Point Transect Sampling Along Linear Features

Summary Distance sampling is a widely used methodology for assessing animal abundance. A key requirement of distance sampling is that samplers (lines or points) are placed according to a randomized design, which ensures that samplers are positioned independently of animals. Often samplers are placed along linear features such as roads, so that bias is expected if animals are not uniformly distributed with respect to distance from the linear feature. We present an approach for analyzing distance data from a survey when the samplers are points placed along a linear feature. Based on results from a simulation study and from a survey of Irish hares in Northern Ireland conducted from roads, we conclude that large bias may result if the position of samplers is not randomized, and analysis methods fail to account for nonuniformity.     

Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure

Although most natural populations are genetically subdivided, they are often analysed as if they were panmictic units. In particular, signals of past demographic size changes are often inferred from genetic data by assuming that the analysed sample is drawn from a population without any internal subdivision. However, it has been shown that a bottleneck signal can result from the presence of some recent immigrants in a population. It thus appears important to contrast these two alternative scenarios in a model choice procedure to prevent wrong conclusions to be made. We use here an Approximate Bayesian Computation (ABC) approach to infer whether observed patterns of genetic diversity in a given sample are more compatible with it being drawn from a panmictic population having gone through some size change, or from one or several demes belonging to a recent finite island model. Simulations show that we can correctly identify samples drawn from a subdivided population in up to 95% of the cases for a wide range of parameters. We apply our model choice procedure to the case of the chimpanzee (Pan troglodytes) and find conclusive evidence that Western and Eastern chimpanzee samples are drawn from a spatially subdivided population.     

The position of the Haplotaxidae in the evolution of oligochaete annelids

The Haplotaxidae have all the characteristics to support the hypothesis that they are the living descendents of the stem forms from which all of the Oligochaeta Clitellata (Orders Lumbriculida, Haplotaxida, Lumbricida, Tubificida) can be derived. The Aphanoneura are distinct from the Clitellata and are raised to a separate Class. There is no evidence to support the view that the elaborate setae of many Tubificida are derived from a polychaete ancestry; both are held to be independent modifications to aquatic life derived from a simple burrowing protoannelid with lumbricine setae.     

Flotation of lipid-protein particles containing triacylglycerol and phospholipid from the cytosol of carnation petals

Lipid-protein particles ranging from 20 to 250 nm in diameter have been isolated from the cytosol of carnation petals by flotation centrifugation and also by ultrafiltration. The cytosolic lipid-protein particles resemble oil bodies, lipid-protein particles found in oil-bearing seeds, in that they contain triacylglycerol, are circumscribed by phospholipid that is not organized in a bilayer, appear to be derived from membranes and can be isolated by flotation. However, the cytosolic particles are distinguishable from oil bodies in that triacylglycerol is not the dominant lipid. Indeed, they contain a spectrum of lipids in addition to phospholipids and triacylglycerol including free fatty acids, sterol and wax esters, phosphatidic acid and diacylglycerol. These same lipids are present in corresponding microsomal membranes as well, but in much smaller proportions relative to phospholipid. The lipid-protein particles from carnation petals contain a 17-kDa protein that is of similar size to oil body oleosin, but does not cross-react with anti-oleosin antibodies. The data indicate that these cytosolic particles are structurally and chemically similar to oil bodies and are consistent with the notion that their genesis may be a means of removing destabilizing lipids from membrane bilayers.     

Impact of gene flow from cultivated beet on genetic diversity of wild sea beet populations

Gene flow and introgression from cultivated plants may have important consequences for the conservation of wild plant populations. Cultivated beets (sugar beet, red beet and Swiss chard: Beta vulgaris ssp. vulgaris) are of particular concern because they are cross-compatible with the wild taxon, sea beet (B.vs. ssp. maritima). Cultivated beet seed production areas are sometimes adjacent to sea beet populations; the numbers of flowering individuals in the former typically outnumber those in the populations of the latter. In such situations, gene flow from cultivated beets has the potential to alter the genetic composition of the nearby wild populations. In this study we measured isozyme allele frequencies of 11 polymorphic loci in 26 accessions of cultivated beet, in 20 sea beet accessions growing near a cultivated beet seed production region in northeastern Italy, and 19 wild beet accessions growing far from seed production areas. We found one allele that is specific to sugar beet, relative to other cultivated types, and a second that has a much higher frequency in Swiss chard and red beet than in sugar beet. Both alleles are typically rare in sea beet populations that are distant from seed production areas, but both are common in those that are near the Italian cultivated beet seed production region, supporting the contention that gene flow from the crop to the wild species can be substantial when both grow in proximity. Interestingly, the introgressed populations have higher genetic diversity than those that are isolated from the crop. The crop-to-wild gene flow rates are unknown, as are the fitness consequences of such alleles in the wild. Thus, we are unable to assess the long-term impact of such introgression. However, it is clear that gene flow from a crop to a wild taxon does not necessarily result in a decrease in the genetic diversity of the native plant.     

Distinguishing structural and functional restraints in evolution in order to identify interaction sites

Structural genomics projects are producing many three-dimensional structures of proteins that have been identified only from their gene sequences. It is therefore important to develop computational methods that will predict sites involved in productive intermolecular interactions that might give clues about functions. Techniques based on evolutionary conservation of amino acids have the advantage over physiochemical methods in that they are more general. However, the majority of techniques neither use all available structural and sequence information, nor are able to distinguish between evolutionary restraints that arise from the need to maintain structure and those that arise from function. Three methods to identify evolutionary restraints on protein sequence and structure are described here. The first identifies those residues that have a higher degree of conservation than expected: this is achieved by comparing for each amino acid position the sequence conservation observed in the homologous family of proteins with the degree of conservation predicted on the basis of amino acid type and local environment. The second uses information theory to identify those positions where environment-specific substitution tables make poor predictions of the overall amino acid substitution pattern. The third method identifies those residues that have highly conserved positions when three-dimensional structures of proteins in a homologous family are superposed. The scores derived from these methods are mapped onto the protein three-dimensional structures and contoured, allowing identification clusters of residues with strong evolutionary restraints that are sites of interaction in proteins involved in a variety of functions. Our method differs from other published techniques by making use of structural information to identify restraints that arise from the structure of the protein and differentiating these restraints from others that derive from intermolecular interactions that mediate functions in the whole organism.     

Serial Monogamy as Polygyny or Polyandry?

Applications of sexual selection theory to humans lead us to expect that because of mammalian sex differences in obligate parental investment there will be gender differences in fitness variances, and males will benefit more than females from multiple mates. Recent theoretical work in behavioral ecology suggests reality is more complex. In this paper, focused on humans, predictions are derived from conventional parental investment theory regarding expected outcomes associated with serial monogamy and are tested with new data from a postreproductive cohort of men and women in a primarily horticultural population in western Tanzania (Pimbwe). Several predictions derived from the view that serial monogamy is a reproductive strategy from which males benefit are not supported. Furthermore, Pimbwe women are the primary beneficiaries of multiple marriages. The implications for applications of sexual selection theory to humans are discussed, in particular the fact that in some populations women lead sexual and reproductive lives that are very different from those derived from a simple Bateman-Trivers model.     

Relatedness of penicillin-binding protein 1a genes from different clones of penicillin-resistant Streptococcus pneumoniae isolated in South Africa and Spain.

Penicillin-resistant strains of Streptococcus pneumoniae have been common in South Africa and Spain for several years. Multilocus enzyme electrophoresis identified one clone of capsular type 6B which was prevalent in Spain and another clone of type 23F that was present in both countries. Genes for penicillin-binding proteins (PBPs) in penicillin-resistant strains are often mosaics where parts of the pneumococcal genes are replaced by homologous genes from other species. We have compared the mosaic structures of the PBP 1a genes from the two clones as well as from genetically distinct South African isolates. Four classes of mosaic PBP 1a genes were found that contained blocks of sequences divergent by 6-22% from those of sensitive genes; two classes contained sequences coming from more than one external source. Data are presented showing that the PBP 1a genes from the 23F and the 6B clone are related, and that the two PBP 1a genes from the South African isolates are also related. We suggest that the type 23F clone originated in Spain prior to distribution into other continents.     

Improved in vitro packaging of coliphage lambda DNA: a one-strain system free from endogenous phage

In previous systems for in vitro packaging of lambda DNA, phages are produced from the packaging components as well as from added DNA. We have developed a new genetic strategy for in vitro packaging that bypasses this endogenous phage problem. Our system employs a single bacterial strain whose lambda prophage codes for all of the packaging proteins but is deleted for cos, the packaging origin. Crude extracts of the single lysogen: (i) are virtually free from endogenous phages, (ii) package added lambda DNA efficiently and (iii) are easy to prepare. Using the cos- in vitro packaging system we show that packaging of lambda linear monomers is a second-order reaction, but that packaging from concatemers prepared by annealing or ligation is first order. We conclude that in our cos- system, linear monomers are a poor substrate for in vitro packaging but that packaging from concatemers works well.     

Morphometric analysis of Chilean blue whales and implications for their taxonomy

In the Southern Hemisphere, blue whales are currently divided into two subspecies, Antarctic blue whales (Balaenoptera musculus intermedia) and pygmy blue whales (B. m. brevicauda), but there is some debate about whether Chilean blue whales should also be considered as a separate subspecies. Here, we provide novel morphometric data to directly address this taxonomic question from a biological survey of 60 blue whales taken during the 1965/1966 Chilean whaling season. The data show that maximum body length and mean body length of both sexually mature females and males for Chilean blue whales are intermediate between pygmy and Antarctic blue whales; and that fluke-anus lengths of Chilean blue whales are significantly different from pygmy blue whales, but not necessarily from Antarctic blue whales. There is also some support from the data that snout-eye measurements are different among all three groups. These data provide further confirmation that Chilean blue whales are a distinct population requiring separate management from other blue whale populations, and are also consistent with suggestions that Chilean blue whales are not the same subspecies as pygmy blue whales.     

A note on the timing of tradeoffs in discrete life history models

We discuss the timing of tradeoffs in discrete life history models. With a simple mathematical example we show that different assumptions about the temporal order of costs and benefits resulting from a reproductive effort can lead to qualitatively different predictions. We examine two models taken from the literature, in which an implicit assumption is that benefits from reproductive efforts are received before the corresponding costs are paid. We show that the reverse assumptions would have led to very different results. Since there is no biological basis for a bias towards a particular set of assumptions, we conclude that a more flexible approach should be used when studying optimality problems that are based on discrete life histories.     

Cultivar‐specific plant odour preferences of a generalist aphid parasitoid Aphidius colemani and a possible mechanism for maternal priming of resistance to toxic plant chemistry

Aphidius colemani Viereck, emerging from Myzus persicae (Sulzer) mummies on the Brussels sprout cultivar ‘Bedford Winter Harvest’ (BWH), responds positively in the olfactometer to the odour of that cultivar in comparison with air. Responses to the odours of other sprout cultivars, cabbage and broad bean could be explained by the humidity from plant leaves. In a choice between BWH and other sprout cultivars, the BWH odour is preferred, or that of cv. ‘Red Delicious’ (RD) if the parasitoids are reared on RD. This confirms previous work showing that the secondary chemistry of a cultivar is learnt from the mummy cuticle during emergence. Adults emerging from pupae excised from the mummy show a similar but less pronounced preference. Parasitoids developing in aphids on an artificial diet do not discriminate between the odours of BWH and RD, unless allowed contact with a mummy from the same cultivar that the mother develops on. This suggests a cultivar‐specific maternal cue. This cue is speculated to consist of a small amount of the secondary chemistry (probably glucosinolates in the present study) that are left in or on the egg at oviposition, which subsequently induces enzymes that detoxify plant‐derived toxins in the aphid host. Indeed, when parasitoids emerging from diet‐reared aphids are released on aphid‐infested sprout plants, fewer mummies are produced than by parasitoids emerging from mummies of plant‐reared aphids or from excised pupae. Only parasitoids that emerge from mummies of plant‐reared aphids prefer the cultivar of origin as shown by the number of mummified hosts.     

Isolation of Drosophila melanogaster Testes

The testes of Drosophila melanogaster provide an important model for the study of stem cell maintenance and differentiation, meiosis, and soma-germline interactions. Testes are typically isolated from adult males 0-3 days after eclosion from the pupal case. The testes of wild-type flies are easily distinguished from other tissues because they are yellow, but the testes of white mutant flies, a common genetic background for laboratory experiments are similar in both shape and color to the fly gut. Performing dissection on a glass microscope slide with a black background makes identifying the testes considerably easier. Testes are removed from the flies using dissecting needles. Compared to protocols that use forceps for testes dissection, our method is far quicker, allowing a well-practiced individual to dissect testes from 200-300 wild-type flies per hour, yielding 400-600 testes. Testes from white flies or from mutants that reduce testes size are harder to dissect and typically yield 200-400 testes per hour.     

Tuning in to the signals controlling photoregulated gene expression in plants.

Plants have developed flexible mechanisms to respond appropriately to environmental signals. These stimuli are transduced by largely unknown signalling pathways that are likely to be modulated by endogenous developmental signals to produce an integrated response that coordinately regulates gene expression. Light is a critical environmental signal that controls many aspects of plant development via a series of photoreceptors that are able to respond to different light wavelengths. Light is also the principal energy source for photosynthesis. The photosynthetic products are carbohydrates which are translocated in the form of sucrose from the photosynthetic (source) to non-photosynthetic (sink) organs. Consequently, the control of photoregulated genes must integrate developmental inputs with signals derived from the photoreceptors, from the photosynthetic apparatus and from metabolites such as sucrose.     

Rare-earth element distribution characteristics of biological chains in rare-earth element-high background regions and their implications

The rare-earth element (REE) contents of water and vegetables from two typical REE-high background regions and a normal region in Gannan, Jiangxi Province, indicated that the REE contents were significantly different from those of water and vegetables, respectively. The average values are 0.03 mg/L and 0.11 mg/L REE for water from regions A and B. As the REE contents of vegetables from region A are different from region B, it is suggested that there are a number of factors controlling the REE distribution from those among plants. By comparing with the normal region, the soluble REE contents of water from the REE-high background regions are higher than those of the normal region by factors of 18 and 68, respectively. The REE contents of most plants and crops from regions A and B are higher than those of the normal region. It is clear that the REEs are the indispensable elements of plants during their growing period. Why are the REE contents of some plants from regions A and B usually higher than those from the normal region? The answer is that the plants and crops have passively absorbed REE during their growth.     

Three-dimensional architecture of phycobilisomes from Nostoc flagelliforme revealed by single particle electron microscopy

Phycobilisomes are protein complexes that harvest light and transfer energy to the photo system. Here, the three dimensional structure of intact phycobilisomes from Nostoc flagelliforme is studied by a combination of negative stain electron microscopy and cryo-electron microscopy. Results show that the intact phycobilisomes are composed of a tricylindrical core and six rods. Each allophycocyanin cylinder presents a double-layered structure when viewed from the side and a triangular shape when viewed from the top. These characteristics indicate that allophycocyanin trimers in the intact phycobilisomes are arranged into hexameric oligomers in a parallel manner.     

Estimating the area under the ROC curve when transporting a prediction model to a target population

We propose methods for estimating the area under the receiver operating characteristic (ROC) curve (AUC) of a prediction model in a target population that differs from the source population that provided the data used for original model development. If covariates that are associated with model performance, as measured by the AUC, have a different distribution in the source and target populations, then AUC estimators that only use data from the source population will not reflect model performance in the target population. Here, we provide identification results for the AUC in the target population when outcome and covariate data are available from the sample of the source population, but only covariate data are available from the sample of the target population. In this setting, we propose three estimators for the AUC in the target population and show that they are consistent and asymptotically normal. We evaluate the finite-sample performance of the estimators using simulations and use them to estimate the AUC in a nationally representative target population from the National Health and Nutrition Examination Survey for a lung cancer risk prediction model developed using source population data from the National Lung Screening Trial.     

Exploiting genomic patterns to discover new supramolecular protein assemblies

Bacterial microcompartments are supramolecular protein assemblies that function as bacterial organelles by compartmentalizing particular enzymes and metabolic intermediates. The outer shells of these microcompartments are assembled from multiple paralogous structural proteins. Because the paralogs are required to assemble together, their genes are often transcribed together from the same operon, giving rise to a distinctive genomic pattern: multiple, typically small, paralogous proteins encoded in close proximity on the bacterial chromosome. To investigate the generality of this pattern in supramolecular assemblies, we employed a comparative genomics approach to search for protein families that show the same kind of genomic pattern as that exhibited by bacterial microcompartments. The results indicate that a variety of large supramolecular assemblies fit the pattern, including bacterial gas vesicles, bacterial pili, and small heat‐shock protein complexes. The search also retrieved several widely distributed protein families of presently unknown function. The proteins from one of these families were characterized experimentally and found to show a behavior indicative of supramolecular assembly. We conclude that cotranscribed paralogs are a common feature of diverse supramolecular assemblies, and a useful genomic signature for discovering new kinds of large protein assemblies from genomic data.     

The composition and relationships of the marine molluscan fauna of the Pitcairn Islands

The recent expedition has doubled the number of marine molluscs known from the Pitcairn Islands. Over 80 taxa are recorded from Ducie and Pitcairn (both still poorly known), 240 from Oeno and 320 from Henderson. A total exceeding 400 taxa is now known from the group as a whole. Most of this increase results from a vastly improved knowledge of the small taxa that had been neglected in earlier surveys. Important faunal differences exist between the four islands in the group which are related to the different character of each island. These totals still underestimate the true diversities, but they provide data that are comparable in quality to those from adjacent regions. In this context the molluscan fauna from the Pitcairn Islands is seen to be impoverished when compared to those from islands further west. Most of the fauna is composed of widespread Indo-West Pacific species, but there are several taxa that have more restricted ranges centred on S.E. Polynesia. A few, including some undescribed taxa discovered on the expedition, appear to be endemic. Significantly, many of these are characterized by non-planktotrophic larval development. Comparison of the modern fauna from Henderson with the fossil fauna from the Pleistocene reef on its plateau reveals important differences. About 25% of the fossil molluscs are currently unknown from the group and about 5% appear to be undescribed. These high rates of turnover demonstrate that the faunas are temporally unstable.