RESUMEN
Vast amounts of pathogen genomic, demographic and spatial data are transforming our understanding of SARS-CoV-2 emergence and spread. We examined the drivers of molecular evolution and spread of 291,791 SARS-CoV-2 genomes from Denmark in 2021. With a sequencing rate consistently exceeding 60%, and up to 80% of PCR-positive samples between March and November, the viral genome set is broadly whole-epidemic representative. We identify a consistent rise in viral diversity over time, with notable spikes upon the importation of novel variants (e.g., Delta and Omicron). By linking genomic data with rich individual-level demographic data from national registers, we find that individuals aged < 15 and > 75 years had a lower contribution to molecular change (i.e., branch lengths) compared to other age groups, but similar molecular evolutionary rates, suggesting a lower likelihood of introducing novel variants. Similarly, we find greater molecular change among vaccinated individuals, suggestive of immune evasion. We also observe evidence of transmission in rural areas to follow predictable diffusion processes. Conversely, urban areas are expectedly more complex due to their high mobility, emphasising the role of population structure in driving virus spread. Our analyses highlight the added value of integrating genomic data with detailed demographic and spatial information, particularly in the absence of structured infection surveys.
Asunto(s)
COVID-19 , Genoma Viral , SARS-CoV-2 , Humanos , Dinamarca/epidemiología , COVID-19/epidemiología , COVID-19/virología , COVID-19/transmisión , SARS-CoV-2/genética , SARS-CoV-2/clasificación , Genoma Viral/genética , Adulto , Persona de Mediana Edad , Anciano , Adolescente , Adulto Joven , Evolución Molecular , Masculino , Femenino , Preescolar , Niño , Filogenia , LactanteRESUMEN
PURPOSE: To report real-time IRP and FR while performing flexible ureteroscopy in porcine kidney model utilizing LithoVue™ Elite (Boston Scientific®) with different irrigation systems, including automated pumps. METHODS: Using an ex-vivo model of porcine kidney, IRPs were measured with LithoVue Elite. Ureteroscopic settings (US) were tested with all permutations of irrigation methods (IM), working channel occupant (WCO), and ureteral access sheaths (UAS). IMs included: Single Action Pumping System (SAPS™, Boston Scientific), Thermedx FluidSmart™ (Stryker®), and ENDOMAT™ (Karl Storz®). Pumps were tested at 50, 100, and 150 mmHg. WCOs included a 1.9Fr zero-tip basket, 200 µm, and 365 µm laser fibers. UASs utilized 11/13Fr and 12/14Fr 36 cm. RESULTS: 84 different US were tested (252 experiments). ENDOMAT had higher IRP but the same FR as Thermedx at the same US for 50 and 100 mmHg (p < 0.01). SAPS had higher IRP and FR than pumps in all US studies (p < 0.01). There was positive correlation between pressure set by the pump and both IRP and FR (rho > 0.9). As the diameter of the WCO increased, lower IRP and FR were observed with the pumps (p < 0.01). With SAPS, IRP was similar regardless of WCO, but FR was decreased with the increased diameter of WCO (p = 0.81 and p < 0.01, respectively). There was significantly higher IRP when using 11/13Fr UAS than 12/14Fr (p < 0.01). CONCLUSION: IRP was higher with SAPS than automated pumps. ENDOMAT showed higher IRP than Thermedx when under 150 mmHg. IRP and FR increase with higher pump pressure and decrease with larger diameter WCO. Likewise, a larger UAS significantly reduced IRP.
Asunto(s)
Riñón , Presión , Irrigación Terapéutica , Ureteroscopía , Animales , Porcinos , Irrigación Terapéutica/instrumentación , Ureteroscopía/instrumentación , Riñón/fisiología , Diseño de Equipo , UreteroscopiosRESUMEN
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art methods rely on carefully designed heuristics for tree search, using different data structures for easy manipulation (e.g., classes in object-oriented programming languages) and readable representation of trees (e.g., Newick-format strings). Here, we present Phylo2Vec, a parsimonious encoding for phylogenetic trees that serves as a unified approach for both manipulating and representing phylogenetic trees. Phylo2Vec maps any binary tree with n leaves to a unique integer vector of length n - 1. The advantages of Phylo2Vec are fourfold: i) fast tree sampling, (ii) compressed tree representation compared to a Newick string, iii) quick and unambiguous verification if two binary trees are identical topologically, and iv) systematic ability to traverse tree space in very large or small jumps. As a proof of concept, we use Phylo2Vec for maximum likelihood inference on five real-world datasets and show that a simple hill-climbing-based optimisation scheme can efficiently traverse the vastness of tree space from a random to an optimal tree.
RESUMEN
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.
Asunto(s)
Cálculos Renales , Láseres de Estado Sólido , Nefrolitotomía Percutánea , Tulio , Humanos , Femenino , Láseres de Estado Sólido/uso terapéutico , Masculino , Nefrolitotomía Percutánea/métodos , Nefrolitotomía Percutánea/instrumentación , Tulio/uso terapéutico , Estudios Retrospectivos , Persona de Mediana Edad , Cálculos Renales/cirugía , Adulto , Resultado del Tratamiento , Posición Supina , Anciano , Litotripsia por Láser/métodos , Litotripsia por Láser/instrumentaciónRESUMEN
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.
Asunto(s)
Aves , Evolución Molecular , Genoma , Filogenia , Animales , Aves/genética , Aves/clasificación , Aves/anatomía & histología , Encéfalo/anatomía & histología , Extinción Biológica , Genoma/genética , Genómica , Densidad de Población , Masculino , FemeninoRESUMEN
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.
Asunto(s)
Evolución Molecular , Modelos Genéticos , Genómica , Genoma , Evolución Biológica , FilogeniaRESUMEN
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.
Asunto(s)
Cálculos Renales , Nefrolitotomía Percutánea , Nefrostomía Percutánea , Humanos , Cálculos Renales/cirugía , Nefrostomía Percutánea/métodos , Riñón , Endoscopía , Nefrolitotomía Percutánea/métodos , Resultado del TratamientoRESUMEN
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.
Asunto(s)
Clasificación , Filogenia , Clasificación/métodos , Modelos Biológicos , Modelos Genéticos , Teorema de Bayes , Tasa de NatalidadRESUMEN
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.
Asunto(s)
Algoritmos , Modelos Genéticos , Filogenia , Simulación por ComputadorRESUMEN
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.
RESUMEN
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.
Asunto(s)
Genoma , Genómica , Animales , Genoma/genética , Filogenia , Flujo Génico , Hibridación Genética , Ballenas/genética , Especiación GenéticaRESUMEN
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.
Asunto(s)
Cálculos Renales , Cálculos Urinarios , Humanos , Urólogos , Cálculos Renales/cirugía , Estruvita , Apatitas , Oxalato de Calcio , Cistina , Cálculos Urinarios/químicaRESUMEN
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.
Asunto(s)
Ureteroscopios , Ureteroscopía , Humanos , Ureteroscopía/métodos , Tecnología de Fibra Óptica , Diseño de EquipoRESUMEN
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.
Asunto(s)
Láseres de Estado Sólido , Litotripsia por Láser , Humanos , Holmio , Litotripsia por Láser/métodos , Tulio , Ureteroscopios , UreteroscopíaRESUMEN
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 (â¼200 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.
Asunto(s)
Antílopes , Mustelidae , Animales , Humanos , Antílopes/genética , Evolución Biológica , Filogenia , Genoma , Mustelidae/genéticaRESUMEN
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.
RESUMEN
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.
Asunto(s)
Paleognatos , Struthioniformes , Animales , Demografía , Genómica , Paleognatos/genética , FilogeniaRESUMEN
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.
Asunto(s)
Mustelidae , Adaptación Fisiológica/genética , Animales , Genoma , Genómica , Mustelidae/genética , FenotipoRESUMEN
The historical signal in nucleotide sequences becomes eroded over time by substitutions occurring repeatedly at the same sites. This phenomenon, known as substitution saturation, is recognized as one of the primary obstacles to deep-time phylogenetic inference using genome-scale data sets. We present a new test of substitution saturation and demonstrate its performance in simulated and empirical data. For some of the 36 empirical phylogenomic data sets that we examined, we detect substitution saturation in around 50% of loci. We found that saturation tends to be flagged as problematic in loci with highly discordant phylogenetic signals across sites. Within each data set, the loci with smaller numbers of informative sites are more likely to be flagged as containing problematic levels of saturation. The entropy saturation test proposed here is sensitive to high evolutionary rates relative to the evolutionary timeframe, while also being sensitive to several factors known to mislead phylogenetic inference, including short internal branches relative to external branches, short nucleotide sequences, and tree imbalance. Our study demonstrates that excluding loci with substitution saturation can be an effective means of mitigating the negative impact of multiple substitutions on phylogenetic inferences. [Phylogenetic model performance; phylogenomics; substitution model; substitution saturation; test statistics.].