The variances of the distributions of the combinations of the sexes within mammalian litters: Notes to mark the centenary of the problem

It is 100 years since Gini noted that in some samples of litters of mice and rabbits, the variances of the distributions of the combinations of the sexes are sub-binomial. In other words, in contrast with binomial expectation, there are too many litters in which the sexes are equally balanced, and there are too few unisexual litters. In the intervening years, this finding has been replicated in a number of further species, but no explanation has become established. Potential explanations are reviewed here, and it is suggested that the most likely cause is that, at the time of formation of the zygotes, p, the probability that a zygote will be male, varies from one zygote to another within litters, thus constituting an example of Poisson variation. And it is a standard result in probability theory that such variation causes sub-binomial variance.     

Assessing the impacts of fire on the vegetation resources that are available to the local communities of the seasonal wetlands of the Okavango, Botswana, in the context of different land uses and key government policies

The Okavango wetlands in north western Botswana are the most fire-prone environment in Botswana. Most of these fires are anthropogenic. The fires in this environment are thought to impact the environment negatively and therefore practices that are associated with extensive use of fire have been strongly criticized. Despite this, there has been little work done to understand how these fires impact the wetlands environment and its dynamics, especially the vegetation resources that are used by the local communities in the wetlands. The objective of the study was to identify fire spatial and temporal trends in relation to settlement distribution, through the use of remote sensing, socio-economic and phytosociological surveys. The fire history results show that geographically there has not been any significant change in vegetation structure and that in fact fires may have promoted biodiversity. The results of analysis show an overall variance on vegetation structure of 23% whereas the rest are unaccounted for. There is a strong association between settlements, ethnicities, literacy and fire occurrences. The most fire-prone areas are inhabited by communities that have used fire in the past for various resource use practices.     

Evolution of the molluscan body plan: the case of the anterior adductor muscle of bivalves

The separated shell plates with the rearranged musculature (adductor muscle) is a novelty for bivalves. Despite its importance in the bivalve bodyplan, the development of the anterior adductor muscle remains unresolved. In this study, we investigate the myogenesis of the bivalve species Septifer virgatus to reveal the developmental origin of the larval muscles in bivalves, focusing on the anterior adductor muscle. We observed that larval retractor muscles are differentiated from the ectomesoderm in bivalves, and that the anterior adductor muscles are derived from primordial larval retractor muscles via segregation of the myoblast during the veliger larval stage. Through the comparative study of myogenesis in bivalves and its related taxa, gastropods, we found that both species possess myoblasts that emerge bilaterally and later meet dorsally. We hypothesize that these myoblasts, which are a major component of the main larval retractor in limpets, are homologous to the anterior adductor muscle in bivalves. These observations imply that the anterior adductor muscle of bivalves evolved as a novel muscle by modifying the attachment sites of an existing muscle.     

On the use of the Price equation

This paper distinguishes two categories of questions that the Price equation can help us answer. The two different types of questions require two different disciplines that are related, but nonetheless move in opposite directions. These disciplines are probability theory on the one hand and statistical inference on the other. In the literature on the Price equation this distinction is not made. As a result of this, questions that require a probability model are regularly approached with statistical tools. In this paper, we examine the possibilities of the Price equation for answering questions of either type. By spending extra attention on mathematical formalities, we avoid the two disciplines to get mixed up. After that, we look at some examples, both from kin selection and from group selection, that show how the inappropriate use of statistical terminology can put us on the wrong track. Statements that are 'derived' with the help of the Price equation are, therefore, in many cases not the answers they seem to be. Going through the derivations in reverse can, however, be helpful as a guide how to build proper (probabilistic) models that do give answers.     

On the role of the engrailed+ gene in the internal organs of Drosophila.

Our purpose is to assess the effects of lethal alleles of engrailed on cells of the internal organs of Drosophila. Using nuclear transplantation we make mosaic flies that contain regions made by engrailed-lethal cells that are genetically labelled. We find that engrailed-lethal cells cause defects in some parts of the epidermis and central nervous system. Most of the internal organs of the fly are assessed and of those, all organs and tissues derived from the endoderm or the splanchnic and somatic mesoderm are normal; flies carrying engrailed-lethal cells in large areas of these organs are viable. We postulate that segments of the mesoderm are single units of cell lineage and that, unlike the ectoderm, they are not subdivided into anterior and posterior compartments.     

On the importance of homology in the age of phylogenomics

Homology is perhaps the most central concept of phylogenetic biology. Molecular systematists have traditionally paid due attention to the homology statements that are implied by their alignments of orthologous sequences, but some authors have suggested that manual gene-by-gene curation is not sustainable in the phylogenomics era. Here, we show that there are multiple ways to efficiently screen for and detect homology errors in phylogenomic data sets. Application of these screening approaches to two phylogenomic data sets, one for birds and another for mammals, shows that these data are replete with homology errors including alignments of different exons to each other, alignments of exons to introns, and alignments of paralogues to each other. The extent of these homology errors weakens the conclusions of studies based on these data sets. Despite advances in automated phylogenomic pipelines, we contend that much of the long, difficult, and sometimes tedious work of systematics is still required to guard against pervasive homology errors. This conclusion is underscored by recent studies that show that just a few outlier genes can impact phylogenetic results at short, tightly spaced internodes that are deep in the Tree of Life. The view that widespread DNA sequence alignment errors are not a major concern for rigorous systematic research is not tenable. If a primary goal of phylogenomics is to resolve the most challenging phylogenetic problems with the abundant data that are now available, researchers must employ effective procedures to screen for and correct homology errors prior to performing downstream phylogenetic analyses.     

Genetic matches and the logic of the law

In a recent article Levine and Kobilinsky (1997) point out that current methods in forensic DNA 'identification' are inadequate because the commercial kits commonly used in forensic practice do not detect the true genotype, but rather a genotype based on convenient categorization. For this reason, Levine and Kobilinsky argue that statistics attached to such categorizations are invalid. The authors believe that the arguments of Levine and Kobilinsky are logically flawed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Evidence from the domestication of apple for the maintenance of autumn colours by coevolution

The adaptive value of autumn colours is still a puzzle for evolutionary biology. It has been suggested that autumn colours are a warning signal to insects that use the trees as a host. I show that aphids (Dysaphis plantaginea) avoid apple trees (Malus pumila) with red leaves in autumn and that their fitness in spring is lower on these trees, which suggests that red leaves are an honest signal of the quality of the tree as a host. Autumn colours are common in wild populations but not among cultivated apple varieties, which are no longer under natural selection against insects. I show that autumn colours remain only in the varieties that are very susceptible to the effects of a common insect-borne disease, fire blight, and therefore are more in need of avoiding insects. Moreover, varieties with red leaves have smaller fruits, which shows that they have been under less effective artificial selection. This suggests a possible trade off between fruit size, leaf colour and resistance to parasites. These results are consistent with the hypothesis that autumn colours are a warning signal to insects, but not with other hypotheses.     

Helix movements and the reconstruction of the haem pocket during the evolution of the cytochrome c family

Analysis of cytochromes c (tuna), c2 (Rhodospirillum rubrum), c550 (Paracoccus denitrificans) and c551 (Pseudomonas aeruginosa) shows that they contain 48 residues identifiable as homologous from superposition of the structures. The other 34 to 64 residues are in loops that vary greatly in sequence, length and conformation, or in alpha-helices that are found in only some of the structures. Of the 48 homologous residues, 17 are in three segments which pack onto the haem faces. In all four structures, these segments have the same conformations, and the same locations relative to the haem. The other 31 residues are in three alpha-helices which are in contact with each other. These form the back and one side of the haem pocket. In cytochrome c551 the positions of the three alpha-helices have shifted and rotated, in comparison with cytochromes c and c2, by up to 5 A and 25 degrees relative to the haem. These shifts, facilitated by mutations at the helix-helix interfaces, are related to the reconstruction of the propionic acid side of the haem pocket described by Almassy & Dickerson (1978). Together these effects produce alternative structures for the haem pocket. This mechanism of adaptation to mutation contrasts with that observed in the globins. In the globins, mutations also produce changes in helix interfaces and shifts of packed helices, but in the globins these shifts are coupled to conserve the structure of the haem pocket.     

Nucleolar targeting: the hub of the matter

The nucleolus is a dynamic structure that has roles in various processes, from ribosome biogenesis to regulation of the cell cycle and the cellular stress response. Such functions are frequently mediated by the sequestration or release of nucleolar proteins. Our understanding of protein targeting to the nucleolus is much less complete than our knowledge of membrane‐spanning translocation systems—such as those involved in nuclear targeting—and the experimental evidence reveals that few parallels exist with these better‐characterized systems. Here, we discuss the current understanding of nucleolar targeting, explore the types of sequence that control the localization of a protein to the nucleolus, and speculate that certain subsets of nucleolar proteins might act as hub proteins that are able to bind to multiple protein targets. In parallel to other subnuclear structures, such as PML bodies, the proteins that are involved in the formation and maintenance of the nucleolus are inexorably linked to nucleolar trafficking.     

Innervation of the anococcygeus muscle of the rat

Summary The innervation of the anococcygeus muscle of the rat was investigated with regard to the histochemical features of nerve fibers within the muscle and to the location of the postganglionic autonomic neurons which are the source of these fibers. Acetylcholinesterase-positive fibers and catecholaminergic fibers are abundant in the anococcygeus as well as the related retractor penis muscle. Neuronal somata, either between muscle bundles of the anococcygeus or in the connective tissue sheath, are also acetylcholinesterase-positive. Nerve fibers and a minority of the ganglion cells in the anococcygeus and retractor penis muscles are immunoreactive for vasoactive intestinal polypeptide. Injection of the retrogradely transported dye Fluorogold into the anococcygeus muscle filled neurons in the abdominopelvic sympathetic chain, pelvic plexus and a small number of neurons in the inferior mesenteric ganglion. In the pelvic plexus, some neurons were located in the major pelvic ganglion but most were found along the main penile nerve and its branches to the anococcygeus muscle. Immunocytochemistry of these identified neurons indicates that about one half of them are positive for vasoactive intestinal polypeptice. These results raise the possibility that both acetylcholine and vasoactive intestinal polypeptide are important neurotransmitters in autonomic nerves to the anococcygeus muscle.     

Involvement of the vacuoles of the endodermis in the early process of shoot gravitropism in Arabidopsis

The endodermal cells of the shoot are thought to be the gravity-sensing cells in Arabidopsis. The amyloplasts in the endodermis that sediment in the direction of gravity may act as statoliths. Endodermis-specific expression of SGR2 and ZIG using the SCR promoter could complement the abnormal shoot gravitropism of the sgr2 and zig mutants, respectively. The abnormalities in amyloplast sedimentation observed in both mutants recovered simultaneously. These results indicate that both genes in the endodermal cell layer are crucial for shoot gravitropism. ZIG encodes AtVTI11, which is a SNARE involved in vesicle transport to the vacuole. The fusion protein of SGR2 and green fluorescent protein localized to the vacuole and small organelles. These observations indicate that ZIG and SGR2 are involved in the formation and function of the vacuole, a notion supported by the results of subcellular analysis of the sgr2 and zig mutants with electron microscopy. These results strongly suggest that the vacuole participates in the early events of gravitropism and that SGR2 and ZIG functions are involved.     

Meiofauna and the origins of the Metazoa*

Possible alternative habitats and life-styles of the original metazoan are considered. It is argued from the dominance of the benthic habitat in present-day groups that the original metazoan habitat was benthic rather than planktonic. Similarly, plesiomorphic metazoan taxa tend to be holobenthic rather than pelago-benthic. It is therefore probable that the early Metazoa were holobenthic. The concept of plesiohabitats and apohabitats in the evolution of taxa is presented. This leads to the proposition that the early metazoans were interstitial bionts of fine sand. Finally, the controversy concerning the aerobic or anaerobic origin of the Metazoa is considered. It is shown that competition theory predicts that plesiomorphic taxa are likely to remain in plesiohabitats. Diagrams showing the possible evolution of major taxa in relation to available habitats are presented. It is concluded that the earliest Metazoa could have evolved in anaerobic marine sand and that the early Plathelminthomorpha and Aschelminthes did so.     

Military Uses of Ocean Space and the Law of the Sea in the New Millennium

Military uses of ocean space consist of both movement rights and operational rights. Only movement rights, which include all rights associated with the mobility of seaborne forces, were codified in the LOS Convention. Operational rights, on the other hand, are primarily customary rights that are governed by the regime of freedom of the seas and defended by the naval power of the United States. This article begins by examining freedom of the seas as a principle of international law, as a bundle of user rights, and as a doctrine. It next examines the major challenges to freedom of the seas in terms of a construct called controlled access. After summarizing the major historical elements of controlled access, the article closes with a brief analysis of the threats to freedom of the seas for military purposes that are posed by multipolarity, the shift in U.S. naval strategy from the open seas to the coastal littorals, and in the withering away of U.S. naval superiority. The major arguments advanced throughout the article are that military uses of ocean space are hegemonic in nature, that their preservation depends on clear maritime superiority, and that they will come under increasing challenge and restriction as the balance of power at sea shifts from unipolarity to multipolarity by the middle of the new millennium.     

ECVAM's role in the implementation of the Three Rs concept in the field of biologicals

Biologicals can be defined as products that are derived from living organisms or are produced by them. They include vaccines, hormones, monoclonal and polyclonal antibodies, blood products and rDNA products. The production of conventionally produced biologicals requires an extensive batch-related quality control, to ensure that these products are both safe and potent. As several of the control tests rely on animal models, it is inevitable that the large numbers of animals are used. Many initiatives have been undertaken in the last few decades to reduce and refine the use of animals in this area. ECVAM has been involved in many activities to support the development, validation and implementation of these Three Rs methods. The role that ECVAM has played in a number of validation studies is summarised. It is concluded that ECVAM should continue to support the activities that have been shown to be successful, preferably in collaboration with the regulatory bodies.     

A computational comparison of the atomic models of the actomyosin interface

Several atomic models of the actomyosin interface have been proposed based on the docking together of their component structures using electron microscopy and resonance energy-transfer measurements. Although these models are in approximate agreement in the location of the binding interfaces when myosin is tightly bound to actin, their relationships to molecular docking simulations based on computational free-energy calculations are investigated here. Both rigid-docking and flexible-docking conformational search strategies were used to identify free-energy minima at the interfaces between atomic models of myosin and actin. These results suggest that the docking model produced by resonance energy-transfer data is closer to a free-energy minimum at the interface than are the available atomic models based on electron microscopy. The conformational searches were performed using both scallop and chicken skeletal muscle myosins and identified similarly oriented actin-binding interfaces that serve to validate that these models are at the global minimum. These results indicate that the existing docking models are close to but not precisely at the lowest-energy initial contact site for strong binding between myosin and actin that should represent an initial contact between the two proteins; therefore, conformational changes are likely to be important during the transition to a strongly bound complex.     

Chemosensory pathways in the capitate tentacles of the hydroid Cladonema

The introduction of an extract of Artemia into the sea water bathing tentacles from the hydroid Cladonema triggers a burst of electrical activity that can be recorded intracellularly from cnidocytes in the capitate tentacles. These bursts, which are composed of a variety of events, including action potentials and EPSPs, are Ca²⁺ dependent, and are abolished by pretreatment with NiCl₂, suggesting that voltage-gated Ca²⁺ channels are involved in their generation or transmission. Intracellular injection of Lucifer Yellow and recordings from pairs of cnidocytes reveal that the cnidocytes are electrically coupled to one another, but that they are not uncoupled by heptanol. The role of these chemosensory pathways in priming the cnidocytes for discharge is discussed.     

The role of the hormone ecdysterone in the control of the activity of the Balbiani rings and the other puffs of Drosophila auraria

The activity of the Balbiani rings and the other puffs of Drosophila auraria salivary gland chromosomes from various stages of development was studied in vitro in the presence or the absence of various concentrations of the hormone ecdysterone. It was found that of 81 sites affected by these conditions, 69 (including the BRs) exhibit changes during normal development as well, while the remaining 12 change only under culture conditions. The results indicate that the normal profiles of certain puffs (and the BRs) are approximated more closely by the lower concentrations of the hormone and it is suggested that such low concentrations are necessary to induce the normal course of events in vivo. Various hypotheses concerning the influence of ecdysterone on the puffing patterns are discussed in view of the data presented in this report.     

Magnetic resonance imaging of the siliceous skeleton of the demosponge Lubomirskia baicalensis

The skeletal elements (spicules) of the demosponge Lubomirskia baicalensis were analyzed; they are composed of amorphous, non-crystalline silica, and contain in a central axial canal the axial filament which consists of the enzyme silicatein. The axial filament, that orients the spicule in its longitudinal axis exists also in the center of the spines which decorate the spicule. During growth of the sponge, new serially arranged modules which are formed from longitudinally arranged spicule bundles are added at the tip of the branches. X-ray analysis revealed that these serial modules are separated from each other by septate zones (annuli). We describe that the longitudinal bundles of spicules of a new module originate from the apex of the earlier module from where they protrude. A cross section through the oscular/apical-basal axis shows that the bundle rays are organized in a concentric and radiate pattern. High resolution magnetic resonance microimaging studies showed that the silica spheres of the spicules in the cone region contain high amounts of 'mobile' water. We conclude that the radiate accretive growth pattern of sponges is initiated in the apical region (cones) by newly growing spicules which are characterized by high amounts of 'mobile' water; subsequently spicule bundles are formed laterally around the cones.