Genetic Load in Natural Populations: Is It Compatible with the Hypothesis That Many Polymorphisms Are Maintained by Natural Selection?

Recent studies of genetically controlled enzyme variation lead to an estimation that at least 30 to 60% of the structural genes are polymorphic in natural populations of many vertebrate and invertebrate species. Some authors have argued that a substantial proportion of these polymorphisms cannot be maintained by natural selection because this would result in an unbearable genetic load. If many polymorphisms are maintained by heterotic natural selection, individuals with much greater than average proportion of homozygous loci should have very low fitness. We have measured in Drosophila melanogaster the fitness of flies homozygous for a complete chromosome relative to normal wild flies. A total of 37 chromosomes from a natural population have been tested using 92 experimental populations. The mean fitness of homozygous flies is 0.12 for second chromosomes, and 0.13 for third chromosomes. These estimates are compatible with the hypothesis that many (more than one thousand) loci are maintained by heterotic selection in natural populations of D. melanogaster.     

Coordinated Cell Death in Isogenic Bacterial Populations: Sacrificing Some for the Benefit of Many?

Antibiotics are classically perceived as biological weapons that bacteria produce to hold their ground against competing species in their natural habitat. But in the context of multicellular differentiation processes, antimicrobial compounds sometimes also play a role in intraspecies competition, resulting in the death of a sub-population of genetically identical siblings for the benefit of the population. Such a strategy is based on the diversification and hence phenotypic heterogeneity of an isogenic bacterial population. This review article will address three such phenomena. In Bacillus subtilis, cannibalism is a differentiation strategy that enhances biofilm formation, prolongs or potentially even prevents full commitment to endospore formation under starvation conditions, and protects cells within the biofilm against competing species. The nutrients released by lysed cells can be used by the toxin producers, thereby delaying the full activation of the master regulator of sporulation. A related strategy is associated with the initiation of competence development under nutrient excess in Streptococcus pneumoniae. This process, termed fratricide, causes allolysis in a sub-population and is thought to enhance genetic diversity within the species. In Myxococcus xanthus, a large fraction of the population undergoes programmed cell death during the formation of fruiting bodies. This sacrifice ensures the survival of the sporulating sub-population by providing nutrients and hence energy to complete this differentiation process. The biological relevance and underlying regulatory mechanisms of these three processes will be discussed in order to extract common features of such strategies. Moreover, open questions and future challenges will be addressed.     

Genetic Structure of Chum Salmon (Oncorhynchus keta) Populations in the Lower Columbia River: Are Chum Salmon in Cascade Tributaries Remnant Populations?

The lower Columbia River drainage once supported a run of over a million chum salmon. By the late 1950s, the run had decreased to often a few hundred fish. With the exception of Grays River near the coast and an aggregation of chum salmon spawning in creeks and the main stem near Bonneville Dam in the Columbia Gorge, most populations were thought to be extinct. However, chum salmon consistently return in low numbers to tributaries originating in the Cascade Range: the Cowlitz, Lewis, and Washougal rivers. To assess whether Cascade spawners were strays or remnants of former populations, chum salmon from the Coastal, Cascade and Gorge ecoregional zones were characterized at 17 microsatellite loci. Significant heterogeneity in genotype distributions was detected between zones and collections formed regional groups in a neighbor-joining tree. Cascade collections had higher allelic richness and private alleles, and the Cowlitz River supported genetically divergent fall and summer runs, the only summer chum salmon run extant in the Columbia River drainage. We propose that chum salmon in the Cascade zone are remnants of original populations. We attribute the divergence between zonal groups to diverse ecological conditions in each zone, which promoted regional genetic adaptation, and to genetic drift experienced in small populations.     

How Many Species Are There? Public Understanding and Awareness of Biodiversity in Switzerland

This paper presents the results of interviews and a questionnaire study on public knowledge of the concept of biodiversity and of plant species richness in Switzerland. Despite its extensive use in science and policy making, the concept of biodiversity is not widely recognized or known to people in Switzerland. Overall, 60% of all study participants (161 grammar school pupils, 110 non-graduates, and 96 graduates in the Canton of Zurich) had never heard the term biodiversity, while the others had come across it primarily in the media. Few study participants considered their school education a relevant source of information about biodiversity. Study participants most frequently referred to the diversity of plants and animals when defining biodiversity, but also quite often believed that biodiversity had something to do with ecological concepts such as the equilibrium between all components of nature. Both young people and adults held widely inaccurate ideas of the plant species richness of communities. Particularly for Switzerland, plant species richness was strongly overestimated.

Can Genetic Estimators Provide Robust Estimates of the Effective Number of Breeders in Small Populations?

The effective population size (N_e) is proportional to the loss of genetic diversity and the rate of inbreeding, and its accurate estimation is crucial for the monitoring of small populations. Here, we integrate temporal studies of the gecko Oedura reticulata, to compare genetic and demographic estimators of N_e. Because geckos have overlapping generations, our goal was to demographically estimate N_bI, the inbreeding effective number of breeders and to calculate the N_bI/N_a ratio (N_a = number of adults) for four populations. Demographically estimated N_bI ranged from 1 to 65 individuals. The mean reduction in the effective number of breeders relative to census size (N_bI/N_a) was 0.1 to 1.1. We identified the variance in reproductive success as the most important variable contributing to reduction of this ratio. We used four methods to estimate the genetic based inbreeding effective number of breeders N_bI(gen) and the variance effective populations size N_eV(gen) estimates from the genotype data. Two of these methods - a temporal moment-based (MBT) and a likelihood-based approach (TM3) require at least two samples in time, while the other two were single-sample estimators - the linkage disequilibrium method with bias correction LDNe and the program ONeSAMP. The genetic based estimates were fairly similar across methods and also similar to the demographic estimates excluding those estimates, in which upper confidence interval boundaries were uninformative. For example, LDNe and ONeSAMP estimates ranged from 14–55 and 24–48 individuals, respectively. However, temporal methods suffered from a large variation in confidence intervals and concerns about the prior information. We conclude that the single-sample estimators are an acceptable short-cut to estimate N_bI for species such as geckos and will be of great importance for the monitoring of species in fragmented landscapes.     

Are Movements Necessary for the Sense of Body Ownership? Evidence from the Rubber Hand Illusion in Pure Hemiplegic Patients

A question still debated within cognitive neuroscience is whether signals present during actions significantly contribute to the emergence of human’s body ownership. In the present study, we aimed at answer this question by means of a neuropsychological approach. We administered the classical rubber hand illusion paradigm to a group of healthy participants and to a group of neurological patients affected by a complete left upper limb hemiplegia, but without any propriceptive/tactile deficits. The illusion strength was measured both subjectively (i.e., by a self-report questionnaire) and behaviorally (i.e., the location of one’s own hand is shifted towards the rubber hand). We aimed at examining whether, and to which extent, an enduring absence of movements related signals affects body ownership. Our results showed that patients displayed, respect to healthy participants, stronger illusory effects when the left (affected) hand was stimulated and no effects when the right (unaffected) hand was stimulated. In other words, hemiplegics had a weaker/more flexible sense of body ownership for the affected hand, but an enhanced/more rigid one for the healthy hand. Possible interpretations of such asymmetrical distribution of body ownership, as well as limits of our results, are discussed. Broadly speaking, our findings suggest that the alteration of the normal flow of signals present during movements impacts on human’s body ownership. This in turn, means that movements have a role per se in developing and maintaining a coherent body ownership.     

Detection and Characterization of Wolbachia Infections in Natural Populations of Aphids: Is the Hidden Diversity Fully Unraveled?

Aphids are a serious threat to agriculture, despite being a rather small group of insects. The about 4,000 species worldwide engage in highly interesting and complex relationships with their microbial fauna. One of the key symbionts in arthropods is Wolbachia, an α-Proteobacterium implicated in many important biological processes and believed to be a potential tool for biological control. Aphids were thought not to harbour Wolbachia; however, current data suggest that its presence in aphids has been missed, probably due to the low titre of the infection and/or to the high divergence of the Wolbachia strains of aphids. The goal of the present study is to map the Wolbachia infection status of natural aphids populations, along with the characterization of the detected Wolbachia strains. Out of 425 samples from Spain, Portugal, Greece, Israel and Iran, 37 were found to be infected. Our results, based mainly on 16S rRNA gene sequencing, indicate the presence of two new Wolbachia supergroups prevailing in aphids, along with some strains belonging either to supergroup B or to supergroup A.     

How Effective Are DNA Barcodes in the Identification of African Rainforest Trees?

Background

DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of rbcL, matK and trnH-psbA plastid DNA markers to identify rain forest trees at two sites in Atlantic central Africa under the assumption that a database is exhaustive in terms of species content, but not necessarily in terms of haplotype diversity within species.

Methodology/Principal Findings

We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95–100% success), but less for species identification (71–88%). Using a single marker, best results for species identification were obtained with trnH-psbA. There was a significant decrease of barcoding success in species-rich clades. When the local database was used to identify the genus of trees from another region and did include all genera from the query individuals but not all species, genus identification success decreased to 84–90%. The GD method performed best but a global multiple sequence alignment is not applicable on trnH-psbA.

Conclusions/Significance

Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications.     

How Frequent Are Eating Disturbances in the Population? Norms of the Eating Disorder Examination-Questionnaire

Objective

The Eating Disorder Examination-Questionnaire (EDE-Q) is a self-report instrument assessing the specific psychopathology and key behaviors of eating disorders. This study sought to determine the prevalence of eating disturbances, and to provide psychometric properties and norms of the EDE-Q, in a representative German population sample.

Methods

A total of 2520 individuals (1166 men, 1354 women) were assessed with the EDE-Q.

Results

Eating disorder psychopathology was higher and most key behaviors were more prevalent in women than in men. Psychopathology declined with age ≥65 in both sexes, and showed a peak at age 55–64 in men. Overall, 5.9% of the women and 1.5% of the men revealed eating disturbances. The prevalence of eating disturbances decreased with age in women and was significantly higher in obese than in normal-weight individuals. Psychometric analyses showed favorable item characteristics. Internal consistencies of EDE-Q composite scores were ≥.80 for women and ≥.70 for men. The factor structure of the EDE-Q was partially reproduced. Sex- and age-specific population norms are reported.

Discussion

This study provides population norms of the EDE-Q for both sexes and across the age range, demonstrates demographic variations in symptomatology, and reveals satisfactory psychometric properties. Further research is warranted on eating disturbances in older adults.     

Using Noun Phrases for Navigating Biomedical Literature on Pubmed: How Many Updates Are We Losing Track of?

Author-supplied citations are a fraction of the related literature for a paper. The "related citations" on PubMed is typically dozens or hundreds of results long, and does not offer hints why these results are related. Using noun phrases derived from the sentences of the paper, we show it is possible to more transparently navigate to PubMed updates through search terms that can associate a paper with its citations. The algorithm to generate these search terms involved automatically extracting noun phrases from the paper using natural language processing tools, and ranking them by the number of occurrences in the paper compared to the number of occurrences on the web. We define search queries having at least one instance of overlap between the author-supplied citations of the paper and the top 20 search results as citation validated (CV). When the overlapping citations were written by same authors as the paper itself, we define it as CV-S and different authors is defined as CV-D. For a systematic sample of 883 papers on PubMed Central, at least one of the search terms for 86% of the papers is CV-D versus 65% for the top 20 PubMed "related citations." We hypothesize these quantities computed for the 20 million papers on PubMed to differ within 5% of these percentages. Averaged across all 883 papers, 5 search terms are CV-D, and 10 search terms are CV-S, and 6 unique citations validate these searches. Potentially related literature uncovered by citation-validated searches (either CV-S or CV-D) are on the order of ten per paper--many more if the remaining searches that are not citation-validated are taken into account. The significance and relationship of each search result to the paper can only be vetted and explained by a researcher with knowledge of or interest in that paper.     

Are Bogs Reservoirs for Emerging Disease Vectors? Evaluation of Culicoides Populations in the Hautes Fagnes Nature Reserve (Belgium)

Several species of Culicoides (Diptera: Ceratopogonidae) biting midges serve as biological vectors for the bluetongue virus (BTV) and the recently described Schmallenberg virus (SBV) in northern Europe. Since their recent emergence in this part of the continent, these diseases have caused considerable economic losses to the sheep and cattle industries. Much data is now available that describe the distribution, population dynamics, and feeding habits of these insects. However, little is known regarding the presence of Culicoides in unusual habitats such as peaty marshes, nor their potential vector capacity. This study evaluated Culicoides biting midges present in the bogs of a Belgian nature reserve compared to those residing at a nearby cattle farm. Culicoides were trapped in 2011 at four different sites (broadleaved and coniferous forested areas, open environments, and at a scientific station) located in the Hautes Fagnes Nature Reserve (Belgium). An additional light trap was operated on a nearby cattle farm. Very high numbers of biting midges were captured in the marshy area and most of them (70 to 95%) were Culicoides impunctatus, a potential vector of BTV and other pathogens. In addition, fewer numbers of C. obsoletus/C. scoticus species, C. chiopterus, and C. dewulfi were observed in the bogs compared to the farm. The wet environment and oligotrophic nature of the soil were probably responsible for these changes in the respective populations. A total of 297,808 Culicoides midges belonging to 27 species were identified during this study and 3 of these species (C. sphagnumensis, C. clintoni and C. comosioculatus) were described in Belgium for the first time.     

The Reason for the Preservation of High Instability at the yellow Gene in Drosophila melanogaster Strains Isolated from the Natural Population of Uman' during the “Mode for Mutation”

Mobile genetic elements are responsible for most spontaneous mutations in Drosophila melanogaster. The discovered in the 1980s phenomenon of frequent change of the wild-type yellow phenotype for a mutant one, and vice-versa, in strains of D. melanogaster isolated from the Uman' natural population can be, according to our data, explained by repeated inversions and reinversions of the gene regulatory region located between the two copies of the hobo transposon. However, most molecular genetic events accompanying the process can occur without the phenotype change. After several generations, the strains, remaining phenotypically unchanged, can possess different molecular genetic properties with respect to yellow. Using genetically homogenous or isogenic strains for the genetic analysis or for production of the new plant cultivars or animal breeds, geneticists and breeders often face the problem of stability of the strains. In the present study, the mechanism underlying the generation of instability at the yellowlocus of D. melanogaster determined by the hobo-induced genome instability is described.     

Are the Young Less Knowledgeable? Local Knowledge of Natural Remedies and Its Transformations in the Andean Highlands

A widespread concern among ethnobiologists is the rapid process of erosion of indigenous environmental knowledge observed worldwide. This paper examines the ongoing transformations of knowledge about natural remedies in the Quechua-speaking Andes. Freelisting exercises and interviews were conducted with 36 households at Bolivian and Peruvian study sites. (Generalized) linear mixed-effects models were used to analyze the effects of age on knowledge about medicinal plants, animals, minerals, and their uses. Our study demonstrates that younger participants knew as much about natural remedies as their elders. However, proportional knowledge about some medicinal use categories of natural remedies varied with age. We conclude that knowledge about natural remedies is generally not being lost at the study sites. Nevertheless, it is undergoing transformations in terms of specific medicinal uses. A careful understanding of these complex transformation processes is needed to better orient initiatives for the conservation of biocultural diversity in the Andes and elsewhere.     

How Universal Are Preferences for Female Waist-to-Hip Ratios? Evidence from the Hadza of Tanzania

Female waist-to-hip ratio (WHR) has been proposed by evolutionary psychologists to be an important component of human male mate choice, because this trait is thought to provide a reliable cue to a woman's reproductive value. Based largely on work conducted in industrialized societies, the claim has been made that preferences for low WHR are culturally invariant. Presumably, the preferences evolved before the advent of agriculture, making foraging populations the best place to test the hypothesis. This was done with the Hadza of Tanzania, who were shown figures of females that varied by weight and waist-to-hip ratio. Low WHR was not preferred. Hadza men did not consider waist-to-hip ratio when expressing preferences for mates. Instead, they were most interested in the weight of potential partners. Research by others with subjects who practice swidden agriculture also revealed that low WHR was not preferred. The data from the Hadza coupled with the information derived from this horticultural group bring into question whether preferences for low WHR are culturally invariant.     

Reintroduction of the European Capercaillie from the Capercaillie Breeding Centre in Wis?a Forest District: Genetic Assessments of Captive and Reintroduced Populations

The Western capercaillie (Tetrao urogallus) is a specific bird species, which, despite its very broad distribution and large global population size, is highly endangered in many Western and Central European countries. According to the species situation, in many countries (including Poland), breeding and reintroduction programmes have been started. One of the most complex and large-scale reintroduction programmes was started in Bory Dolnośląskie Forest, and the Capercaillie Breeding Centre in Wisła Forest District was used as one of the sources of individuals for reintroduction. As genetic tools provide essential knowledge about species biodiversity, which is crucially important during the breeding process and reintroduction, both captive and reintroduced grouse populations were genetically analysed. We were particularly interested in genetic diversity of the individuals in both populations and the genetic relationship between them, as well as between them and other capercaillie representatives from their current range. To fulfil these goals we determined nine microsatellite loci along with a fragment of the mitochondrial control region. Genetic diversity parameters were moderate to high compared to populations from other Central and Western European countries. Both populations were clustered into three distinct genetic clades based on microsatellites. Phylogenetic analysis placed all mitochondrial haplotypes we revealed in the Eurasian clade. The present results will play an important role as they will help to preserve and maximize genetic diversity in captive populations, and will provide a basis for future monitoring of the reintroduction process.     

How Many Sirtuin Genes Are Out There? Evolution of Sirtuin Genes in Vertebrates With a Description of a New Family Member

Studying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural studies to allow a deeper and more precise interpretation of their results in an evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our results show a well-resolved phylogeny that represents an improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin gene family member (SIRT3.2) that was apparently lost in the last common ancestor of amniotes but retained in all other groups of jawed vertebrates. According to our experimental analyses, elephant shark SIRT3.2 protein is located in mitochondria, the overexpression of which leads to an increase in cellular levels of ATP. Moreover, in vitro analysis demonstrated that it has deacetylase activity being modulated in a similar way to mammalian SIRT3. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.     

Are climatic factors responsible for the process of oak decline in Poland?

Oak decline, a complex process leading to increased mortality of this species, has been observed in Europe for many years. Previous studies suggest that climate conditions, especially drought, may be one of the most important factors that trigger this phenomenon. The paper investigates the radial growth and wood anatomy features of pedunculate oak (Quercus robur) trees of various health status as well as their response to climate conditions. Wood samples including all annual increments were taken at two sites (western and central Poland, 15 trees each). Based on the crown defoliation level, three health groups (healthy, weakened and dead oaks) were distinguished. Cross-sections were prepared with sliding microtome and Cell P image analysis software was used for the measurements. Tree-ring width (TRW), earlywood vessels density (VDen) and non-weighted vessels diameter (VD) were determined and correlated with mean monthly values of temperature, precipitation, vapour pressure, and Palmer Drought Severity Index (PDSI). Radial increment and anatomical parameters were significantly higher for the healthy oaks than for the weakened and the dead trees. TRW showed smaller dependence on climate than analysed anatomical attributes. No obvious pattern of relationship was found between oak radial growth and climate regarding tree health status. Our results revealed that the drought has a weak impact on the process of oak decline on investigated sites in Poland.