Daniel P. Faith

Conservation evaluation and phylogenetic diversity

Protecting biological diversity with limited resources may require placing conservation priorities on different taxa. A system of priorities that reflects the value of taxonomic diversity can be achieved by setting priorities such that the subset of taxa that is protected has maximum underlying feature diversity. Such feature diversity of taxon subsets is difficult to estimate directly, but can be predicted by the cladistic/phylogenetic relationships among the taxa. In this study, a simple measure of phylogenetic diversity is defined based on cladistic information. The measure of phylogenetic diversity, PD, is contrasted with a measure of taxic diversity recently developed by Vane-Wright et al. (Biol. Conserv., 55, 1991). In re-examining reserve-selection scenarios based on a phylogeny of bumble bees (Apidae), PD produces quite different priorities for species conservation, relative to taxic diversity. The potential application of PD at levels below that of the species is then illustrated using a mtDNA phylogeny for populations of crested newts Triturus cristatus. Calculation of PD for different population subsets shows that protection of populations at either of two extremes of the geographic range of the group can significantly increase the phylogenetic diversity that is protected.

Compositional dissimilarity as a robust measure of ecological distance

The robustness of quantitative measures of compositional dissimilarity between sites was evaluated using extensive computer simulations of species’ abundance patterns over one and two dimensional configurations of sample sites in ecological space. Robustness was equated with the strength, over a range of models, of the linear and monotonic (rank-order) relationship between the compositional dissimilarities and the corresponding Euclidean distances between sites measured in the ecological space. The range of models reflected different assumptions about species’ response curve shape, sampling pattern of sites, noise level of the data, species’ interactions, trends in total site abundance, and beta diversity of gradients.

COULD A CLADOGRAM THIS SHORT HAVE ARISEN BY CHANCE ALONE?: ON PERMUTATION TESTS FOR CLADISTIC STRUCTURE

Abstract Absolute criteria for evaluating cladistic analyses are useful, not only because cladistic algorithms impose structure, but also because applications of cladistic results demand some assessment of the degree of corroboration of the cladogram. Here, a means of quantitative evaluation is presented based on tree length. The length of the most‐parsimonious tree reflects the degree to which the observed characters co‐vary such that a single tree topology can explain shared character states among the taxa. This “cladistic covariation” can be quantified by comparing the length of the most parsimonious tree for the observed data set to that found for data sets with random covariation of characters. A random data set is defined as one in which the original number of characters and their character states are maintained, but for each character, the states are randomly reassigned to the taxa. The cladistic permutation tail probability, PTP, is defined as the estimate of the proportion of times that a tree can be found as short or shorter than the original tree. Significant cladistic covariation exists if the PTP is less than a prescribed value, for example, 0.05. In case studies based on molecular and morphological data sets, application of the PTP shows that:

Comparative phylogeography and the identification of genetically divergent areas for conservation

Genetic diversity is recognized as a fundamental component of biodiversity and its protection is incorporated in several conventions and policies. However, neither the concepts nor the methods for assessing conservation value of the spatial distribution of genetic diversity have been resolved. Comparative phylogeography can identify suites of species that have a common history of vicariance. In this study we explore the strengths and limitations of Faith’s measure of ‘Phylogenetic Diversity’ (PD) as a method for predicting from multiple intraspecific phylogeographies the underlying feature diversity represented by combinations of areas. An advantage of the PD approach is that information on the spatial distribution of genetic diversity can be combined across species and expressed in a form that allows direct comparison with patterns of species distributions. It also seeks to estimate the same parameter, feature diversity, regardless of the level of biological organization. We extend the PD approach by using Venn diagrams to identify the components of PD, including those unique to or shared among areas and those which represent homoplasy on an area tree or which are shared across all areas. PD estimation should be complemented by analysis of these components and inspection of the contributing phylogeographies. We illustrate the application of the approach using mtDNA phylogeographies from vertebrates resident in the wet tropical rainforests of north‐east Queensland and compare the results to biodiversity assessments based on the distribution of endemic vertebrate species. The genetic vs. species approaches produce different assessments of conservation value, perhaps reflecting differences in the temporal and spatial scale of the determining processes. The two approaches should be seen as complementary and, in this case, conservation planning should incorporate information on both dimensions of biodiversity.

Correlation of environmental variables with patterns of distribution and abundance of common and rare freshwater macroinvertebrates

Abstract This study explores the environmental factors underlying variation in abundance of common and rare freshwater taxa. Hybrid multidimensional scaling is used to model variation in distribution and abundance of freshwater microinvertebrate taxa over 17 sample sites in the upper catchment of the LaTrobe River, Victoria, Australia. Initial analysis of 40 common taxa revealed high correlations of the ordination space with physico-chemical variables related to temperature, stream order, particle size and water chemistry. Analysis of all 269 taxa, or alternatively of the 229 rarer taxa alone, resulted in ordination spaces that showed high correlations for additional physico-chemical variables, particularly relating to water chemistry. Monte Carlo significance tests supported this finding in demonstrating that the analysis of all taxa produced a greater number of significant correlations between the ordination space and physico-chemical variables. The additional important environmental correlates revealed by the analysis of the rare taxa suggested that there might be differences in the set of environmental variables that are related to patterns of distribution and abundance of rare versus common taxa. A Monte Carlo test was carried out to test the null hypothesis that the failure to recover some environmental correlates in the analysis of common taxa simply resulted from the small (40) number of taxa involved. Results of the test generally showed that rareness versus commonness could not be implicated in the greater recovery of these water chemistry variables in the analysis of the rare taxa. The recovery of additional environmental correlates with the inclusion of rare taxa has implications for conservation studies at the community level. Ordination can be used for survey extension where complete information on distribution and abundance of taxa is unavailable. The ability of ordination methods to summarise distribution and abundance of rare taxa, and incorporate their additional information on environmental variation, suggests that representativeness of the ordination space is a useful criterion for reserve selection.

Genetic diversity and taxonomic priorities for conservation

Abstract Crozier (Biol. Conserv., 61, 1992) has proposed two measures for taxon-weighting, a uniqueness index and a product-formula, both based on genetic distances or branch lengths interpreted as estimates of probabilities of evolutionary change. I provide new versions of each measure that correct limitations in their original formulation. However, I also demonstrate other undesirable properties of these measures, including: failure to reflect complementarity among taxa, incompatibility with the additivity property of branch lengths, and poor prediction of underlying feature diversity of taxon subsets. The examples presented here also counter Croziers conjecture that the product-formula measure will tend to yield results similar to the phylogenetic diversity (PD) measure of Faith (Biol. Conserv., 61, 1992). An alternative probabilistic interpretation of branch lengths, based on a Poisson distribution, avoids the problems of Croziers probabilistic measures. The corresponding probabilistic measure derived here is shown to be monotonically related to PD, and so provides a further probabilistic rationale for phylogenetic diversity as an indicator of underlying feature diversity patterns among taxa.

A Comparison of Two Approaches to Beta-Flexible Clustering

We introduce a UPGMA based counterpart to the Lance and Williams (1966) p-flexible clustering strategy. This new method is compared with the original p-flexible technique based on WPGMA for a range of fl values from -0.8 to +0.1. Recovery of the known cluster structure from simulated data was evaluated using the Hubert and Arabie (1985) version of the Rand statistic. The algorithm used to generate the simulated clusters in the study included error-free data as well as three other error conditions. The simulated data also varied the number of clusters, the underlying dimensionality, and the density distribution of points to the clusters. Results showed that the flexible UPGMA gives the best recovery for all generated data configurations. Further, the flexible UPGMA method with a small negative β value performed better than the standard UPGMA method where β is set equal to zero. The flexible UPGMA strategy, employed with a narrow β range, is recommended based upon its ability to recover cluster structure over all error conditions.

Asymmetric binary similarity measures

SummaryAsymmetry in binary data arises when one of the two states (e.g. state “1”) is interpreted as more informative than the other state. A common example in ecology occurs when one state represents presence of some unit and the other state represents absence. The problem of the classification of individuals based upon a set of such characters is related to the goal of group homogeneity. The homogeneity of a group of individuals is defined as the count over all possible pairs of individuals and all characters, of the number of shared 1 states, minus the number of mismatches or 0–1, 1-0 combinations. The shared 0 states are effectively neutral, then, in terms of 1-state homogeneity.The behaviour of some common binary similarity measures is examined in relation to 1-state homogeneity. Although the Jaccard coefficient comes close to having the desired behaviour it exhibits undesirable behaviour for some data values and a proportionality relationship between matches and mismatches that may not always be desirable. A new coefficient, “C”, is introduced which overcomes these problems and leads to homogeneous classifications in the sense described above. Further general recommendations are made for the use of these coefficients in various contexts.

ON CORROBORATION: A REPLY TO CARPENTER

Carpenter’s (1992) characterization of cladistic methods will have a comfortable familiarity for many cladists. Indeed, I agree, as would most cladists, with many of his points: cladistics can be expected to work well because it avoids unwarranted assumptions about the evolutionary process; the fundamental assumption that is made, that of common-ancestry explanations for observed shared-features, is best satisfied by a most-parsimonious tree; the impossibility of knowing, or verifying, the identity of the “true” tree, leads properly to Popperian falsification of hypotheses; those hypotheses resisting falsification, and therefore highly corroborated, form the proper foundation for applications. So where is the disagreement? The key issue raised in Carpenter’s paper, and addressed in this reply, is exactly how Popperian corroboration is or is not achieved in cladistics. Carpenter claims that the most-parsimonious tree (“mpt”) is equivalent to the most highlycorroborated hypothesis among alternative tree-hypotheses, and argues that the PTP randomization test (Faith and Cranston, 1991; see also At-chic, 1989a) contributes nothing to corroboration. In this reply, I will counter both these assertions. I will show that the view of corroboration in cladistics presented by Carpenter fails to satisfy the essential requirement for Popperian corroboration, in that it does not reflect a low probability. Further, I will show that it is exactly this weakness that is overcome through the interpretation (Faith and Cranston, 1992) of the PTP test as providing a measure of corroboration in cladistics.

Homoplasy as pattern: multivariate analysis of morphological convergence in Anseriformes

Abstract— A multivariatc model for taxa and characters is presented that represents taxa as points in an ordination space such that shared derived character states define groups of taxa or regions in this space. This model is compared, in terms of concepts of information content and explanatory power, to the eladistie model that relates characters and taxa to a hierarchical pattern. While a cladogram may be identified with a phylogenetic hypothesis, the ordination pattern may be equated with hypotheses about similarities among the taxa in habitat, feeding mode, or other ecological factors.