Morphological stasis masks ecologically divergent coral species on tropical reefs

Coral reefs are the epitome of species diversity, yet the number of described scleractinian coral species, the framework-builders of coral reefs, remains moderate by comparison. DNA sequencing studies are rapidly challenging this notion by exposing a wealth of undescribed diversity, but the evolutionary and ecological significance of this diversity remains largely unclear. Here, we present an annotated genome for one of the most ubiquitous corals in the Indo-Pacific (Pachyseris speciosa) and uncover, through a comprehensive genomic and phenotypic assessment, that it comprises morphologically indistinguishable but ecologically divergent lineages. Demographic modeling based on whole-genome resequencing indicated that morphological crypsis (across micro- and macromorphological traits) was due to ancient morphological stasis rather than recent divergence. Although the lineages occur sympatrically across shallow and mesophotic habitats, extensive genotyping using a rapid molecular assay revealed differentiation of their ecological distributions. Leveraging "common garden'' conditions facilitated by the overlapping distributions, we assessed physiological and quantitative skeletal traits and demonstrated concurrent phenotypic differentiation. Lastly, spawning observations of genotyped colonies highlighted the potential role of temporal reproductive isolation in the limited admixture, with consistent genomic signatures in genes related to morphogenesis and reproduction. Overall, our findings demonstrate the presence of ecologically and phenotypically divergent coral species without substantial morphological differentiation and provide new leads into the potential mechanisms facilitating such divergence. More broadly, they indicate that our current taxonomic framework for reef-building corals may be scratching the surface of the ecologically relevant diversity on coral reefs, consequently limiting our ability to protect or restore this diversity effectively

J/psi suppression at forward rapidity in Au+Au collisions at sqrt(s_NN)=39 and 62.4 GeV

We present measurements of the J/psi invariant yields in sqrt(s_NN)=39 and 62.4 GeV Au+Au collisions at forward rapidity (1.2<|y|<2.2). Invariant yields are presented as a function of both collision centrality and transverse momentum. Nuclear modifications are obtained for central relative to peripheral Au+Au collisions (R_CP) and for various centrality selections in Au+Au relative to scaled p+p cross sections obtained from other measurements (R_AA). The observed suppression patterns at 39 and 62.4 GeV are quite similar to those previously measured at 200 GeV. This similar suppression presents a challenge to theoretical models that contain various competing mechanisms with different energy dependencies, some of which cause suppression and others enhancement.Comment: 365 authors, 10 pages, 11 figures, 4 tables. Submitted to Phys. Rev. C. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Upsilon (1S+2S+3S) production in d+Au and p+p collisions at sqrt(s_NN)=200 GeV and cold-nuclear matter effects

The three Upsilon states, Upsilon(1S+2S+3S), are measured in d+Au and p+p collisions at sqrt(s_NN)=200 GeV and rapidities 1.2<|y|<2.2 by the PHENIX experiment at the Relativistic Heavy-Ion Collider. Cross sections for the inclusive Upsilon(1S+2S+3S) production are obtained. The inclusive yields per binary collision for d+Au collisions relative to those in p+p collisions (R_dAu) are found to be 0.62 +/- 0.26 (stat) +/- 0.13 (syst) in the gold-going direction and 0.91 +/- 0.33 (stat) +/- 0.16 (syst) in the deuteron-going direction. The measured results are compared to a nuclear-shadowing model, EPS09 [JHEP 04, 065 (2009)], combined with a final-state breakup cross section, sigma_br, and compared to lower energy p+A results. We also compare the results to the PHENIX J/psi results [Phys. Rev. Lett. 107, 142301 (2011)]. The rapidity dependence of the observed Upsilon suppression is consistent with lower energy p+A measurements.Comment: 495 authors, 11 pages, 9 figures, 5 tables. Submitted to Phys. Rev. C. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Medium modification of jet fragmentation in Au+Au collisions at sqrt(s_NN)=200 GeV measured in direct photon-hadron correlations

The jet fragmentation function is measured with direct photon-hadron correlations in p+p and Au+Au collisions at sqrt(s_NN)=200 GeV. The p_T of the photon is an excellent approximation to the initial p_T of the jet and the ratio z_T=p_T^h/p_T^\gamma is used as a proxy for the jet fragmentation function. A statistical subtraction is used to extract the direct photon-hadron yields in Au+Au collisions while a photon isolation cut is applied in p+p. I_ AA, the ratio of jet fragment yield in Au+Au to that in p+p, indicates modification of the jet fragmentation function. Suppression, most likely due to energy loss in the medium, is seen at high z_T. The fragment yield at low z_T is enhanced at large angles. Such a trend is expected from redistribution of the lost energy into increased production of low-momentum particles.Comment: 562 authors, 70 insitutions, 8 pages, and 3 figures. Submitted to Phys. Rev. Lett. v2 has minor changes to improve clarity. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

L\'evy-stable two-pion Bose-Einstein correlations in sNN=200\sqrt{s_{_{NN}}}=200 GeV Au++Au collisions

We present a detailed measurement of charged two-pion correlation functions in 0%-30% centrality $\sqrt{s_{_{NN}}}=200$ GeV Au$+$Au collisions by the PHENIX experiment at the Relativistic Heavy Ion Collider. The data are well described by Bose-Einstein correlation functions stemming from L\'evy-stable source distributions. Using a fine transverse momentum binning, we extract the correlation strength parameter $\lambda$, the L\'evy index of stability $\alpha$ and the L\'evy length scale parameter $R$ as a function of average transverse mass of the pair $m_T$. We find that the positively and the negatively charged pion pairs yield consistent results, and their correlation functions are represented, within uncertainties, by the same L\'evy-stable source functions. The $\lambda(m_T)$ measurements indicate a decrease of the strength of the correlations at low $m_T$. The L\'evy length scale parameter $R(m_T)$ decreases with increasing $m_T$, following a hydrodynamically predicted type of scaling behavior. The values of the L\'evy index of stability $\alpha$ are found to be significantly lower than the Gaussian case of $\alpha=2$, but also significantly larger than the conjectured value that may characterize the critical point of a second-order quark-hadron phase transition.Comment: 448 authors, 25 pages, 11 figures, 4 tables, 2010 data. v2 is version accepted for publication in Phys. Rev. C. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

ϕ\phi meson production in dd++Au collisions at sNN=200\sqrt{s_{_{NN}}}=200 GeV

The PHENIX experiment has measured $\phi$ meson production in $d$$+$Au collisions at $\sqrt{s_{_{NN}}}=200$ GeV using the dimuon and dielectron decay channels. The $\phi$ meson is measured in the forward (backward) $d$-going (Au-going) direction, $1.2<y<2.2$ ($-2.2<y<-1.2$) in the transverse-momentum ($p_T$) range from 1--7 GeV/$c$, and at midrapidity $|y|<0.35$ in the $p_T$ range below 7 GeV/$c$. The $\phi$ meson invariant yields and nuclear-modification factors as a function of $p_T$, rapidity, and centrality are reported. An enhancement of $\phi$ meson production is observed in the Au-going direction, while suppression is seen in the $d$-going direction, and no modification is observed at midrapidity relative to the yield in $p$$+$$p$ collisions scaled by the number of binary collisions. Similar behavior was previously observed for inclusive charged hadrons and open heavy flavor indicating similar cold-nuclear-matter effects.Comment: 484 authors, 16 pages, 12 figures, 6 tables. v1 is the version accepted for publication in Phys. Rev. C. Data tables for the points plotted in the figures are given in the paper itsel

Measurement of higher cumulants of net-charge multiplicity distributions in Au++Au collisions at sNN=7.7−200\sqrt{s_{_{NN}}}=7.7-200 GeV

We report the measurement of cumulants ($C_n, n=1\ldots4$) of the net-charge distributions measured within pseudorapidity ($|\eta|<0.35$) in Au$+$Au collisions at $\sqrt{s_{_{NN}}}=7.7-200$ GeV with the PHENIX experiment at the Relativistic Heavy Ion Collider. The ratios of cumulants (e.g. $C_1/C_2$, $C_3/C_1$) of the net-charge distributions, which can be related to volume independent susceptibility ratios, are studied as a function of centrality and energy. These quantities are important to understand the quantum-chromodynamics phase diagram and possible existence of a critical end point. The measured values are very well described by expectation from negative binomial distributions. We do not observe any nonmonotonic behavior in the ratios of the cumulants as a function of collision energy. The measured values of $C_1/C_2 = \mu/\sigma^2$ and $C_3/C_1 = S\sigma^3/\mu$ can be directly compared to lattice quantum-chromodynamics calculations and thus allow extraction of both the chemical freeze-out temperature and the baryon chemical potential at each center-of-mass energy.Comment: 512 authors, 8 pages, 4 figures, 1 table. v2 is version accepted for publication in Phys. Rev. C as a Rapid Communication. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Systematic study of charged-pion and kaon femtoscopy in Au++Au collisions at sNN\sqrt{s_{_{NN}}}=200 GeV

We present a systematic study of charged pion and kaon interferometry in Au$+$Au collisions at $\sqrt{s_{_{NN}}}$=200 GeV. The kaon mean source radii are found to be larger than pion radii in the outward and longitudinal directions for the same transverse mass; this difference increases for more central collisions. The azimuthal-angle dependence of the radii was measured with respect to the second-order event plane and similar oscillations of the source radii were found for pions and kaons. Hydrodynamic models qualitatively describe the similar oscillations of the mean source radii for pions and kaons, but they do not fully describe the transverse-mass dependence of the oscillations.Comment: 499 authors, 27 pages, 13 figures, and 11 tables. v2 is the version accepted for publication in Phys. Rev. C. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Measurement of Υ\Upsilon(1S+2S+3S) production in pp++pp and Au++Au collisions at sNN=200\sqrt{s_{_{NN}}}=200 GeV

Measurements of bottomonium production in heavy ion and $p$$+$$p$ collisions at the Relativistic Heavy Ion Collider (RHIC) are presented. The inclusive yield of the three $\Upsilon$ states, $\Upsilon(1S+2S+3S)$, was measured in the PHENIX experiment via electron-positron decay pairs at midrapidity for Au$+$Au and $p$$+$$p$ collisions at $\sqrt{s_{_{NN}}}=200$ GeV. The $\Upsilon(1S+2S+3S)\rightarrow e^+e^-$ differential cross section at midrapidity was found to be $B_{\rm ee} d\sigma/dy =$ 108 $\pm$ 38 (stat) $\pm$ 15(syst) $\pm$ 11 (luminosity) pb in $p$$+$$p$ collisions. The nuclear modification factor in the 30\% most central Au$+$Au collisions indicates a suppression of the total $\Upsilon$ state yield relative to the extrapolation from $p$$+$$p$ collision data. The suppression is consistent with measurements made by STAR at RHIC and at higher energies by the CMS experiment at the Large Hadron Collider.Comment: 506 authors, 15 pages, 17 figures, and 7 tables. v3 is as accepted by Phys. Rev. C. v2 has changes to text and figures, plus additional authors. Published version will be at http://www.phenix.bnl.gov/phenix/WWW/info/pp1/1NN/ Plain text data tables are (or will be) at http://www.phenix.bnl.gov/papers.htm