A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.Comment: 30 pages, 1 table, 4 figures, 1 supplementary table, 3 supplementary figure

The functional diversity of fish assemblages in the vicinity of oil and gas pipelines compared to nearby natural reef and soft sediment habitats

We would like to thank skippers John Totterdell and Kylie Skipper who assisted and made data collection possible. We acknowledge David Whillas and Kevin Holden who operated the stereo-ROV on the pipelines. The contributions of Laura Fullwood and Damon Driessen both in the field and with image analysis are gratefully acknowledged, as is Jack Park for his assistance with image analysis. This research project was funded by Chevron through its Anchor Partnership with the UK National Decommissioning Centre. We also acknowledge in-kind support from Net Zero Technology Centre and the University of Aberdeen through their partnership in the UK National Decommissioning Centre.Peer reviewedPublisher PD

Acute effects of ingesting Java Fit™ energy extreme functional coffee on resting energy expenditure and hemodynamic responses in male and female coffee drinkers

<p>Abstract</p> <p>Background</p> <p>The purpose of this study was to examine the effects of a functional coffee beverage containing additional caffeine, green tea extracts, niacin and garcinia cambogia to regular coffee to determine the effects on resting energy expenditure (REE) and hemodynamic variables.</p> <p>Methods</p> <p>Subjects included five male (26 ± 2.1 y, 97.16 ± 10.05 kg, 183.89 ± 6.60 cm) and five female (28.8 ± 5.3 y, 142.2 ± 12.6 lbs) regular coffee drinkers. Subjects fasted for 10 hours and were assessed for 1 hour prior (PRE) and 3 hours following 1.5 cups of coffee ingestion [JavaFit™ Energy Extreme (JF) ~400 mg total caffeine; Folgers (F) ~200 mg total caffeine] in a double-blind, crossover design. REE, resting heart rate (RHR), and systolic (SBP) and diastolic (DBP) blood pressure was assessed at PRE and 1, 2, and 3-hours post coffee ingestion. Data were analyzed by three-factor repeated measures ANOVA (p < 0.05).</p> <p>Results</p> <p>JF trial resulted in a significant main effect for REE (p < 0.01), SBP (p < 0.01), RER (p < 0.01), and VO₂(p < 0.01) compared to F, with no difference between trials on the RHR and DBP variables. A significant interaction for trial and time point (p < 0.05) was observed for the variable REE. The JF trial resulted in a significant overall mean increase in REE of 14.4% (males = 12.1%, females = 17.9%) over the observation period (p < 0.05), while the F trial produced an overall decrease in REE of 5.7%. SBP was significantly higher in the JF trial; however, there was no significant increase from PRE to 3-hours post.</p> <p>Conclusion</p> <p>Results from this study suggest that JavaFit™ Energy Extreme coffee is more effective than Folgers regular caffeinated coffee at increasing REE in regular coffee drinkers for up to 3 hours following ingestion without any adverse hemodynamic effects.</p

The effects of creatine ethyl ester supplementation combined with heavy resistance training on body composition, muscle performance, and serum and muscle creatine levels

Numerous creatine formulations have been developed primarily to maximize creatine absorption. Creatine ethyl ester is alleged to increase creatine bio-availability. This study examined how a seven-week supplementation regimen combined with resistance training affected body composition, muscle mass, muscle strength and power, serum and muscle creatine levels, and serum creatinine levels in 30 non-resistance-trained males. In a double-blind manner, participants were randomly assigned to a maltodextrose placebo (PLA), creatine monohydrate (CRT), or creatine ethyl ester (CEE) group. The supplements were orally ingested at a dose of 0.30 g/kg fat-free body mass (approximately 20 g/day) for five days followed by ingestion at 0.075 g/kg fat free mass (approximately 5 g/day) for 42 days. Results showed significantly higher serum creatine concentrations in PLA (p = 0.007) and CRT (p = 0.005) compared to CEE. Serum creatinine was greater in CEE compared to the PLA (p = 0.001) and CRT (p = 0.001) and increased at days 6, 27, and 48. Total muscle creatine content was significantly higher in CRT (p = 0.026) and CEE (p = 0.041) compared to PLA, with no differences between CRT and CEE. Significant changes over time were observed for body composition, body water, muscle strength and power variables, but no significant differences were observed between groups. In conclusion, when compared to creatine monohydrate, creatine ethyl ester was not as effective at increasing serum and muscle creatine levels or in improving body composition, muscle mass, strength, and power. Therefore, the improvements in these variables can most likely be attributed to the training protocol itself, rather than the supplementation regimen

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales

Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels. © The Author(s) 2012. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved

Adverse Childhood Experiences and Urinary Incontinence in Elementary School Aged Children

Purpose/Background: Adverse Childhood Experiences (ACEs) have an impact on health throughout the lifespan (Filletti et al., 1999; Hughes et al., 2017). These experiences range from physical and mental abuse, substance abuse in the home, parental separation or loss, financial instability, acute illness or injury, witnessing violence in the home or community, and incarceration of family members (Hughes et al., 2017). Understanding and screening for ACEs in children with urinary incontinence can help practitioners identify psychological stress as a potentially modifiable risk factor. Methods: A 5-month chart review was performed identifying English speaking patients ages 6-11 years presenting to the outpatient urology office for an initial visit with a primary diagnosis of urinary incontinence. Charts were reviewed for documentation of individual or family risk factors for ACEs exposure, community risk factors for ACEs exposures, and records where no related documentation was included. Results: For the thirty-nine patients identified, no community risk factors were noted in the charts. Seventy-nine percent of patients had one or more individual or family risk factors documented. Implications for Nursing Practice This chart review indicates that a significant percentage of pediatric, school-aged patients presenting with urinary incontinence have exposure to ACEs. A formal assessment for ACEs at the time of initial presentation would be helpful to identify those at highest risk. References: Felitti VJ, Anda RF, Nordenberg D, Williamson DF, Spitz AM, Edwards V, Koss MP, Marks JS. Relationship of childhood abuse and household dysfunction to many of the leading causes of death in adults: the adverse childhood experiences (ACE) study. Am J Prev Med. 1998;14:245–258 Hughes, K., Bellis, M.A., Hardcastle, K.A., Sethi, D., Butchart, D., Mikton, C., Jones, L., Dunne, M.P. (2017) The effect of multiple adverse childhood experiences on health: a systematic review and meta-analysis. Lancet Public Health, 2(8): e356–e366. Published online 2017 Jul 31.doi: 10.1016/S2468-2667(17)30118-4 Lai, H., Gardner, V., Vetter, J., & Andriole, G. L. (2015). Correlation between psychological stress levels and the severity of overactive bladder symptoms. BMC urology, 15, 14. doi:10.1186/s12894-015-0009-