Origin and evolution of the octoploid strawberry genome.

Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million years ago. Here we report a near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary processes that shaped this complex allopolyploid. We identified the extant relatives of each diploid progenitor species and provide support for the North American origin of octoploid strawberry. We examined the dynamics among the four subgenomes in octoploid strawberry and uncovered the presence of a single dominant subgenome with significantly greater gene content, gene expression abundance, and biased exchanges between homoeologous chromosomes, as compared with the other subgenomes. Pathway analysis showed that certain metabolomic and disease-resistance traits are largely controlled by the dominant subgenome. These findings and the reference genome should serve as a powerful platform for future evolutionary studies and enable molecular breeding in strawberry

Exploring the influence of ancient and historic megaherbivore extirpations on the global methane budget

Globally, large-bodied wild mammals are in peril. Because “megamammals” have a disproportionate influence on vegetation, trophic interactions, and ecosystem function, declining populations are of considerable conservation concern. However, this is not new; trophic downgrading occurred in the past, including the African rinderpest epizootic of the 1890s, the massive Great Plains bison kill-off in the 1860s, and the terminal Pleistocene extinction of megafauna. Examining the consequences of these earlier events yields insights into contemporary ecosystem function. Here, we focus on changes inmethane emissions, produced as a byproduct of enteric fermentation by herbivores. Although methane is ∼200 times less abundant than carbon dioxide in the atmosphere, the greater efficiency of methane in trapping radiation leads to a significant role in radiative forcing of climate. Using global datasets of late Quaternary mammals, domestic livestock, and human population from the United Nations as well as literature sources, we develop a series of allometric regressions relating mammal body mass to population density and CH4 production, which allows estimation of methane production by wild and domestic herbivores for each historic or ancient time period. We find the extirpation ofmegaherbivores reduced global enteric emissions between 2.2–69.6 Tg CH4 y−1 during the various time periods, representing a decrease of 0.8–34.8% of the overall inputs to tropospheric input. Our analyses suggest that large-bodied mammals have a greater influence on methane emissions than previously appreciated and, further, that changes in the source pool from herbivores can influence global biogeochemical cycles and, potentially, climate

X-ray and Multiwavelength Insights into the Nature of Weak Emission-Line Quasars at Low Redshift

(Abridged) We report on the X-ray and multiwavelength properties of 11 radio-quiet quasars with weak or no emission lines identified by the Sloan Digital Sky Survey (SDSS) with redshift z=0.4-2.5. The distribution of relative X-ray brightness for our low-redshift weak-line quasar (WLQ) candidates is significantly different from that of typical radio-quiet quasars, having an excess of X-ray weak sources, but it is consistent with that of high-redshift WLQs. The X-ray weak sources generally show similar UV emission-line properties to those of the X-ray weak quasar PHL 1811; they may belong to the notable class of PHL 1811 analogs. The average X-ray spectrum of these sources is somewhat harder than that of typical radio-quiet quasars. Several other low-redshift WLQ candidates have normal ratios of X-ray-to-optical/UV flux, and their average X-ray spectral properties are also similar to those of typical radio-quiet quasars. The X-ray weak and X-ray normal WLQ candidates may belong to the same subset of quasars having high-ionization "shielding gas" covering most of the wind-dominated broad emission-line region, but be viewed at different inclinations. The mid-infrared-to-X-ray spectral energy distributions (SEDs) of these sources are generally consistent with those of typical SDSS quasars, showing that they are not likely to be BL Lac objects with relativistically boosted continua and diluted emission lines. However, one source in our X-ray observed sample is remarkably strong in X-rays, indicating that a small fraction of low-redshift WLQ candidates may actually be BL Lacs residing in the radio-faint tail of the BL Lac population. We also investigate universal selection criteria for WLQs over a wide range of redshift, finding that it is not possible to select WLQ candidates in a fully consistent way using different prominent emission lines as a function of redshift.Comment: ApJ in press; 26 pages, 11 figures and 7 tables. The full Table 3 is available upon reques

X-ray Insights into the Nature of Weak Emission-Line Quasars at High Redshift

We present Chandra observations of nine high-redshift quasars (z=2.7-5.9) discovered by the Sloan Digital Sky Survey with weak or undetectable high-ionization emission lines in their UV spectra (WLQs). Adding archival X-ray observations of six additional sources of this class has enabled us to place the strongest constraints yet on the X-ray properties of this remarkable class of AGNs. Although our data cannot rule out the possibility that the emission lines are overwhelmed by a relativistically boosted continuum, as manifested by BL Lac objects, we find that WLQs are considerably weaker in the X-ray and radio bands than the majority of BL Lacs found at much lower redshifts. If WLQs are high-redshift BL Lacs, then it is difficult to explain the lack of a large parent population of X-ray and radio bright weak-lined sources at high redshift. We also consider the possibility that WLQs are quasars with extreme properties, and in particular that the emission lines are suppressed by high accretion rates. Using joint spectral fitting of the X-ray spectra of 11 WLQs we find that the mean photon index in the hard X-ray band is consistent with those observed in typical radio-quiet AGNs with no hint of an unusually steep hard-X-ray spectrum. This result poses a challenge to the hypothesis that WLQs have extremely high accretion rates, and we discuss additional observations required to test this idea.Comment: 13 pages (emulateapj), 7 figures. Accepted for publication in Ap

Priority sites for wildfowl conservation in Mexico

A set of priority sites for wildfowl conservation in Mexico was determined using contemporary count data (1991–2000) from the U.S. Fish & Wildlife Service mid-winter surveys. We used a complementarity approach implemented through linear integer programming that addresses particular conservation concerns for every species included in the analysis and large fluctuations in numbers through time. A set of 31 priority sites was identified, which held more than 69% of the mid-winter count total in Mexico during all surveyed years. Six sites were in the northern highlands, 12 in the central highlands, six on the Gulf of Mexico coast and seven on the upper Pacific coast. Twenty-two sites from the priority set have previously been identified as qualifying for designation as wetlands of international importance under the Ramsar Convention and 20 sites are classified as Important Areas for Bird Conservation in Mexico. The information presented here provides an accountable, spatially-explicit, numerical basis for ongoing conservation planning efforts in Mexico, which can be used to improve existing wildfowl conservation networks in the country and can also be useful for conservation planning exercises elsewhere

A Population of X-ray Weak Quasars: PHL 1811 Analogs at High Redshift

We report the results from Chandra and XMM-Newton observations of a sample of 10 type 1 quasars selected to have unusual UV emission-line properties (weak and blueshifted high-ionization lines; strong UV Fe emission) similar to those of PHL 1811, a confirmed intrinsically X-ray weak quasar. These quasars were identified by the Sloan Digital Sky Survey at high redshift (z~2.2); eight are radio quiet while two are radio intermediate. All of the radio-quiet PHL 1811 analogs are notably X-ray weak by a mean factor of ~13. These sources lack broad absorption lines and have blue UV/optical continua, suggesting they are intrinsically X-ray weak. However, their average X-ray spectrum appears to be harder than those of typical quasars, which may indicate the presence of heavy intrinsic X-ray absorption. Our radio-quiet PHL 1811 analogs support a connection between an X-ray weak spectral energy distribution and PHL 1811-like UV emission lines; this connection provides an economical way to identify X-ray weak type 1 quasars. The fraction of radio-quiet PHL 1811 analogs in the radio-quiet quasar population is estimated to be < 1.2%. We have investigated correlations between relative X-ray brightness and UV emission-line properties for a sample combining radio-quiet PHL 1811 analogs, PHL 1811, and typical type 1 quasars. These correlation analyses suggest that PHL 1811 analogs may have extreme wind-dominated broad emission-line regions. Observationally, radio-quiet PHL 1811 analogs appear to be a subset (~30%) of radio-quiet weak-line quasars. The existence of a subset of quasars in which high-ionization "shielding gas" covers most of the BELR, but little more than the BELR, could potentially unify the PHL 1811 analogs and WLQs. The two radio-intermediate PHL 1811 analogs are X-ray bright. One of them appears to have jet-dominated X-ray emission, while the nature of the other remains unclear.Comment: ApJ accepted; 25 pages, 11 figures and 8 table

A High Yield of New Sightlines for the Study of Intergalactic Helium: Far-UV-Bright Quasars from SDSS, GALEX, and HST

Investigations of He II Ly-alpha (304 A rest) absorption toward a half-dozen quasars at z~3-4 have demonstrated the great potential of helium studies of the IGM, but the current critically small sample size of clean sightlines for the He II Gunn-Peterson test limits confidence in cosmological inferences, and a larger sample is required. Although the unobscured quasar sightlines to high redshift are extremely rare, SDSS DR6 provides thousands of z>2.8 quasars. We have cross-correlated these SDSS quasars with GALEX GR2/GR3 to establish a catalog of 200 higher-confidence (~70% secure) cases of quasars at z=2.8-5.1 potentially having surviving far-UV (restframe) flux. We also catalog another 112 likely far-UV-bright quasars from GALEX cross-correlation with other (non-SDSS) quasar compilations. Reconnaissance UV prism observations with HST of 24 of our SDSS/GALEX candidates confirm 12 as detected in the far-UV, with at least 9 having flux extending to very near the He II break; with refinements our success rate is even higher. Our SDSS/GALEX selection approach is thereby confirmed to be an order of magnitude more efficient than previous He II quasar searches, more than doubles the number of spectroscopically confirmed clean sightlines to high redshift, and provides a resource list of hundreds of high-confidence sightlines for upcoming He II and other far-UV studies from HST. Our reconnaissance HST prism spectra suggest some far-UV diversity, confirming the need to obtain a large sample of independent quasar sightlines across a broad redshift range to assess such issues as the epoch(s) of helium reionization, while averaging over individual-object pathology and/or cosmic variance.Comment: 32 pages, 7 figures, accepted by Ap

Systemwide Evaluation of Avian Predation on Juvenile Salmonids from the Columbia River Based on Recoveries of Passive Integrated Transponder Tags

We recovered passive integrated transponder (PIT) tags from nine piscivorous waterbird colonies in the Columbia River basin to evaluate avian predation on Endangered Species Act (ESA)-listed salmonid Oncorhynchus spp. populations during 2007–2010. Avian predation rates were calculated based on the percentage of PIT-tagged juvenile salmonids that were detected as passing hydroelectric dams and subsequently were consumed and deposited by birds on their nesting colonies. Caspian terns Hydroprogne caspia (hereafter, “terns”) and double-crested cormorants Phalacrocorax auritus (hereafter, “cormorants”) nesting on East Sand Island in the Columbia River estuary consumed the highest proportions of available PIT-tagged salmonids, with minimum predation rates ranging from 2.5% for Willamette River spring Chinook salmon O. tshawytscha to 16.0% for Snake River steelhead O. mykiss. Estimated predation rates by terns, cormorants, gulls of two species (California gull Larus californicus and ring-billed gull L. delawarensis), and American white pelicans Pelecanus erythrorhynchos nesting near the confluence of the Snake and Columbia rivers were also substantial; minimum predation rates ranged from 1.4% for Snake River fall Chinook salmon to 13.2% for upper Columbia River steelhead. Predation on ESA-listed salmonids by gulls and American white pelicans were minor (<2.0% per ESA-listed salmonid population) relative to predation by terns and cormorants. Cumulative impacts were greater for Snake River and upper Columbia River salmonids than for salmonids originating closer to the estuary because upriver salmonids must migrate past more bird colonies to reach the ocean. Predation rates adjusted for colony size (per capita rates) were significantly higher for terns and cormorants nesting at inland colonies (upstream of Bonneville Dam) than for those nesting in the estuary, suggesting that inland colonies have a greater reliance on salmonids as a food source. Management actions to increase salmonid survival by reducing avian predation in the estuary could be offset if birds that disperse from the estuary relocate to inland nesting sites on or near the Columbia River.This is the publisher’s final pdf. The article is copyrighted by the American Fisheries Society and published by Taylor & Francis. It can be found at: http://www.tandfonline.com/toc/utaf20/curren

Discovery of underground argon with low level of radioactive 39Ar and possible applications to WIMP dark matter detectors

We report on the first measurement of 39Ar in argon from underground natural gas reservoirs. The gas stored in the US National Helium Reserve was found to contain a low level of 39Ar. The ratio of 39Ar to stable argon was found to be <=4x10-17 (84% C.L.), less than 5% the value in atmospheric argon (39Ar/Ar=8x10-16). The total quantity of argon currently stored in the National Helium Reserve is estimated at 1000 tons. 39Ar represents one of the most important backgrounds in argon detectors for WIMP dark matter searches. The findings reported demonstrate the possibility of constructing large multi-ton argon detectors with low radioactivity suitable for WIMP dark matter searches.Comment: 6 pages, 2 figures, 2 table

Organizational factors and depression management in community-based primary care settings

Abstract Background Evidence-based quality improvement models for depression have not been fully implemented in routine primary care settings. To date, few studies have examined the organizational factors associated with depression management in real-world primary care practice. To successfully implement quality improvement models for depression, there must be a better understanding of the relevant organizational structure and processes of the primary care setting. The objective of this study is to describe these organizational features of routine primary care practice, and the organization of depression care, using survey questions derived from an evidence-based framework. Methods We used this framework to implement a survey of 27 practices comprised of 49 unique offices within a large primary care practice network in western Pennsylvania. Survey questions addressed practice structure (e.g., human resources, leadership, information technology (IT) infrastructure, and external incentives) and process features (e.g., staff performance, degree of integrated depression care, and IT performance). Results The results of our survey demonstrated substantial variation across the practice network of organizational factors pertinent to implementation of evidence-based depression management. Notably, quality improvement capability and IT infrastructure were widespread, but specific application to depression care differed between practices, as did coordination and communication tasks surrounding depression treatment. Conclusions The primary care practices in the network that we surveyed are at differing stages in their organization and implementation of evidence-based depression management. Practical surveys such as this may serve to better direct implementation of these quality improvement strategies for depression by improving understanding of the organizational barriers and facilitators that exist within both practices and practice networks. In addition, survey information can inform efforts of individual primary care practices in customizing intervention strategies to improve depression management.http://deepblue.lib.umich.edu/bitstream/2027.42/78269/1/1748-5908-4-84.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78269/2/1748-5908-4-84-S1.PDFhttp://deepblue.lib.umich.edu/bitstream/2027.42/78269/3/1748-5908-4-84.pdfPeer Reviewe