Holmium:yttrium-aluminium-garnet laser with MOSES technology is more efficient than thulium fibre laser in supine mini-percutaneous nephrolithotomy.

OBJECTIVES: To address the paucity of literature comparing outcomes achieved with utilisation of the high-power holmium:yttrium-aluminium-garnet (Ho:YAG) laser with MOSES technology vs those achieved with the thulium fibre laser (TFL) in mini-percutaneous nephrolithotomy (PCNL). METHODS: A retrospective review was performed of patients undergoing supine mini-PCNL between August 2021 and May 2023. Exclusion criteria were urinary diversion, simultaneous utilisation of >1 laser platform, use of any other form of fragmentation, and ureteric stones. The Ho:YAG platform (Lumenis Pulse P120H™ with MOSES technology, 120W; Boston Scientific®) and the TFL (Soltive SuperPulsed Thulium Fibre [SPTF], 60W; Olympus®) were compared. Data on stone-free rate (SFR) were determined by computed tomography performed on the first postoperative day and presented as absence of stone fragments, no fragments larger than 2 mm, or no fragments larger than 4 mm. RESULTS: A total of 100 patients met the inclusion criteria, 51 mini-PCNLs with the Ho:YAG laser and 49 with the SPTF laser. No significant differences in demographics or stone characteristics were detected between the two groups. The Ho:YAG laser utilised less energy and time, resulting in higher ablation efficiency (P < 0.05) and less total operating time (P < 0.05). Overall, there was no difference in SFR in any category between the Ho:YAG group and the SPTF group (no fragments: relative risk [RR] 0.81, 95% confidence interval [CI] 0.59-1.12, P = 0.21; fragments <2 mm: RR 0.86, 95% CI 0.67-1.10, P = 0.23; fragments <4 mm: RR 0.96, 95% CI 0.80-1.15, P = 0.67). CONCLUSIONS: Although we observed an equivalent postoperative SFR, this study supports a shorter operating time and greater intra-operative laser efficiency with the Ho:YAG laser over the SPTF laser in mini-PCNL.

Complexity of avian evolution revealed by family-level genomes.

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1-3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data.

Phylogenomic data provide valuable opportunities for studying evolutionary rates and timescales. These analyses require theoretical and statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing evolutionary rate signals in phylogenomic data. Here, information about evolutionary rates in branches across gene trees is placed in Euclidean space, allowing data transformation, visualization, and hypothesis testing. ClockstaRX implements formal tests for identifying groups of loci and branches that make a large contribution to patterns of rate variation. This information can then be used to test for drivers of genomic evolutionary rates or to inform models for molecular dating. Drawing on the results of a simulation study, we recommend forms of data exploration and filtering that might be useful prior to molecular-clock analyses.

Impact of Renal Access Angle and Speed of Nephroscope Retrieval Movements on the Vortex Effect.

OBJECTIVE: To analyze the influence of different renal access angles (AAs) and nephroscope retrieval speeds on the efficacy of the vortex effect (VE) in mini-percutaneous nephrolithotomy (mini-PCNL). This study aimed to understand the poorly understood physical components of the VE. MATERIALS AND METHODS: A Pexiglas™ (KUS®) model was built based on the dimensions of a 15/16 F mini-PCNL set (Karl Storz). The flow rate was continuous via an automatic pump and calibrated to achieve hydrodynamic equivalence to the real equipment. One experiment consisted of manually retrieving all 30 stone phantoms (3 mm diameter) utilizing only the VE. Cumulative time to retrieve all stones was measured. An accelerometer recorded instant speeds of the nephroscope every 0.08 seconds (s), and 3 experiments were performed at each angle (0°, 45°, and 90°). A logistic regression model was built utilizing maximum speeds and access angles to predict the effectiveness of the VE. RESULTS: Mean cumulative time for complete stone retrieval was 28.1 seconds at 0° vs 116.5 seconds at 45° vs 101.4 seconds at 90° (P < .01). We noted significantly higher speeds at 0° compared to 45° and 90° (P < .01); however, differences in average and maximum speed between 45° and 90° were not statistically significant (P = .21 and P = .25, respectively). The regression model demonstrated a negative association between increasing maximum speed and VE's effectiveness (OR 0.547, CI 95% 0.350-0.855, P < .01). When controlling for maximum speed, the 0° angle had significantly higher chances of achieving at least a partially effective VE. CONCLUSION: Increasing the renal access angle or nephroscope extraction speed negatively impacts the effectiveness of the VE. This significantly increased procedure time in the laboratory model, suggesting that the VE is less effective at higher sheath angles.

The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference.

Birth-death models are stochastic processes describing speciation and extinction through time and across taxa and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under the constant-rate birth-death (crBD) model tend to differ from empirical trees, for example, with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between the crBD model and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which the crBD model differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD model trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used Bayesian methods and crBD priors with those that used other non-crBD priors and non-Bayesian methods (i.e., maximum likelihood methods), we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using the crBD model in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios but also highlight that empirically observed phylogenetic imbalance is highly improbable under the crBD model, leading to systematic bias in data sets with limited information content.

Leaping through Tree Space: Continuous Phylogenetic Inference for Rooted and Unrooted Trees.

Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains challenging. To address this problem, for the first time, we perform both tree exploration and inference in a continuous space where the computation of gradients is possible. This continuous relaxation allows for major leaps across tree space in both rooted and unrooted trees, and is less susceptible to convergence to local minima. Our approach outperforms the current best methods for inference on unrooted trees and, in simulation, accurately infers the tree and root in ultrametric cases. The approach is effective in cases of empirical data with negligible amounts of data, which we demonstrate on the phylogeny of jawed vertebrates. Indeed, only a few genes with an ultrametric signal were generally sufficient for resolving the major lineages of vertebrates. Optimization is possible via automatic differentiation and our method presents an effective way forward for exploring the most difficult, data-deficient phylogenetic questions.

A genomic assessment of the marine-speciation paradox within the toothed whale superfamily Delphinoidea.

The impact of post-divergence gene flow in speciation has been documented across a range of taxa in recent years, and may have been especially widespread in highly mobile, wide-ranging marine species, such as cetaceans. Here, we studied individual genomes from nine species across the three families of the toothed whale superfamily Delphinoidea (Delphinidae, Phocoenidae and Monodontidae). To investigate the role of post-divergence gene flow in the speciation process, we used a multifaceted approach, including (i) phylogenomics, (ii) the distribution of shared derived alleles and (iii) demographic inference. We found the divergence of lineages within Delphinoidea did not follow a process of pure bifurcation, but was much more complex. Sliding-window phylogenomics reveal a high prevalence of discordant topologies within the superfamily, with further analyses indicating these discordances arose due to both incomplete lineage sorting and gene flow. D-statistics and f-branch analyses supported gene flow between members of Delphinoidea, with the vast majority of gene flow occurring as ancient interfamilial events. Demographic analyses provided evidence that introgressive gene flow has likely ceased between all species pairs tested, despite reports of contemporary interspecific hybrids. Our study provides the first steps towards resolving the large complexity of speciation within Delphinoidea; we reveal the prevalence of ancient interfamilial gene flow events prior to the diversification of each family, and suggest that contemporary hybridisation events may be disadvantageous, as hybrid individuals do not appear to contribute to the parental species' gene pools.

The Vortex Effect in Minimally Invasive Percutaneous Nephrolithotomy.

OBJECTIVE: To describe the physical principles of the vortex effect to better understand its applicability in minimally invasive percutaneous nephrolithotomy (MIP) procedures. METHODS: Two acrylic phantom models were built based on the cross-sectional area (CSA) ratio of a MIP nephroscope and access sheaths (15/16F and 21/22F MIP-M, Karl Storz). The nephroscope phantom was 10 mm in diameter. The access sheaths had diameters of 14 mm (CSA ratio: 0.69) and 20 mm (CSA ratio: 0.30). The models were adapted to generate hydrolysis, and hydrogen bubbles enhanced flow visualization on a green laser background. After calibration, the experimental flow rate was set to 12.0 mL/s. Three 30-second trials assessing the flow were performed with each model. Computational fluid dynamic simulations were completed to determine the speed and pressure profiles. RESULTS: In both models, as the incoming fluid from the nephroscope phantom attempted to move toward the collecting system, a stagnation point was demonstrated. No fluid entered the collecting system phantom. Utilizing the 14 mm sheath, we observed a random generation of several vortices and a pressure gradient (PG) of 114.4 N/m2 between the nephroscope's tip and stagnation point. In contrast, examining the 20 mm sheath revealed a significantly smaller PG (19.4 N/m2) and no noticeable vortices were noted. CONCLUSION: The speed of the fluid and equipment geometry regulate the PG and the vortices field, which are responsible for the production of the vortex effect. Considering the same flow rate, a higher ratio between the CSA of the nephroscope and access sheath results in improved efficacy of the vortex effect.

Optimizing stone harvesting in miniaturized-PCNL: a critical examination of renal access angles, technology, and the role they play in operative efficiency.

PURPOSE: Stone retrieval can be a laborious aspect of percutaneous nephrolithotomy (PCNL). A unique phenomenon of mini-PCNL is the vortex-effect (VE), a hydrodynamic form of stone retrieval. Additionally, the vacuum-assisted sheath (VAS) was recently developed as a new tool for stone extraction. The purpose of our study is to investigate the impact of renal access angle (as a surrogate for patient positioning) on stone retrieval efficiency and compare the efficiency among methods of stone retrieval. METHODS: A kidney model was filled with 3 mm artificial stones. Access to the mid-calyx was obtained using a 15Fr sheath. Stones were retrieved over three minutes at angles of 0°, 25°, and 75° utilizing the VE, VAS, and basket. Stones were weighed for comparison of stones/retraction and stones/minute. Trials were repeated three times at each angle. RESULTS: Renal access angle of 0° was associated with increased stone retrieval for both the VE and VAS (p < 0.05). The VE was the most effective method for stones retrieved per individual retraction at an angle of 0° (p < 0.005), although when analyzed as stones retrieved per minute, the VE and VAS were no longer statistically different (p = 0.08). At 75°, none of the methods were statistically different, regardless if analyzed as stones per retraction or per minute (p = 0.20-0.40). CONCLUSIONS: Renal access angle of 0° is more efficient for stone retrieval than a steep upward angle. There is no difference in stone retrieval efficiency between the VE and VAS methods, although both are superior to the basket at lower sheath angles.

Recanalize ureteral stents with focused ultrasound.

BACKGROUND: Maintaining ureteral patency is imperative to preventing renal injury and systemic infection. Ureteral stents are small conduits connecting the kidney and the bladder. They have been widely used to treat ureteral obstructions and ureteral leaks. The most problematic and frequent stent-associated complication is stent encrustation. This occurs when mineral crystals (e.g. calcium, oxalate, phosphorus, struvite) are deposited onto the surface and internal lumen of the stent. Encrustation can lead to the obstruction of a stent and increases risk of systemic infection. As a result, ureteral stents need to be replaced typically every 2-3 months. PURPOSE: In this study, we present a non-invasive, high-intensity focused ultrasound (HIFU)-based technique to recanalize obstructed stents. By taking advantage of the mechanical force produced by a HIFU beam, including acoustic radiation force, acoustic streaming, and cavitation, HIFU can break up encrustations, clearing the stent of obstruction. METHODS: The ureteral stents for this study were obtained from patients undergoing ureteral stent removal. Under the guidance of ultrasound imaging, the encrustation in the stents were located, and then targeted by HIFU at frequencies of 0.25 and 1 MHz. The duty cycle of HIFU was 10%, and the HIFU burst repetition rate was 1 Hz, while the HIFU amplitude was varied to find the threshold pressure that would displace encrustations. The treatment duration was limited at 2 min (or 120 shots from HIFU). The treatments were carried out in two different orientations (parallel and perpendicular) of the ureteral stent with respect to the HIFU beam. For each setting, five treatments were conducted for a maximum duration of 2 min. During the entire treatment, an ultrasound imaging system was used to monitor the movement of encrustations inside the stent. The peak negative HIFU pressures needed to move the encrustations inside the stent was recorded for quantitative analysis. RESULTS: Our results demonstrated that at both 0.25 and 1 MHz ultrasound frequencies, obstructed stents could be recanalized. At 0.25 MHz, the needed average peak negative pressure was 0.52 MPa in parallel orientation and 0.42 MPa in perpendicular orientation. At 1 MHz, the needed average peak negative pressure was 1.10 MPa in parallel orientation and 1.15 MPa in perpendicular orientation CONCLUSIONS: This first in-vitro study has demonstrated the feasibility of non-invasive HIFU to recanalize ureteral stents. This technology has a potential to reduce the need for ureteral stent exchange.

On the rocks: can urologists identify stone composition based on endoscopic images alone? A worldwide survey of urologists.

PURPOSE: As part of the management of nephrolithiasis, determination of chemical composition of stones is important. Our objective in this study is to assess urologists' accuracy in making visual, intraoperative determinations of stone composition. MATERIALS AND METHODS: We conducted a REDCap survey asking urologists to predict stone composition based on intraoperative images of 10 different pure-composition kidney stones of 7 different types: calcium oxalate monohydrate (COM), calcium oxalate dihydrate (COD), calcium phosphate (CP) apatite, CP brushite, uric acid (UA), struvite (ST) and cystine (CY). To evaluate experience, we examined specific endourologic training, years of experience, and number of ureteroscopy (URS) cases/week. A self-assessment of ability to identify stone composition was also required. RESULTS: With a response rate of 26% (366 completed surveys out of 1,370 deliveries), the overall accuracy of our cohort was 44%. COM, ST, and COD obtained the most successful identification rates (65.9%, 55.7%, and 52.0%, respectively). The most frequent misidentified stones were CP apatite (10.7%) and CY (14.2%). Predictors of increased overall accuracy included self-perceived ability to determine composition and number of ureteroscopies per week, while years of experience did not show a positive correlation. CONCLUSIONS: Although endoscopic stone recognition can be an important tool for surgeons, it is not reliable enough to be utilized as a single method for stone identification, suggesting that urologists need to refine their ability to successfully recognize specific stone compositions intraoperatively.

Breakage Costs in Flexible Ureteroscopy: Digital vs. Fiberoptic Modalities.

OBJECTIVE: To compare the maintenance costs of digital flexible ureteroscopes (DFU) versus fiberoptic flexible ureteroscopes (FFU) to understand the long-term financial impact associated with breakage in a flexible ureteroscopy (f-URS) program. METHODS: Data for breakage of FFU and DFU at an academic institution from 2019 to 2021 were obtained from our vendor (Karl Storz) and analyzed by month. Correlation test was used to evaluate significant differences in number of procedures, number of breakage events, breakage rates, and repair cost per month. Cumulative analyses were utilized to examine the number of procedures before failure (time to failure - TTF) and repair costs per procedure (RCpP). RESULTS: We performed a total of 2,154 f-URS, including 1,355 with FFU and 799 with DFU (P<.001). Although we found a higher number of breakage events in FFU (n=124) than DFU (n=73) (P<.001), the overall breakage rate was similar, 9.9% vs. 8.8%, respectively (P=0.86). On cumulative analysis, both modalities reached the same TTF plateau (11 cases) after 18 months. After 400 cases, the RCpP for DFU was 1.25 times higher than for FFU (P=0.04). CONCLUSION: Overall, we found no difference in overall scope breakage rates between DFU and FFU. Although there was no difference in TTF over time, at the beginning DFU displayed considerable higher durability, leading to lower RCpP. Furthermore, DFU's endurance leveled off to FFU over time, resulting in higher RCpP after 400 cases. This finding may be explained by the presence of renewed scopes after repair.

Image Distortion During Flexible Ureteroscopy: A Laboratory Model Comparing Super Pulsed Thulium Fiber Laser vs High-Power Ho:YAG Laser.

Purpose: Digital ureteroscopes employ "chip-on-the-tip" technology that allows for significant improvement in image resolution. However, image distortion often occurs during laser lithotripsy owing to acoustic wave production. We sought to compare image distortion using different laser power settings and distances from the laser fiber tip to the scope for the Super Pulsed Thulium Fiber (SPTF) laser and high-power Holmium:YAG (Ho:YAG) laser. Materials and Methods: Ureteroscopy was simulated using a silicon kidney-ureter-bladder model fitted with a 12F/14F access sheath and the Lithovue™ (Boston Scientific), disposable digital flexible ureteroscope. At defined laser parameters (10, 20, 30 and 40 W, short pulse), a 200-µm laser fiber was slowly retracted toward the tip of the ureteroscope during laser activation. Image distortion was identified, and distance from the laser tip to the scope tip was determined. Data from the two lasers were compared utilizing t-tests. Results: After controlling for frequency, power, and laser mode, utilizing 1.0 J of energy was significantly associated with less feedback than 0.5 J (-0.091 mm, p ≤ 0.05). Increased power was associated with larger feedback distance (0.016 mm, p ≤ 0.05); however, increase in frequency did not have a significant effect (-0.001 mm, p = 0.39). The SPFT laser had significantly less feedback when compared with all Holmium laser modes. Conclusions: Increased total power results in image distortion occurring at greater distances from the tip of the ureteroscope during laser activation. Image distortion occurs further from the ureteroscope with Ho:YAG laser than with SPTF fibers at the same laser settings. In clinical practice, the tip of the laser fiber should be kept further away from the tip of the scope during ureteroscopy as the power increases as well as when utilizing the Ho:YAG system compared with the SPTF laser platform. The SPTF laser may have a better safety profile in terms of potential scope damage.

Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus).

The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4× mean coverage from a historical specimen (∼200 years old) and one at 2.1× mean coverage from a fossil specimen dating to 9,800-9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction.

Bird lineages colonizing urban habitats have diversified at high rates across deep time.

Aim: Urbanization exposes species to novel ecological conditions. Some species thrive in urban areas, whereas many others are excluded from these human-made environments. Previous analyses suggest that the ability to cope with rapid environmental change is associated with long-term patterns of diversification, but whether the suite of traits associated with the ability to colonize urban environments is linked to this process remains poorly understood. Location: World. Time period: Current. Major taxa studied: Passerine birds. Methods: We applied macroevolutionary models to a large dataset of passerine birds to compare the evolutionary history of urban-tolerant species with that of urban-avoidant species. Specifically, we examined models of state-dependent speciation and extinction to assess the macroevolution of urban tolerance as a binary trait, in addition to models of quantitative trait-dependent diversification based on relative urban abundance. We also ran simulation-based model assessments to explore potential sources of bias. Results: We provide evidence that historically, species with traits promoting urban colonization have undergone faster diversification than urban-avoidant species, indicating that urbanization favours clades with a historical tendency towards rapid speciation or reduced extinction. In addition, we find that past transitions towards states that currently impede urban colonization by passerines have been more frequent than in the opposite direction. Furthermore, we find a portion of urban-avoidant passerines to be recent and to undergo fast diversification. All highly supported models give this result consistently. Main conclusions: Urbanization is mainly associated with the loss of lineages that are inherently more vulnerable to extinction over deep time, whereas cities tend to be colonized by less vulnerable lineages, for which urbanization might be neutral or positive in terms of longer-term diversification. Urban avoidance is associated with high rates of recent diversification for some clades occurring in regions with relatively intact natural ecosystems and low current levels of urbanization.

Genomic insights into the evolutionary relationships and demographic history of kiwi.

Kiwi are a unique and emblematic group of birds endemic to New Zealand. Deep-time evolutionary relationships among the five extant kiwi species have been difficult to resolve, in part due to the absence of pre-Quaternary fossils to inform speciation events. Here, we utilise single representative nuclear genomes of all five extant kiwi species (great spotted kiwi, little spotted kiwi, Okarito brown kiwi, North Island brown kiwi, and southern brown kiwi) and investigate their evolutionary histories with phylogenomic, genetic diversity, and deep-time (past million years) demographic analyses. We uncover relatively low levels of gene-tree phylogenetic discordance across the genomes, suggesting clear distinction between species. However, we also find indications of post-divergence gene flow, concordant with recent reports of interspecific hybrids. The four species for which unbiased levels of genetic diversity could be calculated, due to the availability of reference assemblies (all species except the southern brown kiwi), show relatively low levels of genetic diversity, which we suggest reflects a combination of older environmental as well as more recent anthropogenic influence. In addition, we suggest hypotheses regarding the impact of known past environmental events, such as volcanic eruptions and glacial periods, on the similarities and differences observed in the demographic histories of the five kiwi species over the past million years.

Environmental niche and flight intensity are associated with molecular evolutionary rates in a large avian radiation.

BACKGROUND: Metabolic activity and environmental energy are two of the most studied putative drivers of molecular evolutionary rates. Their extensive study, however, has resulted in mixed results and has rarely included the exploration of interactions among various factors impacting molecular evolutionary rates across large clades. Taking the diverse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with proxies of metabolic demands imposed by flight (wing loading and wing shape) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation). RESULTS: We found weak evidence of a positive effect of environmental and morphological variables on mitochondrial substitution rates. Additionally, we found that temperature and UV radiation interact to explain molecular rates at nucleotide sites affected by selection and population size (non-synonymous substitutions), contrary to the expectation of their impact on sites associated with mutation rates (synonymous substitutions). We also found a negative interaction between wing shape (as described by the hand-wing index) and body mass explaining mitochondrial molecular rates, suggesting molecular signatures of positive selection or reduced population sizes in small-bodied species with greater flight activity. CONCLUSIONS: Our results suggest that the demands of flight and environmental energy pose multiple evolutionary pressures on the genome either by driving mutation rates or via their association with natural selection or population size. Data from whole genomes and detailed physiology across taxa will bring a more complete picture of the impact of metabolism, population size, and the environment on avian genome evolution.

Probing the genomic limits of de-extinction in the Christmas Island rat.

Three principal methods are under discussion as possible pathways to "true" de-extinction; i.e., back-breeding, cloning, and genetic engineering.1,2 Of these, while the latter approach is most likely to apply to the largest number of extinct species, its potential is constrained by the degree to which the extinct species genome can be reconstructed. We explore this question using the extinct Christmas Island rat (Rattus macleari) as a model, an endemic rat species that was driven extinct between 1898 and 1908.3-5 We first re-sequenced its genome to an average of >60× coverage, then mapped it to the reference genomes of different Rattus species. We then explored how evolutionary divergence from the extant reference genome affected the fraction of the Christmas Island rat genome that could be recovered. Our analyses show that even when the extremely high-quality Norway brown rat (R. norvegicus) is used as a reference, nearly 5% of the genome sequence is unrecoverable, with 1,661 genes recovered at lower than 90% completeness, and 26 completely absent. Furthermore, we find the distribution of regions affected is not random, but for example, if 90% completeness is used as the cutoff, genes related to immune response and olfaction are excessively affected. Ultimately, our approach demonstrates the importance of applying similar analyses to candidates for de-extinction through genome editing in order to provide critical baseline information about how representative the edited form would be of the extinct species.

Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae.

Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species-specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.

Preoperative Optimization of Promotility in Robotic Prostatectomy and Minimally Invasive Kidney Surgery.

INTRODUCTION: Patients are routinely discharged postoperative day 1 following minimally invasive surgery (MIS) for prostate cancer and kidney cancer. Delays in discharge are often related to gastrointestinal symptoms such as nausea, abdominal pain and vomiting; however, the role of baseline constipation in these symptoms and resultant delays in discharge is unclear. We conducted a prospective observational study to describe the incidence of baseline constipation among patients undergoing MIS prostate and kidney surgery, and its relationship to length of stay (LOS). METHODS: Consenting adult patients undergoing MIS procedures for kidney and prostate cancer completed constipation symptom questionnaires perioperatively. Clinicopathological data were collected prospectively. Delay in discharge, defined as LOS >2 days, was the primary outcome. Patients were stratified by the primary outcome and preoperative Patient Assessment of Constipation Symptoms (PAC-SYM) scores were compared. RESULTS: A total of 97 patients enrolled, of whom 29 underwent radical nephrectomy, 34 underwent robotic partial nephrectomy and 34 underwent robotic prostatectomy. Constipation symptoms were reported in 67/97 patients (69%). A total of 17/97 patients (18%) had a delay in discharge. Patients who discharged on time had a median PAC-SYM score of 2 (IQR 2-9) compared to 4 (IQR 0-7.5) for those with a delay (p=0.021). Patients who had a delay with gastrointestinal symptoms had a median PAC-SYM score of 5 (IQR 1.5-11.5, p=0.032). CONCLUSIONS: Seven out of 10 patients undergoing routine MIS procedures report constipation symptoms, which may represent a target for preoperative interventions to reduce LOS after surgery.