Comparing the Accuracy of Egg Candling and Egg Flotation to Estimate the Hatching Date of Northern Bobwhite Clutches

Floating and candling avian eggs to assess hatch dates has been used successfully to estimate hatch dates for wild bird clutches for decades. However, there is a dearth of information assessing the accuracy of these techniques to estimate northern bobwhite (Colinus virginianus) hatch dates. We captured and fitted a hen bobwhites with very high frequency transmitters during January and February of 2011–2012. We monitored each bird twice weekly until nesting was initiated. We searched for the nest while the hen was away from the nest (i.e., feeding) to reduce potential abandonment. We used egg floatation and egg candling methods to attempt to estimate wild northern bobwhite clutches during the 2011–2012 nesting seasons. We used a mini MagLite© (97 lumens; Mag Instrument, Inc., Ontario, CA, USA) with the glass lens removed so eggs would sit near the bulb to increase the illumination. We used a dark green 68-cm x 137-cm towel to cover the observer in the field to reduce the naturally occurring light, which might have reduced the visibility of the chick embryo. We based age of the eggs (no. of days since the start of incubation) on the embryo growth stage at the time of nest discovery. We conducted egg flotation at the same time as candling. We used a 100-mL glass beaker with 100-mL of ambient temperature tap water to completely submerge the egg to estimate hatch date. We based the flotation estimation age on the angle at which the egg floated in the water. We also conducted a controlled laboratory experiment using pen-raised quail eggs collected from the breeding colony at the Quail-Tech Alliance breeding facility in Lubbock, Texas. We placed 110 eggs in a commercial incubator that was maintained at 37° C with 55% humidity for the duration of the study. We used 3 novice observers to determine the impact of observer bias on the techniques of estimating hatch date. We placed random groups of eggs (i.e., 5–15 eggs at a time until 110 eggs were obtained) into the incubator at a staggered rate to increase variation in the study. We used the same field techniques for hatch date estimation in the controlled study. We first floated eggs during both controlled and field observations to reduce any potential bias that candling might have on the hatch date estimation (i.e., lack of embryo growth). During the controlled study observers examined the eggs individually. Using the average estimated hatch date (Julian date) as a predictor, we used linear regression to determine the accuracy of the candling and floating methods. We also used a linear regression to determine the accuracy of each estimation technique and observers. When candle and egg floating occurred in a field setting, both methods were found to overestimate the actual hatch date of the clutches discovered (n = 47; R2 = 0.993, P \u3c 0.001; estimated hatch days when using candle: x̄ = 1.21 ± 0.92 days, floating: x̄ = 0.89 ± 0.97 days). However, the mean difference between the candling and flotation was -0.38 days (SE = 1.07 days). Regression analysis suggests that candling and egg flotation are fairly accurate predictors of the actual hatch date for newly discovered bobwhite nests (candling: β = 0.43, t = 3.75, P = 0.001; floating: β = 0.53, t = 4.79, P \u3c 0.001). Use of the candling method appears to be correct 43% of the time whereas egg flotation accurately predicted the estimated hatch date 53% of the time. Under controlled conditions, all 3 observers were new to both techniques of hatch date estimation and were all taught by the same instructor for each method. During the controlled test, we found that observers were highly variable. Two observers could predict the estimated hatch date by using the candling and egg flotation methods to a close estimation of the actual hatch date (floating [observer 1: β = 0.23, t = 2.80, P = 0.006 and observer 2: β = 0.47, t = 5.52, P \u3c 0.001]; candling [observer 1: β = 0.30, t = 4.00, P = 0.006, observer 2: β = 0.219, P \u3c 0.01]). Although observer 3 was unable to predict the estimated hatch date for both estimation methods (floating: β = –0.001, t = –0.013, P = 0.684; candling: β = 0.043, t = 0.40, P = 0.990). We also examined any potential abandonment or hatchability issues that might have risen while using candling or floating to estimate hatch dates for wild clutches. We found that 0.06% (5 of 80 nests) of hens abandoned their clutches during this study. Of the 5 nests that were abandoned zero were abandoned because of measurements obtained during the initial investigation of the nest site. All abandonments were due to either weather (i.e., summer hail), predators, or livestock. Viability and hatchability were unaffected for the remaining clutches that were measured during the field study. We found that candling and egg flotation are both viable methods for estimating hatch dates of bobwhite clutches during an initial measurement when a nest is discovered. When an entire clutch is measured accuracy can be within 1 day of the actual estimated hatch date (based on a 24-day incubation period). However, observers or researchers who will estimate hatch dates for clutches should be properly trained and allowed time to acclimate to the measuring techniques to potentially increase their accuracy at estimating hatch dates for northern bobwhite clutches

Evaluation of a Solar-Recharged Micro-GPS Datalogger for Northern Bobwhite in the Rolling Plains of Texas

The use of Global Positioning Systems (GPS) transmitters on northern bobwhite (Colinus virginianus; hereafter, bobwhite) could increase our understanding of fine-scale movements and habitat use for a declining game bird species. We evaluated solar-recharged micro-GPS dataloggers to determine the effectiveness of the units on free-ranging bobwhite and we conducted a controlled experiment to determine the accuracy of the dataloggers under a variety of canopy cover. We deployed the micro-GPS dataloggers on 25 bobwhites between August 2016 and April 2017 across 4 different ranches in the Rolling Plains of West Texas, USA. Accuracy (± standard error) for the 8 dataloggers across 3 trials for the stationary tests was 25.4 ± 3.8 m. Daily movement of bobwhite averaged 0.96 ± 0.09 km and morning movements averaged 0.49 ± 0.07 km. Average 95% and 50% minimum convex polygons for bobwhite area utilization were 15.2 ha and 3.6 ha, respectively. Our data indicate that solar-recharged micro-GPS dataloggers can be used to monitor bobwhites’ short-term fine-scale movements in West Texas

Genetic Structure of Northern Bobwhite in the Rolling Plains

The recent declines in northern bobwhite quail populations in the Rolling Plains of Texas have raised concerns about habitat connectivity and gene flow. In addition, bobwhites have several life history traits that make them likely to display high levels of spatial genetic structure including low survival, high reproductive rates, and low dispersal rates. To determine if populations within the Rolling Plains have limited gene flow, we investigated the genetic structure of northern bobwhites within the ecoregion. Blood samples were collected at 16 ranches, encompassing 22 million acres, between February 2010 and April 2013. Bobwhites were also samples at a ranch in South Texas to serve as an outgroup. Samples (n = 647) were genotyped at 14 microsatellite loci that averaged 19.00 ± 5.07 alleles per loci. Global Fst indicated significant genetic structure (p = 0.001) between ranches with no isolation by distance signal (p = 0.079). Program STRUCTURE, however, indicated many (n = 30) overlapping subpopulations with no ranch constituting a single subpopulation and individuals from the outgroup ranch were included in 11 subpopulations. It appears that bobwhites within the Rolling Plains have few restrictions to gene flow and dispersal is not limited by the dominant habitat, xeric rangeland. These results suggest that populations in the Rolling Plains are not in danger of becoming isolated nor are bottlenecks present due to the recent decline

Exclosures: An Experimental Technique for Protection of Northern Bobwhite Nests

Nest predation has been implicated as a factor affecting northern bobwhite (Colinus virginianus) recruitment rates. Public stakeholders are increasingly questioning use of lethal methods to manage predation. We evaluated a nonlethal method consisting of single nest treatments using an exclosure to protect nests from potential predators. The exclosure treatment also included use of Amdrot (hydramethylnon) and Snake-a-wayt repellents to deter red-imported fire ants (Solenopsis invicta) and snakes, respectively. We compared nest success of treated (n 1⁄4 8) to untreated nests (n 1⁄4 18). Treated nests were 88% successful which was a 2-fold increase over unprotected nests. We did not observe any difference in hen behavior between treatment and controls. This technique may be useful to study nest success of wild quail and is not intended to be a management technique to influence overall population growth

Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains

.Sequencing of the non-pathogenic Francisella tularensis sub-species novicida U112, and comparison with two pathogenic sub-species, provides insights into the evolution of pathogenicity in these species

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

Online Correction for: https://doi.org/10.1038/s41586-020-2493-4 | Erratum for https://bura.brunel.ac.uk/handle/2438/21299In the version of this article initially published, two members of the ENCODE Project Consortium were missing from the author list. Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) are now included in the author list. These errors have been corrected in the online version of the article : 'Expanded encyclopaedias of DNA elements in the human and mouse genomes'.https://www.nature.com/articles/s41586-021-04226-3https://www.nature.com/articles/s41586-021-04226-

AD51B in Familial Breast Cancer

Common variation on 14q24.1, close to RAD51B, has been associated with breast cancer: rs999737 and rs2588809 with the risk of female breast cancer and rs1314913 with the risk of male breast cancer. The aim of this study was to investigate the role of RAD51B variants in breast cancer predisposition, particularly in the context of familial breast cancer in Finland. We sequenced the coding region of RAD51B in 168 Finnish breast cancer patients from the Helsinki region for identification of possible recurrent founder mutations. In addition, we studied the known rs999737, rs2588809, and rs1314913 SNPs and RAD51B haplotypes in 44,791 breast cancer cases and 43,583 controls from 40 studies participating in the Breast Cancer Association Consortium (BCAC) that were genotyped on a custom chip (iCOGS). We identified one putatively pathogenic missense mutation c.541C>T among the Finnish cancer patients and subsequently genotyped the mutation in additional breast cancer cases (n = 5259) and population controls (n = 3586) from Finland and Belarus. No significant association with breast cancer risk was seen in the meta-analysis of the Finnish datasets or in the large BCAC dataset. The association with previously identified risk variants rs999737, rs2588809, and rs1314913 was replicated among all breast cancer cases and also among familial cases in the BCAC dataset. The most significant association was observed for the haplotype carrying the risk-alleles of all the three SNPs both among all cases (odds ratio (OR): 1.15, 95% confidence interval (CI): 1.11–1.19, P = 8.88 x 10−16) and among familial cases (OR: 1.24, 95% CI: 1.16–1.32, P = 6.19 x 10−11), compared to the haplotype with the respective protective alleles. Our results suggest that loss-of-function mutations in RAD51B are rare, but common variation at the RAD51B region is significantly associated with familial breast cancer risk

Perspectives on ENCODE

Supplementary information is available for this paper at https://doi.org/10.1038/s41586-020- 2449-8.© 2020, The Author(s). The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.NIH grants: U01HG007019, U01HG007033, U01HG007036, U01HG007037, U41HG006992, U41HG006993, U41HG006994, U41HG006995, U41HG006996, U41HG006997, U41HG006998, U41HG006999, U41HG007000, U41HG007001, U41HG007002, U41HG007003, U41HG007234, U54HG006991, U54HG006997, U54HG006998, U54HG007004, U54HG007005, U54HG007010 and UM1HG009442