Platyhelminth phylogenetics - a key to understanding parasitism?

The comparative method, the inference of biological processes from phylogenetic patterns, is founded on the reliability of the phylogenetic tree. In attempting to apply the comparative method to the understanding of the evolution of parasitism in the phylum Platyhelminthes, we have highlighted several points we consider to be of value along with many problems. We discuss four of these topics. Firstly, we view the group at a phylum level, in particular discussing the importance of establishing the sister taxon to the obligate parasite group, the Neodermata, for addressing such questions as the monophyly, parasitism or the endo or ectoparasitic nature of the early parasites. The variety of non-congruent phylogenetic trees presented so far, utilising either or both morphological and molecular data, gives rise to the suggestion that any evolutionary scenarios presented at this stage be treated as interesting hypotheses rather than well-supported theories. Our second point of discussion is the conflict between morphological and molecular estimates of monogenean evolution. The Monogenea presents several well-established morphological autapomorphies, such that morphology consistently estimates the group as monophyletic, whereas molecular sequence analyses indicate paraphyly, with different genes giving different topologies. We discuss the problem of reconciling gene and species trees. Thirdly, we use recent phylogenetic results on the tapeworms to interpret the evolution of strobilation, proglottization, segmentation and scolex structure. In relation to the latter, the results presented indicate that the higher cestodes are diphyletic, with one branch difossate and the other tetrafossate. Finally, we use a SSU rDNA phylogenetic tree of the Trematoda as a basis for the discussion of an aspect of the digenean life-cycle, namely the nature of the first intermediate host. Frequent episodes of host-switching, between gastropod and bivalve hosts or even into annelids, are indicated.

Molecular clocks in reptiles: Life history influences rate of molecular evolution

Life history has been implicated as a determinant of variation in rate of molecular evolution amongst vertebrate species because of a negative correlation between bode size and substitution rate for many Molecular data sets. Both the generality and the cause of the negative bode size trend have been debated, and the validity of key studies has been questioned (particularly concerning the failure to account for phylogenetic bias). In this study, a comparative method has been used to test for an association between a range of life-history variables-such as body size age at maturity, and clutch size-and DNA substitution rate for three genes (NADH4, cytochrome b, and c-mos). A negative relationship between body size and rate of molecular evolution was found for phylogenetically independent pairs of reptile species spanning turtles. lizards. snakes, crocodile, and tuatara. Although this Study was limited by the number of comparisons for which both sequence and lite-history data were available, the results, suggest that a negative bode size trend in rate of molecular evloution may be a general feature of reptile molecular evolution. consistent with similar studies of mammals and birds. This observation has important implications for uncovering the mechanisms of molecular evolution and warns against assuming that related lineages will share the same substitution rate (a local molecular clock) in order to date evolutionary divergences from DNA sequences.

Getting the run around: accessing services for children with developmental co-ordination disorder

Background Accessing services for children with developmental co-ordination disorder (DCD) is frequently difficult for parents who have to navigate both health and education systems to find a diagnosis and appropriate interventions. Method A qualitative study design incorporating a phenomenological perspective was utilized to understand the nature of the experiences of these parents in attempting to access support for their children with DCD. Twelve parents, whose children attended the Kids Skills Clinic at the University of Western Ontario and were identified as having DCD, were interviewed by the second author. Interviews were transcribed verbatim and analysed using constant comparative method. Member checking, peer checking and code-recoding were carried out to enhance rigour in data analysis. Results A number of themes emerged focusing on the common problems experienced leading to occupational therapy referral. Parents' journeys to seek and access services for their children with DCD were characterized by a sense of maternal knowing, experience of frustration, trivialization of the problem, a sense of 'going it alone', and 'getting the run around'. Conclusions Implications for health and educational professionals working with children, in terms of recognition of DCD and referral for services, are described.

Sociality and the rate of molecular evolution

The molecular clock does not tick at a uniform rate in all taxa but maybe influenced by species characteristics. Eusocial species (those with reproductive division of labor) have been predicted to have faster rates of molecular evolution than their nonsocial relatives because of greatly reduced effective population size; if most individuals in a population are nonreproductive and only one or few queens produce all the offspring, then eusocial animals could have much lower effective population sizes than their solitary relatives, which should increase the rate of substitution of nearly neutral mutations. An earlier study reported faster rates in eusocial honeybees and vespid wasps but failed to correct for phylogenetic nonindependence or to distinguish between potential causes of rate variation. Because sociality has evolved independently in many different lineages, it is possible to conduct a more wide-ranging study to test the generality of the relationship. We have conducted a comparative analysis of 25 phylogenetically independent pairs of social lineages and their nonsocial relatives, including bees, wasps, ants, termites, shrimps, and mole rats, using a range of available DNA sequences (mitochondrial and nuclear DNA coding for proteins and RNAs, and nontranslated sequences). By including a wide range of social taxa, we were able to test whether there is a general influence of sociality on rates of molecular evolution and to test specific predictions of the hypothesis: (1) that social species have faster rates because they have reduced effective population sizes; (2) that mitochondrial genes would show a greater effect of sociality than nuclear genes; and (3) that rates of molecular evolution should be correlated with the degree of sociality. We find no consistent pattern in rates of molecular evolution between social and nonsocial lineages and no evidence that mitochondrial genes show faster rates in social taxa. However, we show that the most highly eusocial Hymenoptera do have faster rates than their nonsocial relatives. We also find that social parasites (that utilize the workers from related species to produce their own offspring) have faster rates than their social relatives, which is consistent with an effect of lower effective population size on rate of molecular evolution. Our results illustrate the importance of allowing for phylogenetic nonindependence when conducting investigations of determinants of variation in rate of molecular evolution.

Adverse feedback sequences in exploited marine systems: Are deliberate interruptive actions warranted?

Several mechanisms for self-enhancing feedback instabilities in marine ecosystems are identified and briefly elaborated. It appears that adverse phases of operation may be abruptly triggered by explosive breakouts in abundance of one or more previously suppressed populations. Moreover, an evident capacity of marine organisms to accomplish extensive geographic habitat expansions may expand and perpetuate a breakout event. This set of conceptual elements provides a framework for interpretation of a sequence of events that has occurred in the Northern Benguela Current Large Marine Ecosystem (off south-western Africa). This history can illustrate how multiple feedback loops might interact with one another in unanticipated and quite malignant ways, leading not only to collapse of customary resource stocks but also to degradation of the ecosystem to such an extent that disruption of customary goods and services may go beyond fisheries alone to adversely affect other major global ecosystem concerns (e.g. proliferations of jellyfish and other slimy, stingy, toxic and/or noxious organisms, perhaps even climate change itself, etc.). The wisdom of management interventions designed to interrupt an adverse mode of feedback operation is pondered. Research pathways are proposed that may lead to improved insights needed: (i) to avoid potential 'triggers' that might set adverse phases of feedback loop operation into motion; and (ii) to diagnose and properly evaluate plausible actions to reverse adverse phases of feedback operation that might already have been set in motion. These pathways include the drawing of inferences from available 'quasi-experiments' produced either by short-term climatic variation or inadvertently in the course of biased exploitation practices, and inter-regional applications of the comparative method of science.

A comparative study of iterative Chebyshev and Lanczos implementations of the boundary inhomogeneity method for quantum scattering

We have recently developed a scaleable Artificial Boundary Inhomogeneity (ABI) method [Chem. Phys. Lett.366, 390–397 (2002)] based on the utilization of the Lanczos algorithm, and in this work explore an alternative iterative implementation based on the Chebyshev algorithm. Detailed comparisons between the two iterative methods have been made in terms of efficiency as well as convergence behavior. The Lanczos subspace ABI method was also further improved by the use of a simpler three-term backward recursion algorithm to solve the subspace linear system. The two different iterative methods are tested on the model collinear H+H2 reactive state-to-state scattering.

Comparative study of Li, Na, and K adsorptions on graphite by using ab initio method

A comprehensive study has been conducted to compare the adsorptions of alkali metals (including Li, Na, and K) on the basal plane of graphite by using molecular orbital theory calculations. All three metal atoms prefer to be adsorbed on the middle hollow site above a hexagonal aromatic ring. A novel phenomenon was observed, that is, Na, instead of Li or K, is the weakest among the three types of metal atoms in adsorption. The reason is that the SOMO (single occupied molecular orbital) of the Na atom is exactly at the middle point between the HOMO and the LUMO of the graphite layer in energy level. As a result, the SOMO of Na cannot form a stable interaction with either the HOMO or the LUMO of the graphite. On the other hand, the SOMO of Li and K can form a relatively stable interaction with either the HOMO or the LUMO of graphite. Why Li has a relatively stronger adsorption than K on graphite has also been interpreted on the basis of their molecular-orbital energy levels.

Continuity of care and readmission in two service systems: a comparative Victorian and Groningen case-register study

Objective: We compared service consumption, continuity of care and risk of readmission in a record linkage follow-up study of cohorts of patients with schizophrenia and related disorders in Victoria (Australia) and in Groningen (The Netherlands). These areas are interesting to compare because mental health care is in a different stage of deiustitutionalization. More beds are available in Groningen and more community resources are available in Victoria. Method: The cohorts were followed for 4 years, since discharge from inpatient services using record linkage data available in the psychiatric case-registers in both areas. Survival analysis was used to study continuity of care and risk of readmission. Results: Available indicators showed a higher level of continuity of care in Victoria. While the relative risk of readmission was the same in both areas and not affected by aftercare contact after discharge, the number of days spent in hospital was much higher in the Groningen register area. Conclusion: These findings provide further support for earlier reports that the risk of readmission is predominantly affected by attributes of mental illness. However, the duration of admissions, is strongly affected by service system variables, including the provision of continuity of care.

A comparative mental health literacy survey of psychiatrists and other mental health professionals in Singapore

Objective: The objectives of this study are, first, to replicate and extend an Australian approach to assessing mental health literacy by studying a sample of Singapore mental health professionals, and to focus on differences between judgements made by the psychiatrists in comparison with the other mental health professionals. Second, to compare the psychiatrists' judgements with those of Australian psychiatrists. Method: The Australian questionnaire, assessing responses in relation to vignettes of major depression and to schizophrenia was extended by adding a third vignette of mania, and by the addition of several region-specific response options. Nearly 500 questionnaires were distributed to representative staff (psychiatrists, nurses and allied health) of a large psychiatric institution in Singapore, with a response rate of 81%. Psychiatrists' judgements were compared with all other hospital staff, and with Australian psychiatrists' judgements. Results: The two principal contrast groups (Singapore psychiatrists and other Singapore mental health professionals) differed slightly in terms of diagnostic accuracy. The psychiatrists differed in favouring a more professionally focused model of intervention, while both professional groups viewed traditional healers and their practices as distinctly unhelpful. Direct comparison of psychiatrist ratings generated in Singapore and in Australia revealed quite similar response profiles. Conclusions: In addition to generating data of some intrinsic importance, comparison with Australian survey data allows the potential impact of regional and cultural differences, as well as of varying psychiatric practices, to be identified. Responses identified more similarities than differences in the judgements of the psychiatrists from the two countries.

Methods for prediction of peptide binding to MHC molecules: A comparative study

Background: A variety of methods for prediction of peptide binding to major histocompatibility complex (MHC) have been proposed. These methods are based on binding motifs, binding matrices, hidden Markov models (HMM), or artificial neural networks (ANN). There has been little prior work on the comparative analysis of these methods. Materials and Methods: We performed a comparison of the performance of six methods applied to the prediction of two human MHC class I molecules, including binding matrices and motifs, ANNs, and HMMs. Results: The selection of the optimal prediction method depends on the amount of available data (the number of peptides of known binding affinity to the MHC molecule of interest), the biases in the data set and the intended purpose of the prediction (screening of a single protein versus mass screening). When little or no peptide data are available, binding motifs are the most useful alternative to random guessing or use of a complete overlapping set of peptides for selection of candidate binders. As the number of known peptide binders increases, binding matrices and HMM become more useful predictors. ANN and HMM are the predictive methods of choice for MHC alleles with more than 100 known binding peptides. Conclusion: The ability of bioinformatic methods to reliably predict MHC binding peptides, and thereby potential T-cell epitopes, has major implications for clinical immunology, particularly in the area of vaccine design.

Comparative surface accessibility of a pore-lining threonine residue (T6') in the glycine and GABA(A) receptors

The substituted cysteine accessibility method was used to probe the surface exposure of a pore-lining threonine residue (T6') common to both the glycine receptor (GlyR) and gamma-aminobutyric acid, type A receptor (GABAAR) chloride channels. This residue lies close to the channel activation gate, the ionic selectivity filter, and the main pore blocker binding site. Despite their high amino acid sequence homologies and common role in conducting chloride ions, recent studies have suggested that the GlyRs and GABA(A)Rs have divergent open state pore structures at the 6' position. When both the human alpha1(T6'C) homomeric GlyR and the rat alpha1(T6'C)beta1(T6'C) heteromeric GABA(A)R were expressed in human embryonic kidney 293 cells, their 6' residue surface accessibilities differed significantly in the closed state. However, when a soluble cysteine-modifying compound was applied in the presence of saturating agonist concentrations, both receptors were locked into the open state. This action was not induced by oxidizing agents in either receptor. These results provide evidence for a conserved pore opening mechanism in anion-selective members of the ligand-gated ion channel family. The results also indicate that the GABA(A)R pore structure at the 6' level may vary between different expression systems.

Comparative surface accessibility of a pore-lining threonine residue (T6') in the glycine and GABA(A) receptors

The substituted cysteine accessibility method was used to probe the surface exposure of a pore-lining threonine residue (T6’) common to both the glycine receptor (GlyR) and GABAA receptor (GABAAR) chloride channels. This residue lies close to the channel activation gate, the ionic selectivity filter and the main pore blocker binding site. Recent studies have suggested that the GlyRs and GABAARs have divergent open state pore structures at the 6’ position. When both the human a1T6’C homomeric GlyR and the rat a1T6’Cb1T6’C heteromeric GABAAR were expressed in HEK293 cells, their 6’ residue surface accessibilities differed significantly in the closed state. However, when a soluble cysteine-modifying compound was applied in the presence of saturating agonist concentrations, both receptors were locked into the open state. This action was not induced by oxidising agents in either receptor. These results provide evidence for a conserved pore opening mechanism in anion-selective members of the ligand-gated ion channel family. The results also indicate that the GABAAR pore structure at the 6’ level may vary between different expression systems.

Dendritic branching patterns of pyramidal cells in the visual cortex of the new world marmoset monkey, with comparative notes on the old world macaque monkey

The basal dendritic arbors of 442 supragranular pyramidal cells in visual cortex of the marmoset monkey were compared by fractal analyses. As detailed in a previous study,(1) individual cells were injected with Lucifer Yellow and processed for a DAB reaction product. The basal dendritic arbors were drawn, in the tangential plane, and the fractal dimension (D) determined by the dilation method. The fractal dimensions were compared between cells in ten cortical areas containing cells involved in visual processing, including the primary visual area (Vi), the second visual area (V2), the dorsoanterior area (DA), the dorsomedial area (DM), the dorsolateral. area (DL), the middle temporal area (MT), the posterior parietal area (PP), the fundus of the superior temporal area (FST) and the caudal and rostral subdivisions of inferotemporal cortex (ITc and ITr, respectively). Of 45 pairwise interareal comparisons of the fractal dimension of neurones, 20 were significantly different. Moreover, comparison of data according to previously published visual processing pathways revealed a trend for cells with greater fractal dimensions in higher cortical areas. Comparison of the present results with those in homologous cortical areas in the macaque monkey(2) revealed some similarities between the two species. The similarity in the trends of D values of cells in both species may reflect developmental features which, result in different functional attributes.

Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875)

Comparative phylogeography has proved useful for investigating biological responses to past climate change and is strongest when combined with extrinsic hypotheses derived from the fossil record or geology. However, the rarity of species with sufficient, spatially explicit fossil evidence restricts the application of this method. Here, we develop an alternative approach in which spatial models of predicted species distributions under serial paleoclimates are compared with a molecular phylogeography, in this case for a snail endemic to the rainforests of North Queensland, Australia. We also compare the phylogeography of the snail to those from several endemic vertebrates and use consilience across all of these approaches to enhance biogeographical inference for this rainforest fauna. The snail mtDNA phylogeography is consistent with predictions from paleoclimate modeling in relation to the location and size of climatic refugia through the late Pleistocene-Holocene and broad patterns of extinction and recolonization. There is general agreement between quantitative estimates of population expansion from sequence data (using likelihood and coalescent methods) vs. distributional modeling. The snail phylogeography represents a composite of both common and idiosyncratic patterns seen among vertebrates, reflecting the geographically finer scale of persistence and subdivision in the snail. In general, this multifaceted approach, combining spatially explicit paleoclimatological models and comparative phylogeography, provides a powerful approach to locating historical refugia and understanding species' responses to them.

Comparative analysis of genetic diversity in the mangrove species Avicennia marina (Forsk.) Vierh. (Avicenniaceae) detected by AFLPs and SSRs

Avicennia marina is an important mangrove species with a wide geographical and climatic distribution which suggests that large amounts of genetic diversity are available for conservation and breeding programs. In this study we compare the informativeness of AFLPs and SSRs for assessing genetic diversity within and among individuals, populations and subspecies of A. marina in Australia. Our comparison utilized three SSR loci and three AFLP primer sets that were known to be polymorphic, and could be run in a single analysis on a capillary electrophoresis system, using different-colored fluorescent dyes. A total of 120 individuals representing six populations and three subspecies were samplcd. At the locus level, SSRs were considerably more variable than AFLPs, with a total of 52 alleles and an average heterozygosity of 0.78. Average heterozygosity for AFLPs was 0.193, but all of the 918 bands scored were polymorphic. Thus, AFLPs were considerably more efficient at revealing polymorphic loci than SSRs despite lower average heterozygosities. SSRs detected more genetic differentiation between populations (19 vs 9%) and subspecies (35 vs 11%) than AFLPs. Principal co-ordinate analysis revealed congruent patterns of genetic relationships at the individual, population and subspecific levels for both data sets. Mantel testing confirmed congruence between AFLP and SSR genetic distances among, but not within, population comparisons, indicating that the markers were segregating inde- pendently but that evolutionary groups (populations and subspecies) were similar. Three genetic criteria of importance for defining priorities for ex situ collections or in situ conservation programs (number of alleles, number of locally common alleles and number of private alleles) were correlated between the AFLP and SSR data sets. The congruence between AFLP and SSR data sets suggest that either method, or a combination, is applicable to expanded genetic studies of mangroves. The codominant nature of SSRs makes them ideal for further population-based investigations, such as mating-system analyses, for which the dominant AFLP markers are less well suited. AFLPs may be particularly useful for monitoring propagation programs and identifying duplicates within collections, since a single PCR assay can reveal many loci at once.