Translocating Wild California Valley Quail to Texas: An Evaluation of Survival, Dispersal, Tracking Efficacy, and Roost Preference

Quail translocations are becoming increasingly popular in regions of suitable habitat where local quail populations have declined. In northeastern Texas, USA, northern bobwhite (Colinus virginianus) populations have drastically declined for over a century and have reached undetectable levels in many areas. As a result, the number of quail hunters and quail conservation funding have also declined. California valley quail (Callipepla californica; hereafter, valley quail) have increased across their range and have been translocated to many states and countries. Thus, the goal of this study was to determine whether translocating wild valley quail to Texas was feasible, and evaluate their survival, dispersal, roost location preference, and potential predator impacts. We translocated 748 wild valley quail from Idaho, USA to northeastern Texas in 2019 and 2020. We collected quail location data from very high frequency (VHF) and digital transmitters. Motion-triggered cameras, scent stations, simulated nests, and raptor transects were used to record predator presence and potential predator impacts. Survival of birds with tracking devices was 63% (VHF) in 2019, and 38.8% (VHF) and 92.5% (digital tag) in 2020. Survival was greater for quail with digital transmitters. Median dispersal distance was 633.5 m in 2019 and 246.6 m in 2020 for valley quail with VHF transmitters, and 310.4 m for quail with digital transmitters. Minimum convex polygon area medians were 4.3 ha in 2019 and 3.1 ha in 2020 for quail with VHF transmitters, and 16.1 ha in 2020 for quail with digital transmitters. Roost sites were primarily in young stands of oak trees. Median simulated nest survival was 2 days (minimum [min] = 1, interquartile range [IQR] = 2–5.4, maximum [max] = 23) in 2019, and 7.5 days (min = 2, IQR = 4.5–15.2, max = 23) in 2020. The most frequent mammalian predators observed were raccoons (Procyon lotor), feral hogs (Sus scrofa), and white-tailed deer (Odocoileus virginianus). Red-tailed hawks (Buteo jamaicensis) were the most frequent aerial predator. We completed the first documented translocation of wild California valley quail to Texas, demonstrating it is feasible. Future translocation may benefit from translocating more birds over a longer period of time, with more consistent methodology. The establishment of a sustainable population may require ≥7 years of translocation at a rate of 500 birds per year with \u3e2,000 ha of suitable habitat

Early phase observations of extremely luminous Type Ia Supernova 2009dc

We present early phase observations in optical and near-infrared wavelengths for the extremely luminous Type Ia supernova (SN Ia) 2009dc. The decline rate of the light curve is $\Delta m_{15}(B)=0.65\pm 0.03$, which is one of the slowest among SNe Ia. The peak $V$-band absolute magnitude is $M_{V}=-19.90\pm 0.15$ mag even if the host extinction is $A_{V}=0$ mag. It reaches $M_{V}=-20.19\pm 0.19$ mag for the host extinction of $A_{V}=0.29$ mag as inferred from the observed Na {\sc i} D line absorption in the host. Our $JHK_{s}$-band photometry shows that the SN is one of the most luminous SNe Ia also in near-infrared wavelengths. These results indicate that SN 2009dc belongs to the most luminous class of SNe Ia, like SN 2003fg and SN 2006gz. We estimate the ejected $^{56}$Ni mass of $1.2\pm 0.3$ \Msun for no host extinction case (or 1.6$\pm$ 0.4 M$_{\odot}$ for the host extinction of $A_{V}=0.29$ mag). The C {\sc ii} $\lambda$6580 absorption line keeps visible until a week after maximum, which diminished in SN 2006gz before its maximum brightness. The line velocity of Si {\sc ii} $\lambda$6355 is about 8000 km s$^{-1}$ around the maximum, being considerably slower than that of SN 2006gz, while comparable to that of SN 2003fg. The velocity of the C {\sc ii} line is almost comparable to that of the Si {\sc ii}. The presence of the carbon line suggests that thick unburned C+O layers remain after the explosion. SN 2009dc is a plausible candidate of the super-Chandrasekhar mass SNe Ia

Assortative Mating on Ancestry-Variant Traits in Admixed Latin American Populations

Assortative mating is a universal feature of human societies, and individuals from ethnically diverse populations are known to mate assortatively based on similarities in genetic ancestry. However, little is currently known regarding the exact phenotypic cues, or their underlying genetic architecture, which inform ancestry-based assortative mating. We developed a novel approach, using genome-wide analysis of ancestry-specific haplotypes, to evaluate ancestry-based assortative mating on traits whose expression varies among the three continental population groups – African, European, and Native American – that admixed to form modern Latin American populations. Application of this method to genome sequences sampled from Colombia, Mexico, Peru, and Puerto Rico revealed widespread ancestry-based assortative mating. We discovered a number of anthropometric traits (body mass, height, and facial development) and neurological attributes (educational attainment and schizophrenia) that serve as phenotypic cues for ancestry-based assortative mating. Major histocompatibility complex (MHC) loci show population-specific patterns of both assortative and disassortative mating in Latin America. Ancestry-based assortative mating in the populations analyzed here appears to be driven primarily by African ancestry. This study serves as an example of how population genomic analyses can yield novel insights into human behavior

Population Pharmacogenomics for Precision Public Health in Colombia

While genomic approaches to precision medicine hold great promise, they remain prohibitively expensive for developing countries. The precision public health paradigm, whereby healthcare decisions are made at the level of populations as opposed to individuals, provides one way for the genomics revolution to directly impact health outcomes in the developing world. Genomic approaches to precision public health require a deep understanding of local population genomics, which is still missing for many developing countries. We are investigating the population genomics of genetic variants that mediate drug response in an effort to inform healthcare decisions in Colombia. Our work focuses on two neighboring populations with distinct ancestry profiles: Antioquia and Chocó. Antioquia has primarily European genetic ancestry followed by Native American and African components, whereas Chocó shows mainly African ancestry with lower levels of Native American and European admixture. We performed a survey of the global distribution of pharmacogenomic variants followed by a more focused study of pharmacogenomic allele frequency differences between the two Colombian populations. Worldwide, we found pharmacogenomic variants to have both unusually high minor allele frequencies and high levels of population differentiation. A number of these pharmacogenomic variants also show anomalous effect allele frequencies within and between the two Colombian populations, and these differences were found to be associated with their distinct genetic ancestry profiles. For example, the C allele of the single nucleotide polymorphism (SNP) rs4149056 [Solute Carrier Organic Anion Transporter Family Member 1B1 (SLCO1B1)∗5], which is associated with an increased risk of toxicity to a commonly prescribed statin, is found at relatively high frequency in Antioquia and is associated with European ancestry. In addition to pharmacogenomic alleles related to increased toxicity risk, we also have evidence that alleles related to dosage and metabolism have large frequency differences between the two populations, which are associated with their specific ancestries. Using these findings, we have developed and validated an inexpensive allele-specific PCR assay to test for the presence of such population-enriched pharmacogenomic SNPs in Colombia. These results serve as an example of how population-centered approaches to pharmacogenomics can help to realize the promise of precision medicine in resource-limited settings

The Baryon Oscillation Spectroscopic Survey of SDSS-III

The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large scale structure. BOSS uses 1.5 million luminous galaxies as faint as i=19.9 over 10,000 square degrees to measure BAO to redshifts z<0.7. Observations of neutral hydrogen in the Lyman alpha forest in more than 150,000 quasar spectra (g<22) will constrain BAO over the redshift range 2.15<z<3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Lyman alpha forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance D_A to an accuracy of 1.0% at redshifts z=0.3 and z=0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Lyman alpha forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate D_A(z) and H^{-1}(z) parameters to an accuracy of 1.9% at z~2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS.Comment: 49 pages, 16 figures, accepted by A

The Baryon Oscillation Spectroscopic Survey of SDSS-III

The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large-scale structure. BOSS uses 1.5 million luminous galaxies as faint as i = 19.9 over 10,000 deg(2) to measure BAO to redshifts z < 0.7. Observations of neutral hydrogen in the Ly alpha forest in more than 150,000 quasar spectra (g < 22) will constrain BAO over the redshift range 2.15 < z < 3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Ly alpha forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance d(A) to an accuracy of 1.0% at redshifts z = 0.3 and z = 0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Ly alpha forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate D-A(z) and H-1(z) parameters to an accuracy of 1.9% at z similar to 2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS

Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases

Genome-wide association studies (GWASs) have identified hundreds of susceptibility genes, including shared associations across clinically distinct autoimmune diseases. We performed an inverse χ(2) meta-analysis across ten pediatric-age-of-onset autoimmune diseases (pAIDs) in a case-control study including more than 6,035 cases and 10,718 shared population-based controls. We identified 27 genome-wide significant loci associated with one or more pAIDs, mapping to in silico-replicated autoimmune-associated genes (including IL2RA) and new candidate loci with established immunoregulatory functions such as ADGRL2, TENM3, ANKRD30A, ADCY7 and CD40LG. The pAID-associated single-nucleotide polymorphisms (SNPs) were functionally enriched for deoxyribonuclease (DNase)-hypersensitivity sites, expression quantitative trait loci (eQTLs), microRNA (miRNA)-binding sites and coding variants. We also identified biologically correlated, pAID-associated candidate gene sets on the basis of immune cell expression profiling and found evidence of genetic sharing. Network and protein-interaction analyses demonstrated converging roles for the signaling pathways of type 1, 2 and 17 helper T cells (TH1, TH2 and TH17), JAK-STAT, interferon and interleukin in multiple autoimmune diseases

Genetic ancestry, admixture and health determinants in Latin America

Abstract Background Modern Latin American populations were formed via genetic admixture among ancestral source populations from Africa, the Americas and Europe. We are interested in studying how combinations of genetic ancestry in admixed Latin American populations may impact genomic determinants of health and disease. For this study, we characterized the impact of ancestry and admixture on genetic variants that underlie health- and disease-related phenotypes in population genomic samples from Colombia, Mexico, Peru, and Puerto Rico. Results We analyzed a total of 347 admixed Latin American genomes along with 1102 putative ancestral source genomes from Africans, Europeans, and Native Americans. We characterized the genetic ancestry, relatedness, and admixture patterns for each of the admixed Latin American genomes, finding a spectrum of ancestry proportions within and between populations. We then identified single nucleotide polymorphisms (SNPs) with anomalous ancestry-enrichment patterns, i.e. SNPs that exist in any given Latin American population at a higher frequency than expected based on the population’s genetic ancestry profile. For this set of ancestry-enriched SNPs, we inspected their phenotypic impact on disease, metabolism, and the immune system. All four of the Latin American populations show ancestry-enrichment for a number of shared pathways, yielding evidence of similar selection pressures on these populations during their evolution. For example, all four populations show ancestry-enriched SNPs in multiple genes from immune system pathways, such as the cytokine receptor interaction, T cell receptor signaling, and antigen presentation pathways. We also found SNPs with excess African or European ancestry that are associated with ancestry-specific gene expression patterns and play crucial roles in the immune system and infectious disease responses. Genes from both the innate and adaptive immune system were found to be regulated by ancestry-enriched SNPs with population-specific regulatory effects. Conclusions Ancestry-enriched SNPs in Latin American populations have a substantial effect on health- and disease-related phenotypes. The concordant impact observed for same phenotypes across populations points to a process of adaptive introgression, whereby ancestry-enriched SNPs with specific functional utility appear to have been retained in modern populations by virtue of their effects on health and fitness