Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes

A grant from the One-University Open Access Fund at the University of Kansas was used to defray the author's publication fees in this Open Access journal. The Open Access Fund, administered by librarians from the KU, KU Law, and KUMC libraries, is made possible by contributions from the offices of KU Provost, KU Vice Chancellor for Research & Graduate Studies, and KUMC Vice Chancellor for Research. For more information about the Open Access Fund, please see http://library.kumc.edu/authors-fund.xml.Systems of genetic sex determination and the homology of sex chromosomes in different taxa vary greatly across vertebrates. Much progress remains to be made in understanding systems of genetic sex determination in non-model organisms, especially those with homomorphic sex chromosomes and/or large genomes. We used reduced representation genome sequencing to investigate genetic sex determination systems in the salamander family Cryptobranchidae (genera Cryptobranchus and Andrias), which typifies both of these inherent difficulties. We tested hypotheses of male- or female-heterogamety by sequencing hundreds of thousands of anonymous genomic regions in a panel of known-sex cryptobranchids and characterized patterns of presence/absence, inferred zygosity, and depth of coverage to identify sex-linked regions of these 56 gigabase genomes. Our results strongly support the hypothesis that all cryptobranchid species possess homologous systems of female heterogamety, despite maintenance of homomorphic sex chromosomes over nearly 60 million years. Additionally, we report a robust, non-invasive genetic assay for sex diagnosis in Cryptobranchus and Andrias which may have great utility for conservation efforts with these endangered salamanders. Co-amplification of these W-linked markers in both cryptobranchid genera provides evidence for long-term sex chromosome stasis in one of the most divergent salamander lineages. These findings inform hypotheses about the ancestral mode of sex determination in salamanders, but suggest that comparative data from other salamander families are needed. Our results further demonstrate that massive genomes are not necessarily a barrier to effective genome-wide sequencing and that the resulting data can be highly informative about sex determination systems in taxa with homomorphic sex chromosomes.Cryptobranchid Interest GroupFresno Chaffee ZooSaint Louis Zoo WildCare InstituteUniversity of Kentucky G.F. Ribble FundNational Science Foundation (DEB-0949532 to D.W.W. and DGE-3048109801 to P.M.H.

Measurement of the charged-pion polarisability

The COMPASS collaboration at CERN has investigated pion Compton scattering, $\pi^-\gamma\rightarrow \pi^-\gamma$, at centre-of-mass energy below 3.5 pion masses. The process is embedded in the reaction $\pi^-\mathrm{Ni}\rightarrow\pi^-\gamma\;\mathrm{Ni}$, which is initiated by 190\,GeV pions impinging on a nickel target. The exchange of quasi-real photons is selected by isolating the sharp Coulomb peak observed at smallest momentum transfers, $Q^2<0.0015$\,(GeV/$c$)$^2$. From a sample of 63\,000 events the pion electric polarisability is determined to be $\alpha_\pi\ =\ (\,2.0\ \pm\ 0.6_{\mbox{\scriptsize stat}}\ \pm\ 0.7_{\mbox{\scriptsize syst}}\,) \times 10^{-4}\,\mbox{fm}^3$under the assumption$\alpha_\pi=-\beta_\pi$, which relates the electric and magnetic dipole polarisabilities. It is the most precise measurement of this fundamental low-energy parameter of strong interaction, that has been addressed since long by various methods with conflicting outcomes. While this result is in tension with previous dedicated measurements, it is found in agreement with the expectation from chiral perturbation theory. An additional measurement replacing pions by muons, for which the cross-section behavior is unambigiously known, was performed for an independent estimate of the systematic uncertainty.Comment: Published version: 9 pages, 3 figures, 1 tabl

Spin alignment and violation of the OZI rule in exclusive ω\omega and ϕ\phi production in pp collisions

Exclusive production of the isoscalar vector mesons $\omega$ and $\phi$ is measured with a 190 GeV$/c$ proton beam impinging on a liquid hydrogen target. Cross section ratios are determined in three intervals of the Feynman variable $x_{F}$ of the fast proton. A significant violation of the OZI rule is found, confirming earlier findings. Its kinematic dependence on $x_{F}$ and on the invariant mass $M_{p\mathrm{V}}$ of the system formed by fast proton $p_\mathrm{fast}$ and vector meson $V$ is discussed in terms of diffractive production of $p_\mathrm{fast}V$ resonances in competition with central production. The measurement of the spin density matrix element $\rho_{00}$ of the vector mesons in different selected reference frames provides another handle to distinguish the contributions of these two major reaction types. Again, dependences of the alignment on $x_{F}$ and on $M_{p\mathrm{V}}$ are found. Most of the observations can be traced back to the existence of several excited baryon states contributing to $\omega$ production which are absent in the case of the $\phi$ meson. Removing the low-mass $M_{p\mathrm{V}}$ resonant region, the OZI rule is found to be violated by a factor of eight, independently of $x_\mathrm{F}$.Comment: 23 pages, 13 figures and 5 table

Collins and Sivers asymmetries in muonproduction of pions and kaons off transversely polarised proton

Measurements of the Collins and Sivers asymmetries for charged pions and charged and neutral kaons produced in semi-inclusive deep-inelastic scattering of high energy muons off transversely polarised protons are presented. The results were obtained using all the available COMPASS proton data, which were taken in the years 2007 and 2010. The Collins asymmetries exhibit in the valence region a non-zero signal for pions and there are hints of non-zero signal also for kaons. The Sivers asymmetries are found to be positive for positive pions and kaons and compatible with zero otherwise.Comment: 15 pages, 13 figures and 1 tabl

Search for exclusive photoproduction of Zc±_c^{\pm}(3900) at COMPASS

A search for the exclusive production of the $Z_c^{\pm}(3900)$ hadron by virtual photons has been performed in the channel $Z_c^{\pm}(3900)\rightarrow J/\psi \pi^{\pm}$. The data cover the range from 7 GeV to 19 GeV in the centre-of-mass energy of the photon-nucleon system. The full set of the COMPASS data set collected with a muon beam between 2002 and 2011 has been used. An upper limit for the ratio $BR(Z_c^{\pm}(3900)\rightarrow J/\psi \pi^{\pm} )\times \sigma_{ \gamma~N \rightarrow Z_c^{\pm}(3900)~ N} /\sigma_{\gamma~N \rightarrow J/\psi~ N}$ of $3.7\times10^{-3}$ has been established at the confidence level of 90%.Comment: 8 pages, 3 figures, 1 tabl

Leading-order determination of the gluon polarisation from semi-inclusive deep inelastic scattering data

Using a novel analysis technique, the gluon polarisation in the nucleon is re-evaluated using the longitudinal double-spin asymmetry measured in the cross section of semi-inclusive single-hadron muoproduction with photon virtuality $Q^2>1~({\rm GeV}/c)^2$. The data were obtained by the COMPASS experiment at CERN using a 160 GeV/$c$ polarised muon beam impinging on a polarised $^6$LiD target. By analysing the full range in hadron transverse momentum $p_{\rm T}$, the different $p_{\rm T}$-dependences of the underlying processes are separated using a neural-network approach. In the absence of pQCD calculations at next-to-leading order in the selected kinematic domain, the gluon polarisation $\Delta g/g$ is evaluated at leading order in pQCD at a hard scale of $\mu^2= \langle Q^2 \rangle = 3 ({\rm GeV}/c)^2$. It is determined in three intervals of the nucleon momentum fraction carried by gluons, $x_{\rm g}$, covering the range $0.04 \!<\! x_{ \rm g}\! <\! 0.28$~ and does not exhibit a significant dependence on $x_{\rm g}$. The average over the three intervals, $\langle \Delta g/g \rangle = 0.113 \pm 0.038_{\rm (stat.)}\pm 0.036_{\rm (syst.)}$ at $\langle x_{\rm g} \rangle \approx 0.10$, suggests that the gluon polarisation is positive in the measured $x_{\rm g}$ range.Comment: 14 pages, 6 figure

Resonance Production and ππ\pi\pi S-wave in π−+p→π−π−π++precoil\pi^- + p \rightarrow \pi^- \pi^- \pi^+ + p_{recoil} at 190 GeV/c

The COMPASS collaboration has collected the currently largest data set on diffractively produced $\pi^-\pi^-\pi^+$ final states using a negative pion beam of 190 GeV/c momentum impinging on a stationary proton target. This data set allows for a systematic partial-wave analysis in 100 bins of three-pion mass, $0.5 < m_{3\pi} < 2.5$ GeV/c$^2$ , and in 11 bins of the reduced four-momentum transfer squared, $0.1 < t < 1.0$ (GeV/c)$^2$ . This two-dimensional analysis offers sensitivity to genuine one-step resonance production, i.e. the production of a state followed by its decay, as well as to more complex dynamical effects in nonresonant $3\pi$ production. In this paper, we present detailed studies on selected $3\pi$ partial waves with $J^{PC} = 0^{-+}$, $1^{++}$, $2^{-+}$, $2^{++}$, and $4^{++}$. In these waves, we observe the well-known ground-state mesons as well as a new narrow axial-vector meson $a_1(1420)$ decaying into $f_0(980) \pi$. In addition, we present the results of a novel method to extract the amplitude of the $\pi^-\pi^+$ subsystem with $I^{G}J^{PC} = 0^+ 0^{++}$ in various partial waves from the $\pi^-\pi^-\pi^+$ data. Evidence is found for correlation of the $f_0(980)$ and $f_0(1500)$ appearing as intermediate $\pi^- \pi^+$ isobars in the decay of the known $\pi(1800)$ and $\pi_2(1880)$.Comment: 96 page

Longitudinal double spin asymmetries in single hadron quasi-real photoproduction at high pTp_T

We measured the longitudinal double spin asymmetries $A_{LL}$ for single hadron muo-production off protons and deuterons at photon virtuality $Q^2$ < 1(GeV/$\it c$)$^2$ for transverse hadron momenta $p_T$ in the range 0.7 GeV/$\it c$ to 4 GeV/$\it c$ . They were determined using COMPASS data taken with a polarised muon beam of 160 GeV/$\it c$ or 200 GeV/$\it c$ impinging on polarised $\mathrm{{}^6LiD}$ or $\mathrm{NH_3}$ targets. The experimental asymmetries are compared to next-to-leading order pQCD calculations, and are sensitive to the gluon polarisation $\Delta G$ inside the nucleon in the range of the nucleon momentum fraction carried by gluons $0.05 < x_g < 0.2$

The Spin Structure Function g1pg_1^{\rm p} of the Proton and a Test of the Bjorken Sum Rule

New results for the double spin asymmetry $A_1^{\rm p}$ and the proton longitudinal spin structure function $g_1^{\rm p}$ are presented. They were obtained by the COMPASS collaboration using polarised 200 GeV muons scattered off a longitudinally polarised NH$_3$ target. The data were collected in 2011 and complement those recorded in 2007 at 160\,GeV, in particular at lower values of $x$. They improve the statistical precision of $g_1^{\rm p}(x)$ by about a factor of two in the region $x\lesssim 0.02$. A next-to-leading order QCD fit to the $g_1$ world data is performed. It leads to a new determination of the quark spin contribution to the nucleon spin, $\Delta \Sigma$ ranging from 0.26 to 0.36, and to a re-evaluation of the first moment of $g_1^{\rm p}$. The uncertainty of $\Delta \Sigma$ is mostly due to the large uncertainty in the present determinations of the gluon helicity distribution. A new evaluation of the Bjorken sum rule based on the COMPASS results for the non-singlet structure function $g_1^{\rm NS}(x,Q^2)$ yields as ratio of the axial and vector coupling constants $|g_{\rm A}/g_{\rm V}| = 1.22 \pm 0.05~({\rm stat.}) \pm 0.10~({\rm syst.})$, which validates the sum rule to an accuracy of about 9\%.Comment: 19 pages, 8 figures and table

Multiplicities of charged pions and unidentified charged hadrons from deep-inelastic scattering of muons off an isoscalar target

Multiplicities of charged pions and unidentified hadrons produced in deep-inelastic scattering were measured in bins of the Bjorken scaling variable $x$, the relative virtual-photon energy $y$ and the relative hadron energy $z$. Data were obtained by the COMPASS Collaboration using a 160 GeV muon beam and an isoscalar target ($^6$LiD). They cover the kinematic domain in the photon virtuality $Q^2$ > 1(GeV/c$)^2$, $0.004 < x < 0.4$, $0.2 < z < 0.85$ and $0.1 < y < 0.7$. In addition, a leading-order pQCD analysis was performed using the pion multiplicity results to extract quark fragmentation functions