Spectral Line Selection for HMI: A Comparison of Fe I 6173 and Ni I 6768

We present a study of two spectral lines, Fe I 6173 Angstroms and Ni I 6768 Angstroms, that were candidates to be used in the Helioseismic and Magnetic Imager (HMI) for observing Doppler velocity and the vector magnetic field. The line profiles were studied using the Mt. Wilson Observatory, the Advanced Stokes Polarimeter and the Kitt Peak McMath telescope and one meter Fourier transform spectrometer atlas. Both Fe I and Ni I profiles have clean continua and no blends that threaten instrument performance. The Fe I line is 2% deeper, 15% narrower and has a 6% smaller equivalent width than the Ni I line. The potential of each spectral line to recover pre-assigned solar conditions is tested using a least-squares minimization technique to fit Milne-Eddington models to tens of thousands of line profiles that have been sampled at five spectral positions across the line. Overall, the Fe I line has a better performance than the Ni I line for vector magnetic field retrieval. We selected the Fe I spectral line for use in HMI due to its better performance for magnetic diagnostics while not sacrificing velocity information

Use of >100,000 NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium whole genome sequences improves imputation quality and detection of rare variant associations in admixed African and Hispanic/Latino populations

Most genome-wide association and fine-mapping studies to date have been conducted in individuals of European descent, and genetic studies of populations of Hispanic/Latino and African ancestry are limited. In addition, these populations have more complex linkage disequilibrium structure. In order to better define the genetic architecture of these understudied populations, we leveraged >100,000 phased sequences available from deep-coverage whole genome sequencing through the multi-ethnic NHLBI Trans-Omics for Precision Medicine (TOPMed) program to impute genotypes into admixed African and Hispanic/Latino samples with genome-wide genotyping array data. We demonstrated that using TOPMed sequencing data as the imputation reference panel improves genotype imputation quality in these populations, which subsequently enhanced gene-mapping power for complex traits. For rare variants with minor allele frequency (MAF) 86%. Subsequent association analyses of TOPMed reference panel-imputed genotype data with hematological traits (hemoglobin (HGB), hematocrit (HCT), and white blood cell count (WBC)) in ~21,600 African-ancestry and ~21,700 Hispanic/Latino individuals identified associations with two rare variants in the HBB gene (rs33930165 with higher WBC [p = 8.8x10-15] in African populations, rs11549407 with lower HGB [p = 1.5x10-12] and HCT [p = 8.8x10-10] in Hispanics/Latinos). By comparison, neither variant would have been genome-wide significant if either 1000 Genomes Project Phase 3 or Haplotype Reference Consortium reference panels had been used for imputation. Our findings highlight the utility of the TOPMed imputation reference panel for identification of novel rare variant associations not previously detected in similarly sized genome-wide studies of under-represented African and Hispanic/Latino populations

Phenotypic plasticity in adult life‐history strategies compensates for a poor start in life in Trinidadian Guppies (Poecilia reticulata)

Low food availability during early growth and development can have long‐term negative consequences for reproductive success. Phenotypic plasticity in adult life‐history decisions may help to mitigate these potential costs, yet adult life‐history responses to juvenile food conditions remain largely unexplored. I used a food‐manipulation experiment with female Trinidadian guppies (Poecilia reticulata) to examine age‐related changes in adult life‐history responses to early food conditions, whether these responses varied across different adult food conditions, and how these responses affected overall reproductive success. Guppy females reared on low food as juveniles matured at a later age, at a smaller size, and with less energy reserves than females reared on high food as juveniles. In response to this setback, they changed their investment in growth, reproduction, and fat storage throughout the adult stage such that they were able to catch up in body size, increase their reproductive output, and restore their energy reserves to levels comparable to those of females reared on high food as juveniles. The net effect was that adult female guppies did not merely mitigate but surprisingly were able to fully compensate for the potential long‐term negative effects of poor juvenile food conditions on reproductive success

First description of the nest, eggs, young, and breeding behavior of the Great Antpitta (Grallaria excelsa)

We provide the first description of the nest, eggs, young, and breeding behavior of the Great Antpitta (Grallaria excelsa) in Yacambu National Park, Venezuela. The nests (n = 3) were large, bulky, open-cup structures composed of a dense assortment of live and dead mosses, rootlets, wet leaves, small stems, detritus, and live and dead fern fronds, and were lined with a thick mesh of black rootlets and rhizomorphs. Nests were built >3.8 m above the ground in live trees where dense clusters of aroid plants, epiphytes, and lianas secured them to either a vertical fork or against the trunk itself. Both adults participated in nest building; incubating two unmarked, turquoise eggs; and feeding nestlings. Mean nest attentiveness (time spent on the nest/total video time when corrected for human disturbance) was 98.8 ± 1.8% SD, and nestling feeding rates were low (one visit by each adult/5 hr total video time)

A model for optimal offspring size in fish, including live-bearing and parental effects

Since Smith and Fretwell’s seminal article in 1974 on the optimal offspring size, most theory has assumed a trade-off between offspring number and offspring fitness, where larger offspring have better survival or fitness, but with diminishing returns. In this article, we use two ubiquitous biological mechanisms to derive the shape of this trade-off: the offspring’s growth rate combined with its size-dependent mortality (predation). For a large parameter region, we obtain the same sigmoid relationship between offspring size and offspring survival as Smith and Fretwell, but we also identify parameter regions where the optimal offspring size is as small or as large as possible. With increasing growth rate, the optimal offspring size is smaller. We then integrate our model with strategies of parental care. Egg guarding that reduces egg mortality favors smaller or larger offspring, depending on how mortality scales with size. For live-bearers, the survival of offspring to birth is a function of maternal survival; if the mother’s survival increases with her size, then the model predicts that larger mothers should produce larger offspring. When using parameters for Trinidadian guppies Poecilia reticulata, differences in both growth and size-dependent predation are required to predict observed differences in offspring size between wild populations from high- and low-predation environments

Nesting biology of the Black-bellied Wren (Thryothorus fasciatoventris) in central Panama

We describe the nest and nest site, and provide the first description of the eggs and nesting behavior of the Black-bellied Wren (Thryothorus fasciatoventris) in central Panama. Nine nests were found near tree-fall gaps, swamps, and roads in moist tropical forests. Nests were dome-shaped with a circular side entrance. They were composed chiefly of strips of dead palm fronds, and were generally built in places where leaf litter and other debris had accumulated at the convergence of several vines near the forest floor. Both males and females participated in building the nest. Clutch size was three, and eggs were laid on consecutive days. Egg color varied from creamy to beige with faint to dark brown speckles that were more concentrated at the blunt end. Females were the sole incubators, but males fed the incubating females. Only the female brooded the nestlings once they hatched, but both parents fed the nestlings

Fine-scale local adaptation in life histories along a continuous environmental gradient in Trinidadian guppies

<p>1. Theoretical models of life-history evolution predict a continuum of fast to slow life histories, yet most of empirical support for this theory comes from studies that have considered dichotomous environments (i.e. high vs. low food, presence or absence of major predators). Although this approach has been very successful in identifying the signature of local adaptation, it might limit our ability to identify the causes of underlying patterns of phenotypic variation. By studying the variation in life-history traits along continuous gradients, we can gain better insight into the diversity of adaptations exhibited by natural populations.</p> <p>2. We studied the evolution of life-history traits along a gradient of predation pressure in the Trinidadian guppy (Poecilia reticulata). Six localities along the Guanapo–Caroni River drainage were selected with respect to their predator community, going from upstream localities where guppies only coexist with a single gape-limited fish predator, to lowland sites where guppies coexist with a complex fish community. Along this gradient, we characterized the field pattern of phenotypic variation in age and size at maturity and reproductive effort. Further, to determine the genetic basis of this variation, we measured these traits in second-generation laboratory-born fish from the same localities sampled in the wild.</p> <p>3. In nature, we found a fine-scale pattern of phenotypic variation in most life-history traits that paralleled the continuous predation gradient. In the laboratory, we observed that reproductive allocation and brood size progressively decrease while age at maturity and interbrood interval progressively increase with a reduction in the predator community, suggesting a genetic basis to the parallel patterns observed in the field for reproductive allocation and offspring number.</p> <p>4. However, there were some exceptions to the observed pattern of variation. Females from one low-predation locality matured younger and reproduced more frequently than expected based upon the simple nature of the fish community. We also found significant differences between our field and laboratory results for embryo size, suggesting that this trait is highly plastic.</p> <p>5. Our results imply that local adaptation in guppies occurs at a finer scale than has previously been shown. Furthermore, while our results are consistent with predator-driven life-history variation, we also find patterns of plasticity that would not be apparent in the traditional dichotomous approach.</p&gt

Life-history and ecological correlates of geographic variation in egg and clutch mass among passerine species

Broad geographic patterns in egg and clutch mass are poorly described, and potential causes of variation remain largely unexamined. We describe interspecific variation in avian egg and clutch mass within and among diverse geographic regions and explore hypotheses related to allometry, clutch size, nest predation, adult mortality, and parental care as correlates and possible explanations of variation. We studied 74 species of Passeriformes at four latitudes on three continents: the north temperate United States, tropical Venezuela, subtropical Argentina, and south temperate South Africa. Egg and clutch mass increased with adult body mass in all locations, but differed among locations for the same body mass, demonstrating that egg and clutch mass have evolved to some extent independent of body mass among regions. A major portion of egg mass variation was explained by an inverse relationship with clutch size within and among regions, as predicted by life-history theory. However, clutch size did not explain all geographic differences in egg mass; eggs were smallest in South Africa despite small clutch sizes. These small eggs might be explained by high nest predation rates in South Africa; life-history theory predicts reduced reproductive effort under high risk of offspring mortality. This prediction was supported for clutch mass, which was inversely related to nest predation but not for egg mass. Nevertheless, clutch mass variation was not fully explained by nest predation, possibly reflecting interacting effects of adult mortality. Tests of the possible effects of nest predation on egg mass were compromised by limited power and by counterposing direct and indirect effects. Finally, components of parental investment, defined as effort per offspring, might be expected to positively coevolve. Indeed, egg mass, but not clutch mass, was greater in species that shared incubation by males and females compared with species in which only females incubate eggs. However, egg and clutch mass were not related to effort of parental care as measured by incubation attentiveness. Ecological and life-history correlates of egg and clutch mass variation found here follow from theory, but possible evolutionary causes deserve further study

SPIN: an inversion code for the photospheric spectral line

Inversion codes are the most useful tools to infer the physical properties of the solar atmosphere from the interpretation of Stokes profiles. In this paper, we present the details of a new Stokes Profile INversion code (SPIN) developed specifically to invert the spectro-polarimetric data of the Multi-Application Solar Telescope (MAST) at Udaipur Solar Observatory. The SPIN code has adopted Milne–Eddington approximations to solve the polarized radiative transfer equation (RTE) and for the purpose of fitting a modified Levenberg–Marquardt algorithm has been employed. We describe the details and utilization of the SPIN code to invert the spectro-polarimetric data. We also present the details of tests performed to validate the inversion code by comparing the results from the other widely used inversion codes (VFISV and SIR). The inverted results of the SPIN code after its application to Hinode/SP data have been compared with the inverted results from other inversion codes.by Rahul Yadav, Shibu K. Mathew and Alok Ranjan Tiwar