Patterns and Processes Shaping Avian Diversity in the Hawaiian Islands

Ph.D

Use of genomic data to resolve gene tree discordance in a Southeast Asian genus: Readdressing paraphyly in the spiderhunter (Nectariniidae, Arachnothera) phylogeny

Reduced representation genomic sequencing methods provide a fast and relatively inexpensive way to gather sequence data from thousands of loci throughout the genome. These data can be used to test previous phylogenetic hypotheses produced from limited numbers of mitochondrial and nuclear loci that often revealed intriguing, but conflicting results. In this paper, we use phylogenomic data to revisit molecular phylogenetic work that while clarifying taxonomic relationships within spiderhunters (Aves: Arachnothera), also questioned monophyly of this distinctive genus. Previous phylogenetic analysis of two molecular markers (one mitochondrial and one nuclear locus) produced conflicting topologies, yet both strongly supported non-monophyly of Arachnothera. This present study assesses the nature of pervasive gene tree discordance in these birds and investigates phylogenetic relationships within spiderhunters. To accomplish this, we used target-capture of ultra conserved elements (UCEs) to produce a phylogenomic data matrix used to infer the evolutionary history of Arachnothera. Although we recovered many gene tree topologies, concatenated and species-tree methods of analysis converged on a phylogeny with strong support for monophyly of Arachnothera. The consistency in analytical results confers confidence that gene tree conflict has been resolved in this enigmatic genus

Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus: Piranga)

This is a pre-copyedited, author-produced version of an article accepted for publication in Systematic Biology following peer review. The version of record, Joseph D. Manthey, Luke C. Campillo, Kevin J. Burns, Robert G. Moyle; Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus: Piranga), Systematic Biology, Volume 65, Issue 4, 1 July 2016, Pages 640–650, is available online at: ttps://doi.org/10.1093/sysbio/syw005.Restriction-site associated DNA sequencing (RAD-seq) and target capture of specific genomic regions, such as ultraconserved elements (UCEs), are emerging as two of the most popular methods for phylogenomics using reduced-representation genomic data sets. These two methods were designed to target different evolutionary timescales: RAD-seq was designed for population-genomic level questions and UCEs for deeper phylogenetics. The utility of both data sets to infer phylogenies across a variety of taxonomic levels has not been adequately compared within the same taxonomic system. Additionally, the effects of uninformative gene trees on species tree analyses (for target capture data) have not been explored. Here, we utilize RAD-seq and UCE data to infer a phylogeny of the bird genus Piranga. The group has a range of divergence dates (0.5–6 myr), contains 11 recognized species, and lacks a resolved phylogeny. We compared two species tree methods for the RAD-seq data and six species tree methods for the UCE data. Additionally, in the UCE data, we analyzed a complete matrix as well as data sets with only highly informative loci. A complete matrix of 189 UCE loci with 10 or more parsimony informative (PI) sites, and an approximately 80% complete matrix of 1128 PI single-nucleotide polymorphisms (SNPs) (from RAD-seq) yield the same fully resolved phylogeny of Piranga. We inferred non-monophyletic relationships of Pirangalutea individuals, with all other a priori species identified as monophyletic. Finally, we found that species tree analyses that included predominantly uninformative gene trees provided strong support for different topologies, with consistent phylogenetic results when limiting species tree analyses to highly informative loci or only using less informative loci with concatenation or methods meant for SNPs alone

Gull plumages are, and are not, what they appear to human vision

Clear correlations between human and bird visual assessments of color have been documented, and are often assumed, despite fundamental differences in human and avian visual physiology and morphology. Analyses of plumage colors with avian perceptual models have shown widespread hidden inter-sexual and inter-specific color variation among passerines perceived as monochromatic to humans, highlighting the uncertainty of human vision to predict potentially relevant variation in color. Herein, we use reflectance data from 13 Larus gull species as an exemplar data set to study concordance between human vision and avian visual modeling of feather colors near, or below, the human threshold for discrimination. We found little evidence among gulls for sexual dichromatism hidden from human vision, but did find inter-specific color variation among gulls that is not seen by humans. Neither of these results were predictable a priori, and we reassert that reflectance measurements of actual feather colors, analyzed with avian relevant visual models, represent best practice when studying bird coloration

Acute Effects of Different Inter-Repetition Rest Intervals During ‘Composite’ Training on Fast Stretch-Shortening Cycle and Neuromuscular Performance in Hurling Players: A Pilot Study

One study to date has compared inter-repetition rest intervals when employing ‘composite’ training. Thus, the purpose of this study was to compare the acute effects of 2-, 3- and 4-mins ‘composite’ training inter-repetition rest intervals on fast stretch shortening cycle (SSC) and neuromuscular performance. A randomized crossover research design was employed. Drop jump (DJ), 20m sprint (with 5 and 10m splits), countermovement jump (CMJ) and isometric mid-thigh pull (IMTP) tests were performed pre-session, post-session, and 7 days post-session to observe if supercompensation occurred. A 2-min rest interval showed enhancements in fast SSC DJ performance where supercompensation may have occurred in height, velocity, force and power (Cohen’s d = 0.22-0.55). A 3-minute rest interval elicited responses in 5 and 20m sprint performance (Cohen’s d = -0.29 to -0.30) and isometric RFD (Cohen’s d = 0.35-0.60) 7 days post-session. CMJ measures (Cohen’s d = 0.22-0.76) appeared to have experienced supercompensation when employing a 4-minute rest period. Significant (p < 0.05) decreases in performance pre- to post-session were found for certain sprint, CMJ and IMTP variables. The ‘composite’ training inter-repetition rest interval used, appears dependent on the primary goal of a training cycle. However, a 3-min rest interval may be used if there are multiple goals of a training cycle due to enhancements in sprint performance, isometric RFD and CMJ height. ‘Composite’ training is a time-efficient method of enhancing jump, sprint, and maximal strength, which is suitable for practitioners working in sports such as hurling where time is limited

Micro-combs: a novel generation of optical sources

The quest towards the integration of ultra-fast, high-precision optical clocks is reflected in the large number of high-impact papers on the topic published in the last few years. This interest has been catalysed by the impact that high-precision optical frequency combs (OFCs) have had on metrology and spectroscopy in the last decade [1–5]. OFCs are often referred to as optical rulers: their spectra consist of a precise sequence of discrete and equally-spaced spectral lines that represent precise marks in frequency. Their importance was recognised worldwide with the 2005 Nobel Prize being awarded to T.W. Hänsch and J. Hall for their breakthrough in OFC science [5]. They demonstrated that a coherent OFC source with a large spectrum – covering at least one octave – can be stabilised with a self-referenced approach, where the frequency and the phase do not vary and are completely determined by the source physical parameters. These fully stabilised OFCs solved the challenge of directly measuring optical frequencies and are now exploited as the most accurate time references available, ready to replace the current standard for time. Very recent advancements in the fabrication technology of optical micro-cavities [6] are contributing to the development of OFC sources. These efforts may open up the way to realise ultra-fast and stable optical clocks and pulsed sources with extremely high repetition-rates, in the form of compact and integrated devices. Indeed, the fabrication of high-quality factor (high-Q) micro-resonators, capable of dramatically amplifying the optical field, can be considered a photonics breakthrough that has boosted not only the scientific investigation of OFC sources [7–13] but also of optical sensors and compact light modulators [6,14]

Elective cancer surgery in COVID-19-free surgical pathways during the SARS-CoV-2 pandemic: An international, multicenter, comparative cohort study

PURPOSE As cancer surgery restarts after the first COVID-19 wave, health care providers urgently require data to determine where elective surgery is best performed. This study aimed to determine whether COVID-19–free surgical pathways were associated with lower postoperative pulmonary complication rates compared with hospitals with no defined pathway. PATIENTS AND METHODS This international, multicenter cohort study included patients who underwent elective surgery for 10 solid cancer types without preoperative suspicion of SARS-CoV-2. Participating hospitals included patients from local emergence of SARS-CoV-2 until April 19, 2020. At the time of surgery, hospitals were defined as having a COVID-19–free surgical pathway (complete segregation of the operating theater, critical care, and inpatient ward areas) or no defined pathway (incomplete or no segregation, areas shared with patients with COVID-19). The primary outcome was 30-day postoperative pulmonary complications (pneumonia, acute respiratory distress syndrome, unexpected ventilation). RESULTS Of 9,171 patients from 447 hospitals in 55 countries, 2,481 were operated on in COVID-19–free surgical pathways. Patients who underwent surgery within COVID-19–free surgical pathways were younger with fewer comorbidities than those in hospitals with no defined pathway but with similar proportions of major surgery. After adjustment, pulmonary complication rates were lower with COVID-19–free surgical pathways (2.2% v 4.9%; adjusted odds ratio [aOR], 0.62; 95% CI, 0.44 to 0.86). This was consistent in sensitivity analyses for low-risk patients (American Society of Anesthesiologists grade 1/2), propensity score–matched models, and patients with negative SARS-CoV-2 preoperative tests. The postoperative SARS-CoV-2 infection rate was also lower in COVID-19–free surgical pathways (2.1% v 3.6%; aOR, 0.53; 95% CI, 0.36 to 0.76). CONCLUSION Within available resources, dedicated COVID-19–free surgical pathways should be established to provide safe elective cancer surgery during current and before future SARS-CoV-2 outbreaks

Elective Cancer Surgery in COVID-19-Free Surgical Pathways During the SARS-CoV-2 Pandemic: An International, Multicenter, Comparative Cohort Study.

PURPOSE: As cancer surgery restarts after the first COVID-19 wave, health care providers urgently require data to determine where elective surgery is best performed. This study aimed to determine whether COVID-19-free surgical pathways were associated with lower postoperative pulmonary complication rates compared with hospitals with no defined pathway. PATIENTS AND METHODS: This international, multicenter cohort study included patients who underwent elective surgery for 10 solid cancer types without preoperative suspicion of SARS-CoV-2. Participating hospitals included patients from local emergence of SARS-CoV-2 until April 19, 2020. At the time of surgery, hospitals were defined as having a COVID-19-free surgical pathway (complete segregation of the operating theater, critical care, and inpatient ward areas) or no defined pathway (incomplete or no segregation, areas shared with patients with COVID-19). The primary outcome was 30-day postoperative pulmonary complications (pneumonia, acute respiratory distress syndrome, unexpected ventilation). RESULTS: Of 9,171 patients from 447 hospitals in 55 countries, 2,481 were operated on in COVID-19-free surgical pathways. Patients who underwent surgery within COVID-19-free surgical pathways were younger with fewer comorbidities than those in hospitals with no defined pathway but with similar proportions of major surgery. After adjustment, pulmonary complication rates were lower with COVID-19-free surgical pathways (2.2% v 4.9%; adjusted odds ratio [aOR], 0.62; 95% CI, 0.44 to 0.86). This was consistent in sensitivity analyses for low-risk patients (American Society of Anesthesiologists grade 1/2), propensity score-matched models, and patients with negative SARS-CoV-2 preoperative tests. The postoperative SARS-CoV-2 infection rate was also lower in COVID-19-free surgical pathways (2.1% v 3.6%; aOR, 0.53; 95% CI, 0.36 to 0.76). CONCLUSION: Within available resources, dedicated COVID-19-free surgical pathways should be established to provide safe elective cancer surgery during current and before future SARS-CoV-2 outbreaks

Contrasting Response to Predator and Brood Parasite Signals in the Song Sparrow (melospiza melodia)

Student paper, BIOL 3811, 2009The Song Sparrow is a widespread north American songbird that is preyed upon by the Cooper’s Hawk and is subject to nest parasitism by the Brown-Headed Cowbird. This study uses the response of twelve Song Sparrows, located around Itasca State Park, in terms of the frequencies of alarm call and song to investigate which threat is greater to this species in late June. The results show that the Song Sparrows do not consider the cowbird as a threat, but they certainly do consider the Cooper’s Hawk a threat with greatly suppressed song frequency.Campillo, Luke; Claus, Aaron. (2010). Contrasting Response to Predator and Brood Parasite Signals in the Song Sparrow (melospiza melodia). Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/97294