The use of phylogenetic information in conservation biology and community ecology relies highly on the assumption that shared features are due to a shared evolutionary history.

2. Up until now, confusion between the conservation biology and community ecology frameworks may have resulted to a misuse of phylogenetic information in many cases.

3. In conservation biology, the interest is to maintain option values through feature variation. Strategies that do not consider the phylogenetic complementarity of sites and species do not allow maximizing the chances to preserve option values, but some may have a practical interest.

4. In community ecology, phylogenetic information may help to disentangle the process at the origin of diversity patterns and community assembly in a given area, but phylogenetic complementarity among sites is not always essential.

5. Yet, it should be noted that limitations in the relationship between features and evolutionary history may lead to misunderstandings and misinterpretations in both conservation biology and community ecology.

6. Understanding and considering the conditions to use phylogenies for conservation and community ecology purposes is challenging, but recent progress has been made. For example, alternative indices to phylogenetic diversity have been proposed to include factors at the origin of shifts in the relation between evolutionary and trait variation.

7. Improving our knowledge on the relation between evolutionary history and trait variation is important as it has implications in various fields of ecology such as the understanding of ecological interactions, ecological functions, and the potential future benefits of biodiversity to societies.

Figure 1 .

 1 Figure 1. THREE PRIORITIZATION STRATEGIES BASED ON PD. PD is measured as the sum of

  , Heightened Evolutionary Distinctiveness and Global Endangerment (HEDGE; Steel et al. 2007), Biogeographical weighted Evolutionary Distinctiveness (Cadotte and Davies 2010), Loss-significant Evolutionary Distinctive Globally Enduring (LEDGE; Faith 2015), or After Downlisting Expected Phylogenetic Diversity (ADEPD; Nunes et al. 2015).

Figure 2 :

 2 Figure 2: Comparison of PD and ED in maximizing feature variationThis figure represents the

Glossary

Character: All observable characters of an organism, including morphological, anatomical, chemical, and molecular.

Diversification:

The process that lead species to diversify; the sum of speciation and extinction events.

Evolutionary History:

The history of species evolution that links all species on Earth in a unique natural classification.

Extinction: In its modern definition, a species is considered extinct when there is no reasonable doubt that the last individual has died.

Natural Selection: Darwin's natural selection theory stated that the most useful variations of species in their environment (i.e., a new fitness) favored the individuals and thus persisted, and that those advantageous variations were inheritable.

Niche Complementarity: This hypothesis states that for coexistence to occur high overlap in one dimension of the niche must be compensated by low overlap in another.

Option Value: Biodiversity values that provide benefits and uses, often unanticipated, for future generations.

Operational Taxonomic Unit (OTU): An operational definition used to classify groups of closely related individuals.

Phylogenetic Root:

The root represents the common ancestor to all taxa on a tree and is their oldest ancestor.

Phylogenetic Signal:

The tendency for related species to resemble each other more than they resemble species drawn at random from the phylogenetic tree.

Species: Defined for language convention as reproductively isolated populations. Speciation: Lineage-splitting event that produces two or more separate species.

Trait: The diversity of morphological, biochemical, behavioral, and physiological characters of species.

Tree of Life: Phylogenetic tree depicting the links uniting all of the species on Earth.