Comparison of Linear,Nonlinear and Semiparametric Mixed‐effects Models for Estimating HIV Dynamic Parameters

The potency of antiretroviral agents in AIDS clinical trials can be assessed on the basis of an early viral response such as viral decay rate or change in viral load (number of copies of HIV RNA) of the plasma. Linear, parametric nonlinear, and semiparametric nonlinear mixed‐effects models have been proposed to estimate viral decay rates in viral dynamic models. However, before applying these models to clinical data, a critical question that remains to be addressed is whether these models produce coherent estimates of viral decay rates, and if not, which model is appropriate and should be used in practice. In this paper, we applied these models to data from an AIDS clinical trial of potent antiviral treatments and found significant incongruity in the estimated rates of reduction in viral load. Simulation studies indicated that reliable estimates of viral decay rate were obtained by using the parametric and semiparametric nonlinear mixed‐effects models. Our analysis also indicated that the decay rates estimated by using linear mixed‐effects models should be interpreted differently from those estimated by using nonlinear mixed‐effects models. The semiparametric nonlinear mixed‐effects model is preferred to other models because arbitrary data truncation is not needed. Based on real data analysis and simulation studies, we provide guidelines for estimating viral decay rates from clinical data. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Effects of species and habitat positional errors on the performance and interpretation of species distribution models

Aim A key assumption in species distribution modelling is that both species and environmental data layers contain no positional errors, yet this will rarely be true. This study assesses the effect of introduced positional errors on the performance and interpretation of species distribution models. Location Baixo Alentejo region of Portugal. Methods Data on steppe bird occurrence were collected using a random stratified sampling design on a 1‐km² pixel grid. Environmental data were sourced from satellite imagery and digital maps. Error was deliberately introduced into the species data as shifts in a random direction of 0–1, 2–3, 4–5 and 0–5 pixels. Whole habitat layers were shifted by 1 pixel to cause mis‐registration, and the cumulative effect of one to three shifted layers investigated. Distribution models were built for three species using three algorithms with three replicates. Test models were compared with controls without errors. Results Positional errors in the species data led to a drop in model performance (larger errors having larger effects – typically up to 10% drop in area under the curve on average), although not enough for models to be rejected. Model interpretation was more severely affected with inconsistencies in the contributing variables. Errors in the habitat layers had similar although lesser effects. Main conclusions Models with species positional errors are hard to detect, often statistically good, ecologically plausible and useful for prediction, but interpreting them is dangerous. Mis‐registered habitat layers produce smaller effects probably because shifting entire layers does not break down the correlation structure to the same extent as random shifts in individual species observations. Spatial autocorrelation in the habitat layers may protect against species positional errors to some extent but the relationship is complex and requires further work. The key recommendation must be that positional errors should be minimised through careful field design and data processing.     

The spatial pattern of soil-dwelling termites in primary and logged forest in Sabah, Malaysia

Abstract.  1. Primary and logged lowland dipterocarp forest sites were sampled for subterranean termites using soil pits located on a grid system in order to detect any patchiness in their distribution.
2. A spatial pattern in termite distributions was observed in the primary and logged sites, but the response differed between soil-feeding and non-soil-feeding termites.
3. Spatial analysis showed that soil-feeding termites were homogeneously distributed in the primary forest but significantly aggregated in the logged forest. This pattern was reversed for non-soil-feeding termites and may result from differences in resource provisioning between the two sites.
4. Gaps in termite distribution comprised a greater area than patches for both feeding groups and sites, but gaps dominated the logged site.
5. A significant association between soil-feeding and non-soil-feeding termite distributions occurred at both sites. This arose from an association between patches in the primary forest and between gaps in the logged forest.
6. Termite spatial pattern was optimally observed at a minimum extent of 64 m and lag of 2 m.
7. The spatially explicit SADIE (Spatial Analysis by Distances IndicEs) analyses were more successful than (non-spatially explicit) multivariate analysis (Canonical Correspondence Analysis) at detecting associations between termite spatial distributions and that of other biotic and abiotic variables.     

Roles of endothermy in niche differentiation for ball-rolling dung beetles (Coleoptera: Scarabaeidae) along an altitudinal gradient

Abstract.  1. An analysis of whether niche differentiation in ball-rolling dung beetles can be explained by the way in which they regulate their body temperature was conducted.
2.  A priori assumptions were: (i) if thermoregulation affects niche partitioning, sympatric species must have different endothermic strategies that minimise encounters; or, alternatively (ii) if two co-occurring species show the same thermoregulation pattern and their flight periods overlap, they might be avoiding competition by exhibiting different resource preferences or different food relocation behaviour.
3. The ball-rolling dung beetles studied showed a hierarchical structure based on the species' endothermic capacity, measured as temperature excess [ T _ex= difference between body temperature ( T _b) and ambient temperature ( T _a)]. Those with a high T _ex (10–15 °C) were located exclusively at altitudes >1000 m a.s.l. On the coastal plains, species with a high T _ex were restricted to flying at night when the T _a was lower. Species with a lower T _ex (less than 10 °C higher than T _a) were found in the coastal plains zone.
4. Where there was sympatry with similar trophic habits, the species involved showed very different thermal niches, and where there was significant overlap of thermal niches between sympatric species, trophic habits of species were very different.
5. The results suggest that it is possible to use the concept of the thermal niche as a tool to explain interspecific interactions and the spatial distribution of species.     

Seamounts: centres of endemism or species richness for ophiuroids?

Aim To test the hypotheses that seamounts exhibit high rates of endemism and/or species richness compared to surrounding areas of the continental slope and oceanic ridges. Location The south‐west Pacific Ocean from 19–57° S to 143–171° E. Methods Presence/absence museum data were compiled for seamount and non‐seamount areas at depths between 100 and 1500 m for the Ophiuroidea (brittle‐stars), an abundant and speciose group of benthic invertebrates. Large‐scale biogeographical gradients were examined through multivariate analyses at two spatial scales, at the scale of seamounts (< 1° of latitude/longitude) and regions (5–9°). The robustness of these patterns to spatially inconsistent sampling effort was tested using Monte Carlo‐style simulations. Levels of local endemism and species richness over numbers of samples were compared for seamount and non‐seamount areas using linear regressions. Non‐seamount populations were randomly generated from areas and depth ranges that reflected the typical sampling profile of seamounts. Results Seamount ophiuroid assemblages did not exhibit elevated levels of species richness or narrow‐range endemism compared with non‐seamount areas. Seamounts can exhibit high overall species richness for low numbers of samples, particularly on seamounts supporting a dense coral matrix, but this does not increase with additional sampling at the rates found in non‐seamount areas. There were relatively few identifiable seamount specialists. In general, seamount faunas reflected those found at similar depths in surrounding areas, including the continental slope. Seamount and non‐seamount faunas within the study area exhibited congruent latitudinal and bathymetric species turnover. Main conclusions Seamount faunas were variable for ophiuroid faunal composition, species richness and narrow‐range endemism, reflecting their environmental diversity and complex history. The continental slope was also variable, with some areas being particularly species rich. Broad geomorphological habitat categories such as ‘seamounts’ or ‘continental slope’ may be at the wrong scale to be useful for conservation planning.     

Influence of geographical extent on typology- and model-based assessments of taxonomic completeness of river macroinvertebrates

1. River InVertebrate Prediction and Classification System (RIVPACS)‐type predictive models are increasingly used to assess the biological condition of freshwaters, but management schemes may also be based on a priori groupings of similar water bodies (typologies) to control for natural variation in biota. The two approaches may lead to disagreements of the biological status of a site, depending on, for example, the spatial scale at which assessments are conducted. 2. We used data from 96 reference and 134 potentially impacted sites from Western and Central Finland to compare RIVPACS‐type models and a simple size‐based typology of rivers for the assessment of taxonomic completeness (the quotient of the Observed‐to‐Expected number of predicted taxa, O / E) of riffle macroinvertebrates. We specifically examined how geographical extent influences bioassessment performance (accuracy, precision and sensitivity to detect impact) of the two approaches. To fully examine the behaviour of the O / E‐index with the two approaches at differing spatial scales, we performed all assessments with a full range of thresholds for predicted taxa occurrence probabilities (p_t from 0+ to 0.9). 3. Both approaches performed consistently better than the corresponding null models. At the larger extent (i.e. assessment encompassing the whole study area), the RIVPACS‐approach performed in all aspects better than the typology‐approach. However, at the smaller extent (i.e. regional assessments) the RIVPACS‐type models and the typologies showed similar accuracy to predict the actual fauna (mean E), similar precision (SD) of cross‐validated O / E and similar sensitivity to detect sites with human impairment. 4. SD(O / E) decreased (i.e. precision increased) consistently with increasing p_t. However, both approaches were most sensitive at intermediate p_t:s (c. 0.2–0.6) when taxa with low predicted occurrence probabilities were excluded. 5. Our results show that RIVPACS‐type predictive models are less susceptible to variations in spatial scale, whereas the performance of a priori typologies increases with decreasing spatial extent. Thus, RIVPACS‐type models are more efficient for large‐scale bioassessments, but at restricted spatial scales, or with an otherwise biologically meaningful stratification, simple a priori classifications can be equally useful for the assessment of taxonomic completeness of river macroinvertebrates.     

Sex and the selfish herd: sexual segregation within nonmating whirligig groups

The fitness costs and benefits at different positions in fishshoals, bird flocks, and insect swarms can be asymmetric; agroup's edge may provide more feeding opportunities, but alsogreater predator risk. Animals make trade-offs between theseselection pressures based on individual differences in traitsincluding satiation level, ability to avoid predators, and sex.Previous studies did not evaluate the impact of sex on grouppositioning in these types of nonhierarchical, nonmating groupscalled congregations. A controlled laboratory experiment wasconducted, using marked whirligig beetles (Coleoptera: Gyrinidae),to test for sexual segregation and why different sexes mightchoose different positions. Soon after a disturbance, malesoften were found at the periphery and females at the centerof groups. There was also an overlying influence of feedingon position; satiated individuals moved toward the center andhungry individuals toward the periphery. Several minutes aftera disturbance, sexual segregation disappeared, but segregationdue to hunger persisted. Sexual segregation in this study wasbest explained by the predator avoidance hypothesis, not theenergy needs hypothesis. Females weighed less than males; thismay make them more at risk to predation because of reduced swimmingspeed or less mechanical protection from their exoskeleton.No difference between the sexes was found in the volume of theirdefensive chemicals. This is one of the first studies to showthat sex influences position of individuals within simple nonmatinggroups (congregations) and suggests that more attention shouldbe given to positional sex differences within shoals, flocks,herds, and swarms.     

Carbon dioxide increase: the implications at the ecosystem level*

Abstract Possible effects of increased atmospheric concentrations of CO₂ on forest ecosystems are discussed and as an example a simulation case study using a set of mixed-age and mixed-species forest stand models is presented. The responses of the models to a simple scenario (uniform growth increase of all trees as a response to CO₂ enrichment) include increases in biomass that are considerably less than the increases in growth rate of the trees. These simulations and more general discussion of the possible effects of increased photosynthetic production identify the problem of scaling-up small time-scale and space-scale measurements of plant responses to CO₂ enrichment to the ecosystem level.     

Models of development for blowfly sister species Chrysomya chloropyga and Chrysomya putoria

Abstract Developmental curves for the sister species Chrysomya chloropyga (Wiedemann, 1818) and Chrysomya putoria (Wiedemann, 1830) (Diptera: Calliphoridae) were established at eight and 10 different constant temperatures, respectively, using developmental landmarks and body length as measures of age. The thermal summation constants (K) and developmental threshold (D₀) were calculated for five developmental landmarks using a previously described method. Isomorphen and isomegalen diagrams were also constructed for the purpose of estimating postmortem intervals (PMIs). Chrysomya chloropyga had an average developmental threshold value (D₀) of 10.91 °C (standard error [SE] = 0.94 °C, n = 5), significantly lower than that of C. putoria (13.42 °C, SE = 0.45 °C, n = 5) (paired t‐test: t = ? 4.63, d.f. = 8, P < 0.00). Similarly, K values for C. chloropyga were larger than those for C. putoria for all developmental events except onset of the wandering phase. These are the first data that can be used to calculate minimum PMIs and predict population growth of C. chloropyga and C. putoria in Africa; the data indicate that developmental data for one of these species cannot be used as surrogate data for the sister species.     

A Bayesian Long‐term Survival Model Parametrized in the Cured Fraction

The main goal of this paper is to investigate a cure rate model that comprehends some well‐known proposals found in the literature. In our work the number of competing causes of the event of interest follows the negative binomial distribution. The model is conveniently reparametrized through the cured fraction, which is then linked to covariates by means of the logistic link. We explore the use of Markov chain Monte Carlo methods to develop a Bayesian analysis in the proposed model. The procedure is illustrated with a numerical example.