Molecular phylogenetic relationships and phenotypic diversity in miniaturized toadlets, genus Brachycephalus (Amphibia: Anura: Brachycephalidae)

Toadlets of the genus Brachycephalus are endemic to the Atlantic rainforests of southeastern and southern Brazil. The 14 species currently described have snout-vent lengths less than 18. mm and are thought to have evolved through miniaturization: an evolutionary process leading to an extremely small adult body size. Here, we present the first comprehensive phylogenetic analysis for Brachycephalus, using a multilocus approach based on two nuclear (Rag-1 and Tyr) and three mitochondrial (Cyt b, 12S, and 16S rRNA) gene regions. Phylogenetic relationships were inferred using a partitioned Bayesian analysis of concatenated sequences and the hierarchical Bayesian method (BEST) that estimates species trees based on the multispecies coalescent model. Individual gene trees showed conflict and also varied in resolution. With the exception of the mitochondrial gene tree, no gene tree was completely resolved. The concatenated gene tree was completely resolved and is identical in topology and degree of statistical support to the individual mtDNA gene tree. On the other hand, the BEST species tree showed reduced significant node support relative to the concatenate tree and recovered a basal trichotomy, although some bipartitions were significantly supported at the tips of the species tree. Comparison of the log likelihoods for the concatenated and BEST trees suggests that the method implemented in BEST explains the multilocus data for Brachycephalus better than the Bayesian analysis of concatenated data. Landmark-based geometric morphometrics revealed marked variation in cranial shape between the species of Brachycephalus. In addition, a statistically significant association was demonstrated between variation in cranial shape and genetic distances estimated from the mtDNA and nuclear loci. Notably, B. ephippium and B. garbeana that are predicted to be sister-species in the individual and concatenated gene trees and the BEST species tree share an evolutionary novelty, the hyperossified dorsal plate.Facultad de Ciencias Naturales y Muse

Molecular phylogenetic relationships and phenotypic diversity in miniaturized toadlets, genus Brachycephalus (Amphibia: Anura: Brachycephalidae)

Toadlets of the genus Brachycephalus are endemic to the Atlantic rainforests of southeastern and southern Brazil. The 14 species currently described have snout-vent lengths less than 18. mm and are thought to have evolved through miniaturization: an evolutionary process leading to an extremely small adult body size. Here, we present the first comprehensive phylogenetic analysis for Brachycephalus, using a multilocus approach based on two nuclear (Rag-1 and Tyr) and three mitochondrial (Cyt b, 12S, and 16S rRNA) gene regions. Phylogenetic relationships were inferred using a partitioned Bayesian analysis of concatenated sequences and the hierarchical Bayesian method (BEST) that estimates species trees based on the multispecies coalescent model. Individual gene trees showed conflict and also varied in resolution. With the exception of the mitochondrial gene tree, no gene tree was completely resolved. The concatenated gene tree was completely resolved and is identical in topology and degree of statistical support to the individual mtDNA gene tree. On the other hand, the BEST species tree showed reduced significant node support relative to the concatenate tree and recovered a basal trichotomy, although some bipartitions were significantly supported at the tips of the species tree. Comparison of the log likelihoods for the concatenated and BEST trees suggests that the method implemented in BEST explains the multilocus data for Brachycephalus better than the Bayesian analysis of concatenated data. Landmark-based geometric morphometrics revealed marked variation in cranial shape between the species of Brachycephalus. In addition, a statistically significant association was demonstrated between variation in cranial shape and genetic distances estimated from the mtDNA and nuclear loci. Notably, B. ephippium and B. garbeana that are predicted to be sister-species in the individual and concatenated gene trees and the BEST species tree share an evolutionary novelty, the hyperossified dorsal plate.Facultad de Ciencias Naturales y Muse

Skull diversity and evolution in miniaturized amphibians, genus Brachycephalus (Anura: Brachycephalidae)

Miniaturized amphibians of the genus Brachycephalus are phenotypically diverse. The species of Brachycephalus have bufoniform or leptodactyliform baupläne and any of three skeletal states: nonhyperossified, hyperossified without dorsal shield, and hyperossified with dorsal shield. We integrate high-resolution microcomputed tomography, geometric morphometrics, and an estimate of molecular phylogenetic relationships to investigate skull diversity in shape and size-shape space in selected species of Brachycephalus. Skull diversity amongst species of Brachycephalus can be partitioned into shape and size-shape space according to the four conditions of skeletal states-baupläne, namely, nonhyperossified leptodactyliform, nonhyperossified bufoniform, hyperossified bufoniform without dorsal shield, and hyperossified bufoniform with dorsal shield. Skull diversity in shape and size-shape space in nonhyperossified leptodactyliform species of Brachycephalus is markedly larger, when compared to skull diversity in species of the three other conditions of skeletal states-baupläne. Variation in skull shape scales with size across Brachycephalus and, therefore, can be explained by allometry. Skull diversity, baupläne, and skeletal states covary to a large extent with monophyletic lineages of Brachycephalus, as revealed by a mitochondrial DNA species tree. Nonhyperossified bufoniform species and hyperossified bufoniform species with or without dorsal shield are monophyletic lineages, as inferred from a mitochondrial DNA species tree. Nonhyperossified leptodactyliform species of Brachycephalus do not share, however, a most recent common ancestor. The nonhyperossified leptodactyliform species of Brachycephalus, due to their marked skull diversity and lack of monophyly, emerge as evolutionarily complex. Therefore, further sampling of the nonhyperossified leptodactyliform condition of skeletal states-baupläne will be necessary to further understand the evolutionary history of Brachycephalus.Fil: dos Reis, Sérgio F.. Universidade Estadual de Campinas. Instituto de Biología; BrasilFil: Clemente Carvalho, Rute B.G.. Queens University; CanadáFil: dos Santos, Caio M. S. F. F.. Universidade Federal do Rio de Janeiro; BrasilFil: Lopes, Ricardo T.. Universidade Federal do Rio de Janeiro; BrasilFil: Von Zuben, Fernando J.. Universidade Estadual de Campinas; BrasilFil: Laborda, Prianda R.. Universidade Estadual de Campinas. Instituto de Biología; BrasilFil: Perez, Sergio Ivan. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Departamento Científico de Antropología; Argentin

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

Performance and Operation of the CMS Electromagnetic Calorimeter

The operation and general performance of the CMS electromagnetic calorimeter using cosmic-ray muons are described. These muons were recorded after the closure of the CMS detector in late 2008. The calorimeter is made of lead tungstate crystals and the overall status of the 75848 channels corresponding to the barrel and endcap detectors is reported. The stability of crucial operational parameters, such as high voltage, temperature and electronic noise, is summarised and the performance of the light monitoring system is presented

Biodiversidade.

Neste capítulo, foi adotada uma definição ampla da biodiversidade, incorporando não apenas a complexidade do conceito, mas uma percepção de seu mecanismo, na geração de serviços ecossistêmicos. Essa visão holística da biodiversidade tem implicações importantes para políticas públicas, englobando a conservação de regiões biologicamente relevantes e seus processos ecológicos associados, além da pura proteção das espécies. O Brasil, reconhecido pela sua megabiodiversidade, possui a maior cobertura de florestas tropicais e a flora mais rica do mundo, além de abrigar uma fauna igualmente importante. Abriga diversos biomas terrestres e aquáticos onde se expressa frequentemente, de forma endêmica, o mais vasto e diversificado conjunto de espécies do planeta. Apesar dos avanços nas pesquisas para conhecimento da biodiversidade brasileira, ainda há muitas lacunas sobre a estrutura e composição dos ecossistemas e a maneira adequada de manejá-los, visando sua preservação. Um País megadiverso como o Brasil, com taxas tão altas de biodiversidade e endemismo, também tem grande responsabilidade de preservar sua rica biota e seus ecossistemas. De fato, o patrimônio natural do País inclui dois hotspots de biodiversidade (Mata Atlântica e Cerrado), seis Reservas da Biosfera, reconhecidas pela Organização das Nações Unidas para a Educação, a Ciência e a Cultura (Unesco), 12 ecorregiões prioritárias, definidas pelo Global 200 (WWF, 2001), 11 sítios Ramsar2, para a proteção de zonas úmidas, e quase 1.500 unidades de conservação. Este capítulo traz um panorama das forças motrizes, pressões, estados, impactos e respostas sobre a biodiversidade brasileira. SUMÁRIO: CAPÍTULO 4 – BIODIVERSIDADE; INTRODUÇÃO; ESPÉCIES E ECOSSISTEMAS: Alterações de comunidades e populações; Tráfico de animais silvestres; Espécies exóticas invasoras; Biodiversidade em números; Plantas, algas e fungos; Fauna aquática e terrestre; Avaliação do estado de conservação da biodiversidade brasileira; Espécies ameaçadas; Espécies da flora ameaçadas; Espécies da fauna ameaçadas; Plano de ação para a conservação e regulação do uso de espécies; Flora nativa; Fauna nativa; Espécies exóticas e invasoras; Perda de habitat, fragmentação e deterioração dos ecossistemas; Áreas e ações prioritárias para conservação, utilização sustentável e repartição dos benefícios da biodiversidade brasileira; RECURSOS GENÉTICOS: Biopirataria; Legislação nacional de proteção do patrimônio genético nacional e do conhecimento tradicional associado; Efeitos da política pública de proteção do patrimônio genético nacional, e do conhecimento tradicional associado, na conservação dos recursos genéticos; Proteção, gestão e uso sustentável dos recursos genéticos; Ratificação do Protocolo de Nagoia pelo Brasil; Conservação dos recursos genéticos vegetais e microbianos; GOVERNANÇA: Estratégia e Plano de Ação Nacionais para a Biodiversidade (Epanb); Avaliação das metas nacionais da biodiversidade; BIODIVERSIDADE E SAÚDE: Usos da biodiversidade: dos saberes tradicionais à biotecnologia; Biodiversidade e segurança alimentar; Emergência de zoonoses e biodiversidade; CONSIDERAÇÕES FINAIS; REFERÊNCIAS.ODS 2, ODS 3, ODS 9, ODS 12, ODS 14, ODS 15, ODS 17

Calibration of the CMS Drift Tube Chambers and Measurement of the Drift Velocity with Cosmic Rays

Peer reviewe

Measurements of long-range azimuthal anisotropies and associated Fourier coefficients for pp collisions at √s=5.02 and 13 TeV and p+Pb collisions at √sNN=5.02 TeV with the ATLAS detector

ATLAS measurements of two-particle correlations are presented for √s=5.02 and 13 TeV ppcollisions and for √sNN=5.02 TeV p+Pb collisions at the LHC. The correlation functions are measured as a function of relative azimuthal angle Δϕ, and pseudorapidity separation Δη, using charged particles detected within the pseudorapidity interval |η|2, is studied using a template fitting procedure to remove a “back-to-back” contribution to the correlation function that primarily arises from hard-scattering processes. In addition to the elliptic, cos (2Δϕ), modulation observed in a previous measurement, the pp correlation functions exhibit significant cos (3Δϕ) and cos (4Δϕ) modulation. The Fourier coefficients vn, n associated with the cos (nΔϕ) modulation of the correlation functions for n=2–4 are measured as a function of charged-particle multiplicity and charged-particle transverse momentum. The Fourier coefficients are observed to be compatible with cos (nϕ) modulation of per-event single-particle azimuthal angle distributions. The single-particle Fourier coefficients vn are measured as a function of charged-particle multiplicity, and charged-particle transverse momentum for n=2–4. The integrated luminosities used in this analysis are, 64nb−1 for the √s=13 TeV pp data, 170 nb−1 for the √ s = 5.02 TeV pp data, and 28 nb−1 for the √sNN = 5.02 TeV p+Pb data

Alignment of the CMS silicon tracker during commissioning with cosmic rays

The CMS silicon tracker, consisting of 1440 silicon pixel and 15 148 silicon strip detector modules, has been aligned using more than three million cosmic ray charged particles, with additional information from optical surveys. The positions of the modules were determined with respect to cosmic ray trajectories to an average precision of 3-4 microns RMS in the barrel and 3-14 microns RMS in the endcap in the most sensitive coordinate. The results have been validated by several studies, including laser beam cross-checks, track fit self-consistency, track residuals in overlapping module regions, and track parameter resolution, and are compared with predictions obtained from simulation. Correlated systematic effects have been investigated. The track parameter resolutions obtained with this alignment are close to the design performance

Dark matter interpretations of ATLAS searches for the electroweak production of supersymmetric particles in s√=8 s=8 TeV proton-proton collisions

A selection of searches by the ATLAS experiment at the LHC for the electroweak production of SUSY particles are used to study their impact on the constraints on dark matter candidates. The searches use 20 fb−1 of proton-proton collision data at s √ =8 s=8 TeV. A likelihood-driven scan of a five-dimensional effective model focusing on the gaugino-higgsino and Higgs sector of the phenomenological minimal supersymmetric Standard Model is performed. This scan uses data from direct dark matter detection experiments, the relic dark matter density and precision flavour physics results. Further constraints from the ATLAS Higgs mass measurement and SUSY searches at LEP are also applied. A subset of models selected from this scan are used to assess the impact of the selected ATLAS searches in this five-dimensional parameter space. These ATLAS searches substantially impact those models for which the mass m(χ ~ 0 1 ) m(χ~10) of the lightest neutralino is less than 65 GeV, excluding 86% of such models. The searches have limited impact on models with larger m(χ ~ 0 1 ) m(χ~10) due to either heavy electroweakinos or compressed mass spectra where the mass splittings between the produced particles and the lightest supersymmetric particle is small