A biologist's guide to Bayesian phylogenetic analysis.

Bayesian methods have become very popular in molecular phylogenetics due to the availability of user-friendly software implementing sophisticated models of evolution. However, Bayesian phylogenetic models are complex, and analyses are often carried out using default settings, which may not be appropriate. Here, we summarize the major features of Bayesian phylogenetic inference and discuss Bayesian computation using Markov chain Monte Carlo (MCMC), the diagnosis of an MCMC run, and ways of summarising the MCMC sample. We discuss the specification of the prior, the choice of the substitution model, and partitioning of the data. Finally, we provide a list of common Bayesian phylogenetic software and provide recommendations as to their use

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case.

Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the Cretaceous-Paleogene (K-Pg) boundary and the timing of diversification of the main crown groups remain controversial. Here, we analysed a data set of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (autocorrelated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the autocorrelated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene

Evaluating Reflective Writing Fostering and Evaluating Reflective Capacity in Medical Education: Developing the REFLECT Rubric for Assessing Reflective Writing

Abstract Purpose Reflective writing (RW) curriculum initiatives to promote reflective capacity are proliferating within medical education. The authors developed a new evaluative tool that can be effectively applied to assess students' reflective levels and assist with the process of providing individualized written feedback to guide reflective capacity promotion. Method Following a comprehensive search and analysis of the literature, the authors developed an analytic rubric through repeated iterative cycles of development, including empiric testing and determination of interrater reliability, reevaluation and refinement, and redesign. Rubric iterations were applied in successive development phases to Warren Alpert Medical School of Brown University students' 2009 and 2010 RW narratives with determination of intraclass correlations (ICCs). Results The final rubric, the Reflection Evaluation for Learners' Enhanced Competencies Tool (REFLECT), consisted of four reflective capacity levels ranging from habitual action to critical reflection, with focused criteria for each level. The rubric also evaluated RW for transformative reflection and learning and confirmatory learning. ICC ranged from 0.376 to 0.748 for datasets and rater combinations and was 0.632 for the final REFLECT iteration analysis. Conclusions The REFLECT is a rigorously developed, theory-informed analytic rubric, demonstrating adequate interrater reliability, face validity, feasibility, and acceptability. The REFLECT rubric is a reflective analysis innovation supporting development of a reflective clinician via formative assessment and enhanced crafting of faculty feedback to reflectiv

Genetic polymorphisms and coronary artery disease in the portuguese population: the GENEMACOR Study

PosterMultiple studies have showed an association between genetic polymorphisms and the risk of coronary artery disease (CAD). Initially, studies focused mainly in variants acting in pathophysiological axis of CAD or its risk factors. Genome-Wide Association Studies (GWAS) revealed other genes that, besides having an unknown mechanism, are statistically significant. The importance of these in the development of CAD in the Portuguese population is unknown. Objective: Analyze the genetic polymorphisms associated with the development of CAD in a Portuguese population. Methods: We performed a case-control study with 1321 consecutive coronary patients (mean age 53.4 ± 8.1 years, 78.8% male) and 1148 controls (adjusted for age and sex) selected from GENEMACOR Study, an ongoing study designed to analyze the genetic profile of a Portuguese population. We evaluated, in both groups, 29 genetic variants previously associated with CAD: ACE I/D, AGT235 M/T, ATIR A/C, MTHFR C/T and 1298 A/C, PON192 Q/R and 55 L/M,LPA T/C, APO E, Locus 9p21.3 (rs1333049), CDKN2B (rs4977574), GJA4 C/T, PCSK9 A/G, TAS2R50 A/G, KIF6 C/T, IGF2BP2 G/T, ADAMTS7 A/G, MC4R T/C, PPARG Pro12 Ala, ZNF259 C/G, SMAD3 C/T, MIA3 C/A, MTHFD1L A/G, SLC30A8 C/T, TCF7L2 C/T, HNF4 C/G, FTO A/C and ADIPOQ C/G. Allele and genotypic frequencies of individuals with and without CAD were compared and the strength of association was expressed by the OR as well as by CI 95%. Results: The variants rs4340 (ACE I/D), rs266729 (ADIPOQ C/G), rs458560 (PON55 L/M), rs429358 (APOE2), LPA T/C, rs1333049 (locus 9p21.3) and rs4977574 (CDKN2B A/G) were significantly associated with CAD (p<0.05) (Table). Conclusions: In our population, the genetic polymorphisms significantly related to CAD were: ACE, associated with hypertension; ADIPOQ, associated with obesity; PON55, associated with oxidation; APOE and LPA, associated with dyslipidemia and finally the locus 9p21.3 with a unclear mechanism so far.info:eu-repo/semantics/publishedVersio

Unexpected drop of dynamical heterogeneities in colloidal suspensions approaching the jamming transition

As the glass (in molecular fluids\cite{Donth}) or the jamming (in colloids and grains\cite{LiuNature1998}) transitions are approached, the dynamics slow down dramatically with no marked structural changes. Dynamical heterogeneity (DH) plays a crucial role: structural relaxation occurs through correlated rearrangements of particle ``blobs'' of size $\xi$\cite{WeeksScience2000,DauchotPRL2005,Glotzer,Ediger}. On approaching these transitions, $\xi$ grows in glass-formers\cite{Glotzer,Ediger}, colloids\cite{WeeksScience2000,BerthierScience2005}, and driven granular materials\cite{KeysNaturePhys2007} alike, strengthening the analogies between the glass and the jamming transitions. However, little is known yet on the behavior of DH very close to dynamical arrest. Here, we measure in colloids the maximum of a ``dynamical susceptibility'', $\chi^*$, whose growth is usually associated to that of $\xi$\cite{LacevicPRE}. $\chi^*$ initially increases with volume fraction $\phi$, as in\cite{KeysNaturePhys2007}, but strikingly drops dramatically very close to jamming. We show that this unexpected behavior results from the competition between the growth of $\xi$ and the reduced particle displacements associated with rearrangements in very dense suspensions, unveiling a richer-than-expected scenario.Comment: 1st version originally submitted to Nature Physics. See the Nature Physics website fro the final, published versio

Determinants of the income velocity of money in Portugal: 1891–1998

This paper performs a long-run time series analysis of the behaviour of the income velocity of money in Portugal between 1891 and 1998 by assessing the importance of both macroeconomic and institutional factors and looking for particularities in the Portuguese case. We estimate two cointegration vectors for the income velocity of money, macroeconomic variables and institutional variables. It is apparent that one of these vectors reflects the relationship between income velocity and macroeconomic variables, while the other reflects the relationship between income velocity and institutional variables. Moreover, a regression analysis reveals that the usual U-shaped pattern is displayed with a relatively late inflection point located around 1970, which is consistent with the Spanish case. It is further noted that this is a feature of countries with a late economic and institutional development process.info:eu-repo/semantics/publishedVersio

How consistent are the transcriptome changes associated with cold acclimation in two species of the Drosophila virilis group?

This work was financially support by a Marie Curie Initial Training Network grant, “Understanding the evolutionary origin of biological diversity” (ITN-2008–213780 SPECIATION), grants from the Academy of Finland to A.H. (project 132619) and M.K. (projects 268214 and 272927), a grant from NERC, UK to M.G.R. (grant NE/J020818/1), and NERC, UK PhD studentship to D.J.P. (NE/I528634/1).For many organisms the ability to cold acclimate with the onset of seasonal cold has major implications for their fitness. In insects, where this ability is widespread, the physiological changes associated with increased cold tolerance have been well studied. Despite this, little work has been done to trace changes in gene expression during cold acclimation that lead to an increase in cold tolerance. We used an RNA-Seq approach to investigate this in two species of the Drosophila virilis group. We found that the majority of genes that are differentially expressed during cold acclimation differ between the two species. Despite this, the biological processes associated with the differentially expressed genes were broadly similar in the two species. These included: metabolism, cell membrane composition, and circadian rhythms, which are largely consistent with previous work on cold acclimation/cold tolerance. In addition, we also found evidence of the involvement of the rhodopsin pathway in cold acclimation, a pathway that has been recently linked to thermotaxis. Interestingly, we found no evidence of differential expression of stress genes implying that long-term cold acclimation and short-term stress response may have a different physiological basis.PostprintPeer reviewe