An Excess of Gene Expression Divergence on the X Chromosome in Drosophila Embryos: Implications for the Faster-X Hypothesis

The X chromosome is present as a single copy in the heterogametic sex, and this hemizygosity is expected to drive unusual patterns of evolution on the X relative to the autosomes. For example, the hemizgosity of the X may lead to a lower chromosomal effective population size compared to the autosomes, suggesting that the X might be more strongly affected by genetic drift. However, the X may also experience stronger positive selection than the autosomes, because recessive beneficial mutations will be more visible to selection on the X where they will spend less time being masked by the dominant, less beneficial allele—a proposal known as the faster-X hypothesis. Thus, empirical studies demonstrating increased genetic divergence on the X chromosome could be indicative of either adaptive or non-adaptive evolution. We measured gene expression in Drosophila species and in D. melanogaster inbred strains for both embryos and adults. In the embryos we found that expression divergence is on average more than 20% higher for genes on the X chromosome relative to the autosomes; but in contrast, in the inbred strains, gene expression variation is significantly lower on the X chromosome. Furthermore, expression divergence of genes on Muller's D element is significantly greater along the branch leading to the obscura sub-group, in which this element segregates as a neo-X chromosome. In the adults, divergence is greatest on the X chromosome for males, but not for females, yet in both sexes inbred strains harbour the lowest level of gene expression variation on the X chromosome. We consider different explanations for our results and conclude that they are most consistent within the framework of the faster-X hypothesis

Untangling the imprints of climate, geography and land use/cover on bird diversity in the South American Gran Chaco

To evaluate the structure of bird communities throughout the South American Gran Chaco determining the effects of climate, geography and land use/land cover in bird beta diversity, as well as to understand the beta diversity processes underlying land use changes across broad spatial ranges. Location: South American Gran Chaco. Taxon: Birds. Methods: We constructed a site-by-species matrix with occurrence probabilities of 293 bird species across 2,669 spatial units tiling completely the study area. Based on this matrix, we calculated pairwise dissimilarities scores and performed a hierarchical cluster analysis for describing the spatial configuration of dissimilarities. The clustering result was spatially represented through an original venation map with boundaries between sites widened in the function of their distance in the dendrogram. We used the Generalized Dissimilarity Modelling approach to model beta diversity, using geographic distance, climatic and land use/land cover information as predictors. We mapped beta diversity patterns using colour theory and the HSV colour model. We identified two main clusters of sites across the Gran Chaco, which represent environmentally different sites and harbour very distinct assemblages of species. These main groups are separated by two natural delimiters: The Bermejo-Pilcomayo interfluvium and the Lower Paraná floodplain. Overall, we observed that the percentage of cropland and climatic variables were important shapers of bird beta diversity. Main conclusions: We provide the first area-wide assessment of land use/land cover effects on bird beta diversity for the Gran Chaco. The distribution of croplands has a marked influence on bird beta diversity at regional scale highlighting the role of anthropic changes in reshaping bird beta diversity within the ecoregion. Taking into account the global increasing conversion of forests into croplands, a growing footprint of land use changes over geographical patterns of bird diversity in forest biomes can be anticipated.Fil: Nazaro, María Gabriela. Universidad Nacional de Tucumán. Instituto de Ecología Regional. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Ecología Regional; ArgentinaFil: Dos Santos, Daniel Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Biodiversidad Neotropical. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo. Instituto de Biodiversidad Neotropical. Instituto de Biodiversidad Neotropical; ArgentinaFil: Torres, Ricardo Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; ArgentinaFil: Baumann, Matthias. Humboldt-universitat Zu Berlin. Geography Department.; AlemaniaFil: Blendinger, Pedro Gerardo. Universidad Nacional de Tucumán. Instituto de Ecología Regional. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Ecología Regional; Argentin

Evidence for a spin-aligned neutron-proton paired phase from the level structure of 92^{92}Pd

The general phenomenon of shell structure in atomic nuclei has been understood since the pioneering work of Goeppert-Mayer, Haxel, Jensen and Suess.They realized that the experimental evidence for nuclear magic numbers could be explained by introducing a strong spin-orbit interaction in the nuclear shell model potential. However, our detailed knowledge of nuclear forces and the mechanisms governing the structure of nuclei, in particular far from stability, is still incomplete. In nuclei with equal neutron and proton numbers ($N = Z$), the unique nature of the atomic nucleus as an object composed of two distinct types of fermions can be expressed as enhanced correlations arising between neutrons and protons occupying orbitals with the same quantum numbers. Such correlations have been predicted to favor a new type of nuclear superfluidity; isoscalar neutron-proton pairing, in addition to normal isovector pairing (see Fig. 1). Despite many experimental efforts these predictions have not been confirmed. Here, we report on the first observation of excited states in $N = Z = 46$ nucleus $^{92}$Pd. Gamma rays emitted following the $^{58}$Ni($^{36}$Ar,2$n$)$^{92}$Pd fusion-evaporation reaction were identified using a combination of state-of-the-art high-resolution {\gamma}-ray, charged-particle and neutron detector systems. Our results reveal evidence for a spin-aligned, isoscalar neutron-proton coupling scheme, different from the previous prediction. We suggest that this coupling scheme replaces normal superfluidity (characterized by seniority coupling) in the ground and low-lying excited states of the heaviest N = Z nuclei. The strong isoscalar neutron- proton correlations in these $N = Z$ nuclei are predicted to have a considerable impact on their level structures, and to influence the dynamics of the stellar rapid proton capture nucleosynthesis process.Comment: 13 pages, 3 figure

Towards an Evolutionary Model of Transcription Networks

DNA evolution models made invaluable contributions to comparative genomics, although it seemed formidable to include non-genomic features into these models. In order to build an evolutionary model of transcription networks (TNs), we had to forfeit the substitution model used in DNA evolution and to start from modeling the evolution of the regulatory relationships. We present a quantitative evolutionary model of TNs, subjecting the phylogenetic distance and the evolutionary changes of cis-regulatory sequence, gene expression and network structure to one probabilistic framework. Using the genome sequences and gene expression data from multiple species, this model can predict regulatory relationships between a transcription factor (TF) and its target genes in all species, and thus identify TN re-wiring events. Applying this model to analyze the pre-implantation development of three mammalian species, we identified the conserved and re-wired components of the TNs downstream to a set of TFs including Oct4, Gata3/4/6, cMyc and nMyc. Evolutionary events on the DNA sequence that led to turnover of TF binding sites were identified, including a birth of an Oct4 binding site by a 2nt deletion. In contrast to recent reports of large interspecies differences of TF binding sites and gene expression patterns, the interspecies difference in TF-target relationship is much smaller. The data showed increasing conservation levels from genomic sequences to TF-DNA interaction, gene expression, TN, and finally to morphology, suggesting that evolutionary changes are larger at molecular levels and smaller at functional levels. The data also showed that evolutionarily older TFs are more likely to have conserved target genes, whereas younger TFs tend to have larger re-wiring rates

Aristotelian Essentialism: Essence in the Age of Evolution

The advent of contemporary evolutionary theory ushered in the eventual decline of Aristotelian Essentialism (Æ) – for it is widely assumed that essence does not, and cannot have any proper place in the age of evolution. This paper argues that this assumption is a mistake: if Æ can be suitably evolved, it need not face extinction. In it, I claim that if that theory’s fundamental ontology consists of dispositional properties, and if its characteristic metaphysical machinery is interpreted within the framework of contemporary evolutionary developmental biology, an evolved essentialism is available. The reformulated theory of Æ offered in this paper not only fails to fall prey to the typical collection of criticisms, but is also independently both theoretically and empirically plausible. The paper contends that, properly understood, essence belongs in the age of evolution

Final results from the PERUSE study of first-line pertuzumab plus trastuzumab plus a taxane for HER2-positive locally recurrent or metastatic breast cancer, with a multivariable approach to guide prognostication

Background: The phase III CLinical Evaluation Of Pertuzumab And TRAstuzumab (CLEOPATRA) trial established the combination of pertuzumab, trastuzumab and docetaxel as standard first-line therapy for human epidermal growth factor receptor 2 (HER2)-positive locally recurrent/metastatic breast cancer (LR/mBC). The multicentre single-arm PERtUzumab global SafEty (PERUSE) study assessed the safety and efficacy of pertuzumab and trastuzumab combined with investigator-selected taxane in this setting. Patients and methods: Eligible patients with inoperable HER2-positive LR/mBC and no prior systemic therapy for LR/mBC (except endocrine therapy) received docetaxel, paclitaxel or nab-paclitaxel with trastuzumab and pertuzumab until disease progression or unacceptable toxicity. The primary endpoint was safety. Secondary endpoints included progression-free survival (PFS) and overall survival (OS). Prespecified subgroup analyses included subgroups according to taxane, hormone receptor (HR) status and prior trastuzumab. Exploratory univariable analyses identified potential prognostic factors; those that remained significant in multivariable analysis were used to analyse PFS and OS in subgroups with all, some or none of these factors. Results: Of 1436 treated patients, 588 (41%) initially received paclitaxel and 918 (64%) had HR-positive disease. The most common grade 653 adverse events were neutropenia (10%, mainly with docetaxel) and diarrhoea (8%). At the final analysis (median follow-up: 5.7 years), median PFS was 20.7 [95% confidence interval (CI) 18.9-23.1] months overall and was similar irrespective of HR status or taxane. Median OS was 65.3 (95% CI 60.9-70.9) months overall. OS was similar regardless of taxane backbone but was more favourable in patients with HR-positive than HR-negative LR/mBC. In exploratory analyses, trastuzumab-pretreated patients with visceral disease had the shortest median PFS (13.1 months) and OS (46.3 months). Conclusions: Mature results from PERUSE show a safety and efficacy profile consistent with results from CLEOPATRA and median OS exceeding 5 years. Results suggest that paclitaxel is a valid alternative to docetaxel as backbone chemotherapy. Exploratory analyses suggest risk factors that could guide future trial design