Computational aspects of host-parasite phylogenies

Computational aspects of host-parasite phylogenies form part of a set of general associations between areas and organisms, hosts and parasites, and species and genes. The problem is not new and the commonalities of exploring vicariance biogeography (organisms tracking areas) and host-parasite co-speciation (parasites tracking hosts) have been recognised for some time. Methods for comparing host-parasite phylogenies are now well established and fall within two basic categories defined in terms of the way the data are interpreted in relation to the comparison of host-parasite phylogenies, so-called a posteriori, eg Brooks' Parsimony Analysis (BPA), or a priori, eg reconciled trees and other model-based methods, as implemented in the program TreeMap; the relative merits of the two philosophies inherent in these two approaches remain hotly debated. This paper reviews the computational methods currently available to analyse host-parasite relationships.     

Male morphological variation and the determinants of body size in two Otiteselline fig wasps

The chalcid wasps (Hymenoptera) that develop in fig tree inflorescences(Ficus: Moraceae) have often been used to study alternativereproductive behaviors. However, recent work suggests that suchbehaviors are more complex than previously thought. We investigatedthis in Otitesella longicauda and O. rotunda. In addition toknown dimorphisms in the two species (each have "religiosa"males that use their mandibles to fight for mates in the fig,and "digitata" males that disperse from the fig to mate), wefound that religiosa males below species-specific body sizeswitch points have relatively larger mandibles and are lesssclerotized than those above. Thus, they are actually trimorphic.We suggest that the religiosa morph variation is linked to fighter/nonfighteralternative mating behaviors, with small (nonfighting) maleshaving relatively larger mandibles because they also use themto pull females out of their galls before mating. Also, we investigatedthe determinants of wasp body size, and whether females (foundresses)adjust their offspring allocation strategies according to expectedoffspring size. We found that wasp size is larger in ovariesnear the center of the fig, and more females and fewer religiosamales are laid in such ovaries than in those further away. Thisprobably indicates that foundresses lay females when they areexpected to be large because their fitness is more body size–dependentthan that of religiosa males. We then discuss the implicationsof our findings for the study of alternative reproductive behaviorsand foundress offspring allocation strategies.     

Control of kernel weight and kernel water relations by post-flowering source-sink ratio in maize

The maize (Zea mays L.) kernel undergoes large changes in water content during its development. Whether such changes regulate the pattern of kernel development or are simply a consequence of it has not yet been established because other factors, such as assimilate supply, can also affect the rate and duration of kernel growth. This study was conducted to determine whether variation in kernel weight (KW) in response to source-sink treatments is mediated by a change in kernel water relations. Two hybrids were sown at three stand densities (one, eight and 18 plants m-2), and kernel numbers were restricted to control the post-flowering source-sink ratio within each stand density. Kernel development and water relations [water content, water potential (psiw), osmotic potential (psis) and turgor] were monitored throughout grain filling. Final KW varied from 253 to 372 mg per kernel in response to source-sink treatments. For both genotypes, variation in KW was a result of a change in kernel growth rate (r2 = 0.91; P < 0.001) and not in the duration of kernel filling. Final KW was closely correlated with maximum kernel water content (r2 = 0.94; P < 0.001) achieved during rapid dry matter accumulation. However, variation in KW was not reflected in kernel water status parameters (psiw, psis or turgor), which remained fairly stable across treatments. These results indicate that maximum water content provides an easily quantifiable measure of kernel sink capacity in maize. Kernel water status parameters may affect the duration of grain filling, but have no discernible impact on kernel growth rate.     

Comparative ecophysiological measurements on the light responses,water relations and desiccation tolerance of the filmy ferns Hymenophyllum wilsonii Hook. and H. tunbrigense (L.) Smith

Chlorophyll-fluorescence and infrared gas analyser measurements show saturation of photosynthetic electron flow and CO(2) uptake at generally lower irradiances in Hymenophyllum tunbrigense than in H. wilsonii, but with wide variation in both species (63-189 micromol m(-2) s(-1) PPFD in H. tunbrigense, 129-552 micro mol m(-2) s(-1) PPFD in H. wilsonii), probably related to both site and season. Non-photochemical quenching (at 400 micromol m(-2) s(-1) PPFD) ranged from 2.1 to 8.1, with no significant difference between the species. Pressure-volume curves from thermocouple-psychrometer measurements give full-turgor osmotic potentials of approx. -1.4 MPa in both species, and indicate low apoplast fractions and high cell-wall elastic moduli. Leaves of H. tunbrigense recovered within 24 h from up to 7 d desiccation at water potentials ranging from -40 MPa (74 % relative humidity, RH) to -220 MPa (20 % RH); after 15 or 30 d, desiccation recovery was slower and less complete, and leaves were severely damaged at the highest and lowest humidities. Hymenophyllum wilsonii recovered well from up to 30 d desiccation at -114 and -220 MPa, but at -40 MPa it showed signs of damage after 15 d, and was severely damaged or killed after 30 d. Results are discussed in relation to the ecological and geographical distributions of the two species, and to the adaptive strategies of filmy ferns in general.     

Enforced Expression of Oxygen-Regulated Protein,ORP150, Induces Vacuolar Degeneration in Mouse Myocardium

Although the 150 kDa oxygen-regulated protein (ORP150) is known as a protein induced by low oxygen tension or ischemical insult, its possible role has not been fully investigated in vivo. To investigate the intracellular function of this protein, we generated the ORP150 over-expressing transgenic mice (ORP-Tg mice) under -actin promoter, and established three independent lines of the transgene expressed mice. All lines invariably showed growth retardation. Over-expression of ORP150 was confirmed by western blotting in heart, brain, spleen, skeletal muscle, pancreas, lung, thymus, and kidney. To ascertain the relationship between the over-expression of the ORP150 and the growth retardation in the transgenic mice, we examined pathological changes in the transgenics. In the ORP-Tg mice, vacuolar degeneration appeared in the heart. The degeneration in the myocytes became conspicuous with advancing age. Immunostaining demonstrated ORP150 in the vacuoles of degenerating myocytes. Electron microscopical findings revealed striking development of intracellular membrane system, for example, rough endoplasmic reticula (rER), vacuoles and Golgi bodies, swelling of sarcoplasmic reticulum, and lysis of myofibrils and mitochondria. These findings indicate that ORP150 may locate in the rER and other outer compartment of ER, and that constitutive over-expression of ORP150 in the heart induces vacuolar degeneration in myocytes, resulting in growth retardation of the transgenics.     

Combined association,segregation and aggregation analysis on case-control family data

Recently genetic epidemiologists have begun using case-control family study designs to investigate the role of genetic and environmental risk factors in disease etiology. The objective of these studies is to assess the association of environmental factors with the disease trait; to characterize the disease genes using segregation analysis; and to quantify the residual familial aggregation after controlling for environmental and genetic factors. Typically these objectives are achieved by conducting separate studies and analysis. This paper describes an estimating equation based approach for a combined association, segregation and aggregation analysis on data from case-control family studies. Simulations indicate that the method performs well in a variety of settings. The method is illustrated using simulated family history data made available to participants in a recent Genetic Analysis Workshop.     

Some general points in estimating heterogeneity variance with the DerSimonian-Laird estimator

In this paper we consider estimating heterogeneity variance with the DerSimonian-Laird (DSL) estimator as typically used in meta-analysis. In its general form the DSL estimator requires inverse population-averaged study-specific variances as weights, in which case the estimator is unbiased. It has become common practice, however, to use estimates of the study-specific variances instead of their population-averaged versions. This can lead to considerable bias. Simulations illustrate these findings.     

On the conservative nature of the leaf mass-area relationship

In a previous empirical study, Hughes and colleagues showed that for several herbaceous species there is apparently a unique species-specific relationship between the area and mass of leaves. We tested this proposition using measurements from 15 broad-leaved species. We found that to a reasonable approximation, leaf area was proportional to leaf mass within a given species despite relatively large variations in both leaf thickness and the mass fraction of liquid matter. These observations show that the inverse density-thickness of leaves from a given species, which we call the Hughes constant, is approximately conserved. We conclude that the Hughes constant is likely to be more conservative than other traits traditionally used to describe leaves.     

Tillering in grain sorghum over a wiide range of population densities: modelling dynamics of tiller fertility

The prediction of tillering is poor or absent in existing sorghum crop models even though fertile tillers contribute significantly to grain yield. The objective of this study was to identify general quantitative relationships underpinning tiller dynamics of sorghum for a broad range of assimilate availabilities. Emergence, phenology, leaf area development and fertility of individual main culms and tillers were quantified weekly in plants grown at one of four plant densities ranging from two to 16 plants m(-2). On any given day, a tiller was considered potentially fertile (a posteriori) if its number of leaves continued to increase thereafter. The dynamics of potentially fertile tiller number per plant varied greatly with plant density, but could generally be described by three determinants, stable across plant densities: tiller emergence rate aligned with leaf ligule appearance rate; cessation of tiller emergence occurred at a stable leaf area index; and rate of decrease in potentially fertile tillers was linearly related to the ratio of realized to potential leaf area growth. Realized leaf area growth is the measured increase in leaf area, whereas potential leaf area growth is the estimated increase in leaf area if all potentially fertile tillers were to continue to develop. Procedures to predict this ratio, by estimating realized leaf area per plant from intercepted radiation and potential leaf area per plant from the number and type of developing axes, are presented. While it is suitable for modelling tiller dynamics in grain sorghum, this general framework needs to be validated by testing it in different environments and for other cultivars.