Character correlation and its use for identification

A method is presented for correlating phylogenetic characters through cladistic analysis. It extends the use of phylogenetic datasets for diagnostic purposes. It improves matrix-based identification tools by predicting novel character-state combinations that were not observed when the key was constructed. By interpreting homoplasy as analytical error, hypothetical character-state combinations are tested for the homoplasy that they would add to the shortest tree(s). The correlation is equal to the homoplasy summed across all state combinations, divided by a maximum possible value. The results depend on uncertainty about the sequence of state transitions and their overlap among characters. A correlation index r is proposed for sets of non-additive characters; it is a kind of multiple-regression value, and its ensemble value R is a statistic of a whole matrix. This approach can be used to select sets of the best "proxy" characters to substitute for unobservable characters of interest. The concept can be extended to continuous characters. Worked examples are given with datasets of various insect orders.

Influence of different modes of morphological character correlation on phylogenetic tree inference

Phylogenetic analysis algorithms require the assumption of character independence - a condition generally acknowledged to be violated by morphological data. Correlation between characters can originate from intra-organismal features, shared phylogenetic history or forced by particular character-state coding schemes. Although the two first sources can be investigated by biologists a posteriori and the third one can be avoided a priori with good practices, phylogenetic software do not distinguish between any of them.In this study, we propose a new metric of raw character difference as a proxy for character correlation. Using thorough simulations, we test the effect of increasing or decreasing character differences on tree topology. Overall, we found an expected positive effect of reducing character correlations on recovering the correct topology. However, this effect is less important for matrices with a small number of taxa (25 in our simulations) where reducing character correlation is not more effective than randomly drawing characters. Furthermore, in bigger matrices (350 characters), there is a strong effect of the inference method with Bayesian trees being consistently less affected by character correlation than maximum parsimony trees.These results suggest that ignoring the problem of character correlation or independence can often impact topology in phylogenetic analysis. However, encouragingly, they also suggest that, unless correlation is actively maximised or minimised, probabilistic methods can easily accommodate for a random correlation between characters.

Identity of Pourthiaea podocarpifolia (Rosaceae)

Based on extensive field observations, population sampling, examination of a large number of specimens, and subsequent statistical analysis, we found that the characters used previously to distinguish between Pourthiaea blinii and P. podocarpifolia (Rosaceae), i.e. the density of indumentum on the lower surface of leaf blade and inflorescences, are extremely various within a population and continuous in variation, and show no character correlation. These characters are therefore of little value for delimiting these two species. Here we reduce P. podocarpifolia to the synonymy of P. blinii. Lectotypification is made for both Cotoneaster blinii (basionym of Pourthiaea blinii) and Photinia podocarpifolia (basionym of Pourthiaea podocarpifolia).

Multiple shifts between violet and ultraviolet vision in a family of passerine birds with associated changes in plumage coloration

Colour vision in diurnal birds falls into two discrete classes, signified by the spectral sensitivity of the violet- (VS) or ultraviolet-sensitive (UVS) short wavelength-sensitive type 1 (SWS1) single cone. Shifts between sensitivity classes are rare; three or four are believed to have happened in the course of avian evolution, one forming UVS higher passerines. Such shifts probably affect the expression of shortwave-dominated plumage signals. We have used genomic DNA sequencing to determine VS or UVS affinity in fairy-wrens and allies, Maluridae, a large passerine family basal to the known UVS taxa. We have also spectrophotometrically analysed male plumage coloration as perceived by the VS and UVS vision systems. Contrary to any other investigated avian genus, Malurus (fairy-wrens) contains species with amino acid residues typical of either VS or UVS cone opsins. Three bowerbird species (Ptilonorhynchidae) sequenced for outgroup comparison carry VS opsin genes. Phylogenetic reconstructions render one UVS gain followed by one or more losses as the most plausible evolutionary scenario. The evolution of avian ultraviolet sensitivity is hence more complex, as a single shift no longer explains its distribution in Passeriformes. Character correlation analysis proposes that UVS vision is associated with shortwave-reflecting plumage, which is widespread in Maluridae.

A Wesleyan Spirituality: Implications for Clinical Practice

This article seeks to integrate Wesleyan spirituality with psychology and clinical practice. Three particular aspects in the Wesleyan tradition are explored: human freedom, the doctrine of sanctification, and religious affections. The thesis of this article is that all three key points can be well integrated into psychology and clinical practice. The following clinical implications are proposed: God-given human freedom empowers the client and therapist; healthy relationships are seen as a critical measure of spiritual maturity; and religious affections are seen to contribute to psychological health in their ability to experientially build character. Correlation between Wesley's focus on mature relationships and certain emphases in object relations theory are also proposed.