Oecologia (2008) 157:485–495 DOI 10.1007/s00442-008-1082-2 COMMUNITY ECOLOGY - METHODS PAPER A comparative test of phylogenetic diversity indices Oliver Schweiger · Stefan Klotz · Walter Durka · Ingolf Kühn Received: 5 June 2007 / Accepted: 19 May 2008 / Published online: 20 June 2008 © Springer-Verlag 2008 Abstract Traditional measures of biodiversity, such as distinctiveness values for particular species across the com- species richness, usually treat species as being equal. As munity. It is therefore strongly linked to species richness this is obviously not the case, measuring diversity in terms and reXects phylogeny per se weakly but satisWes set mono- of features accumulated over evolutionary history provides tonicity. We suggest that AvTD and J are best applied to additional value to theoretical and applied ecology. Several studies that compare spatially or temporally rather indepen- phylogenetic diversity indices exist, but their behaviour has dent communities that potentially vary strongly in their not yet been tested in a comparative framework. We pro- phylogenetic composition—i.e. where set monotonicity is a vide a test of ten commonly used phylogenetic diversity more negligible issue, but independence of species richness indices based on 40 simulated phylogenies of varying is desired. In contrast, we suggest that TTD be used in stud- topology. We restrict our analysis to a topological fully ies that compare rather interdependent communities where resolved tree without information on branch lengths and changes occur more gradually by species extinction or species lists with presence–absence data. A total of 38,000 introduction. Calculating AvTD or TTD, depending on the artiWcial communities varying in species richness covering research question, in addition to species richness is strongly 5–95% of the phylogenies were created by random resam- recommended. pling. The indices were evaluated based on their ability to meet a priori deWned requirements. No index meets all Keywords Phylogenetic tree · Pure diversity · requirements, but three indices turned out to be more suit- Quadratic entropy · Taxic weights · Taxonomic distinctness able than others under particular conditions. Average taxo- nomic distinctness (AvTD) and intensive quadratic entropy (J) are calculated by averaging and are, therefore, unbiased Introduction by species richness while reXecting phylogeny per se well. However, averaging leads to the violation of set monotonic- Many ecological studies, especially large-scale ones, rely ity, which requires that species extinction cannot increase on species richness as a measure of biodiversity because the index. Total taxonomic distinctness (TTD) sums up time and money constraints often impede eVorts to obtain more detailed information. However, the use of species richness as the sole reXection of biodiversity may be of lim- Communicated by Wolf Mooij. ited value since it treats all species as being equal and does not take into account phylogenetic relationships (Vane- O. Schweiger (&) · S. Klotz · W. Durka · I. Kühn Wright et al. 1991). The diVerences in the evolutionary his- Department of Community Ecology, UFZ—Helmholtz Centre for Environmental Research, tory of community members result in a diversity of mor- Theodor-Lieser-Street 4, 06210 Halle, Germany phological, physiological, and behavioural characters e-mail: [email protected] (Williams and Humphries 1996) and of their features (Faith 1992), where a feature means a particular state of a charac- O. Schweiger · S. Klotz · I. Kühn Virtual Institute for Macroecology, ter. Many of the characters may represent functional traits Theodor-Lieser-Street 4, 06120 Halle, Germany (e.g. Woodward and Cramer 1996; Lavorel et al. 1997; 123 486 Oecologia (2008) 157:485–495 Diaz and Cabido 2001), and the feature richness of a com- based on morphological or functional diVerences (Izsak and munity may be closely related to its functional diversity Papp 1995), on Linnean taxonomy (Warwick and Clarke (e.g. Tilman et al. 1997; Petchey and Gaston 2002; Petchey 1995), on branch lengths of phylogenies based on molecu- et al. 2004). lar data (Solow et al. 1993; Pavoine et al. 2005) or, if Sechrest et al. (2002) showed that biodiversity hotspots branch lengths are not known, on the number of nodes sep- across the globe harbour even greater amounts of evolu- arating each pair of species (Faith 1992). The values within tionary history than would be expected based on species the distance matrix can be interpreted as the distinctiveness richness. Heard and Mooers (2000) demonstrated that phy- between each pair of species or each particular species and logenetic relationships are one of the most important fac- all other species (Rao 1982; Izsak and Papp 2000; Ricotta tors determining species extinction, and Strauss et al. and Avena 2003). Several summary statistics have been (2006) showed that the degree of phylogenetic distance proposed to obtain an index for the whole community. Rao may determine the invasion success of exotic taxa. Hence, (1982), for example, proposed a diversity index termed phylogenetic information may be a better indicator of con- quadratic entropy (QE) that is based on both relative spe- servation value than species richness alone. cies abundances and a measure of the pairwise distances The application of information obtained by phylogenetic between community species. When information about any relationships therefore represents a promising approach kind of distance measure is lacking, QE reduces to the (Webb et al. 2002). Several authors have proposed a variety Simpson index. When abundance data are lacking (or they of indices other than species richness which also take into are equal), QE will be a function of the species number account phylogenetic diversity; however, these diVer (also called intensive quadratic entropy, J, in Izsak and greatly in their method of calculation (Vane-Wright et al. Papp 2000). A similar index, average taxonomic distinct- 1991; Faith 1992; Solow et al. 1993; Faith 1994; Warwick ness (AvTD), was developed by Warwick and Clarke and Clarke 1998; Izsak and Papp 2000; Clarke and War- (1995), which measures the mean distance between two wick 2001a; Rodrigues and Gaston 2002). These indices randomly chosen species. can be separated in two categories: topology based and dis- Krajewski (1994) investigated the behaviour of some tance based (Krajewski 1994). Vane-Wright et al. (1991) phylogenetic diversity indices using the avian family Grui- were the Wrst to propose the application of topology-based dae. Based on a comparison of the ability of these indices to methods, which reXect the phylogenetic branching order rank species and contribute to phylogenetic diversity, he within a monophyletic group. In this approach, each species reported a serious disagreement between the indices, espe- of a community is weighted by the inverse number of nodes cially at intermediate levels of ranking, and concluded that between that species and the root of the phylogenetic tree, “until some working consensus is reached […], phyloge- in a way that the most distinctive (close-to-root) species netic indices are unlikely to supersede more traditional have the highest weights. Community distinctness (as a measures of biodiversity”. Consequently, as long as the measure of phylogenetic diversity) is then obtained simply mathematical and ecological qualities of these indices are by summing the weights of the species. In this paper, we not suYciently investigated in a comparative way, relying use the terms “distinctiveness” and “distinctness” sensu on species richness, for example, would be preferable since Warwick and Clarke (2001). Following their deWnition, the selection of an index to account for phylogenetic rela- “distinctiveness” describes the relation of a particular spe- tionships, and possibly the results and potential conserva- cies to the rest of the community, whereas “distinctness” tion recommendations, will be quite arbitrary. represents a property of the community as a whole. While Krajewski (1994) investigated the ability of the Distance-based methods use either a minimum spanning indices to identify “phylogenetically unique” species, path or a pairwise distance approach. The minimum span- which was motivated by an individual species-focussed ning path measures the phylogenetic diversity of a commu- conservation context, we focus on their ability to measure nity by summing up the branch lengths of the subtree that phylogenetic diversity at the community level. Community- includes the community’s species (PD in Faith 1992). wide phylogenetic diversity patterns can also be used for Branch lengths indicate the expected number of molecular conservation concerns (e.g. the selection of priority areas; “features” accumulated over evolutionary history. Common Posadas et al. 2001), but they are also highly suited for branches reXect shared molecular information inherited monitoring the eVects of environmental change on overall from common ancestors, while the branch length of a single community structure (e.g. Warwick and Clarke 1995; species not shared by others reXects exclusive information. Knapp et al. 2008). By analogy with studies investigating While the minimum spanning path approach measures the behaviour of evenness indices (Smith and Wilson 1996) overall phylogenetic information of a community, the pair- or functional diversity indices (Mason et al. 2003), we pro- wise distance approach is based on a distance matrix vide a comparison