Population genetic diversity in an Iraqi population and gene flow across the Arabian Peninsula

Abstract: Y-STRs have emerged as important forensic and population genetic markers for human identification and population differentiation studies. Therefore, population databases for these markers have been developed for almost all major populations around the world. The Iraqi population encompasses several ethnic groups that need to be genetically characterised and evaluated for possible substructures. Previous studies on the Iraqi population based on Y-STR markers were limited by a restricted number of markers. A larger database for Iraqi Arab population needed to be developed to help study and compare the population with other Middle Eastern populations. Twenty-three Y-STR loci included in the PowerPlex Y23 (Promega, Madison, WI, USA) were typed in 254 males from the Iraqi Arab population. Global and regional Y-STR analysis demonstrated regional genetic continuity among the populations of Iraq, the Arabian Peninsula and the Middle East. The Iraqi Arab haplotypes were used to allocate samples to their most likely haplogroups using Athey’s Haplogroup Predictor tool. Prediction indicated predominance (36.6%) of haplogroup J1 in Iraqi Arabs. The migration rate between other populations and the Iraqis was inferred using coalescence theory in the Migrate-n program. Y-STR data were used to test different out-of-Africa migration models as well as more recent migrations within the Arabian Peninsula. The migration models demonstrated that gene flow to Iraq began from East Africa, with the Levantine corridor the most probable passageway out of Africa. The data presented here will enrich our understanding of genetic diversity in the region and introduce a PowerPlex Y23 database to the forensic community

Muscle-related traits in cattle: The role of the myostatin gene in the South Devon breed

In this paper, we examined the effects of an 11-bp mutation within the GDF-8 gene, originally identified in Belgian Blue cattle, in the South Devon breed. The mutation was found at moderate frequency (0.37) in the South Devon population. We quantified the effects of this mutation on growth, body composition and calving traits in South Devon cattle. We found that the mutation significantly increased muscle score and calving difficulty and decreased fat depth. The mutation did not significantly affect weight at 200 and 400 days or muscle depth. Its effect on muscle score and fat depth was additive while its effect on calving difficulty was recessive. The mutation accounted for a significant proportion of the phenotypic variance in muscle score and calving difficulty. There was an economic benefit of the mutation for this data set, however, calculations were sensitive to changes in the parameter values. Additional data would be required to refine these calculations

Diet modulates the relationship between immune gene expression and functional immune responses

Nutrition is vital to health and the availability of resources has long been acknowledged as a key factor in the ability to fight off parasites, as investing in the immune system is costly. Resources have typically been considered as something of a "black box", with the quantity of available food being used as a proxy for resource limitation. However, food is a complex mixture of macro- and micronutrients, the precise balance of which determines an animal's fitness. Here we use a state-space modelling approach, the Geometric Framework for Nutrition (GFN), to assess for the first time, how the balance and amount of nutrients affects an animal's ability to mount an immune response to a pathogenic infection. Spodoptera littoralis caterpillars were assigned to one of 20 diets that varied in the ratio of macronutrients (protein and carbohydrate) and their calorie content to cover a large region of nutrient space. Caterpillars were then handled or injected with either live or dead Xenorhabdus nematophila bacterial cells. The expression of nine genes (5 immune, 4 non-immune) was measured 20 h post immune challenge. For two of the immune genes (PPO and Lysozyme) we also measured the relevant functional immune response in the haemolymph. Gene expression and functional immune responses were then mapped against nutritional intake. The expression of all immune genes was up-regulated by injection with dead bacteria, but only those in the IMD pathway (Moricin and Relish) were substantially up-regulated by both dead and live bacterial challenge. Functional immune responses increased with the protein content of the diet but the expression of immune genes was much less predictable. Our results indicate that diet does play an important role in the ability of an animal to mount an adequate immune response, with the availability of protein being the most important predictor of the functional (physiological) immune response. Importantly, however, immune gene expression responds quite differently to functional immunity and we would caution against using gene expression as a proxy for immune investment, as it is unlikely to be reliable indicator of the immune response, except under specific dietary conditions. [Abstract copyright: Copyright © 2019. Published by Elsevier Ltd.

A transiting M-dwarf showing beaming effect in the field of Ruprecht 147

We report the discovery and characterization of an eclipsing M5Vdwarf star, orbiting a slightly evolved F7V main sequence star. In contrast to previous claims in the literature, we confirm that the system does not belong to the galactic open cluster Ruprecht 147. We determine its fundamental parameters combining K2 time-series data with spectroscopic observations from the McDonald Observatory, FIES@NOT, and HIRES@KECK. The very precise photometric data from the K2 mission allows us to measure variations caused by the beaming effect (relativistic doppler boosting), ellipsoidal variation, reflection, and the secondary eclipse. We determined the radial velocity using spectroscopic observations and compare it to the radial velocity determined from the beaming effect observed in the photometric data. The M5V star has a radius of 0.200+0.007−0.008  R⊙ and a mass of 0.187+0.012−0.013  M⊙. The primary star has a radius of 1.518+0.038−0.049 R⊙ and a mass of 1.008+0.081−0.097 M⊙. The orbital period is 5.441995 ± 0.000007 d. The system is one of the few eclipsing systems with observed beaming effect and spectroscopic radial velocity measurements and it can be used as a test case for the modelling of the beaming effect. Current and forthcoming space missions such as TESS and PLATO might benefit from the analysis of the beaming effect to estimate the mass of transiting companions without the need for radial velocity follow up observations, provided that the systematic sources of noise affecting this method are well understood.Funding for the K2 mission is provided by the NASA Science Mission directorate. HJD acknowledges support by grant ESP2015-65712-C5-4-R of the Spanish Secretary of State for R&D&i (MINECO). ME and WDC were supported by NASA grant NNX16AE70G to The University of Texas at Austin

Microsatellites reveal that genetic mixing commonly occurs between invasive fall armyworm populations in Africa

Abstract: Understanding the population structure and movements of the invasive fall armyworm (FAW, Spodoptera frugiperda) is important as it can help mitigate crop damage, and highlight areas at risk of outbreaks or evolving insecticide resistance. Determining population structure in invasive FAW has been a challenge due to genetic mutations affecting the markers traditionally used for strain and haplotype identification; mitochondrial cytochrome oxidase I (COIB) and the Z-chromosome-linked Triosephosphate isomerase (Tpi). Here, we compare the results from COIB and Tpi markers with highly variable repeat regions (microsatellites) to improve our understanding of FAW population structure in Africa. There was very limited genetic diversity using the COIB marker, whereas using the TpiI4 marker there was greater diversity that showed very little evidence of genetic structuring between FAW populations across Africa. There was greater genetic diversity identified using microsatellites, and this revealed a largely panmictic population of FAW alongside some evidence of genetic structuring between countries. It is hypothesised here that FAW are using long-distance flight and prevailing winds to frequently move throughout Africa leading to population mixing. These approaches combined provide important evidence that genetic mixing between invasive FAW populations may be more common than previously reported

EPIC 219388192 b - an inhabitant of the brown dwarf desert in the Ruprecht 147 open cluster

We report the discovery of EPIC 219388192 b, a transiting brown dwarf in a 5.3-day orbit around a member star of Ruprecht-147, the oldest nearby open cluster association, which was photometrically monitored by K2 during its Campaign 7. We combine the K2 time-series data with ground-based adaptive optics imaging and high resolution spectroscopy to rule out false positive scenarios and determine the main parameters of the system. EPIC 219388192 b has a radius of $R_\mathrm{b}$=$0.937\pm0.042$~$\mathrm{R_{Jup}}$ and mass of $M_\mathrm{b}$=$36.50\pm0.09$~$\mathrm{M_{Jup}}$, yielding a mean density of $59.0\pm8.1$~$\mathrm{g\,cm^{-3}}$. The host star is nearly a Solar twin with mass $M_\star$=$0.99\pm0.05$~$\mathrm{M_{\odot}}$, radius $R_\star$=$1.01\pm0.04$~$\mathrm{R_{\odot}}$, effective temperature $\mathrm{T_{eff}}$=$5850\pm85$~K and iron abundance [Fe/H]=$0.03\pm0.08$~dex. Its age, spectroscopic distance, and reddening are consistent with those of Ruprecht-147, corroborating its cluster membership. EPIC 219388192 b is the first brown dwarf with precise determinations of mass, radius and age, and serves as benchmark for evolutionary models in the sub-stellar regime.Comment: 13 pages, 11 figures, 4 tables, submitted to AAS Journal

Three Small Planets Transiting a Hyades Star

We present the discovery of three small planets transiting K2-136 (LP 358 348, EPIC 247589423), a late K dwarf in the Hyades. The planets have orbital periods of $7.9757 \pm 0.0011$, $17.30681^{+0.00034}_{-0.00036}$, and $25.5715^{+0.0038}_{-0.0040}$ days, and radii of $1.05 \pm 0.16$, $3.14 \pm 0.36$, and $1.55^{+0.24}_{-0.21}$ $R_\oplus$, respectively. With an age of 600-800 Myr, these planets are some of the smallest and youngest transiting planets known. Due to the relatively bright (J=9.1) host star, the planets are compelling targets for future characterization via radial velocity mass measurements and transmission spectroscopy. As the first known star with multiple transiting planets in a cluster, the system should be helpful for testing theories of planet formation and migration.Comment: Accepted to The Astronomical Journa

Exoplanets around Low-mass Stars Unveiled by K2

We present the detection and follow-up observations of planetary candidates around low-mass stars observed by the K2 mission. Based on light-curve analysis, adaptive-optics imaging, and optical spectroscopy at low and high resolution (including radial velocity measurements), we validate 16 planets around 12 low-mass stars observed during K2 campaigns 5-10. Among the 16 planets, 12 are newly validated, with orbital periods ranging from 0.96-33 days. For one of the planets (K2-151b) we present ground-based transit photometry, allowing us to refine the ephemerides. Combining our K2 M-dwarf planets together with the validated or confirmed planets found previously, we investigate the dependence of planet radius $R_p$ on stellar insolation and metallicity [Fe/H]. We confirm that for periods $P\lesssim 2$ days, planets with a radius $R_p\gtrsim 2\,R_\oplus$ are less common than planets with a radius between 1-2$\,R_\oplus$. We also see a hint of the "radius valley" between 1.5 and 2$\,R_\oplus$ that has been seen for close-in planets around FGK stars. These features in the radius/period distribution could be attributed to photoevaporation of planetary envelopes by high-energy photons from the host star, as they have for FGK stars. For the M dwarfs, though, the features are not as well defined, and we cannot rule out other explanations such as atmospheric loss from internal planetary heat sources, or truncation of the protoplanetary disk. There also appears to be a relation between planet size and metallicity: those few planets larger than about 3 $R_\oplus$ are found around the most metal-rich M dwarfs.Comment: 29 pages, 21 figures, 6 tables, Accepted in Astronomical Journa

The transiting multi-planet system HD3167: a 5.7 MEarth Super-Earth and a 8.3 MEarth mini-Neptune

HD3167 is a bright (V=8.9 mag) K0V star observed by the NASA's K2 space mission during its Campaign 8. It has been recently found to host two small transiting planets, namely, HD3167b, an ultra short period (0.96 d) super-Earth, and HD3167c, a mini-Neptune on a relatively long-period orbit (29.85 d). Here we present an intensive radial velocity follow-up of HD3167 performed with the FIES@NOT, [email protected], and HARPS-N@TNG spectrographs. We revise the system parameters and determine radii, masses, and densities of the two transiting planets by combining the K2 photometry with our spectroscopic data. With a mass of 5.69+/-0.44 MEarth, radius of 1.574+/-0.054 REarth, and mean density of 8.00(+1.0)(-0.98) g/cm^3, HD3167b joins the small group of ultra-short period planets known to have a rocky terrestrial composition. HD3167c has a mass of 8.33 (+1.79)(-1.85) MEarth and a radius of 2.740(+0.106)(-0.100) REarth, yielding a mean density of 2.21(+0.56)(-0.53) g/cm^3, indicative of a planet with a composition comprising a solid core surrounded by a thick atmospheric envelope. The rather large pressure scale height (about 350 km) and the brightness of the host star make HD3167c an ideal target for atmospheric characterization via transmission spectroscopy across a broad range of wavelengths. We found evidence of additional signals in the radial velocity measurements but the currently available data set does not allow us to draw any firm conclusion on the origin of the observed variation.Comment: 18 pages, 11 figures, 5 table

K2-60b and K2-107b. A Sub-Jovian and a Jovian Planet from the K2 Mission

We report the characterization and independent detection of K2-60b, as well as the detection and characterization of K2-107b, two transiting hot gaseous planets from the K2 space mission. We confirm the planetary nature of the two systems and determine their fundamental parameters combining the K2 time-series data with FIES @ NOT and HARPS-N @ TNG spectroscopic observations. K2-60b has a radius of 0.683 +/- 0.037 R-Jup and a mass of 0.426 +/- 0.037 M-Jup and orbits a G4 V star with an orbital period of 3.00267 +/- 0.00006 days. K2-107b has a radius of 1.44 +/- 0.15 R-Jup and a mass of 0.84 +/- 0.08 M-Jup and orbits an F9 IV star every 3.31392 +/- 0.00002 days. K2-60b is among the few planets at the edge of the so-called desert of short-period sub-Jovian planets. K2107b is a highly inflated Jovian planet orbiting an evolved star about to leave the main sequence