Ancient DNA Reveals Genetic Continuity in Mountain Woodland Caribou of the Mackenzie and Selwyn Mountains, Northwest Territories, Canada

We examine the mitochondrial genetic stability of mountain woodland caribou (Rangifer tarandus caribou) in the Mackenzie and Selwyn Mountains, Northwest Territories, over the last 4000 years. Unlike caribou populations in the Yukon, populations in the Northwest Territories show no evidence for mitochondrial genetic turnover during that period, which indicates that they were not adversely affected by the widespread deposition of the White River tephra around 1200 years ago. We detect moderate genetic differentiation between mountain woodland and barren-ground caribou in both territories, lending support to the current subspecies designations. In addition, we identify moderate genetic differentiation between Northwest Territories and western Yukon mountain woodland caribou, suggesting that there has been minimal mixing of matrilines between these herds.Nous examinons la stabilité génétique mitochondriale des caribous des bois des montagnes (Rangifer tarandus caribou) qui ont évolué dans les monts Mackenzie et dans la chaîne de Selwyn, Territoires du Nord-Ouest, ces 4 000 dernières années. Contrairement aux populations de caribou du Yukon, les populations de caribou des Territoires du Nord-Ouest ne montrent aucun signe de rotation génétique mitochondriale pendant cette période, ce qui indique qu’ils n’ont pas été affectés de manière défavorable par le dépôt à grande échelle du téphra de la rivière White, il y a environ 1 200 ans. Nous détectons une différentiation génétique modérée entre le caribou des bois des montagnes et le caribou de la toundra dans les deux territoires, ce qui vient appuyer les désignations actuelles de sous-espèces. Par ailleurs, nous avons dénoté une différenciation génétique modérée entre le caribou des bois des montagnes des Territoires du Nord-Ouest et celui de l’ouest du Yukon, ce qui laisse croire qu’il y aurait eu peu de mélanges matrilinéaires entre ces troupeaux

The Neurovascular Relation in Oxygen-induced Retinopathy

Purpose: Longitudinal studies in rat models of retinopathy of prematurity (ROP) have demonstrated that abnormalities of retinal vasculature and function change hand-in-hand. In the developing retina, vascular and neural structures are under cooperative molecular control. In this study of rats with oxygen-induced retinopathy (OIR) models of ROP, mRNA expression of vascular endothelial growth factor (VEGF), semaphorin (Sema), and their neuropilin receptor (NRP) were examined during the course of retinopathy to evaluate their roles in the observed neurovascular congruency. Methods: Oxygen exposures designed to induce retinopathy were delivered to Sprague-Dawley rat pups (n=36) from postnatal day (P) 0 to P14 or from P7 to P14. Room-air-reared controls (n=18) were also studied. Sensitivities of the rod photoreceptors ($S_{rod}$) and the postreceptor cells (Sm) were derived from electroretinographic (ERG) records. Arteriolar tortuosity, $T_A$, was derived from digital fundus images using Retinal Image multi-Scale Analysis (RISA) image analysis software. mRNA expression of $VEGF_{164}$, semaphorin IIIA (Sema3A), and neuropilin-1 (NRP-1) was evaluated by RT–PCR of retinal extracts. Tests were performed at P15–P16, P18–P19, and P25–P26. Relations among ERG, RISA, and PCR parameters were evaluated using linear regression on log transformed data. Results: Sm was low and $T_A$ was high at young ages, then both resolved by P25–P26. $VEGF_{164}$ and Sema3A mRNA expression were also elevated early and decreased with age. Low Sm was significantly associated with high $VEGF_{164}$ and Sema3A expression. Low Srod was also significantly associated with high VEGF164. $S_{rod}$ and Sm were both correlated with $T_A$. NRP-1 expression was little affected by OIR. Conclusions: The postreceptor retina appears to mediate the vascular abnormalities that characterize OIR. Because of the relationships revealed by these data, early treatment that targets the neural retina may mitigate the effects of ROP

Natural selection shaped the rise and fall of passenger pigeon genomic diversity.

The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. Although theory predicts that large populations will be more genetically diverse, passenger pigeon genetic diversity was surprisingly low. To investigate this disconnect, we analyzed 41 mitochondrial and 4 nuclear genomes from passenger pigeons and 2 genomes from band-tailed pigeons, which are passenger pigeons' closest living relatives. Passenger pigeons' large population size appears to have allowed for faster adaptive evolution and removal of harmful mutations, driving a huge loss in their neutral genetic diversity. These results demonstrate the effect that selection can have on a vertebrate genome and contradict results that suggested that population instability contributed to this species's surprisingly rapid extinction

The TESS-Keck Survey: Science Goals and Target Selection

Space-based transit missions such as Kepler and TESS have demonstrated that planets are ubiquitous. However, the success of these missions heavily depends on ground-based radial velocity (RV) surveys, which combined with transit photometry can yield bulk densities and orbital properties. While most Kepler host stars are too faint for detailed follow-up observations, TESS is detecting planets orbiting nearby bright stars that are more amenable to RV characterization. Here we introduce the TESS-Keck Survey (TKS), an RV program using ~100 nights on Keck/HIRES to study exoplanets identified by TESS. The primary survey aims are investigating the link between stellar properties and the compositions of small planets; studying how the diversity of system architectures depends on dynamical configurations or planet multiplicity; identifying prime candidates for atmospheric studies with JWST; and understanding the role of stellar evolution in shaping planetary systems. We present a fully-automated target selection algorithm, which yielded 103 planets in 86 systems for the final TKS sample. Most TKS hosts are inactive, solar-like, main-sequence stars (4500 K < Teff < 6000 K) at a wide range of metallicities. The selected TKS sample contains 71 small planets (Rp < 4 Re), 11 systems with multiple transiting candidates, 6 sub-day period planets and 3 planets that are in or near the habitable zone of their host star. The target selection described here will facilitate the comparison of measured planet masses, densities, and eccentricities to predictions from planet population models. Our target selection software is publicly available (at https://github.com/ashleychontos/sort-a-survey) and can be adapted for any survey which requires a balance of multiple science interests within a given telescope allocation.Comment: 23 pages, 10 figures, 5 table

The TESS-Keck Survey XVII: Precise Mass Measurements in a Young, High Multiplicity Transiting Planet System using Radial Velocities and Transit Timing Variations

We present a radial velocity (RV) analysis of TOI-1136, a bright TESS system with six confirmed transiting planets, and a seventh single-transiting planet candidate. All planets in the system are amenable to transmission spectroscopy, making TOI-1136 one of the best targets for intra-system comparison of exoplanet atmospheres. TOI-1136 is young ($\sim$ 700 Myr), and the system exhibits transit timing variations (TTVs). The youth of the system contributes to high stellar variability on the order of 50 m s$^{-1}$, much larger than the likely RV amplitude of any of the transiting exoplanets. Utilizing 359 HIRES and APF RVs collected as a part of the TESS-Keck Survey (TKS), and 51 HARPS-N RVs, we experiment with a joint TTV-RV fit. With seven possible transiting planets, TTVs, more than 400 RVs, and a stellar activity model, we posit that we may be presenting the most complex mass recovery of an exoplanet system in the literature to date. By combining TTVs and RVs, we minimized GP overfitting and retrieved new masses for this system: (m$_{b-g}$ = 3.50$^{+0.8}_{-0.7}$, 6.32$^{+1.1}_{-1.3}$, 8.35$^{+1.8}_{-1.6}$, 6.07$^{+1.09}_{-1.01}$, 9.7$^{+3.9}_{-3.7}$, 5.6$^{+4.1}_{-3.2}$ M$_{\oplus}$). We are unable to significantly detect the mass of the seventh planet candidate in the RVs, but we are able to loosely constrain a possible orbital period near 80 days. Future TESS observations might confirm the existence of a seventh planet in the system, better constrain the masses and orbital properties of the known exoplanets, and generally shine light on this scientifically interesting system.Comment: Accepted for publication in the Astronomical Journa

The TESS-Keck Survey. XII. A Dense 1.8 R ⊕ Ultra-short-period Planet Possibly Clinging to a High-mean-molecular-weight Atmosphere after the First Gigayear

The extreme environments of ultra-short-period planets (USPs) make excellent laboratories to study how exoplanets obtain, lose, retain, and/or regain gaseous atmospheres. We present the confirmation and characterization of the USP TOI-1347 b, a 1.8±0.1 R⊕ planet on a 0.85 day orbit that was detected with photometry from the TESS mission. We measured radial velocities of the TOI-1347 system using Keck/HIRES and HARPS-N and found the USP to be unusually massive at 11.1±1.2 M⊕. The measured mass and radius of TOI-1347 b imply an Earth-like bulk composition. A thin H/He envelope (&gt;0.01% by mass) can be ruled out at high confidence. The system is between 1 and 1.8 Gyr old; therefore, intensive photoevaporation should have concluded. We detected a tentative phase curve variation (3σ) and a secondary eclipse (2σ) in TESS photometry, which if confirmed could indicate the presence of a high-mean-molecular-weight atmosphere. We recommend additional optical and infrared observations to confirm the presence of an atmosphere and investigate its composition

The TESS-Keck Survey. XXII. A Sub-Neptune Orbiting TOI-1437

Exoplanet discoveries have revealed a dramatic diversity of planet sizes across a vast array of orbital architectures. Sub-Neptunes are of particular interest; due to their absence in our own solar system, we rely on demographics of exoplanets to better understand their bulk composition and formation scenarios. Here, we present the discovery and characterization of TOI-1437 b, a sub-Neptune with a 18.84 day orbit around a near-solar analog (M⋆ = 1.10 ± 0.10 M☉, R⋆=1.17 ± 0.12 R☉). The planet was detected using photometric data from the Transiting Exoplanet Survey Satellite (TESS) mission and radial velocity (RV) follow-up observations were carried out as a part of the TESS-Keck Survey using both the HIRES instrument at Keck Observatory and the Levy Spectrograph on the Automated Planet Finder telescope. A combined analysis of these data reveal a planet radius of Rp = 2.24 ± 0.23 R⊕ and a mass measurement of Mp = 9.6 ± 3.9 M⊕). TOI-1437 b is one of few (∼50) known transiting sub-Neptunes orbiting a solar-mass star that has a RV mass measurement. As the formation pathway of these worlds remains an unanswered question, the precise mass characterization of TOI-1437 b may provide further insight into this class of planet

The TESS-Keck Survey. XV. Precise Properties of 108 TESS Planets and Their Host Stars

We present the stellar and planetary properties for 85 TESS Objects of Interest (TOIs) hosting 108 planet candidates which comprise the TESS-Keck Survey (TKS) sample. We combine photometry, high-resolution spectroscopy, and Gaia parallaxes to measure precise and accurate stellar properties. We then use these parameters as inputs to a lightcurve processing pipeline to recover planetary signals and homogeneously fit their transit properties. Among these transit fits, we detect significant transit-timing variations among at least three multi-planet systems (TOI-1136, TOI-1246, TOI-1339) and at least one single-planet system (TOI-1279). We also reduce the uncertainties on planet-to-star radius ratios $R_p/R_\star$ across our sample, from a median fractional uncertainty of 8.8$\%$ among the original TOI Catalog values to 3.0$\%$ among our updated results. With this improvement, we are able to recover the Radius Gap among small TKS planets and find that the topology of the Radius Gap among our sample is broadly consistent with that measured among Kepler planets. The stellar and planetary properties presented here will facilitate follow-up investigations of both individual TOIs and broader trends in planet properties, system dynamics, and the evolution of planetary systems.Comment: Accepted at The Astronomical Journal; 21 pages, 9 figure

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts