Polytene chromosomes as indicators of phylogeny in several species groups of Drosophila.

BackgroundPolytene chromosome banding patterns have long been used by Drosophila evolutionists to infer degree of relatedness among taxa. Recently, nucleotide sequences have preempted this traditional method. We place the classical Drosophila evolutionary biology tools of polytene chromosome inversion analysis in a phylogenetic context and assess their utility in comparison to nucleotide sequences.ResultsA simultaneous analysis framework was used to examine the congruence of the chromosomal inversion data with more recent DNA sequence data in four Drosophila species groups - the melanogaster, virilis, repleta, and picture wing. Inversions and nucleotides were highly congruent with one another based on incongruence length difference and partitioned Bremer support values. Inversion phylogenies were less resolved because of fewer numbers of characters. Partitioned Bremer supports, corrected for the number of characters in each matrix, were higher for inversion matrices.ConclusionsPolytene chromosome data are highly congruent with DNA sequence data and, when placed in a simultaneous analysis framework, are shown to be more information rich than nucleotide data

Pilot study of the influence of self-coding on empathy within an introductory motivational interviewing training

Background: Motivational interviewing (MI) is a framework for addressing behavior change that is often used by healthcare professionals. Expression of empathy during MI is associated with positive client outcomes, while absence of empathy may produce iatrogenic effects. Although training in MI is linked to increased therapeutic empathy in learners, no research has investigated individual training components' contribution to this increase. The objective of this study was to test whether a self-coding MI exercise using smartphones completed at hour 6 of an 8-h MI training was superior in engendering empathy to training as usual (watching an MI expert perform in a video clip for the same duration at the same point in the training). Methods: This was a pilot study at two sites using randomization and control groups with 1:1 allocation. Allocation was achieved via computerized assignment (site 1, United Kingdom) or facedown playing card distribution (site 2, United States). Participants were 58 students attending a university class at one of two universities, of which an 8-h segment was dedicated to a standardized MI training. Fifty-five students consented to participate and were randomized. The intervention was an MI self-coding exercise using smartphone recording and a standardized scoring sheet. Students were encouraged to reflect on areas of potential improvement based on their self-coding results. The main outcome measure was score on the Helpful Responses Questionnaire, a measure of therapeutic empathy, collected prior to and immediately following the 8-h training. Questionnaire coding was completed by 2 blinded external reviewers and assessed for interrater reliability, and students were assigned averaged empathy scores from 6 to 30. Analyses were conducted via repeated-measures ANOVA using the general linear model. Results: Fifty-five students were randomized, and 2 were subsequently excluded from analysis at site 2 due to incomplete questionnaires. The study itself was feasible, and overall therapeutic empathy increased significantly and substantially among students. However, the intervention was not superior to the control condition in this study. Conclusions: Replacing a single passive learning exercise with an active learning exercise in an MI training did not result in a substantive boost to therapeutic empathy. However, consistently with prior research, this study identified significant overall increases in empathy following introductory MI training. A much larger study examining the impact of selected exercises and approaches would likely be useful and informative

Population genetic structuring in pacu (Piaractus mesopotamicus) across the Paraná-Paraguay basin: evidence from microsatellites

The Paraná-Paraguay basin encompasses central western Brazil, northeastern Paraguay, eastern Bolivia and northern Argentina. The Pantanal is a flooded plain with marked dry and rainy seasons that, due to its soil characteristics and low declivity, has a great water holding capacity supporting abundant fish fauna. Piaractus mesopotamicus, or pacu, endemic of the Paraná-Paraguay basin, is a migratory species economically important in fisheries and ecologically as a potential seed disperser. In this paper we employ eight microsatellite loci to assess the population structure of 120 pacu sampled inside and outside the Pantanal of Mato Grosso. Our main objective was to test the null hypothesis of panmixia and to verify if there was a different structuring pattern between the Pantanal were there were no physical barriers to fish movement and the heavily impounded Paraná and Paranapanema rivers. All loci had moderate to high levels of polymorphism, the number of alleles varied from three to 18. The average observed heterozygosity varied from 0.068 to 0.911. After the Bonferroni correction three loci remained significant for deviations from Hardy-Weinberg, and for those the frequency of null alleles was estimated. F ST and R ST pairwise comparisons detected low divergence among sampling sites, and differentiation was significant only between Paranapanema and Cuiabá and Paranapanema and Taquari. No correlation between genetic distance and the natural logarithm of the geographic distance was detected. Results indicate that for conservation purposes and for restoration programs small genetic differences detected in the Cuiabá and Paranapanema rivers should be taken in consideration.A bacia Paraná-Paraguai compreende o oeste do Brasil, nordeste do Paraguai, leste da Bolívia e o norte da Argentina. O Pantanal do Mato Grosso é uma planície inundada com estações de chuva e seca bem definidas, as características do solo e baixa declividade favorecem a retenção de água proporcionando abrigo para uma abundante ictiofauna. O Piaractus mesopotamicus, ou pacu, endêmico da bacia do Paraná-Paraguai, é uma espécie migratória com importância econômica na pesca e ecológica como potencial dispersor de sementes. Neste estudo utilizamos oito loci de microssatélites para verificar a estrutura populacional de 120 pacus coletados dentro e fora do Pantanal do Mato Grosso. Nosso principal objetivo foi testar a hipótese de panmixia e verificar se haviam diferentes padrões de estruturação entre o Pantanal onde não existem barreiras físicas ao movimento migratório desses peixes em relação aos rios Paraná e Paranapanema com suas inúmeras barragens. Todos os loci apresentaram níveis de polimorfismo de moderado a alto e o número de alelos variou de três a 18. A heterozigosidade média observada variou de 0,068 a 0,911. Depois da correção usando o método de Bonferroni três loci permaneceram estatisticamente significantes para desvios de Hardy-Weinberg, para estes a frequência de alelos nulos foi calculada. Comparações par a par de F ST e R ST detectaram baixa divergência genética entre os locais de coleta e as diferenças foram significantes apenas entre amostras do Paranapanema e Cuiabá e Paranapanema e Taquari. Não foi detectada correlação entre a diversidade genética e o logaritmo natural da distância geográfica. Os resultados indicam que as pequenas diferenças genéticas encontradas nos rios Cuiabá e Paranapanema devem ser levadas em consideração quando se tratar de programas de conservação desta espécie.FAPES

Should Networks Supplant Tree Building?

Recent studies suggested that network methods should supplant tree building as the basis of genealogical analysis. This proposition is based upon two arguments. First is the observation that bacterial and archaeal lineages experience processes oppositional to bifurcation and hence the representation of the evolutionary process in a tree like structure is illogical. Second is the argument tree building approaches are circular—you ask for a tree and you get one, which pins a verificationist label on tree building that, if correct, should be the end of phylogenetic analysis as we currently know it. In this review, we examine these questions and suggest that rumors of the death of the bacterial tree of life are exaggerated at best

A DNA Virus of Drosophila

Little is known about the viruses infecting most species. Even in groups as well-studied as Drosophila, only a handful of viruses have been well-characterized. A viral metagenomic approach was used to explore viral diversity in 83 wild-caught Drosophila innubila, a mushroom feeding member of the quinaria group. A single fly that was injected with, and died from, Drosophila C Virus (DCV) was added to the sample as a control. Two-thirds of reads in the infected sample had DCV as the best BLAST hit, suggesting that the protocol developed is highly sensitive. In addition to the DCV hits, several sequences had Oryctes rhinoceros Nudivirus, a double-stranded DNA virus, as a best BLAST hit. The virus associated with these sequences was termed Drosophila innubila Nudivirus (DiNV). PCR screens of natural populations showed that DiNV was both common and widespread taxonomically and geographically. Electron microscopy confirms the presence of virions in fly fecal material similar in structure to other described Nudiviruses. In 2 species, D. innubila and D. falleni, the virus is associated with a severe (∼80–90%) loss of fecundity and significantly decreased lifespan

SLAM : Solutions lexicales automatique pour métaphores

30 pagesInternational audienceThis article presents SLAM, an Automatic Solver for Lexical Metaphors like “déshabiller* une pomme” (to undress* an apple). SLAM calculates a conventional solution for these productions. To carry on it, SLAM has to intersect the paradigmatic axis of the metaphorical verb “déshabiller*”, where “peler” (“to peel”) comes closer, with a syntagmatic axis that comes from a corpus where “peler une pomme” (to peel an apple) is semantically and syntactically regular. We test this model on DicoSyn, which is a “small world” network of synonyms, to compute the paradigmatic axis and on Frantext.20, a French corpus, to compute the syntagmatic axis. Further, we evaluate the model with a sample of an experimental corpus of the database of Flexse

Potential Costs of Acclimatization to a Warmer Climate: Growth of a Reef Coral with Heat Tolerant vs. Sensitive Symbiont Types

One of the principle ways in which reef building corals are likely to cope with a warmer climate is by changing to more thermally tolerant endosymbiotic algae (zooxanthellae) genotypes. It is highly likely that hosting a more heat-tolerant algal genotype will be accompanied by tradeoffs in the physiology of the coral. To better understand one of these tradeoffs, growth was investigated in the Indo-Pacific reef-building coral Acropora millepora in both the laboratory and the field. In the Keppel Islands in the southern Great Barrier Reef this species naturally harbors nrDNA ITS1 thermally sensitive type C2 or thermally tolerant type D zooxanthellae of the genus Symbiodinium and can change dominant type following bleaching. We show that under controlled conditions, corals with type D symbionts grow 29% slower than those with type C2 symbionts. In the field, type D colonies grew 38% slower than C2 colonies. These results demonstrate the magnitude of trade-offs likely to be experienced by this species as they acclimatize to warmer conditions by changing to more thermally tolerant type D zooxanthellae. Irrespective of symbiont genotype, corals were affected to an even greater degree by the stress of a bleaching event which reduced growth by more than 50% for up to 18 months compared to pre-bleaching rates. The processes of symbiont change and acute thermal stress are likely to act in concert on coral growth as reefs acclimatize to more stressful warmer conditions, further compromising their regeneration capacity following climate change

Réseaux lexicaux, métaphore, acquisition : une approche interdisciplinaire et inter-linguistique du lexique verbal

When speakers have no access to the conventional label for an object or an event, they tend to extend, consciously or not, the meaning of another available lexical label. This phenomenon often occurs during the lexical acquisition stage of young children. When a such overextension goes beyond the conventional object or event category denoted by the produced label, it is a categorical overextension and the produced utterance is metaphorical: for instance, ``to undress an apple'' for the action to peel an apple is metaphorical.During this thesis, I developed SLAM, a computational system that automatically gives lexical solutions to metaphors filling a lexical gap. SLAM is based on a syntactic analysis of large corpora and on the Hierarchical Small World structure of synonymy networks. For instance, when the produced utterances are ``elle déshabille* une pomme'' ( ``she undresses* an apple'') or ``les bras* de l'arbr'' (``the arms* of the tree''), SLAM gives the interpretations here after: respectively, ``elle pèle une pomme'' (``she peels an apple'') and ``les branches de l'arbre'' (``the branches of the tree'').Then, I studied the dynamics of verb lexicon acquisition that is longer than noun lexicon acquisition. On the one hand, I built methodological tools for inter-linguistic studies of the dynamics of verb lexicon acquisition: (a) a methodological frame to build procedures to identify categorical overextensions of verbs; (b) a methodology to detect visual stimuli containing actions without cultural bias. On the other hand, I highlighted the links between the structure of synonymy networks and the dynamics of verbs lexicon acquisition in french and mandarin. This study has indicated differences in dynamics of verb lexicon acquisition between french and mandarin native speakers. Finally, I built REFLEX, a score that indicates the degree of verb lexicon acquisition and automatically categorizes young children vs adults in french and mandarin.Souvent, lorsque les locuteurs d'une langue n'ont pas accès à l'item conventionnel pour étiqueter un objet ou un événement, ils étendent, consciemment ou inconsciemment, le sens d'un autre item lexical disponible. Ce phénomène se produit particulièrement au cours de la phase d'acquisition lexicale des jeunes enfants. Lorsqu'une telle sur-extension sémantique va au-delà de la catégorie d'objet ou d'événement conventionnellement dénotée par l'item lexical produit, il s'agit d'une sur-extension catégorielle et l'énoncé produit est d'allure métaphorique: par exemple, « déshabiller la pomme » pour l'action peler une pomme est un énoncé d'allure métaphorique. Tout d'abord, cette thèse a permis de développer SLAM, un système de résolution lexicale automatique des métaphores produites en situation de manque du mot. SLAM s'appuie, d'une part, sur l'analyse syntaxique de grands corpus et, d'autre part, sur la structure Petit Monde Hiérarchique des réseaux lexicaux de synonymie. Par exemple, à partir des énoncés « elle déshabille* la pomme » ou « les bras* de l'arbre », SLAM permet d'obtenir les interprétations suivantes: respectivement, « elle pèle une pomme » et « les branches de l'arbre ».Ensuite, cette thèse a permis d'étudier spécifiquement la dynamique d'acquisition du lexique des verbes qui se stabilise après celui des noms. D'une part, des outils méthodologiques pour l'étude inter-linguistique de la dynamique d'acquisition du lexique des verbes ont été élaborés: (a) un cadre méthodologique pour la construction de procédures d'identification des sur-extensions sémantiques catégorielles des verbes; (b) une méthodologie pour le repérage des stimuli visuels d'action sans biais culturel. D'autre part, les liens entre la structure des réseaux lexicaux de synonymie et la dynamique d'acquisition du lexique des verbes en français et en mandarin ont été mis au jour. Après avoir pointé des différences dans la dynamique d'acquisition du lexique des verbes par les jeunes enfants natifs du français et du mandarin, cette étude a servi à construire le score REFLEX, mesure du degré d'acquisition du lexique des verbes, qui permet de catégoriser automatiquement les jeunes enfants vs adultes en français et en mandarin

Testing the Effect of Metabolic Rate on DNA Variability at the Intra-Specific Level

We tested the metabolic rate hypothesis (whereby rates of mtDNA evolution are postulated to be mediated primarily by mutagenic by-products of respiration) by examining whether mass-specific metabolic rate was correlated with root-to-tip distance on a set of mtDNA trees for the springtail Cryptopygus antarcticus travei from sub-Antarctic Marion Island