Analysis of Diallel Table for Experiments Carried Out in BIB Designs-Mixed Model

In this paper the analysis of genotypes obtained in a diallel crossing system, including parents, one set of F₁′s and reciprocal F₁′s, is given. This analysis is presented for data obtained from the experiments carried out in a block design in which block effects are random. The analysis of variance, estimators of reciprocal effects, estimators of general and specific combining abilities are considered. Also statistics for testing hypotheses concerning some genetical parameters are given.     

Applications of a Vectorized MANOVA-Model

If the observation matrix of n independent p-dimensional normal vectors with common covariance matrix is transformed into an np-vector, linear models and hypotheses on the expectations can be formulated, that are not attainable in standard MANOVA or GMANOVA models. The distribution of an earlier proposed test procedure for this vectorized model is derived for p = 2, and its application is demonstrated for crossover and repeated measurement designs. Numerical results are compared in situations, in which both the standard and the vectorized model are applicable.     

Genome-scale metabolic models as platforms for strain design and biological discovery

Genome-scale metabolic models (GEMs) have been developed and used in guiding systems’ metabolic engineering strategies for strain design and development. This strategy has been used in fermentative production of bio-based industrial chemicals and fuels from alternative carbon sources. However, computer-aided hypotheses building using established algorithms and software platforms for biological discovery can be integrated into the pipeline for strain design strategy to create superior strains of microorganisms for targeted biosynthetic goals. Here, I described an integrated workflow strategy using GEMs for strain design and biological discovery. Specific case studies of strain design and biological discovery using Escherichia coli genome-scale model are presented and discussed. The integrated workflow presented herein, when applied carefully would help guide future design strategies for high-performance microbial strains that have existing and forthcoming genome-scale metabolic models.     

Optimal design of the Wilcoxon–Mann–Whitney‐test

In scientific research, many hypotheses relate to the comparison of two independent groups. Usually, it is of interest to use a design (i.e., the allocation of sample sizes m and n for fixed ) that maximizes the power of the applied statistical test. It is known that the two‐sample t‐tests for homogeneous and heterogeneous variances may lose substantial power when variances are unequal but equally large samples are used. We demonstrate that this is not the case for the nonparametric Wilcoxon–Mann–Whitney‐test, whose application in biometrical research fields is motivated by two examples from cancer research. We prove the optimality of the design in case of symmetric and identically shaped distributions using normal approximations and show that this design generally offers power only negligibly lower than the optimal design for a wide range of distributions.     

Scale-dependent mechanisms in the population dynamics of an insect herbivore

A multiscale approach has lead to significant advances in the understanding of species population dynamics. The scale-dependent nature of population processes has been particularly clearly illustrated for insect herbivores. However, one of the most well-studied insect herbivores, the galling sawfly Euura lasiolepis, has to date been examined almost exclusively at fine spatial scales. The preference-performance, plant vigour and larval survival hypotheses are well supported by this species. Here, we test these hypotheses at a spatial scale larger than that previously considered, i.e. across a landscape in northern Arizona represented by an altitudinal gradient encompassing a series of drainages. We also develop a qualitative model for understanding the population dynamics of E. lasiolepis based on patterns of survival and mortality found in this study and previous ones. Gall density was highly variable across the altitudinal gradient, not explained by host plant variables, and thus a poor surrogate fot population abundance. These findings for the first time fail to support the plant vigour and preference hierarchy hypotheses for E. lasiolepis. Dispersal limitation most likely explains the lack of support for these hypotheses at this scale. By contrast, sawfly survival, gall abortion, parasitism and larval mortality were well explained by host plant quality variables and altitude. The larval survival hypothesis was well supported and is thus comparatively scale-invariant. A qualitative model developed here highlighted the importance of both willow water status and disturbance in determining host plant quality, as well as an apparent trade off between shoot length and plant moisture status in determining vital rates across the altitudinal gradient. This study thus demonstrated for the first time the scale-dependent nature of mechanisms underlying the population dynamics E. lasiolepis, and identified the interaction between parasitism and altitude as a novel mechanism underlying spatial patterns in the survival and mortality patterns of this species.     

Evolution of anuran brains: disentangling ecological and phylogenetic sources of variation

Variation in ecological selection pressures has been implicated to explain variation in brain size and architecture in fishes, birds and mammals, but little is known in this respect about amphibians. Likewise, the relative importance of constraint vs. mosaic hypotheses of brain evolution in explaining variation in brain size and architecture remains contentious. Using phylogenetic comparative methods, we studied interspecific variation in brain size and size of different brain parts among 43 Chinese anuran frogs and explored how much of this variation was explainable by variation in ecological factors (viz. habitat type, diet and predation risk). We also evaluated which of the two above‐mentioned hypotheses best explains the observed patterns. Although variation in brain size explained on average 80.5% of the variation in size of different brain parts (supporting the constraint hypothesis), none of the three ecological factors were found to explain variation in overall brain size. However, habitat and diet type explained a significant amount of variation in telencephalon size, as well in three composite measures of brain architecture. Likewise, predation risk explained a significant amount of variation in bulbus olfactorius and optic tecta size. Our results show that evolution of anuran brain accommodates features compatible with both constraint (viz. strong allometry among brain parts) and mosaic (viz. independent size changes in response to ecological factors in certain brain parts) models of brain size evolution.     

The selection and design of marine protected areas: Australia as a case study

Recently there has been increased interest in the use of Marine Protected Areas (MPAs) as tools for the conservation of marine habitats and species. This has resulted in the declaration of many MPAs around the world. Despite this activity there have been few tests of hypotheses about the design criteria for selection and management of these areas, resulting in a haphazard and ad hoc selection of protected areas, with conflicting and inconsistent terminology and objectives. The application of appropriately tested scientific information to the design of MPAs will increase the likelihood of success in the future.To 1st January 1992, 267 MPAs had been declared in Australia, covering a total area of ca 400 019 km². The history of their declaration has been sporadic and uneven. Conflicts over State and Federal legislation and, within states, conflicts over jurisdiction among agencies caused by overlapping responsibilities, have at times slowed the declaration of MPAs. In this paper, the history of MPAs in Australia is used as a case study to discuss the problems, both biological and administrative, of declaring MPAs.     

Analysis of Covariance in Split Block Design

In this paper the analysis of covariance in the split block design with many concomitant variables is presented. The problems concerning the estimation of parametric functions and testing hypotheses are discussed. In the presentation of the model three kinds of regression coefficients for individual sources of variation are taken into consideration. It is shown that for every estimable function of fixed effects, the best linear unbiased estimator under the assumed model is the same as the best linear unbiased estimator under the model with covariance matrix equal to identity matrix multiplied by a positive constant. A variance of this estimator can be calculated by the method presented here. Test functions for standard hypotheses concerning fixed effects are obtained.     

Confidence Intervals and Tests of Hypotheses on Variance Components in an Unbalanced Two-fold Nested Design

Confidence intervals and tests of hypotheses on variance components are required in studies that employ a random effects design. The unbalanced random two-fold nested design is considered in this paper and confidence intervals are proposed for the variance components σ2/A and σ2/B. Computer simulation is used to show that even in very unbalanced designs, these intervals generally maintain the stated confidence coefficient. The hypothesis test for σ2/A based on the lower bound of the recommended confidence interval is shown to be better than previously proposed approximate tests.     

GAMETE INTERACTIONS AND GENETIC DIFFERENTIATION AMONG THREE SYMPATRIC POLYCHAETES

The evolution of gamete incompatibility between free-spawning marine invertebrate species has been explained by three hypotheses: (1) independent divergence at gamete recognition loci; (2) selection against hybrids; and (3) a process of sexual selection involving polymorphic gamete recognition loci (Metz and Palumbi 1996). The first two hypotheses predict that gamete incompatibility appears only after gene flow has been halted for other reasons and the third that gamete incompatibility appears simultanously with blocks to gene flow. Here I show that gametes of three sympatric polychaetes in the genus Arctonoe are compatible in all crosses, over a broad range of gamete concentrations and contact times. Although at least some hybrid crosses produce fertile adults, allozyme and mitochondrial DNA sequence data indicate that the three species do not regularly exchange genes. These data are consistent with predictions of the first two hypotheses for the evolution of gamete incompatibility, but allow rejection of the third hypothesis. Gametes of the three species are compatible despite estimated divergence times of 1–3 M.Y.B.P.; in several other marine invertebrates, divergence times of the same magnitude are associated with asymmetric or complete gamete incompatibility. It appears likely that segregation of symbiotic adults on their respective host species restricts mating opportunities, and thus gene flow, among Arctonoe species.     

Spain: an extreme case of successful integration of second-generation immigrants with transfers of best practices applicable to other European countries?

This volume presents cutting-edge research on integration and adaptation processes of second-generation immigrant adolescents in Spain that no doubt constitutes an important and timely contribution to the migration-integration debate. Principal findings of the Investigación Longitudinal de la Segunda Generación study indicate a comparatively smooth integration of second-generation immigrant adolescents, arguably best explained by the theoretical hypotheses of neo-assimilationism and segmented assimilation. The major strengths of the study pertain to research design and methodology, and theoretical grounding that enables it to have far-reaching implications for future research on migrant youth in Spain and beyond. The focus here is primarily on questions of transferability of major findings to other European countries, such as Sweden. In essence, the authors’ findings raise a number of important questions regarding the feasibility (or infeasibility) of Spain’s laissez-a-faire approach to integration in countries with contrasting modes of incorporation.     

Turning over a new ‘leaf’: multiple functional significances of leaves versus phyllodes in Hawaiian Acacia koa

Hawaiian endemic tree Acacia koa is a model for heteroblasty with bipinnately compound leaves and phyllodes. Previous studies suggested three hypotheses for their functional differentiation: an advantage of leaves for early growth or shade tolerance, and an advantage of phyllodes for drought tolerance. We tested the ability of these hypotheses to explain differences between leaf types for potted plants in 104 physiological and morphological traits, including gas exchange, structure and composition, hydraulic conductance, and responses to varying light, intercellular CO₂, vapour pressure deficit (VPD) and drought. Leaf types were similar in numerous traits including stomatal pore area per leaf area, leaf area‐based gas exchange rates and cuticular conductance. Each hypothesis was directly supported by key differences in function. Leaves had higher mass‐based gas exchange rates, while the water storage tissue in phyllodes contributed to greater capacitance per area; phyllodes also showed stronger stomatal closure at high VPD, and higher maximum hydraulic conductance per area, with stronger decline during desiccation and recovery with rehydration. While no single hypothesis completely explained the differences between leaf types, together the three hypotheses explained 91% of differences. These findings indicate that the heteroblasty confers multiple benefits, realized across different developmental stages and environmental contexts.     

Do plant secondary compounds determine feeding preferences of snowshoe hares?

Summary We investigated the food preferences of captive snowshoc hares (Lepus americanus) in winter to test three hypotheses proposed to explain food choices by hares: (1) that food choice is related to the protein content of twigs; 92) that defensive chemicals present in twigs are negatively correlated with hare food preferences; and (3) that hares eat less-preferred but protein-rich twigs when their diet is buffered by large amounts of palatable food. Hares exhibited striking and consistent preferences for different species and, in general, preferred mature twigs to juvenile growth stages. Preferences across species among mature twigs were not, however, the same as preferences for juvenile growth stages across species. None of the three hypotheses adequately explained food choice by hares. Hares did not (1) select twigs that were high in protein content. They also did not (2) consistently select twigs that were low in resins or phenols. Finally (3), hares generally ate less, not more of non-preferred twigs in the presence of a protein and energy rich alternative food, commercial rabbit chow. Food preferences of hares must presumably have some chemical basis, but no simple theory has yet explained what this is. We suggest that hares may not be under severe dietary constraints imposed by chemical defenses in winter.     

Application of the Biased Spring Balance Weighing Design Theory to Estimation of Differences of Line Effects for Legume Content

The incidence matrix of a BIB design for v treatments has been used to construct a biased spring balance weighing design. Conditions under which an optimum biased spring balance weighing design exists are given. It is also shown how this theory may be utilized to obtain treatment and experiment designs to estimate differences in legume content between pair of lines in an experiment overseeded with grass species.     

SPATIAL RELATIONSHIP AND GENE FLOW PATHS BETWEEN POPULATIONS OF THE ALPINE SNAIL ARIANTA ARBUSTORUM (PULMONATA: HELICIDAE)

The alpine snail Arianta arbustorum (Pulmonata, Helicidae) was sampled along an 8-km contour line in the Swiss Alps orthogonal to well-known altitudinal clines in life history and shell traits. The allele frequencies and the morphs of 16 populations were compared with habitats. Two hypotheses about the recolonization of the mountain slopes after the last glaciation were tested against the present population structure. The allele frequencies are best explained by the spatial structure whereas the morphs are better explained by the habitats. The genotypic distances point to a historical explanation by recolonization processes, the phenotypical dissimilarities to a selectionistic interpretation of the present distribution of the populations. The following conclusions are from the study of the spatial relationship and the gene flow paths for A. arbustorum at Mount Martegnas: (1) Streams are the main gene flow paths; gene flow is low, allowing differentiation of local populations. (2) Morphs and habitats are correlated, but the interpretation has to be made carefully. The spatial dependence of habitats has to be included into the analysis of selection. (3) The random assumption for gene flow of A. arbustorum is not a spatial isolation-by-distance model, but a functional isolation-by-distance model, assuming gene flow over the drainage system.     

‘Out‐of‐Africa’ dispersal of tropical floras during the Miocene climatic optimum: evidence from Uvaria (Annonaceae)

Aim African–Asian disjunctions are common in palaeotropical taxa, and are typically explained by reference to three competing hypotheses: (1) ‘rafting’ on the Indian tectonic plate, enabling Africa‐to‐Asia dispersal; (2) migration via Eocene boreotropical forests; and (3) transoceanic long‐distance dispersal. These hypotheses are tested using Uvaria (Annonaceae), which is distributed in tropical regions of Africa, Asia and Australasia. Recent phylogenetic reconstructions of the genus show a clear correlation with geographical provenance, indicating a probable origin in Africa and subsequent dispersal to Asia and then Australasia. Ancestral areas and migration routes are inferred and compared with estimates of divergence times in order to distinguish between the prevailing dispersal hypotheses. Location Palaeotropics. Methods Divergence times in Uvaria are estimated by analysing the sequences of four DNA regions (matK, psbA–trnH spacer, rbcL and trnL–F) from 59 Uvaria species and 77 outgroup species, using a Bayesian uncorrelated lognormal (UCLD) relaxed molecular clock. The ancestral area of Uvaria and subsequent dispersal routes are inferred using statistical dispersal–vicariance analysis (s‐diva ). Results Uvaria is estimated to have originated in continental Africa 31.6 Ma [95% highest posterior density (HPD): 38.4–25.1 Ma] between the Middle Eocene and Late Oligocene. Two main migration events during the Miocene are identified: dispersal into Madagascar around 17.0 Ma (95% HPD: 22.3–12.3 Ma); and dispersal into Asia between 21.4 Ma (95% HPD: 26.7–16.7 Ma) and 16.1 Ma (95% HPD: 20.1–12.1 Ma). Main conclusions Uvaria fruits are widely reported to be consumed by primates, and are therefore unlikely candidates for successful long‐distance transoceanic dispersal. The other biogeographical hypotheses, involving rafting on the Indian tectonic plate, and dispersal via the European boreotropical forests associated with the Eocene thermal maximum, can be discounted due to incongruence with the divergence time estimates. An alternative scenario is suggested, involving dispersal across Arabia and central Asia via the tropical forests that developed during the late Middle Miocene thermal maximum (17–15 Ma), associated with the ‘out‐of‐Africa’ dispersal of primates. The probable route and mechanism of overland dispersal between Africa and Asia for tropical plant groups during the Miocene climatic optimum are clarified based on the Uvaria data.     

Biogeography and diversity among montane populations of mouse shrew (Soricidae: Myosorex) in Tanzania

We assess variation in morphological and molecular characters among three species of Myosorex (the mouse shrew) –Myosorex geata, Myosorex kihaulei, and Myosorex zinki– as a means to test previously proposed biogeographic hypotheses for Tanzanian ‘sky islands’ and systematic hypotheses for Tanzanian mouse shrews. We analyse 17 cranial and dental variables using multivariate statistics and perform phylogenetic and phylogeographic analyses on sequences of mitochondrial and nuclear DNA; samples are drawn from every known Tanzanian population of Myosorex. Morphometric and phylogenetic analyses reveal that M. zinki is distinct, but that currently isolated populations of M. geata and M. kihaulei are relatively similar to one another, and may not have been isolated over geological time scales. Analyses of molecular variance identify statistically significant, but limited, genetic variation within and between isolated populations of M. geata and M. kihaulei. Between two putative regional biogeographic boundaries, greater genetic variation is explained by grouping populations on either side of the Ruaha River than by grouping populations on either side of the Makambako Gap. Our results are in agreement with recent studies illustrating the close relationship between faunas of the Southern Highlands and southern Eastern Arc Mountains, diminishing the apparent importance of the Makambako Gap as a historical biogeographic barrier. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 669–680.     

Effects of variation in Eucalyptus essential oil yield on insect growth and grazing damage

Summary Levels of insect attack and yields of leaf essential oils in Eucalyptus vary widely within and among species. We tested the hypotheses that 1) metabolic cost of oil detoxification increases with increasing oil yield, resulting in lower herbivore growth rates and, consequently, 2) in lower herbivore damage to plants. Distribution of insect damage, eggs, immature insects and adults and feeding rates, growth and survivorship of insects do not support the hypotheses, although a threshold level of oil may be necessary to influence herbivorous insects. Herbivorous beetles tested do not detoxify essential oils. Levels of leaf nitrogen, rather than oil content, explained differences in insect feeding and growth.     

Optimal Split-plot Designs for a Mixed Model

Exact tests are given, for the usual hypotheses on split-plot models with random blocks and fixed treatment effects, considering different numbers of blocks for each level of whole-plot treatment and assuming normally distributed observations. U- and D-optimal designs are considered with respect to the tests of main effects and interactions as well as to estimation of parameters.