Case studies of conservation plans that incorporate geodiversity.

Geodiversity has been used as a surrogate for biodiversity when species locations are unknown, and this utility can be extended to situations where species locations are in flux. Recently, scientists have designed conservation networks that aim to explicitly represent the range of geophysical environments, identifying a network of physical stages that could sustain biodiversity while allowing for change in species composition in response to climate change. Because there is no standard approach to designing such networks, we compiled 8 case studies illustrating a variety of ways scientists have approached the challenge. These studies show how geodiversity has been partitioned and used to develop site portfolios and connectivity designs; how geodiversity-based portfolios compare with those derived from species and communities; and how the selection and combination of variables influences the results. Collectively, they suggest 4 key steps when using geodiversity to augment traditional biodiversity-based conservation planning: create land units from species-relevant variables combined in an ecologically meaningful way; represent land units in a logical spatial configuration and integrate with species locations when possible; apply selection criteria to individual sites to ensure they are appropriate for conservation; and develop connectivity among sites to maintain movements and processes. With these considerations, conservationists can design more effective site portfolios to ensure the lasting conservation of biodiversity under a changing climate.

Evidence from 12S ribosomal RNA sequences that onychophorans are modified arthropods.

The evolutionary relationships of the onychophorans (velvet worms) and the monophyly of the arthropods have generated considerable debate. Cladistic analyses of 12S ribosomal RNA sequences indicate that arthropods are monophyletic and include the onychophorans. Maximum parsimony analyses and monophyly testing within arthropods indicate that myriapods (millipedes and centipedes) form a sister group to all other assemblages, whereas crustaceans (shrimps and lobsters) plus hexapods (insects and allied groups) form a well-supported monophyletic group. Parsimony analysis further suggests that onychophorans form a sister group to chelicerates (spiders and scorpions) and crustaceans plus hexapods, but this relationship is not well supported by monophyly testing. These relationships conflict with current hypotheses of evolutionary pathways within arthropods.

Why and how might genetic and phylogenetic diversity be reflected in the identification of key biodiversity areas?

'Key biodiversity areas' are defined as sites contributing significantly to the global persistence of biodiversity. The identification of these sites builds from existing approaches based on measures of species and ecosystem diversity and process. Here, we therefore build from the work of Sgró et al. (2011 Evol. Appl. 4, 326-337. (doi:10.1111/j.1752-4571.2010.00157.x)) to extend a framework for how components of genetic diversity might be considered in the identification of key biodiversity areas. We make three recommendations to inform the ongoing process of consolidating a key biodiversity areas standard: (i) thresholds for the threatened species criterion currently consider a site's share of a threatened species' population; expand these to include the proportion of the species' genetic diversity unique to a site; (ii) expand criterion for 'threatened species' to consider 'threatened taxa' and (iii) expand the centre of endemism criterion to identify as key biodiversity areas those sites holding a threshold proportion of the compositional or phylogenetic diversity of species (within a taxonomic group) whose restricted ranges collectively define a centre of endemism. We also recommend consideration of occurrence of EDGE species (i.e. threatened phylogenetic diversity) in key biodiversity areas to prioritize species-specific conservation actions among sites.

Environmental service payments: evaluating biodiversity conservation trade-offs and cost-efficiency in the Osa Conservation Area, Costa Rica.

The cost-efficiency of payments for environmental services (PES) to private landowners in the Osa Conservation Area, Costa Rica, is evaluated in terms of the trade-off between biodiversity representation and opportunity costs of conservation to agricultural and forestry land-use. Using available GIS data and an 'off-the-shelf' software application called TARGET, we find that the PES allocation criteria applied by authorities in 2002-2003 were more than twice as cost-efficient as criteria applied during 1999-2001. Results show that a policy relevant assessment of the cost-effectiveness of PES relative to other conservation policies can be carried out at regional level using available studies and GIS data. However, there are a number of data and conceptual limitations to using heuristic optimisation algorithms in the analysis of the cost-efficiency of PES. Site specific data on probabilities of land-use change, and a detailed specification of opportunity costs of farm land, labour and capital are required to use algorithms such as TARGET for ranking individual sites based on cost-efficiency. Despite its conceptual soundness for regional conservation analysis, biodiversity complementarity presents a practical challenge as a criterion for PES eligibility at farm level because it varies depending on the set of areas under PES contracts at any one time.

A model of immunological distances in systematics.

While immunological distances among taxa have had wide use in systematics, there has been some doubt about their utility because of the observed non-metricity of such distance matrices. A model is presented here relating observed immunological distance to the actual number of antigenic site differences between taxa. This model accounts for the observed departures of these distances from the metric condition of reciprocity and triangle inequality. Based upon the model, two procedures are suggested for the transformation of immunological distances to metric distances appropriate for phylogenetic analysis. The model implies that the usual scaling adjustments applied to the immunological distance matrix are inappropriate; however, the same transformation applied instead to an initial similarity matrix will solve a scaling problem. Non-reciprocity of the distances is shown to remain a problem independent of this initial scaling problem. It is suggested that further transformation of these re-scaled distances may be obtained through an extension of the ADCLUS procedure developed in psychology. This approach suggests a general strategy for a transformation to metric distances, given a particular model of non-metricity for the data.

Benthic macroinvertebrates in biological surveillance: Monte carlo significance tests on functional groups' responses to environmental gradients.

Functional feeding groups are evaluated as summaries of benthic macroinvertebrate communities for the Upper La Trobe river system of Victoria, Australia. Two related questions are addressed. First, 'what is the form of response of functional groups to environmental gradients?' Second, 'are observed group patterns significant insofar as they are unlikely to arise in randomly defined groups of taxa?'Five functional feeding groups are evaluated relative to an environmental space defined at the structural, taxonomic level. A three-dimensional multidimensional scaling ordination of the sample sites, based upon this structural data, reveals a strong correlation with stream order in one direction in the space, and with particle size and benthic organic matter in another orthogonal direction. With the exception of filterers, the observed high correlations of functional group abundance with this space also would have occurred in randomly-defined groups. Scrapers, while not significant as a group in terms of linear response, are significant in terms of unimodal or clumped response to this environmental space. The utilization of such clumped responses in ordination space for biological surveillance programs is discussed.

Phylogenetic pattern and the quantification of organismal biodiversity.

Biodiversity can be explored at a number of different levels and in principle may be separately quantified at each. Phylogenetic pattern has the potential to quantify and estimate biodiversity at the finest scale, that is, variation among species in features or attributes. This scale is an important one for conservation, as it should form the basis for prioritizing conservation efforts at the species level. Further, recent published objections to differentially weighting species are answered by defining option value at this feature-level. Unfortunately, there has been no consensus on exactly how phylogeny can be used to value species, possibly because proper consideration of the link between pattern and underlying features generally has been unresolved. 'Phylogenetic diversity' (PD) represents just one of several approaches that do consider diversity at the feature-level explicitly. These alternative approaches are discussed in the context of a general framework for using pattern to quantify diversity at a level below that of the original objects. The pattern framework highlights that estimation of biodiversity at a lower level using pattern will require decisions about the nature of the units of diversity, the kind of pattern to be used, the model relating unit items to pattern, and finally how this implies a pattern-based measure reflecting biodiversity. An alternative published model for relating features to a particular form of phylogenetic pattern is considered, and shown to make unwarranted assumptions. A possible alternative definition of the underlying units of diversity is examined, which may represent a different form of option value, also quantifiable using phylogeny. A possible alternative pattern to a phylogenetic tree for the prediction of feature diversity is also discussed. The appeal of these alternative approaches depends on the goals of conservation; in addition, justification for prioritizing or weighting requires that any practical approach avoid arbitrary, unwarranted, assumptions.

Towards an inclusive philosophy for phylogenetic inference.

We defend and expand on our earlier proposal for an inclusive philosophical framework for phylogenetics, based on an interpretation of Popperian corroboration that is decoupled from the popular falsificationist interpretation of Popperian philosophy. Any phylogenetic inference method can provide Popperian "evidence" or "test statements" based on the method's goodness-of-fit values for different tree hypotheses. Corroboration, or the severity of that test, requires that the evidence is improbable without the hypothesis, given only background knowledge that includes elements of chance. This framework contrasts with attempted Popperian justifications for cladistic parsimony--in which evidence is the data, background knowledge is restricted to descent with modification, and "corroboration," as a by-product of nonfalsification, is to be measured by cladistic parsimony. Recognition that cladistic "corroboration" reflects only goodness-of-fit, not corroboration/severity, makes it clear that standard cladistic prohibitions, such as restrictions on the evolutionary models to be included in "background knowledge," have no philosophical status. The capacity to assess Popperian corroboration neither justifies nor excludes any phylogenetic method, but it does provide a framework in phylogenetics for learning from errors--cases where apparent good evidence is probable even without the hypothesis. We explore these issues in the context of corroboration assessments applied to likelihood methods and to a new form of parsimony. These different forms of evidence and corroboration assessment point also to a new way to combine evidence--not at the level of overall fit, but at the level of overall corroboration/severity. We conclude that progress in an inclusive phylogenetics will be well served by the rejection of cladistic philosophy.

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 ß value performed better than the standard UPGMA method where ß is set equal to zero. The flexible UPGMA strategy, employed with a narrow ß range, is recommended based upon its ability to recover cluster structure over all error conditions.