52 research outputs found
Insights into the influence of priors in posterior mapping of discrete morphological characters: a case study in Annonaceae
No full textBackground - Posterior mapping is an increasingly popular hierarchical Bayesian based method used to infer character histories and reconstruct ancestral states at nodes of molecular phylogenies, notably of morphological characters. As for all Bayesian analyses specification of prior values is an integrative and important part of the analysis. He we provide an example of how alternative prior choices can seriously influence results and mislead interpretations. Methods/Principal Findings - For two contrasting discrete morphological characters, namely a slow and a fast evolving character found in the plant family Annonaceae, we specified a total of eight different prior distributions per character. We investigated how these prior settings affected important summary statistics. Our analyses showed that the different prior distributions had marked effects on the results in terms of average number of character state changes. These differences arise because priors play a crucial role in determining which areas of parameter space the values of the simulation will be drawn from, independent of the data at hand. However, priors seemed to fit the data better if they would result in a more even sampling of parameter space (normal posterior distribution), in which case alternative standard deviation values had little effect on the results. The most probable character history for each character was affected differently by the prior. For the slower evolving character, the same character history always had the highest posterior probability independent of the priors used. In contrast, the faster evolving character showed different most probable character histories depending on the prior. These differences could be related to the level of homoplasy exhibited by each character. Conclusions - Although our analyses were restricted to two morphological characters within a single family, our results underline the importance of carefully choosing prior values for posterior mapping. Prior specification will be of crucial importance when interpreting the results in a meaningful way. It is hard to suggest a statistically sound method for prior specification without more detailed studies. Meanwhile, we propose that the data could be used to estimate the prior value of the gamma distribution placed on the transformation rate in posterior mappin
Taxonomic novelties in the genus Campylospermum (Ochnaceae)
No full textFour new species, one with two subspecies, of the genus Campylospermum are described, all endemic or sub-endemic to Gabon. These are C. auriculatum, C. gabonensis, C. gabonensis subsp. australis, C. glaucifolium and C. occidentalis. Distribution maps and scans of the holotypes are provided as well as preliminary IUCN Red List assessments. New combinations for nine species formerly assigned to the genus Ouratea and/or Gomphia are proposed: C. andongensis, C. glomeratum, C. longestipulatum, C. lunzuensis, C. lutambensis, C. nutans, C. plicatum and C. warneckei. Finally, one taxon is raised from the variety to species level, leading to the new combination C. costatum
Molecular phylogenetics reveal multiple tertiary vicariance origins of the African rain forest trees
No full textBackground - Tropical rain forests are the most diverse terrestrial ecosystems on the planet. How this diversity evolved remains largely unexplained. In Africa, rain forests are situated in two geographically isolated regions: the West-Central Guineo-Congolian region and the coastal and montane regions of East Africa. These regions have strong floristic affinities with each other, suggesting a former connection via an Eocene pan-African rain forest. High levels of endemism observed in both regions have been hypothesized to be the result of either 1) a single break-up followed by a long isolation or 2) multiple fragmentation and reconnection since the Oligocene. To test these hypotheses the evolutionary history of endemic taxa within a rain forest restricted African lineage of the plant family Annonaceae was studied. Molecular phylogenies and divergence dates were estimated using a Bayesian relaxed uncorrelated molecular clock assumption accounting for both calibration and phylogenetic uncertainties. Results - Our results provide strong evidence that East African endemic lineages of Annonaceae have multiple origins dated to significantly different times spanning the Oligocene and Miocene epochs. Moreover, these successive origins (c. 33, 16 and 8 million years ¿ Myr) coincide with known periods of aridification and geological activity in Africa that would have recurrently isolated the Guineo-Congolian rain forest from the East African one. All East African taxa were found to have diversified prior to Pleistocene times. Conclusion - Molecular phylogenetic dating analyses of this large pan-African clade of Annonaceae unravels an interesting pattern of diversification for rain forest restricted trees co-occurring in West/Central and East African rain forests. Our results suggest that repeated reconnections between the West/Central and East African rain forest blocks allowed for biotic exchange while the break-ups induced speciation via vicariance, enhancing the levels of endemicity. These results provide an explanation for present day distribution patterns and origins of endemicity for African rain forest trees. Moreover, given the pre-Pleistocene origins of all the studied endemic East African genera and species, these results also offer important insights for setting conservation priorities in these highly diversified but threatene
Contingent Protection Measures and the Management of the Softwood Lumber Trade in North America
No full textThis article examines CanadaÂ’s softwood lumber dispute with the United States in the context of new juridical models of international dispute settlement and an evolving trade policy environment in North America. Two questions are of central importance to this study. First, what does the rise of contingent protection measures mean for CanadaÂ’s regulatory model? Strong antidumping legislation has created a new order of trade conflict at a time when intrasectoral competition has increased state support in a number of sectors. Second, how do American antidumping trade remedy measures come to bear in this dispute? In the softwood case, dispute settlement has been less effective because Canada, as the smaller economy, faces the challenge of enforcing panel decisions when the respondent has the power to avoid compliance.Antidumping, countervailing duties, dispute settlement, softwood, trade policy, WTO, International Relations/Trade,
Revision of the African genus Hexalobus (Annonaceae)
No full textThe genus Hexalobus consists of five species characterized by six basally fused petal lobes that are transversally folded in bud, which is unique within Annonaceae. The genus is widespread across tropical Africa occurring in rain forest, savanna, and woodland. The species H. callicarpus, occurring in Madagascar, is excluded from Hexalobus, so the genus is now restricted to continental Africa. The present revision provides a synthesis of previously published information and discussions on morphology, taxonomy, phylogeny, and palynology. Conservation status assessments are provided for each species, as well as a diagnostic key and detailed species descriptions. Furthermore, four species are illustrated and all species are mapped
Dopamine restores reward prediction errors in old age
No full textSenescence affects the ability to utilize information about the likelihood of rewards for optimal decision-making. Using functional magnetic resonance imaging in humans, we found that healthy older adults had an abnormal signature of expected value, resulting in an incomplete reward prediction error (RPE) signal in the nucleus accumbens, a brain region that receives rich input projections from substantia nigra/ventral tegmental area (SN/VTA) dopaminergic neurons. Structural connectivity between SN/VTA and striatum, measured by diffusion tensor imaging, was tightly coupled to inter-individual differences in the expression of this expected reward value signal. The dopamine precursor levodopa (L-DOPA) increased the task-based learning rate and task performance in some older adults to the level of young adults. This drug effect was linked to restoration of a canonical neural RPE. Our results identify a neurochemical signature underlying abnormal reward processing in older adults and indicate that this can be modulated by L-DOPA
Experimental & Theoretical Aspects of the Electroweak Sector
No full textThe electroweak sector of the Standard Model (SM) has been extremely successful in predicting and matching observations. The basic form of it was sketched out some fifty years ago with the elucidation of the Higgs mechanism in a non-Abelian Yang-Mills gauge theory, yet the existence of a central player in the story, the (or a) Higgs boson, was confirmed only in 2012. In the intervening years, a great deal of experimental research was done to measure parameters of the model and confirm other predictions. In this sense, it has been an extremely fruitful theory in addition to being robust.
But questions regarding the origin of the values of certain parameters in the theory, and especially regarding obvious but unexplained hierarchies between them, beg to be answered. The question of the technical naturalness of the Higgs mass has been one of the most significant motivating factors behind theories of beyond-the-Standard-Model (BSM) physics, though other striking features (for instance, the large discrepancy between quark masses) have also motivated theories (for instance, 2-Higgs-doublet models and models with Yukawa unification). Thus the electroweak sector has also proven fruitful for BSM theorists.
The present paper may be divided into two parts: a description and characterization of the electroweak sector as it exists in the Standard Model on the one hand (a SM part), and an exploration of what may lie beyond it on the other (a BSM part).
In the SM part, we first review the conceptual development of the electroweak model of Glashow, Weinberg, and Salam (touching on Yang-Mills theory and the Higgs mechanism), then present the key phenomenology of the electroweak theory. This leads into a presentation of this author's work in studying nal-state radiation (FSR) uncertainties in a measurement of sin2 W, with W being the weak mixing angle, done by the Compact Muon Solenoid (CMS) group at the Large Hadron Collider (LHC) in 2011. The framework necessary to understand the analysis is laid out in the text but this author played only the small role described in the section on FSR. The full analysis was presented in the papers by N. Tran and the CMS Collaboration, referenced in the text.
The BSM part begins with an interlude that includes a review one of the most discussed puzzles of the SM and a discussion of "naturalness." We then present some of the basics of supersymmetry, including its history, the SUSY algebra, and the MSSM. SUSY is probably the leading contender for an explanation of seemingly "unnatural" parameters. In the next chapter, we present a supersymmetric model in which a new generation of \vector-like" quarks (as opposed to chiral) mixes with the third generation. Such a mixing raises the value of the top Yukawa yt necessary to give a top quark of the observed mass, mt = 173 GeV. Since the one-loop quantum corrections to the Higgs mass scale as yt to the fourth power , even a minor increase in yt can have a large effect. With current experimental bounds, yt may increase by as much as 6%, which implies the top's contribution to the Higgs mass increases by up to 26%. The model preserves gauge unification and gives a Higgs mass mh ~ 125.5 GeV without requiring soft supersymmetry-breaking masses above 1 TeV while satisfying all experimental constraints and predicting new quarks around the TeV scale, discoverable at the LHC. We conclude with a summary of the model and remarks on future prospects
Trans-eQTLs Reveal That Independent Genetic Variants Associated with a Complex Phenotype Converge on Intermediate Genes, with a Major Role for the HLA
No full textThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
The African timber tree Entandrophragma congoense (Pierre ex De Wild.) A.Chev. is morphologically and genetically distinct from Entandrophragma angolense (Welw.) C.DC
No full textInterpreting morphological variability in terms of species delimitation can be challenging. However, correcting species delineation can have strong implications for the sustainable management of exploited species. Up to now, species delimitation between two putative timber species from African forests, Entandrophragma congoense and E. angolense, remained unclear. To investigate their differences, we applied an integrated approach which combines morphological traits and genetic markers. We defined 13 morphological characters from 81 herbarium specimens and developed 15 new polymorphic microsatellite markers to genotype 305 samples (herbarium samples and specimens collected in the field across the species distribution ranges). Principal component analysis (PCA) of morphological data and the Bayesian clustering analyses of genetic data were used to assess differentiation between putative species. These analyses support two well-differentiated groups (FST = 0.30) occurring locally in sympatry. Moreover, these two groups present distinct morphological characters at the level of the trunk, leaflets, and seeds. Our genetic markers identified few individuals (4%) that seem to be hybrids, though there is no evidence of genetic introgression from geographic patterns of genetic variation. Hence, our results provide clear support to recognize E. congoense as a species distinct from E. angolense, with a much lower genetic diversity than the latter, and that should be managed accordingly. This work highlights the power of microsatellite markers in resolving species boundaries.SCOPUS: ar.jinfo:eu-repo/semantics/publishe
Finding A Voice: Exploring the Biographical Narratives of Adults with Selective Mutism
No full textThis research explores the lived experiences of adults with selective mutism using interpretative phenomenological analysis. Existing literature has typically positioned selective mutism as a disorder of childhood and as a result little is known about the difficulties faced by individuals who continue to experience the effects of selective mutism throughout adolescence and adulthood. This research seeks to gain an understanding of the phenomenology of selective mutism as a lived experience and to allow participant's voices to be heard.
In-depth narrative interviews were conducted with six individuals who had continued to experience selective mutism throughout their adult life. Data from my own experience of suffering from SM were also included. Interpretative phenomenological analysis was used to identify five essential themes. These findings provide an insight into the embodied experience of selective mutism, the process of sense making in which individuals engage to negotiate their identities and the effects of social isolation. Furthermore this research explores the experiences of therapy and help seeking which were important topics within participant narratives.
This research encourages a thoughtful reflection on the lives of those whose realities have been profoundly affected by selective mutism. This research and the exploratory nature of phenomenological inquiry will hopefully encourage further investigations into selective mutism as it exists beyond childhood
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