Abalone I: Analyzing Mark-Recapture-Recovery Data Incorporating Growth and Delayed Recovery

Abalone are semimobile marine gastropods that form the basis of Australia's second most valuable fishery. A site off the coast of Port Arthur, Tasmania, was visited on six occasions. On each occasion, any unmarked live abalone found were marked with a unique identification number and were recorded. Any previously marked abalone found had its identification number and whether or not it was still alive recorded. This results in integrated mark-recapture-recovery data, as in Catchpole et al. (1998, Biometrics 54, 33-46). During the study period, abalone grew in size, and we model the survival of individuals as a function of their size, estimated from a fitted growth curve. The shells of dead animals are long lasting, and we extend existing methodology to allow for the possibility that an animal found dead may have been dead but overlooked for several visits.     

Cervical screening in Luxembourg: 1990–1999

For quality assurance purposes, the results of the 1990's obtained by the National Cervical Cancer Screening Programme (NCCSP) launched in 1962 were reviewed. The positive cytodiagnosis, the histologically verified in situ and invasive cervical cancers and the mortality rates were reported.     

Describing Ordinal Odds Ratios for Stratified r × c Tables

For an r × ctable with ordinal responses, odds ratios are commonly used to describe the relationship between the row and column variables. This article shows two types of ordinal odds ratios where local‐global odds ratios are used to compare several groups on a c‐category ordinal response and a global odds ratio is used to measure the global association between a pair of ordinal responses. When there is a stratification factor, we consider Mantel‐Haenszel (MH) type estimators of these odds ratios to summarize the association from several strata. Like the ordinary MH estimator of the common odds ratio for several 2 × 2 contingency tables, the estimators are used when the association is not expected to vary drastically among the strata. Also, the estimators are consistent under the ordinary asymptotic framework in which the number of strata is fixed and also under sparse asymptotics in which the number of strata grows with the sample size. Compared to the maximum likelihood estimators, simulations find that the MH type estimators perform better especially when each stratum has few observations. This article provides variances and covariances formulae for the local‐global odds ratios estimators and applies the bootstrap method to obtain a standard error for the global odds ratio estimator. At the end, we discuss possible ways of testing the homogeneity assumption.     

Fishers' Knowledge of Marine Species Assemblages: Bridging between Scientific and Local Ecological Knowledge in Southeastern Puerto Rico

Increasingly, local ecological knowledge (LEK) held by groups of people engaging directly with their ecosystems for food production is recognized as a valuable tool for understanding environmental change, as well as for ecosystem management and conservation. However, the acceptance of LEK for resource management has been partly hindered by difficulties in translating local knowledge into a form that can be applied directly to Western scientific endeavors. Anthropology's focus on cultural meaning makes its practitioners uniquely qualified to find common ground between different systems of knowledge. Here, I report the use of ethnographic methods to represent Puerto Rican small-scale fishers' knowledge about tropical coastal habitat connectivity and the composition of species assemblages by underwater habitats. These two topics are of current interest for tropical fishery science and their study can benefit from fishers' extensive experience with the coastal environments on which they depend.     

Ecology and biogeography of plant communities associated with the post Plio-Pleistocene relict Rhododendron ponticum subsp. baeticum in southern Spain

Aims Rhododendron ponticum L. is reputed to be a post Plio‐Pleistocene relict plant species with a disjunct distribution that comprises the Iberian Peninsula to the west and the Euxinian region plus some restricted Mediterranean areas to the east. We analysed the ecological range (of subsp. baeticum) in the western area (Aljibe Mountains, north of the Strait of Gibraltar) to understand the factors determining the present area limitation. Location Sierra del Aljibe, north of the Strait of Gibraltar (Iberian Peninsula). Methods We selected 20 riparian sites where R. ponticum is common, and compiled data on the ecological diversity of associated woody species and ferns. We established a 500‐m main transect in each site, along the stream or river course, in which we placed five 20‐m‐long plots at regular intervals. We recorded physiographic habitat features, woody plants and fern abundance, and the number of R. ponticum individuals. Results Rhododendron ponticum in southern Spain is restricted to riparian forests in acidic soils (pH 4.0–6.4), and is mainly found on the banks of inclined and enclosed streams. In our inventory we recorded 59 woody taxa and 12 ferns, with R. ponticum being the dominant species of the understorey (mean abundance 78.6%). The communities are characterized by a high incidence of the humid warm temperate element, both in number of species (18.8 ± 3.7 per site) and abundance; meanwhile, the presence of the modern Mediterranean element (mean number of species 3.4 ± 3.8 per site) appears to be favoured by disturbance. These ecological–historical groups of taxa also show distinct patterns of typological habit, frequency of endemism, infrageneric diversity and geographical range. Populations of R. ponticum are characterized by a very variable density of seedlings in many sites, and the virtual lack of juveniles. Main conclusions Riparian forests of the Aljibe Mountains constitute a refuge for R. ponticum where the species persists, but populations appear to be in decline. The narrow ecological range of R. ponticum in the area strongly contrasts with its wide amplitude in the eastern natural area, mainly the Euxinian region, where R. ponticum probably finds better conditions due to the environmental heterogeneity of the region, and the lack of a hot dry season.     

Suboptimal thermoregulation in male adders (Vipera berus) after hibernation imposed by spermiogenesis

In ectotherms, the main behavioural option for thermoregulation is the adjustment of daily and seasonal activity to the thermal quality of the environment. While active, ectotherms thermoregulate by shuttling in between thermally differing microhabitat patches. Here, we focused on the question of whether other behavioural or physiological processes could force ectotherms to maintain activity during thermally unfavourable periods, when accurate thermoregulation is impossible. Using laboratory experiments and field data we compared the thermoregulation of male adders ( Vipera berus ) between two periods in spring when (1) only males and (2) also females and juveniles had terminated their winter hibernation. We found that males thermoregulated actively both in the lab and in the field. Accurate thermoregulation was only possible during the second period because of the low thermal quality of the environment. Male adders maintained a lower mean body temperature in the field than in the laboratory within both periods, and in addition their body temperature during the first period was on average 4 °C lower than during the second period. The thermal qualities of the natural basking sites showed a similar pattern. We discuss the results in the context of a potential trade-off between spermiogenesis and thermoregulation, where the benefits of early spermiogenesis coupled with inaccurate thermoregulation are higher than the associated costs. The results support the contention that the earlier spring emergence of the male compared with female adders is explainable by natural selection favouring early initiation of spermiogenesis, and hence sex differences in phenology.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 19–27.     

Parametric and Nonparametric Analyses of Repeated Ordinal Categorical Data

We compare two models for the analysis of repeated ordinal categorical data: the classical parametric model for means of scores assigned to the categories of the response variable and a nonparametric model based on relative effects derived from the marginal distribution functions of the response. An example in the field of Dentistry is used to illustrate and to compare the models. We also consider a simulation study to evaluate the type‐I error rates and the power of tests under both models in a balanced design setup. The simulation results suggest that both approaches behave similarly for equally spaced scores but may perform differently otherwise. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Optimum prediction of three-way crosses from single crosses in forage maize (Zea mays L.)

Summary Three-way cross means were predicted with formulae involving linear functions of general (GCA) and specific combining ability (SCA) effects estimated from single-cross factorials between genetically divergent populations. Data from an experiment with 66 single-cross and 66 three-way cross forage maize (Zea mays L.) hybrids was used for comparing the prediction formulae. The genotypic correlation (r) between observed and predicted three-way crosses increased with increasing , the weighting factor of SCA effects, for plant height and ear dry matter (DM) content. It displayed slightly convex curves for total and stover DM yield, ear percentage, and metabolizable energy content of stover. For Jenkins' method B, r was considerably less than 1.0 for all traits, indicating the presence of epistasis. The square root of heritability (h) of the predicted means decreased with increasing , the reduction being small with a greater number of test environments. Using the product r·h as a criterion of efficiency, none of the prediction methods was consistently superior and the differences among them were rather small (< 7.5%) for all traits, irrespective of the number of test environments. We recommend evaluating the GCA of a greater number of lines from each parent population in testcrosses with a small number of elite lines from the opposite population. All possible three-way or double crosses between both sets of lines should be predicted by Jenkins's method C. This procedure allows one to select with a higher intensity among the predicted hybrids and thus should increase the genetic gain.Extended version of a paper (Geiger et al. 1986) read at the sixth meeting of the EUCARPIA Section Biometrics in Plant Breeding held at Birmingham, UK, July 28–August 1, 1986