Population genomics of eusocial insects: the costs of a vertebrate-like effective population size

The evolution of reproductive division of labour and social life in social insects has lead to the emergence of several life-history traits and adaptations typical of larger organisms: social insect colonies can reach masses of several kilograms, they start reproducing only when they are several years old, and can live for decades. These features and the monopolization of reproduction by only one or few individuals in a colony should affect molecular evolution by reducing the effective population size. We tested this prediction by analysing genome-wide patterns of coding sequence polymorphism and divergence in eusocial vs. noneusocial insects based on newly generated RNA-seq data. We report very low amounts of genetic polymorphism and an elevated ratio of nonsynonymous to synonymous changes - a marker of the effective population size - in four distinct species of eusocial insects, which were more similar to vertebrates than to solitary insects regarding molecular evolutionary processes. Moreover, the ratio of nonsynonymous to synonymous substitutions was positively correlated with the level of social complexity across ant species. These results are fully consistent with the hypothesis of a reduced effective population size and an increased genetic load in eusocial insects, indicating that the evolution of social life has important consequences at both the genomic and population levels.

La teoría de los códigos. Desigualdades lingüísticas en educación

Las desigualdades lingüísticas en educación constituyen un problema que puede acentuarse con el cambio de sociedad. Este artículo recupera la teoría de los códigos de Basil Bernstein desde una perspectiva culturalista para aclarar sus aspectos más polémicos y, al mismo tiempo, introducir un nuevo modelo de análisis que pone en relación el capital cultural de las familias con el nivel de desarrollo lingüístico de los adolescentes. Se observa que el nivel de estudios alcanzado por los padres adquiere una notable importancia en el desarrollo de la competencia comunicativa, especialmente en el desarrollo de las habilidades correspondientes al lenguaje escrito en los adolescentes de primer curso de Educación Secundaria Obligatoria.

Do we need to revise the tripartite subdivision hypothesis of the human subthalamic nucleus (STN)? Response to Alkemade and Forstmann.

Recently in this journal, Alkemade and Forstmann again challenged the evidence for a tripartite organisation to the subthalamic nucleus (STN) (Alkemade & Forstmann 2014). Additionally, they raised specific issues with the earlier published results using 3T MRI to perform in vivo diffusion weighted imaging (DWI) based segmentation of the STN (Lambert et al. 2012). Their comments reveal a common misconception related to the underlying methodologies used, which we clarify in this reply, in addition to highlighting how their current conclusions are synonymous with our original paper. The ongoing debate, instigated by the controversies surrounding STN parcellation, raises important implications for the assumptions and methodologies employed in mapping functional brain anatomy, both in vivo and ex vivo, and reveals a fundamental emergent problem with the current techniques. These issues are reviewed, and potential strategies that could be developed to manage them in the future are discussed further.

DnaSP Version 5. DNA Sequence Polymorphism

DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguadé (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form.

Effect of the MC1R gene on sexual dimorphism in melanin-based colorations.

Variants of the melanocortin-1 receptor (MC1R) gene result in abrupt, naturally selected colour morphs. These genetic variants may differentially affect sexual dimorphism if one morph is naturally selected in the two sexes but another morph is naturally or sexually selected only in one of the two sexes (e.g. to confer camouflage in reproductive females or confer mating advantage in males). Therefore, the balance between natural and sexual selections can differ between MC1R variants, as suggest studies showing interspecific correlations between sexual dimorphism and the rate of nonsynonymous vs. synonymous amino acid substitutions at the MC1R. Surprisingly, how MC1R is related to within-species sexual dimorphism, and thereby to sex-specific selection, has not yet been investigated. We tackled this issue in the barn owl (Tyto alba), a species showing pronounced variation in the degree of reddish pheomelanin-based coloration and in the number and size of black feather spots. We found that a valine (V)-to-isoleucine (I) substitution at position 126 explains up to 30% of the variation in the three melanin-based colour traits and in feather melanin content. Interestingly, MC1R genotypes also differed in the degree of sexual colour dimorphism, with individuals homozygous for the II MC1R variant being 2 times redder and 2.5 times less sexually dimorphic than homozygous individuals for the VV MC1R variant. These findings support that MC1R interacts with the expression of sexual dimorphism and suggest that a gene with major phenotypic effects and weakly influenced by variation in body condition can participate in sex-specific selection processes.

A common BACE1 polymorphism is a risk factor for sporadic Creutzfeldt-Jakob disease

The β site APP cleaving enzyme 1 (BACE1) is the rate-limiting β-secretase enzyme in the amyloidogenic processing of APP and Aβ formation, and therefore it has a prominent role in Alzheimer"s disease (AD) pathology. Recent evidence suggests that the prion protein (PrP) interacts directly with BACE1 regulating its β-secretase activity. Moreover, PrP has been proposed as the cellular receptor involved in the impairment of synaptic plasticity and toxicity caused by Aβ oligomers. Provided that common pathophysiologic mechanisms are shared by Alzheimer"s and Creutzfeldt-Jakob (CJD) diseases, we investigated for the first time to the best of our knowledge a possible association of a common synonymous BACE1 polymorphism (rs638405) with sporadic CJD (sCJD). Our results indicate that BACE1 C-allele is associated with an increased risk for developing sCJD, mainly in PRNP M129M homozygous subjects with early onset. These results extend the very short list of genes (other than PRNP) involved in the development of human prion diseases; and support the notion that similar to AD, in sCJD several loci may contribute with modest overall effects to disease risk. These findings underscore the interplay in both pathologies of APP, Aβ oligomers, ApoE, PrP and BACE1, and suggest that aging and perhaps vascular risk factors may modulate disease pathologies in part through these key players

Annonaceae substitution rates: a codon model perspective

The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.

Local effects drive heterozygosity-fitness correlations in an outcrossing long-lived tree.

Heterozygosity-fitness correlations (HFCs) have been used to understand the complex interactions between inbreeding, genetic diversity and evolution. Although frequently reported for decades, evidence for HFCs was often based on underpowered studies or inappropriate methods, and hence their underlying mechanisms are still under debate. Here, we used 6100 genome-wide single nucleotide polymorphisms (SNPs) to test for general and local effect HFCs in maritime pine (Pinus pinaster Ait.), an iconic Mediterranean forest tree. Survival was used as a fitness proxy, and HFCs were assessed at a four-site common garden under contrasting environmental conditions (total of 16 288 trees). We found no significant correlations between genome-wide heterozygosity and fitness at any location, despite variation in inbreeding explaining a substantial proportion of the total variance for survival. However, four SNPs (including two non-synonymous mutations) were involved in significant associations with survival, in particular in the common gardens with higher environmental stress, as shown by a novel heterozygosity-fitness association test at the species-wide level. Fitness effects of SNPs involved in significant HFCs were stable across maritime pine gene pools naturally growing in distinct environments. These results led us to dismiss the general effect hypothesis and suggested a significant role of heterozygosity in specific candidate genes for increasing fitness in maritime pine. Our study highlights the importance of considering the species evolutionary and demographic history and different spatial scales and testing environments when assessing and interpreting HFCs.

Entre la discapacitat i la diversitat funcional: El professional davant dels canvis de paradigmes i no només de paraules

En qualsevol disciplina els canvis en el vocabulari són importants pel fet que hi ha una evolució en la disciplina mateixa. Pel que fa a la discapacitat i la diversitat funcional no només hi ha un canvi de paraules sinó un canvi conceptual que genera substitucions de vocabulari però no com a sinònims. Els canvis de paradigma als quals fem referència en la darrera dècada comencen a prendre rellevància a molts nivells, com l’acadèmic, el social i el polític, com si fossin un engranatge en què, quan hi ha canvis en una peça, convé també plantejar-los en les altres. Des d’aquest punt de vista alteracions de la concepció de discapacitat i diversitat funcional generen canvis significatius en la manera de generar serveis si calgués. Però a més adquireixen molta importància les novetats a nivell actitudinal i de relació que estableixen els professionals de l’educació social o del treball social sobre les persones amb diversitat funcional.

Det pedagogiska övervägandet : en uppmärksamhetsriktande studie i och genom humanvetenskaplig handlingsteori

Det övergripande syftet med avhandlingen är att bidra till en handlingsinriktad diskurs. Ambitionen är att rikta uppmärksamheten mot den pedagogiska övervägande handlingen genom att pröva konkreta exempel från en pedagogisk praktik mot en begreppsapparat inspirerad av den humanvetenskapliga handlingsteorin. Forskningsfrågorna lyder: Vad är en övervägande handling? Hur byggs den upp och vad förutsätter den? Bakgrunden till intresset att belysa den övervägande handlingen är en önskan att överbrygga klyftan mellan teori och praktik och att hitta ett sätt att samtala om ”tyst kunskap” och den konkreta pedagogiska verkligheten så att denna kan utvecklas på ett meningsfullt sätt. Förhållandet mellan intentionalitet och instrumentella handlingar är av särskilt intresse. Den aristoteliska begreppsapparaten som avser att belysa den mänskliga handlingen används i studien som både utgångspunkt och analysredskap. Retoriken ses som den vetenskap som kan beskriva och förklara hur vi skapar mening med hjälp av språket. Fyra fokussamtal med sammanlagt fem studerande på musikanimatörutbildningen genomfördes under vårterminen 2006. Referaten från samtalen bearbetades till en berättelse. I konstruktionen av berättelsen användes dels en fenomenologisk analys, dels narrativ bearbetning. De aristoteliska begreppen poíesis, praxis och theoria tillämpades och prövades på berättelsen varefter en retorisk analys genomfördes. Berättelsen visar två konkurrerande praxis. Utbildningen framstår i berättelsen dels som en horisontell ”alla kan”-utbildning, dels som en vertikal och lärarstyrd verksamhet. Berättelsen ger inte så många exempel på pedagogiska överväganden men tydliggör ändå den övervägande handlingen. Det pedagogiska övervägandet innebär ett väljande utifrån teoretiskt tänkbara och med praxis förenliga handlingsalternativ. Reflektion ingår i övervägandet men är inte detsamma som övervägande. Övervägandet är inte enbart en rationellt kalkylerande aktivitet. Holistiska och intuitiva procedurer är en viktig del i processen. Övervägande förutsätter dessutom ansvar.

Rummet i vårdandets värld

This study is made in the context of basic research within the field ofcaring science. The aim is to make a theoretical and ontological investigation of what the space is in the world of caring. The basic proposition is that the space, as a fundamental dimension, has an impact on how the appreciation of one's mental health and suffering is shaped, and vice versa. The overall purpose is to develop a theoretical model of space from the caring science point of view andalso to offer an ideal concept of space to caring science. Guided by a theoretical horizon (Eriksson 1993, Eriksson 1995, Eriksson 2001) and methodological approach grounded in Gadamer's philosophic and existential hermeneutics a three-stage analysis and interpretation is conducted. The hermeneutic spiral of this investigation starts through a procedure in accordance with Eriksson's model (1997) of concept definition. The goal is to clarify the etymology of the concept as well as semantic differences between synonymous concepts, i.e. to identify the different extents of the concept of `space` (`rum`) in order to bring these closer for an exploration. The second phase is to analyse and interpret a sample of narratives in order to explicate the ontological nature and meaning of the space. The material used here is literary texts. The goal is to clarify the characteristics of the very inside of the space when it is shaped in relation to the human being in encountering suffering. In the third phase an interview study is taken place. The focus of the study is directed towards the phenomenon of space as it is known by a patient in a landscape of psychiatric care, i.e. what the space is in a contextual meaning. Then, a gradual hermeneutic understanding of the space is attempted by using theories from the field of caring science as well as additional theories from other disciplines. Metaphors are used as they are vivid and expressive tools for generating meaning. Different metaphoric space formations depict here a variety of purports that, although not quite the same, share extensive elements. Six metaphorically summarized entities of meaning emerged. The comprehensive form of space is pointed out as the Mobile-Immobile Room. Furthermore, the Standby, the Asylum, the Wall and the Place. In the further dialogue with the texts the understanding has deepened ontologically. The theoretical model ofthe space sums up the vertical, horizontal and the inward extent of deepness inthe movement of mental health. Three entities of ontological meaning have emerged as three significant rooms: the Common Land emerges as the ideal concept of mutual creation in the freedom of doing, being and becoming health. On the interpersonal level it means freedom, which includes sovereignty, choice and dignity of the human being. The Ice World signifies, ultimately, the space as a kind of frozenness of despair which "wallpapers" the person's entire being in the world in the drama of suffering. The Spiritual Home is shaped when the human being has acquired the very core of his/her inner and outer placeness as a kind of "at-homeness" and rootedness. Time is a central element and the inward extent of deepness of this trialectic space. Each of the metaphors is then the human being's unique, although even paradoxical, way of conceiving reality, and mastering spiritual suffering. They condense characteristic structures and patterns of dynamic scenery, which take place within the movement of health. The space encloses a contradictory spatiality constituted through the dynamic field of meaningfulness and meaninglessness. Anyway, it is not through a purging of these contradictions but through bringing them together in a drama of suffering that the space is shaped as ontologically good and meaningful in the world of caring.

Molecular Basis for Resistance to Fluazifop-P-Butyl in Itchgrass (Rottboellia cochinchinensis) from Costa Rica

Rottboellia cochinchinensis is an annual grass weed species known as itchgrass, or "caminadora" in America´s Spanish speaking countries, and has become a major and troublesome weed in several crops. The application of fluazifop-P-butyl at recommended rates (125 g a.i. ha-1) was observed to be failing to control itchgrass in a field in San José, Upala county, Alajuela province, Costa Rica. Plants from the putative resistant R. cochinchinensis population survived fluazifop-P-butyl when treated with 250 g a.i. ha-1 (2X label rate) at the three- to four-leaf stage under greenhouse conditions. PCR amplification and sequencing of partial carboxyl transferase domain (CT) of the acetyl-CoA carboxylase (ACCase) gene were used to determine the molecular mechanism of resistance. A single non-synonymous point mutation from TGG (susceptible plants) to TGC (putative resistant plants) that leads to a Trp-2027-Cys substitution was found. This Trp-2027-Cys mutation is known to confer resistance to all aryloxyphenoxyproprionate (APP) herbicides to which fluazifop-P-butyl belongs. To the best of our knowledge, this is the first report of fluazifop-P-butyl resistance and a mutation at position 2027 for a Costa Rican R. cochinchinensis population.

L1 sequence of a new human papillomavirus type-58 variant associated with cervical intraepithelial neoplasia

The present study on molecular characterization of a human papillomavirus (HPV) isolated in Central Brazil describes the L1 gene sequence from a new variant of HPV-58, the isolate Bsb-02. The sample was from a smear obtained from a woman with cervical intraepithelial neoplasia grade II. The whole L1 gene from isolate Bsb-02 was sequenced automatically, showing 99.1% nucleotide identity with the gene from the HPV-58 reference. The clustering between Bsb-02 and HPV-58 reference sequence was also supported by phylogenetic analysis. Fourteen nucleotide substitutions were observed: eight were synonymous and six were associated with amino acid substitutions. A10V and V144I have not been previously described. At GenBank, the only complete L1 sequence from HPV-58 in addition to the HPV-58 reference one is that of Bsb-02. These data provide information that may be relevant to HPV diagnosis and to rational vaccine strategies. HPV variants may also be associated with host immune responses and with the risk of cervical neoplasia.

High baseline serum total and LDL cholesterol levels are associated with MDR1 haplotypes in Brazilian hypercholesterolemic individuals of European descent

The MDR1 gene encodes the P-glycoprotein, an efflux transporter with broad substrate specificity. P-glycoprotein has raised great interest in pharmacogenetics because it transports a variety of structurally divergent drugs, including lipid-lowering drugs. The synonymous single-nucleotide polymorphism C3435T and the nonsynonymous single-nucleotide polymorphism G2677T/A in MDR1 have been indicated as potential determinants of variability in drug disposition and efficacy. In order to evaluate the effect of G2677T/A and C3435T MDR1 polymorphisms on serum levels of lipids before and after atorvastatin administration, 69 unrelated hypercholesterolemic individuals from São Paulo city, Brazil, were selected and treated with 10 mg atorvastatin orally once daily for four weeks. MDR1 polymorphisms were analyzed by PCR-RFLP. C3435T and G2677T polymorphisms were found to be linked. The allelic frequencies for C3435T polymorphism were 0.536 and 0.464 for the 3435C and 3435T alleles, respectively, while for G2677T/A polymorphism allele frequencies were 0.580 for the 2677G allele, 0.384 for the 2677T allele and 0.036 for the 2677A allele. There was no significant relation between atorvastatin response and MDR1 polymorphisms (repeated measures ANOVA; P > 0.05). However, haplotype analysis revealed an association between T/T carriers and higher basal serum total (TC) and LDL cholesterol levels (TC: 303 ± 56, LDL-C: 216 ± 57 mg/dl, respectively) compared with non-T/T carriers (TC: 278 ± 28, LDL-C: 189 ± 24 mg/dl; repeated measures ANOVA/Tukey test; P < 0.05). These data indicate that MDR1 polymorphism may have an important contribution to the control of basal serum cholesterol levels in Brazilian hypercholesterolemic individuals of European descent.

Guava Jam packaging determinant attributes in consumer buying decision

Using packaging and labels to lure consumers and to communicate product benefits directly on the shelf is a competitive advantage factor in the food industry sector. The label is especially effective since besides supplying basic details, such as weight, ingredients, and instructions in compliance with governmental regulations, it attracts consumers' attention and the desire to buy and which often becomes synonymous to the brand name. The objective of this study was to obtain detailed information on consumers' attitudes, opinions, behavior, and concepts regarding guava jam packaging using the focus group technique. The results showed that label color and design, packaging type and information, and brand name and price are determinant attributes in the consumers' decision to buy guava jam.