Great Genetic Differentiation among Populations of Meconopsis integrifolia and Its Implication for Plant Speciation in the Qinghai-Tibetan Plateau

The complex tectonic events and climatic oscillations in the Qinghai-Tibetan Plateau (QTP), the largest and highest plateau in the world, are thought to have had great effects on the evolutionary history of the native plants. Of great interest is to investigate plant population genetic divergence in the QTP and its correlation with the geologic and climatic changes. We conducted a range-wide phylogeographical analysis of M. integrifolia based on the chloroplast DNA (cpDNA) trnL-trnF and trnfM-trnS regions, and defined 26 haplotypes that were phylogenetically divided into six clades dated to the late Tertiary. The six clades correspond, respectively, to highly differentiated population groups that do not overlap in geographic distribution, implying that the mountain ranges acting as corridors or barriers greatly affected the evolutionary history of the QTP plants. The older clade of M. integrifolia only occurs in the southwest of the species' range, whereas the distributions of younger clades extend northeastward in the eastern QTP, suggesting that climatic divergence resulting from the uplift of the QTP triggered the initial divergence of M. integrifolia native to the plateau. Also, the nrDNA ITS region was used to clarify the unexpected phylogenetic relationships of cpDNA haplotypes between M. integrifolia and M. betonicifolia. The topological incongruence between the two phylogenies suggests an ancestral hybridization between the two species. Our study indicates that geographic isolation and hybridization are two important mechanisms responsible for the population differentiation and speciation of Meconopsis, a species-rich genus with complex polyploids

Phylogeography of the Patagonian otter Lontra provocax: adaptive divergence to marine habitat or signature of southern glacial refugia?

<p>Abstract</p> <p>Background</p> <p>A number of studies have described the extension of ice cover in western Patagonia during the Last Glacial Maximum, providing evidence of a complete cover of terrestrial habitat from 41°S to 56°S and two main refugia, one in south-eastern Tierra del Fuego and the other north of the Chiloé Island. However, recent evidence of high genetic diversity in Patagonian river species suggests the existence of aquatic refugia in this region. Here, we further test this hypothesis based on phylogeographic inferences from a semi-aquatic species that is a top predator of river and marine fauna, the huillín or Southern river otter (<it>Lontra provocax</it>).</p> <p>Results</p> <p>We examined mtDNA sequences of the control region, ND5 and Cytochrome-b (2151 bp in total) in 75 samples of <it>L. provocax </it>from 21 locations in river and marine habitats. Phylogenetic analysis illustrates two main divergent clades for <it>L. provocax </it>in continental freshwater habitat. A highly diverse clade was represented by haplotypes from the marine habitat of the Southern Fjords and Channels (SFC) region (43°38' to 53°08'S), whereas only one of these haplotypes was paraphyletic and associated with northern river haplotypes.</p> <p>Conclusions</p> <p>Our data support the hypothesis of the persistence of <it>L. provocax </it>in western Patagonia, south of the ice sheet limit, during last glacial maximum (41°S latitude). This limit also corresponds to a strong environmental change, which might have spurred <it>L. provocax </it>differentiation between the two environments.</p

One thousand plant transcriptomes and the phylogenomics of green plants

Abstract: Green plants (Viridiplantae) include around 450,000–500,000 species1, 2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life

Search for new physics in high-mass diphoton events from proton-proton collisions at √s = 13 TeV

Results are presented from a search for new physics in high-mass diphoton events from proton-proton collisions at √s = 13 TeV. The data set was collected in 2016–2018 with the CMS detector at the LHC and corresponds to an integrated luminosity of 138 fb−1. Events with a diphoton invariant mass greater than 500 GeV are considered. Two different techniques are used to predict the standard model backgrounds: parametric fits to the smoothly-falling background and a first-principles calculation of the standard model diphoton spectrum at next-to-next-to-leading order in perturbative quantum chromodynamics calculations. The first technique is sensitive to resonant excesses while the second technique can identify broad differences in the invariant mass shape. The data are used to constrain the production of heavy Higgs bosons, Randall-Sundrum gravitons, the large extra dimensions model of Arkani-Hamed, Dimopoulos, and Dvali (ADD), and the continuum clockwork mechanism. No statistically significant excess is observed. The present results are the strongest limits to date on ADD extra dimensions and RS gravitons with a coupling parameter greater than 0.1

Measurement of the Higgs boson mass and width using the four-lepton final state in proton-proton collisions at √s =13 TeV

A measurement of the Higgs boson mass and width via its decay to two (Formula presented) bosons is presented. Proton-proton collision data collected by the CMS experiment, corresponding to an integrated luminosity of (Formula presented) at a center-of-mass energy of 13 TeV, is used. The invariant mass distribution of four leptons in the on-shell Higgs boson decay is used to measure its mass and constrain its width. This yields the most precise single measurement of the Higgs boson mass to date, (Formula presented), and an upper limit on the width (Formula presented) at 95% confidence level. A combination of the on- and off-shell Higgs boson production decaying to four leptons is used to determine the Higgs boson width, assuming that no new virtual particles affect the production, a premise that is tested by adding new heavy particles in the gluon fusion loop model. This result is combined with a previous CMS analysis of the off-shell Higgs boson production with decay to two leptons and two neutrinos, giving a measured Higgs boson width of (Formula presented), in agreement with the standard model prediction of 4.1 MeV. The strength of the off-shell Higgs boson production is also reported. The scenario of no off-shell Higgs boson production is excluded at a confidence level corresponding to 3.8 standard deviations

Search for CP violation in D0 → KS0KS0 decays in proton-proton collisions at √s=13TeV

A search is reported for charge-parity CP violation in D0 → K0 SK0 S decays, using data collected in proton– proton collisions at √s = 13 TeV recorded by the CMS experiment in 2018. The analysis uses a dedicated data set that corresponds to an integrated luminosity of 41.6 fb−1 , which consists of about 10 billion events containing a pair of b hadrons, nearly all of which decay to charm hadrons. The flavor of the neutral D meson is determined by the pion charge in the reconstructed decays D∗+ → D0 π+ and D∗− → D0 π−. The CP asymmetry in D0 → K0 SK0 S is measured to be ACP(K0 SK0 S) = (6.2 ± 3.0 ± 0.2 ± 0.8)%, where the three uncertainties represent the statistical uncertainty, the systematic uncertainty, and the uncertainty in the measurement of theCP asymmetry in the D0 → K0 Sπ+π− decay. This is the first CP asymmetry measurement by CMS in the charm sector as well as the first to utilize a fully hadronic final state

Luminosity determination using Z boson production at the CMS experiment

The measurement of Z&nbsp;boson production is presented as a method to determine the integrated luminosity of CMS data sets. The analysis uses proton–proton collision data, recorded by the CMS experiment at the CERN LHC in 2017 at a center-of-mass energy of 13 TeV . Events with Z&nbsp;bosons decaying into a pair of muons are selected. The total number of Z&nbsp;bosons produced in a fiducial volume is determined, together with the identification efficiencies and correlations from the same data set, in small intervals of 20 pb-1 of integrated luminosity, thus facilitating the efficiency and rate measurement as a function of time and instantaneous luminosity. Using the ratio of the efficiency-corrected numbers of Z&nbsp;bosons, the precisely measured integrated luminosity of one data set is used to determine the luminosity of another. For the first time, a full quantitative uncertainty analysis of the use of Z bosons for the integrated luminosity measurement is performed. The uncertainty in the extrapolation between two data sets, recorded in 2017 at low and high instantaneous luminosity, is less than 0.5%. We show that the Z&nbsp;boson rate measurement constitutes a precise method, complementary to traditional methods, with the potential to improve the measurement of the integrated luminosity

Elliptic anisotropy measurement of the f0(980) hadron in proton-lead collisions and evidence for its quark-antiquark composition

Despite the f0(980) hadron having been discovered half a century ago, the question about its quark content has not been settled: it might be an ordinary quark-antiquark (qq) meson, a tetraquark (qqqq) exotic state, a kaon-antikaon (KK) molecule, or a quark-antiquark-gluon (qqg) hybrid. This paper reports strong evidence that the f0(980) state is an ordinary qq meson, inferred from the scaling of elliptic anisotropies (v2) with the number of constituent quarks (nq), as empirically established using conventional hadrons in relativistic heavy ion collisions. The f0(980) state is reconstructed via its dominant decay channel f0(980) → π+π−, in proton-lead collisions recorded by the CMS experiment at the LHC, and its v2 is measured as a function of transverse momentum (pT). It is found that the nq = 2 (qq state) hypothesis is favored over nq = 4 (qqqq or KK states) by 7.7, 6.3, or 3.1 standard deviations in the pT &lt; 10, 8, or 6 GeV/c ranges, respectively, and over nq = 3 (qqg hybrid state) by 3.5 standard deviations in the pT &lt; 8 GeV/c range. This result represents the first determination of the quark content of the f0(980) state, made possible by using a novel approach, and paves the way for similar studies of other exotic hadron candidates

Search for heavy neutral resonances decaying to tau lepton pairs in proton-proton collisions at s=13 TeV

A search for heavy neutral gauge bosons ((Formula presented)) decaying into a pair of tau leptons is performed in proton-proton collisions at (Formula presented) at the CERN LHC. The data were collected with the CMS detector and correspond to an integrated luminosity of (Formula presented). The observations are found to be in agreement with the expectation from standard model processes. Limits at 95% confidence level are set on the product of the (Formula presented) production cross section and its branching fraction to tau lepton pairs for a range of (Formula presented) boson masses. For a narrow resonance in the sequential standard model scenario, a (Formula presented) boson with a mass below 3.5 TeV is excluded. This is the most stringent limit to date from this type of search