| 1. |
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| 2. |
- Santangelo, James S., et al.
(author)
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Global urban environmental change drives adaptation in white clover
- 2022
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 375
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Journal article (peer-reviewed)abstract
- Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural dines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.
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| 3. |
- Feng, Shaohong, et al.
(author)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Journal article (peer-reviewed)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 4. |
- Howard, Andrew W., et al.
(author)
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The California planet survey. I. four new giant exoplanets
- 2010
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In: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 721:2, s. 1467-1481
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Journal article (peer-reviewed)abstract
- We present precise Doppler measurements of four stars obtained during the past decade at Keck Observatory by the California Planet Survey (CPS). These stars, namely, HD 34445, HD 126614, HD 13931, and Gl 179, all show evidence for a single planet in Keplerian motion. We also present Doppler measurements from the Hobby-Eberly Telescope (HET) for two of the stars, HD 34445 and Gl 179, that confirm the Keck detections and significantly refine the orbital parameters. These planets add to the statistical properties of giant planets orbiting near or beyond the ice line, and merit follow-up by astrometry, imaging, and space-borne spectroscopy. Their orbital parameters span wide ranges of planetary minimum mass (M sin i = 0.38-1.9 M-Jup), orbital period (P = 2.87-11.5 yr), semimajor axis (a = 2.1-5.2 AU), and eccentricity (e = 0.02-0.41). HD 34445 b (P = 2.87 yr, M sin i = 0.79 MJup, e = 0.27) is a massive planet orbiting an old, G-type star. We announce a planet, HD 126614 Ab, and an M dwarf, HD 126614 B, orbiting the metal-rich star HD 126614 (which we now refer to as HD 126614 A). The planet, HD 126614 Ab, has minimum mass M sin i = 0.38 MJup and orbits the stellar primary with period P = 3.41 yr and orbital separation a = 2.3 AU. The faint M dwarf companion, HD 126614 B, is separated from the stellar primary by 489 mas (33 AU) and was discovered with direct observations using adaptive optics and the PHARO camera at Palomar Observatory. The stellar primary in this new system, HD 126614 A, has the highest measured metallicity ([ Fe/ H] = + 0.56) of any known planet-bearing star. HD 13931 b (P = 11.5 yr, M sin i = 1.88 MJup, e = 0.02) is a Jupiter analog orbiting a near solar twin. Gl 179 b (P = 6.3 yr, M sin i = 0.82 M-Jup, e = 0.21) is a massive planet orbiting a faint M dwarf. The high metallicity of Gl 179 is consistent with the planet-metallicity correlation among M dwarfs, as documented recently by Johnson & Apps.
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| 5. |
- Howard, Andrew W., et al.
(author)
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The NASA-UC Eia-earth program. II. a planet orbiting HD 156668 with a minimum mass of four earth masses
- 2011
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In: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 726:2, s. 73-
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Journal article (peer-reviewed)abstract
- We report the discovery of HD 156668 b, an extrasolar planet with a minimum mass of M-P sin i = 4.15 M-circle plus. This planet was discovered through Keplerian modeling of precise radial velocities from Keck-HIRES and is the second super-Earth to emerge from the NASA-UC Eta-Earth Survey. The best-fit orbit is consistent with circular and has a period of P = 4.6455 days. The Doppler semi-amplitude of this planet, K = 1.89 m s(-1), is among the lowest ever detected, on par with the detection of GJ 581 e using HARPS. A longer period (P approximate to 2.3 years), low-amplitude signal of unknown origin was also detected in the radial velocities and was filtered out of the data while fitting the short-period planet. Additional data are required to determine if the long-period signal is due to a second planet, stellar activity, or another source. Photometric observations using the Automated Photometric Telescopes at Fairborn Observatory show that HD 156668 (an old, quiet K3 dwarf) is photometrically constant over the radial velocity period to 0.1 mmag, supporting the existence of the planet. No transits were detected down to a photometric limit of similar to 3 mmag, ruling out transiting planets dominated by extremely bloated atmospheres, but not precluding a transiting solid/liquid planet with a modest atmosphere.
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| 6. |
- Howard, Andrew W., et al.
(author)
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THE NASA-UC ETA-EARTH PROGRAM : I. A SUPER-EARTH ORBITING HD 7924
- 2009
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In: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 696:1, s. 75-83
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Journal article (peer-reviewed)abstract
- We report the discovery of the first low-mass planet to emerge from the NASA-UC Eta-Earth Program, a super-Earth orbiting the K0 dwarf HD 7924. Keplerian modeling of precise Doppler radial velocities reveals a planet with minimum mass M-P sin i = 9.26M(circle plus) in a P = 5.398 d orbit. Based on Keck-HIRES measurements from 2001 to 2008, the planet is robustly detected with an estimated false alarm probability of less than 0.001. Photometric observations using the Automated Photometric Telescopes at Fairborn Observatory show that HD 7924 is photometrically constant over the radial velocity period to 0.19 mmag, supporting the existence of the planetary companion. No transits were detected down to a photometric limit of similar to 0.5 mmag, eliminating transiting planets with a variety of compositions. HD 7924b is one of only eight planets detected by the radial velocity technique with M-P sini < 10 M-circle plus and as such is a member of an emerging family of low-mass planets that together constrain theories of planet formation.
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| 7. |
- Howard, Andrew W., et al.
(author)
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THE NASA-UC ETA-EARTH PROGRAM. III. A SUPER-EARTH ORBITING HD 97658 AND A NEPTUNE-MASS PLANET ORBITING G1 785
- 2011
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In: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 730:1, s. 10-
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Journal article (peer-reviewed)abstract
- We report the discovery of planets orbiting two bright, nearby early K dwarf stars, HD 97658 and G1 785. These planets were detected by Keplerian modeling of radial velocities measured with Keck-HIRES for the NASA-UC Eta-Earth Survey. HD 97658 b is a close-in super-Earth with minimum mass M sin i = 8.2 +/- 1.2 M-circle plus, orbital period P = 9.494 +/- 0.005 days, and an orbit that is consistent with circular. G1 785 b is a Neptune-mass planet with M sin i = 21.6 +/- 2.0 M-circle plus, P = 74.39 +/- 0.12 days, and orbital eccentricity e = 0.30 +/- 0.09. Photometric observations with the T12 0.8 m automatic photometric telescope at Fairborn Observatory show that HD 97658 is photometrically constant at the radial velocity period to 0.09 mmag, supporting the existence of the planet.
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| 8. |
- Fischer, Debra A., et al.
(author)
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M2K. II. A Triple-Planet System Orbiting Hip 57274
- 2012
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In: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 745:1, s. 21-
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Journal article (peer-reviewed)abstract
- Doppler observations from Keck Observatory have revealed a triple-planet system orbiting the nearby K4V star, HIP 57274. The inner planet, HIP 57274b, is a super-Earth with M sin i = 11.6 M-circle plus (0.036 M-Jup), an orbital period of 8.135 +/- 0.004 days, and slightly eccentric orbit e = 0.19 +/- 0.1. We calculate a transit probability of 6.5% for the inner planet. The second planet has M sin i = 0.4 M-Jup with an orbital period of 32.0 +/- 0.02 days in a nearly circular orbit (e = 0.05 +/- 0.03). The third planet has M sin i = 0.53 M-Jup with an orbital period of 432 +/- 8 days (1.18 years) and an eccentricity e = 0.23 +/- 0.03. This discovery adds to the number of super-Earth mass planets with M sin i < 12 M-circle plus that have been detected with Doppler surveys. We find that 56% +/- 18% of super-Earths are members of multi-planet systems. This is certainly a lower limit because of observational detectability limits, yet significantly higher than the fraction of Jupiter mass exoplanets, 20% +/- 8%, that are members of Doppler-detected, multi-planet systems.
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| 9. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 10. |
- Llop-Sayson, Jorge, et al.
(author)
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Constraining the Orbit and Mass of epsilon Eridani b with Radial Velocities, Hipparcos IAD-Gaia DR2 Astrometry, and Multiepoch Vortex Coronagraphy Upper Limits
- 2021
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In: Astronomical Journal. - : Institute of Physics Publishing (IOPP). - 0004-6256 .- 1538-3881. ; 162:5
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Journal article (peer-reviewed)abstract
- epsilon Eridani is a young planetary system hosting a complex multibelt debris disk and a confirmed Jupiter-like planet orbiting at 3.48 au from its host star. Its age and architecture are thus reminiscent of the early Solar System. The most recent study of Mawet et al., which combined radial-velocity data and Ms-band direct imaging upper limits, started to constrain the planet's orbital parameters and mass, but are still affected by large error bars and degeneracies. Here we make use of the most recent data compilation from three different techniques to further refine epsilon Eridani b's properties: RVs, absolute astrometry measurements from the Hipparcos and Gaia missions, and new Keck/NIRC2 Ms-band vortex coronagraph images. We combine this data in a Bayesian framework. We find a new mass, M-b = 0.66(-0.09)(+0.12) M-Jup, and inclination, i = 78.81(-22.41 degrees)(+29.34), with at least a factor 2 of improvement over previous uncertainties. We also report updated constraints on the longitude of the ascending node, the argument of the periastron, and the time of periastron passage. With these updated parameters, we can better predict the position of the planet at any past and future epoch, which can greatly help define the strategy and planning of future observations and with subsequent data analysis. In particular, these results can assist the search for a direct detection with JWST and the Nancy Grace Roman Space Telescope's coronagraph instrument.
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