Phylogenomics and the rise of the angiosperms

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

The macroevolutionary singularity of snakes

Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.

Global hotspots of plant phylogenetic diversity

Regions harbouring high unique phylogenetic diversity (PD) are priority targets for conservation. Here, we analyse the global distribution of plant PD, which remains poorly understood despite plants being the foundation of most terrestrial habitats and key to human livelihoods. Capitalising on a recently completed, comprehensive global checklist of vascular plants, we identify hotspots of unique plant PD and test three hypotheses: (1) PD is more evenly distributed than species diversity; (2) areas of highest PD (often called 'hotspots') do not maximise cumulative PD; and (3) many biomes are needed to maximise cumulative PD. Our results support all three hypotheses: more than twice as many regions are required to cover 50% of global plant PD compared to 50% of species; regions that maximise cumulative PD substantially differ from the regions with outstanding individual PD; and while (sub-)tropical moist forest regions dominate across PD hotspots, other forest types and open biomes are also essential. Safeguarding PD in the Anthropocene (including the protection of some comparatively species-poor areas) is a global, increasingly recognised responsibility. Having highlighted countries with outstanding unique plant PD, further analyses are now required to fully understand the global distribution of plant PD and associated conservation imperatives across spatial scales.

Compositional shifts associated with major evolutionary transitions in plants

Heterogeneity in gene trees, morphological characters, and composition has been associated with several major plant clades. Here, we examine heterogeneity in composition across a large transcriptomic dataset of plants to better understand whether locations of shifts in composition are shared across gene regions and whether directions of shifts within clades are shared across gene regions. We estimate mixed models of composition for both nucleotide and amino acids across a recent large-scale transcriptomic dataset for plants. We find shifts in composition across both nucleotide and amino acid datasets, with more shifts detected in nucleotides. We find that Chlorophytes and lineages within experience the most shifts. However, many shifts occur at the origins of land, vascular, and seed plants. While genes in these clades do not typically share the same composition, they tend to shift in the same direction. We discuss potential causes of these patterns. Compositional heterogeneity has been highlighted as a potential problem for phylogenetic analysis, but the variation presented here highlights the need to further investigate these patterns for the signal of biological processes.

FieldPrism: A system for creating snapshot vouchers from field images using photogrammetric markers and QR codes

Premise

Field images are important sources of information for research in the natural sciences. However, images that lack photogrammetric scale bars, including most iNaturalist observations, cannot yield accurate trait measurements. We introduce FieldPrism, a novel system of photogrammetric markers, QR codes, and software to automate the curation of snapshot vouchers.

Methods and Results

Our photogrammetric background templates (FieldSheets) increase the utility of field images by providing machine-readable scale bars and photogrammetric reference points to automatically correct image distortion and calculate a pixel-to-metric conversion ratio. Users can generate a QR code flipbook derived from a specimen identifier naming hierarchy, enabling machine-readable specimen identification for automatic file renaming. We also developed FieldStation, a Raspberry Pi-based mobile imaging apparatus that records images, GPS location, and metadata redundantly on up to four USB storage devices and can be monitored and controlled from any Wi-Fi connected device.

Conclusions

FieldPrism is a flexible software tool designed to standardize and improve the utility of images captured in the field. When paired with the optional FieldStation, researchers can create a self-contained mobile imaging apparatus for quantitative trait data collection.

From leaves to labels: Building modular machine learning networks for rapid herbarium specimen analysis with LeafMachine2

Premise

Quantitative plant traits play a crucial role in biological research. However, traditional methods for measuring plant morphology are time consuming and have limited scalability. We present LeafMachine2, a suite of modular machine learning and computer vision tools that can automatically extract a base set of leaf traits from digital plant data sets.

Methods

LeafMachine2 was trained on 494,766 manually prepared annotations from 5648 herbarium images obtained from 288 institutions and representing 2663 species; it employs a set of plant component detection and segmentation algorithms to isolate individual leaves, petioles, fruits, flowers, wood samples, buds, and roots. Our landmarking network automatically identifies and measures nine pseudo-landmarks that occur on most broadleaf taxa. Text labels and barcodes are automatically identified by an archival component detector and are prepared for optical character recognition methods or natural language processing algorithms.

Results

LeafMachine2 can extract trait data from at least 245 angiosperm families and calculate pixel-to-metric conversion factors for 26 commonly used ruler types.

Discussion

LeafMachine2 is a highly efficient tool for generating large quantities of plant trait data, even from occluded or overlapping leaves, field images, and non-archival data sets. Our project, along with similar initiatives, has made significant progress in removing the bottleneck in plant trait data acquisition from herbarium specimens and shifted the focus toward the crucial task of data revision and quality control.

Fish Welfare in Public Aquariums and Zoological Collections

A wide variety of fish species have been displayed in public aquariums and zoological collections for over 150 years. Though the issue of pain perception in fish is still being debated, there is no disagreement that negative impacts on their welfare can significantly affect their health and wellbeing. A general description of the basic biological requirements for maintaining fish in captive environments is presented, but species-specific information and guidelines should be developed for the multitude of species being maintained. A combination of behavioral, performance, and physiological indicators can be used to assess the well-being of these animals. Ultimately, the goal for optimizing the welfare of fish should be to provide the best possible environment, husbandry, and social interactions to promote natural species-specific behaviors of the fish in captivity.

Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method

Applications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes. We then employ an improved framework with a coalescent simulation approach to test and confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization. The new ancestral niche method flexibly models the shape of niche while incorporating diverse sources of uncertainty and will be an important addition to the current comparative methods toolkit. [Ancestral niche reconstruction; hybridization; paleoclimate; pleistocene.].

The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data

The angiosperm family Primulaceae is morphologically diverse and distributed nearly worldwide. However, phylogenetic uncertainty has obstructed the identification of major morphological and biogeographic transitions within the clade. We used target capture sequencing with the Angiosperms353 probes, taxon-sampling encompassing nearly all genera of the family, tree-based sequence curation, and multiple phylogenetic approaches to investigate the major clades of Primulaceae and their relationship to other Ericales. We generated dated phylogenetic trees and conducted broad-scale biogeographic analyses as well as stochastic character mapping of growth habit. We show that Ardisia, a pantropical genus and the largest in the family, is not monophyletic, with at least 19 smaller genera nested within it. Neotropical members of Ardisia and several smaller genera form a clade, an ancestor of which arrived in the Neotropics and began diversifying about 20 Ma. This Neotropical clade is most closely related to Elingamita and Tapeinosperma, which are most diverse on islands of the Pacific. Both Androsace and Primula are non-monophyletic by the inclusion of smaller genera. Ancestral state reconstructions revealed that there have either been parallel transitions to an herbaceous habit in Primuloideae, Samolus, and at least three lineages of Myrsinoideae, or a common ancestor of nearly all Primulaceae was herbaceous. Our results provide a robust estimate of phylogenetic relationships across Primulaceae and show that a revised classification of Myrsinoideae and several other clades within the family is necessary to render all genera monophyletic.

First isolation of Carnobacterium maltaromaticum from farmed Rainbow Trout in Virginia

OBJECTIVE

Carnobacterium maltaromaticum is considered an emerging pathogen of salmonids in the United States and around the world.

METHODS

Bacterial cultures obtained from the posterior kidney and skin of moribund Rainbow Trout Oncorhynchus mykiss from a commercial aquaculture facility in Virginia, USA, grew C. maltaromaticum, which was confirmed by additional phenotypic and molecular characterization.

RESULT

A presumptive diagnosis based on the clinical signs, necropsy observations, histopathology, and bacterial cultures was bacterial septicemia due to C. maltaromaticum.

CONCLUSION

This represents the first documentation of C. maltaromaticum in Rainbow Trout from Virginia.

Lagrange-NG: The next generation of Lagrange

Computing ancestral ranges via the Dispersion Extinction and Cladogensis (DEC) model of biogeography is characterized by an exponential number of states relative to the number of regions considered. This is because the DEC model requires computing a large matrix exponential, which typically accounts for up to 80% of overall runtime. Therefore, the kinds of biogeographical analyses that can be conducted under the DEC model are limited by the number of regions under consideration. In this work, we present a completely redesigned efficient version of the popular tool Lagrange which is up to 49 times faster with multi-threading enabled, and is also 26 times faster when using only one thread. We call this new version Lagrange-NG (Lagrange-Next Generation). The increased computational efficiency allows Lagrange-NG to analyze datasets with a large number of regions in a reasonable amount of time, up to 12 regions in approximately 18 minutes. We achieve these speedups using a relatively new method of computing the matrix exponential based on Krylov subspaces. In order to validate the correctness of Lagrange-NG, we also introduce a novel metric on range distributions for trees so that researchers can assess the difference between any two range inferences. Finally, Lagrange-NG exhibits substantially higher adherence to coding quality standards. It improves a respective software quality indicator as implemented in the SoftWipe tool from average (5.5; Lagrange) to high (7.8; Lagrange-NG). Lagrange-NG is freely available under GPL2.

Analysis of the core bacterial community associated with consumer-ready Eastern oysters (Crassostrea virginica)

Shellfish, such as the Eastern oyster (Crassostrea virginica), are an important agricultural commodity. Previous research has demonstrated the importance of the native microbiome of oysters against exogenous challenges by non-native pathogens. However, the taxonomic makeup of the oyster microbiome and the impact of environmental factors on it are understudied. Research was conducted quarterly over a calendar year (February 2020 through February 2021) to analyze the taxonomic diversity of bacteria present within the microbiome of consumer-ready-to-eat live Eastern oysters. It was hypothesized that a core group of bacterial species would be present in the microbiome regardless of external factors such as the water temperature at the time of harvest or post-harvesting processing. At each time point, 18 Chesapeake Bay (eastern United States) watershed aquacultured oysters were acquired from a local grocery store, genomic DNA was extracted from the homogenized whole oyster tissues, and the bacterial 16S rRNA gene hypervariable V4 region was PCR-amplified using barcoded primers prior to sequencing via Illumina MiSeq and bioinformatic analysis of the data. A core group of bacteria were identified to be consistently associated with the Eastern oyster, including members of the phyla Firmicutes and Spirochaetota, represented by the families Mycoplasmataceae and Spirochaetaceae, respectively. The phyla Cyanobacterota and Campliobacterota became more predominant in relation to warmer or colder water column temperature, respectively, at the time of oyster harvest.

Development of a Controlled Laboratory-scale Inoculation System to Study Vibrio parahaemolyticus-oyster Interactions

Prevalence of seafood-borne gastroenteritis caused by the human pathogen Vibrio parahaemolyticus is increasing globally despite current preventative measures. The United States Centers for Disease Control have designated V. parahaemolyticus as a reportable emerging human pathogen. The Eastern oyster (Crassostrea virginica) is a natural reservoir of the bacterium in marine environments, but little is actually known regarding interactions between oysters and V. parahaemolyticus. Therefore, a laboratory-scale Biosafety Level-2 (BSL2) inoculation system was developed wherein Chesapeake Bay region oysters harvested during summer or winter months, were exposed to the clinical RIMD2210633 strain carrying a chloramphenicol-selective marker (VP RIMDmC). Homogenized whole oyster tissues were spread on selective and differential agar medium to measure viable VP RIMDmC levels. Endogenous Vibrio spp. cell numbers were significantly reduced followed chloramphenicol treatment and this likely contributed to higher VP RIMDmC oyster-associated levels, especially using winter-harvested animals. Summer-harvested oysters had significantly higher existing Vibrio levels and a lower level of artificial oyster-associated VP RIMDmC. Thus, the pre-existing microbiome appears to afford some protection from an external V. parahaemolyticus challenge. Overall, this system successfully enabled controlled manipulation of parameters influencing V. parahaemolyticus-oyster interactions and will be useful in safely testing additional pertinent environmental variables and potential mitigation strategies.

Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree

Phylogenetic analyses fail to yield a satisfactory resolution of some relationships in the tree of life even with genome-scale datasets, so the failure is unlikely to reflect limitations in the amount of data. Gene tree conflicts are particularly notable in studies focused on these contentious nodes, and taxon sampling, different analytical methods, and/or data type effects can further confound analyses. Although many efforts have been made to incorporate biological conflicts, few studies have curated individual genes for their efficiency in phylogenomic studies. Here, we conduct an edge-based analysis of Neoavian evolution, examining the phylogenetic efficacy of two recent phylogenomic bird datasets and three datatypes (ultraconserved elements [UCEs], introns, and coding regions). We assess the potential causes for biases in signal-resolution for three difficult nodes: the earliest divergence of Neoaves, the position of the enigmatic Hoatzin (Opisthocomus hoazin), and the position of owls (Strigiformes). We observed extensive conflict among genes for all data types and datasets even after meticulous curation. Edge-based analyses (EBA) increased congruence and provided information about the impact of data type, GC content variation (GC_CV), and outlier genes on each of nodes we examined. First, outlier gene signals appeared to drive different patterns of support for the relationships among the earliest diverging Neoaves. Second, the placement of Hoatzin was highly variable, although our EBA did reveal a previously unappreciated data type effect with an impact on its position. It also revealed that the resolution with the most support here was Hoatzin + shorebirds. Finally, GC_CV, rather than data type (i.e., coding vs non-coding) per se, was correlated with a signal that supports monophyly of owls + Accipitriformes (hawks, eagles, and vultures). Eliminating high GC_CV loci increased the signal for owls + mousebirds. Categorical EBA was able to reveal the nature of each edge and provide a way to highlight especially problematic branches that warrant a further examination. The current study increases our understanding about the contentious parts of the avian tree, which show even greater conflicts than appreciated previously.

OUP accepted manuscript

Phylogenetic analyses are increasingly being performed with data sets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene trees and the species tree is not accounted for, the temporal duration of branches in regions of the species tree that are affected by incongruence is underestimated, whilst the duration of other branches is considerably overestimated. This effect becomes more pronounced with higher levels of topological incongruence. We show that this pattern results from the erroneous estimation of the number of substitutions along branches in the species tree, although the effect is modulated by the assumptions inherent to divergence time estimation, such as those relating to the fossil record or among-branch-substitution-rate variation. By only analyzing loci with gene trees that are topologically congruent with the species tree, or only taking into account the branches from each gene tree that are topologically congruent with the species tree, we demonstrate that the effects of topological incongruence can be ameliorated. Nonetheless, even when topologically congruent gene trees or topologically congruent branches are selected, error in divergence time estimates remains. This stems from temporal incongruences between divergence times in species trees and divergence times in gene trees, and more importantly, the difficulty of incorporating necessary assumptions for divergence time estimation. [Divergence time estimation; gene trees; species tree; topological incongruence.]

White matter tracts that overlap with the thalamus and the putamen are protected against multiple sclerosis pathology

BACKGROUND

The thalamus and the putamen are highly connected hubs implicated in multiple sclerosis (MS) pathology. It remains unclear if white matter (WM) tracts, which pass through them, have a different susceptibility to MS pathology, and if so, if their impact on disability predominates over that exerted by disease in other WM tracts. We hypothesized that WM tracts connected to and passing through these hubs (subsequently termed hub+ tracts) would be more susceptible to MS-related pathology than tracts that do not pass through them (hub- tracts) due to retrograde and anterograde distant degeneration. Thus, we compared the lesion load and neurite orientation dispersion and density imaging (NODDI) derived metrics between hub+ and hub- tracts and assessed the relationship between these MRI metrics and those of physical impairment.

METHODS

Eighteen patients (mean age of 45.5 years, 12 females) had 3 Tesla MRI consisting of T1-weighted and T2-weighted Fluid Attenuated Inversion Recovery (FLAIR), and NODDI from which the orientation dispersion index (ODI), neurite density index (NDI), and isotropic volume fraction (IVF) were derived. Forty-nine WM tracts, i.e., 12 hub+ and 37 hub- tracts, were segmented out. Exploratory analyses of the differences in lesion burden, whole tract and normal appearing WM (NAWM) NODDI metrics were carried out between the two types of tracts using a Mann-Whitney U test. Correlations with physical impairment, quantified using the expanded disability status scale (EDSS) and timed 25-foot walk (T25FW) test were assessed using Spearman correlation analyses.

RESULTS

Hub- tracts had larger T1- (p<0.001) and T2-lesion (p<0.001) volumes; lower ODI (p<0.001), NDI (p<0.001) and higher IVF (p = 0.020) in comparison to hub+ tracts. Measures of tissue injury in hub+ tracts correlated with those of clinical disability, though less strongly than in hub- tracts.

CONCLUSIONS

Contrary to our hypothesis, our exploratory pilot study results suggest that WM tracts that overlap with the thalamus and the putamen have a lower degree of lesional and non-lesional tissue injury, suggesting a protective role of the hubs against MS pathology or a higher degree of vulnerability of those not passing through hub stations. We also show a weaker association between disability impairment and hub+ pathology, compared to that in hub- tracts. Our findings point to a potential role of disease location in relation to hubs as guidance for treatment personalization in MS.

Temporal and spatial comparisons of angiosperm diversity between eastern Asia and North America

Eastern Asia (EA) and North America north of Mexico (NA) have comparable latitude, land area, and climate, but the overall plant diversity is much higher in EA than in NA. Despite intensive studies on disjunct taxa of the two regions, the temporal and spatial diversity patterns between the two floras remain unclear. Here we explore the floristic differences between EA and NA using the well-studied floras of China and the United States of America (USA) as exemplars, while also employing a newly generated dated phylogeny covering ∼90% of the angiosperm genera of the two countries and comprehensive spatial distribution data. We find that China possesses both higher richness and phylogenetic diversity (PD) for angiosperm genera than the USA. Notably, most lineages contribute to the PD anomaly between the two floras, with 46 of 58 lineages having higher PD in China. Temporally, China has a higher proportion of genera that originated before the Miocene than found in the USA (29.9% vs 23.2%). The eastern USA has more genera that originated during the Paleogene than does the western USA, but the reverse pattern is observed after the middle Miocene, with more genera originating in the west. Spatially, China shows a more distinct east-west deviation in diversity than the USA with eastern China possessing much higher generic richness and PD and more ancient lineages than western China. However, the eastern USA possesses lower generic richness, but higher PD and more ancient lineages than the western USA. Both the floras in China and the USA share a signature of an older east and a younger west, and this pattern may be largely driven by regional orogenic activities and climatic changes in the west of the two regions. Finally, our study indicates that more efforts are needed to enhance biodiversity conservation in southern China and the eastern USA by identifying and protecting phylodiversity hotspots.

The evolutionary assembly of forest communities along environmental gradients: recent diversification or sorting of pre-adapted clades?

Recent studies have demonstrated that ecological processes that shape community structure and dynamics change along environmental gradients. However, much less is known about how the emergence of the gradients themselves shape the evolution of species that underlie community assembly. In this study, we address how the creation of novel environments leads to community assembly via two nonmutually exclusive processes: immigration and ecological sorting of pre-adapted clades (ISPC), and recent adaptive diversification (RAD). We study these processes in the context of the elevational gradient created by the uplift of the Central Andes. We develop a novel approach and method based on the decomposition of species turnover into within- and among-clade components, where clades correspond to lineages that originated before mountain uplift. Effects of ISPC and RAD can be inferred from how components of turnover change with elevation. We test our approach using data from over 500 Andean forest plots. We found that species turnover between communities at different elevations is dominated by the replacement of clades that originated before the uplift of the Central Andes. Our results suggest that immigration and sorting of clades pre-adapted to montane habitats is the primary mechanism shaping tree communities across elevations.

Chloranthus genome provides insights into the early diversification of angiosperms

Chloranthales remain the last major mesangiosperm lineage without a nuclear genome assembly. We therefore assemble a high-quality chromosome-level genome of Chloranthus spicatus to resolve enigmatic evolutionary relationships, as well as explore patterns of genome evolution among the major lineages of mesangiosperms (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales). We find that synteny is highly conserved between genomic regions of Amborella, Vitis, and Chloranthus. We identify an ancient single whole-genome duplication (WGD) (κ) prior to the divergence of extant Chloranthales. Phylogenetic inference shows Chloranthales as sister to magnoliids. Furthermore, our analyses indicate that ancient hybridization may account for the incongruent phylogenetic placement of Chloranthales + magnoliids relative to monocots and eudicots in nuclear and chloroplast trees. Long genes and long introns are found to be prevalent in both Chloranthales and magnoliids compared to other angiosperms. Overall, our findings provide an improved context for understanding mesangiosperm relationships and evolution and contribute a valuable genomic resource for future investigations.

Phase II study of ceralasertib (AZD6738) in combination with durvalumab in patients with advanced/metastatic melanoma who have failed prior anti-PD-1 therapy

BACKGROUND

Modulating the DNA damage response and repair (DDR) pathways is a promising strategy for boosting cancer immunotherapy. Ceralasertib (AZD6738) is an oral inhibitor of the serine/threonine protein kinase ataxia telangiectasia and Rad3-related protein, which is crucial for DDR.

PATIENTS AND METHODS

This phase II trial evaluated ceralasertib plus durvalumab for the treatment of patients with metastatic melanoma who had failed anti-programmed cell death protein 1 therapy.

RESULTS

Among the 30 patients, we observed an overall response rate of 31.0% and a disease control rate of 63.3%. Responses were evident across patients with acral, mucosal, and cutaneous melanoma. The median duration of response was 8.8 months (range, 3.8-11.7 months). The median progression-free survival was 7.1 months (95% confidence interval, 3.6-10.6 months), and the median overall survival was 14.2 months (95% confidence interval, 9.3-19.1 months). Common adverse events were largely hematologic and manageable with dose interruptions and reductions. Exploratory biomarker analysis suggested that tumors with an immune-enriched microenvironment or alterations in the DDR pathway were more likely to respond to the study treatment.

CONCLUSION

We conclude that ceralasertib in combination with durvalumab has promising antitumor activity among patients with metastatic melanoma who have failed anti-programmed cell death protein 1 therapy, and constitute a population with unmet needs.

New Ileostomy Formation and Subsequent Community-onset Acute and Chronic Kidney Disease: A Population-based Cohort Study

OBJECTIVE

The aim of this study was to examine relationships between ileostomy formation and subsequent kidney disease.

SUMMARY AND BACKGROUND DATA

Colonic absorptive capacity loss from ileostomy formation can cause volume depletion and could result in kidney disease.

METHODS

We conducted a population-based cohort study comparing patients who underwent ileostomy formation with or without bowel resection (ileostomy group) to patients who underwent bowel resection without ileostomy formation (reference group). Adjusted odds ratios (aORs) for community-onset acute kidney injury (AKI) within 3 months and new-onset chronic kidney disease (CKD) within 1 year following hospital discharge were determined.

RESULTS

Among 19,889 patients, 4136 comprised the ileostomy group and 15,753 comprised the reference group; 1350 patients experienced community-onset AKI and 464 developed new-onset CKD. The aOR for community-onset AKI with ileostomy formation was 4.08 [95% confidence interval (CI) = 3.62-4.61] for any stage AKI, 7.08 (95% CI = 5.66-8.85) for stage ≥2 injury, and 7.67 (95% CI = 5.06-11.63) for stage 3 injuries. Community-onset AKI modified associations between ileostomy formation and new-onset CKD (P = 0.002). Odds of new-onset CKD were increased in the ileostomy group relative to the reference group for patients both with (aOR = 4.99; 95% CI = 3.42-7.28) and without (aOR = 2.45; 95% CI = 1.85-2.23) previous community-onset AKI episodes. In analyses comparing patients that underwent ileostomy formation and subsequent reversal within 1 year to the reference group without ileostomy, the relationship with new-onset CKD was attenuated for patients both with (aOR = 2.49; 95% CI = 1.50-4.12) and without (aOR = 0.97; 95% CI = 0.67-1.40) previous community-onset AKI episodes.

CONCLUSIONS

Ileostomy formation is strongly associated with subsequent kidney disease. Vigilance for this complication and new strategies for prevention and treatment are necessary.

Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms

Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity across the tree of life is a major challenge in evolutionary biology. In green plants, polyploidy (or whole-genome duplication, WGD) is known to play a major role in microevolution and speciation, but the extent to which WGD has shaped macroevolutionary patterns of diversification and phenotypic innovation across plant phylogeny remains an open question. Here, we examine the relationship of various facets of genomic evolution-including gene and genome duplication, genome size, and chromosome number-with macroevolutionary patterns of phenotypic innovation, species diversification, and climatic occupancy in gymnosperms. We show that genomic changes, such as WGD and genome-size shifts, underlie the origins of most major extant gymnosperm clades, and notably, our results support an ancestral WGD in the gymnosperm lineage. Spikes of gene duplication typically coincide with major spikes of phenotypic innovation, while increased rates of phenotypic evolution are typically found at nodes with high gene-tree conflict, representing historic population-level dynamics during speciation. Most shifts in gymnosperm diversification since the rise of angiosperms are decoupled from putative WGDs and instead are associated with increased rates of climatic occupancy evolution, particularly in cooler and/or more arid climatic conditions, suggesting that ecological opportunity, especially in the later Cenozoic, and environmental heterogeneity have driven a resurgence of gymnosperm diversification. Our study provides critical insight on the processes underlying diversification and phenotypic evolution in gymnosperms, with important broader implications for the major drivers of both micro- and macroevolution in plants.

Concordance-based approaches for the inference of relationships and molecular rates with phylogenomic datasets

Gene tree conflict is common and finding methods to analyze and alleviate the negative effects that conflict has on species tree analysis is a crucial part of phylogenomics. This study aims to expand the discussion of inferring species trees and molecular branch lengths when conflict is present. Conflict is typically examined in two ways: inferring its prevalence, and inferring the influence of the individual genes (how strongly one gene supports any given topology compared to an alternative topology). Here, we examine a procedure for incorporating both conflict and the influence of genes in order to infer evolutionary relationships. All supported relationships in the gene trees are analyzed and the likelihood of the genes constrained to these relationships is summed to provide a likelihood for the relationship. Consensus tree assembly is conducted based on the sum of likelihoods for a given relationship and choosing relationships based on the most likely relationship assuming it does not conflict with a relationship that has a higher likelihood score. If it is not possible for all most likely relationships to be combined into a single bifurcating tree then multiple trees are produced and a consensus tree with a polytomy is created. This procedure allows for more influential genes to have greater influence on an inferred relationship, does not assume conflict has arisen from any one source, and does not force the dataset to produce a single bifurcating tree. Using this approach on three empirical datasets, we examine and discuss the relationship between influence and prevalence of gene tree conflict. We find that in one of the datasets, assembling a bifurcating consensus tree solely composed of the most likely relationships is impossible. To account for conflict in molecular rate analysis we also introduce a concordance-based approach to the summary and estimation of branch lengths suitable for downstream comparative analyses. We demonstrate through simulation that even under high levels of stochastic conflict, the mean and median of the concordant rates recapitulate the true molecular rate better than using a supermatrix approach. Using a large phylogenomic dataset, we examine rate heterogeneity across concordant genes with a focus on the branch subtending crown angiosperms. Notably, we find highly variable rates of evolution along the branch subtending crown angiosperms. The approaches outlined here have several limitations, but they also represent some alternative methods for harnessing the complexity of phylogenomic datasets and enrich our inferences of both species' relationships and evolutionary processes.

Mammary carcinoma arising in an adenoma in a ewe

A large, firm, multi-cystic mammary gland mass grew slowly over 4 y in a 12-y-old, female Finn-Shetland cross sheep. A diagnosis of epithelial malignancy was suspected following fine-needle aspiration cytology at 30 mo after initial observation. The sheep was euthanized when the flock was downsized 18 mo later. A field postmortem examination revealed a large mammary mass, but an absence of metastases to internal organs. Imprint cytology of the mammary tissue supported a benign proliferative process. Histologically, mammary tissue was obliterated by cystic, tubular, and papillary adenomatous arrangements of mammary epithelium, with an anaplastic component, consistent with mammary carcinoma arising in an adenoma. IHC showed strong nuclear positivity to the antibody against progesterone receptor and minimal positivity to the antibody against estrogen receptor alpha expression. Intrinsic subtyping for basal or luminal epithelial origin was attempted through adaptation of companion animal IHC classification panels; high- and low-molecular-weight cytokeratins (CK5, CK8, CK18) failed to stain, but p63 expression for basal epithelium was positive.

Angiotensin-Converting Enzyme Inhibitor/Receptor Blocker, Diuretic, or Nonsteroidal Anti-inflammatory Drug Use After Major Surgery and Acute Kidney Injury: A Case-Control Study

BACKGROUND

Acute kidney injury (AKI) is common after surgery and associated with increased mortality, costs, and lengths of hospitalization. We examined associations between angiotensin-converting enzyme inhibitor (ACEI)/angiotensin receptor blocker (ARB), diuretic, or nonsteroidal anti-inflammatory drug (NSAID) use after major surgery and AKI.

MATERIALS AND METHODS

We conducted a nested case-control study of patients who underwent major cardiac, thoracic, general, or vascular surgery in Calgary, Alberta, Canada. Cases with AKI were matched on age, gender, and surgery type with up to five controls without AKI within 30-d after surgery. Adjusted odds ratios (ORs) for AKI were determined based on postoperative administration of ACEIs/ARBs, diuretics, or NSAIDs.

RESULTS

Among 33,648 patients in the cohort, 2911 cases with AKI were matched to 9309 controls without AKI. Postoperative diuretic [OR = 1.96; 95% confidence interval (CI) = 1.68-2.29], but not ACEI/ARB (OR = 0.83; 95% CI = 0.72-0.95) or NSAID (OR = 1.12; 95% CI = 0.96-1.31), use was independently associated with higher odds of AKI (including stages 1 and 2/3 AKI) after all types of major surgery. There were increased adjusted odds of AKI 1 to 5 d after first exposure to diuretics and 1 d after first exposure to NSAIDs (but not after later exposures). Relationships between ACEI/ARB use and AKI varied by surgery type (p-interaction = 0.004), with lower odds of AKI observed among ACEI/ARB use after cardiac surgery (OR = 0.70; 95% CI = 0.57-0.81), but no difference after other major surgeries.

CONCLUSIONS

Postoperative administration of diuretics and NSAIDs was associated with increased odds of AKI after major surgery. These findings characterize potentially modifiable medication exposures associated with AKI after surgery.

Cryptobia iubilans Infections in Discus Fish in Trinidad and Tobago

Discus (Symphysodon spp.) are costly and prized specimens in the international ornamental fish trade. The majority of discus submitted to the Aquatic Animal Health Unit at the University of the West Indies School of Veterinary Medicine for necropsy between September 2010 and September 2015 had lesions consistent with Cryptobia iubilans infection, thus prompting this study. To determine the prevalence of the flagellated gastrointestinal protozoan C. iubilans in discus fish, 32 discus were sourced from 10 suppliers, including breeders, importers, and hobbyists across Trinidad. Fish were euthanized, and the internal organs, particularly the stomach and intestine, were observed under a light microscope for characteristic granulomatous lesions and/or live C. iubilans parasites. All wet-mount slides on which granulomas were observed were also Ziehl-Neelsen acid-fast stained to presumptively exclude the presence of Mycobacterium spp., the main differential when diagnosing C. iubilans-associated granulomatous gastritis or to determine the presence of dual infections. Further histological analyses were performed on stomach and intestinal sections, and transmission electron microscopy was used to confirm the parasite in stomach sections. The prevalence of C. iubilans infection was found to be 81.3%, and the prevalence of presumptive dual infections with Mycobacterium spp. was found to be 21.9%. To the best of our knowledge, this is the first documented study of C. iubilans infections in the wider Caribbean region.

Is the age of plant communities predicted by the age, stability and soil composition of the underlying landscapes? An investigation of OCBILs

Old, climatically buffered, infertile landscapes (OCBILs) have been hypothesized to harbour an elevated number of persistent plant lineages and are predicted to occur across different parts of the globe, interspersed with other types of landscapes. We tested whether the mean age of a plant community is associated with occurrence on OCBILs, as predicted by climatic stability and poor soil environments. Using digitized occurrence data for seed plants occurring in Australia (7033 species), sub-Saharan Africa (3990 species) and South America (44 482 species), regions that comprise commonly investigated OCBILs (Southwestern Australian Floristic Region, Greater Cape Floristic Region and campos rupestres), and phylogenies pruned to match the species occurrences, we tested for associations between environmental data (current climate, soil composition, elevation and climatic stability) and two novel metrics developed here that capture the age of a community (mean tip length and mean node height). Our results indicate that plant community ages are influenced by a combination of multiple environmental predictors that vary globally; we did not find statistically strong associations between the environments of OCBIL areas and community age, in contrast to the prediction for these landscapes. The Cape Floristic Region was the only OCBIL that showed a significant, although not strong, overlap with old communities.

Intragenic Conflict in Phylogenomic Data Sets

Most phylogenetic analyses assume that a single evolutionary history underlies one gene. However, both biological processes and errors can cause intragenic conflict. The extent to which this conflict is present in empirical data sets is not well documented, but if common, could have far-reaching implications for phylogenetic analyses. We examined several large phylogenomic data sets from diverse taxa using a fast and simple method to identify well-supported intragenic conflict. We found conflict to be highly variable between data sets, from 1% to &gt;92% of genes investigated. We analyzed four exemplar genes in detail and analyzed simulated data under several scenarios. Our results suggest that alignment error may be one major source of conflict, but other conflicts remain unexplained and may represent biological signal or other errors. Whether as part of data analysis pipelines or to explore biologically processes, analyses of within-gene phylogenetic signal should become common.

Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective

Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger data sets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, which we augmented with publicly available sequences for an additional 17 taxa. Using a locus-by-locus approach, we evaluated support for alternative topologies at 17 contentious nodes in the phylogeny. We identified shared properties of conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests of nodal conflict to previous phylogenomic studies, we confidently resolve 9 of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups. [Anchored hybrid enrichment (AHE); gene tree conflict; molecular evolution; phylogenomic concordance; target capture; ultraconserved elements (UCE).].

Evolution of l-DOPA 4,5-dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales

The evolution of l-DOPA 4,5-dioxygenase activity, encoded by the gene DODA, was a key step in the origin of betalain biosynthesis in Caryophyllales. We previously proposed that l-DOPA 4,5-dioxygenase activity evolved via a single Caryophyllales-specific neofunctionalisation event within the DODA gene lineage. However, this neofunctionalisation event has not been confirmed and the DODA gene lineage exhibits numerous gene duplication events, whose evolutionary significance is unclear. To address this, we functionally characterised 23 distinct DODA proteins for l-DOPA 4,5-dioxygenase activity, from four betalain-pigmented and five anthocyanin-pigmented species, representing key evolutionary transitions across Caryophyllales. By mapping these functional data to an updated DODA phylogeny, we then explored the evolution of l-DOPA 4,5-dioxygenase activity. We find that low l-DOPA 4,5-dioxygenase activity is distributed across the DODA gene lineage. In this context, repeated gene duplication events within the DODA gene lineage give rise to polyphyletic occurrences of elevated l-DOPA 4,5-dioxygenase activity, accompanied by convergent shifts in key functional residues and distinct genomic patterns of micro-synteny. In the context of an updated organismal phylogeny and newly inferred pigment reconstructions, we argue that repeated convergent acquisition of elevated l-DOPA 4,5-dioxygenase activity is consistent with recurrent specialisation to betalain synthesis in Caryophyllales.

Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l

Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The data set included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations. [Amaranthaceae; gene tree discordance; hybridization; incomplete lineage sorting; phylogenomics; species network; species tree; transcriptomics.]

------Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods

Cytosine methylation is an ancient epigenetic modification yet its function and extent within genomes is highly variable across eukaryotes. In mammals, methylation controls transposable elements and regulates the promoters of genes. In insects, DNA methylation is generally restricted to a small subset of transcribed genes, with both intergenic regions and transposable elements (TEs) depleted of methylation. The evolutionary origin and the function of these methylation patterns are poorly understood. Here we characterise the evolution of DNA methylation across the arthropod phylum. While the common ancestor of the arthropods had low levels of TE methylation and did not methylate promoters, both of these functions have evolved independently in centipedes and mealybugs. In contrast, methylation of the exons of a subset of transcribed genes is ancestral and widely conserved across the phylum, but has been lost in specific lineages. A similar set of genes is methylated in all species that retained exon-enriched methylation. We show that these genes have characteristic patterns of expression correlating to broad transcription initiation sites and well-positioned nucleosomes, providing new insights into potential mechanisms driving methylation patterns over hundreds of millions of years.

Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

PREMISE

Discordance between nuclear and organellar phylogenies (cytonuclear discordance) is a well-documented phenomenon at shallow evolutionary levels but has been poorly investigated at deep levels of plant phylogeny. Determining the extent of cytonuclear discordance across major plant lineages is essential not only for elucidating evolutionary processes, but also for evaluating the currently used framework of plant phylogeny, which is largely based on the plastid genome.

METHODS

We present a phylogenomic examination of a major angiosperm clade (Asteridae) based on sequence data from the nuclear, plastid, and mitochondrial genomes as a means of evaluating currently accepted relationships inferred from the plastome and exploring potential sources of genomic conflict in this group.

RESULTS

We recovered at least five instances of well-supported cytonuclear discordance concerning the placements of major asterid lineages (i.e., Ericales, Oncothecaceae, Aquifoliales, Cassinopsis, and Icacinaceae). We attribute this conflict to a combination of incomplete lineage sorting and hybridization, the latter supported in part by previously inferred whole-genome duplications.

CONCLUSIONS

Our results challenge several long-standing hypotheses of asterid relationships and have implications for morphological character evolution and for the importance of ancient whole-genome duplications in early asterid evolution. These findings also highlight the value of reevaluating broad-scale angiosperm and green-plant phylogeny with nuclear genomic data.

A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales

PREMISE

Large genomic data sets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications.

METHODS

We used a hierarchical clustering approach, with tree-based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene-wise edge-based analyses, concatenation, and coalescent-based methods, and is summarized in a consensus framework.

RESULTS

Our consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships because of lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole-genome duplication before the radiation of all or most ericalean families, and demonstrate that tree topology and heterogeneous evolutionary rates affect the inferred placement of genome duplications.

CONCLUSIONS

We provide several hypotheses regarding the history of Ericales, and confidently resolve most nodes, but demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.

Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants

Studies have demonstrated that pervasive gene tree conflict underlies several important phylogenetic relationships where different species tree methods produce conflicting results. Here, we present a means of dissecting the phylogenetic signal for alternative resolutions within a data set in order to resolve recalcitrant relationships and, importantly, identify what the data set is unable to resolve. These procedures extend upon methods for isolating conflict and concordance involving specific candidate relationships and can be used to identify systematic error and disambiguate sources of conflict among species tree inference methods. We demonstrate these on a large phylogenomic plant data set. Our results support the placement of Amborella as sister to the remaining extant angiosperms, Gnetales as sister to pines, and the monophyly of extant gymnosperms. Several other contentious relationships, including the resolution of relationships within the bryophytes and the eudicots, remain uncertain given the low number of supporting gene trees. To address whether concatenation of filtered genes amplified phylogenetic signal for relationships, we implemented a combinatorial heuristic to test combinability of genes. We found that nested conflicts limited the ability of data filtering methods to fully ameliorate conflicting signal amongst gene trees. These analyses confirmed that the underlying conflicting signal does not support broad concatenation of genes. Our approach provides a means of dissecting a specific data set to address deep phylogenetic relationships while also identifying the inferential boundaries of the data set. [Angiosperms; coalescent; gene-tree conflict; genomics; phylogenetics; phylogenomics.]

Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments

Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many families within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae, and Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examined potential correlates between molecular evolution and adaptation to harsh environments. Our phylogenetic results were largely congruent with previous analyses, but we identified several early diverging nodes characterized by extensive gene tree conflict. For particularly contentious nodes, we present detailed information about the phylogenetic signal for alternative relationships. We also analyzed the frequency of gene duplications, confirmed previously identified whole genome duplications (WGD), and proposed a previously unidentified WGD event within the Didiereaceae. We found that the WGD events were typically associated with shifts in climatic niche but did not find a direct association with WGDs and diversification rate shifts. Diversification shifts occurred within the Portulacaceae, Cactaceae, and Anacampserotaceae, and whereas these did not experience WGDs, the Cactaceae experienced extensive gene duplications. We examined gene family expansion and molecular evolutionary patterns with a focus on genes associated with environmental stress responses and found evidence for significant gene family expansion in genes with stress adaptation and clades found in extreme environments. These results provide important directions for further and deeper examination of the potential links between molecular evolutionary patterns and adaptation to harsh environments.

Quantification of DTI in the Pediatric Spinal Cord: Application to Clinical Evaluation in a Healthy Patient Population

BACKGROUND AND PURPOSE

The purpose of the study is to characterize diffusion tensor imaging indices in the developing spinal cord, evaluating differences based on age and cord region. Describing the progression of DTI indices in the pediatric cord increases our understanding of spinal cord development.

MATERIALS AND METHODS

A retrospective analysis was performed on DTI acquired in 121 pediatric patients (mean, 8.6 years; range, 0.3-18.0 years) at Monroe Carell Jr. Children's Hospital at Vanderbilt from 2017 to 2018. Diffusion-weighted images (15 directions; b = 750 s/mm²; slice thickness, 5 mm; in-plane resolution, 1.0 × 1.0 mm²) were acquired on a 3T scanner in the cervicothoracic and/or thoracolumbar cord. Manual whole-cord segmentation was performed. Images were masked and further segmented into cervical, upper thoracic, thoracolumbar, and conus regions. Analyses of covariance were performed for each DTI-derived index to investigate how age affects diffusion across cord regions, and 95% confidence intervals were calculated across age for each derived index and region. Post hoc testing was performed to analyze regional differences.

RESULTS

Analyses of covariance revealed significant correlations of age with axial diffusivity, mean diffusivity, and fractional anisotropy (all, P < .001). There were also significant differences among cord regions for axial diffusivity, radial diffusivity, mean diffusivity, and fractional anisotropy (all, P < .001).

CONCLUSIONS

This research demonstrates that diffusion evolves in the pediatric spinal cord during development, dependent on both cord region and the diffusion index of interest. Future research could investigate how diffusion may be affected by common pediatric spinal pathologies.

Trace minerals in tilapia fillets: Status in the United States marketplace and selenium supplementation strategy for improving consumer's health

This goal of this study was to highlight the importance of minerals in the diet of fish for meeting micronutrient requirements in the human diet. First arsenic, calcium, cadmium, copper, iron, molybdenum, magnesium, manganese, sodium, phosphorus, potassium, selenium, and zinc concentrations of twelve commercially available tilapia samples were measured. The nutritional value of fillets in regard to their mineral content were assessed to establish potential health benefits or risks for consumers. The health benefit value of selenium was also calculated. Positive health benefit values indicate that tilapia fillets in the United States marketplace of this study do not pose health risks associated with mercury exposures. Selenium was the trace mineral of interest. After the market study, a seven-week fish feeding trial was conducted to study the influence of organic versus inorganic dietary selenium on Nile tilapia (Oreochromis niloticus). Fish were fed two different diets enriched with the same concentration (0.01g kg-1) of selenium in form of inorganic (sodium selenite) or organic (seleno-L-methionine) selenium in triplicate groups. There were no significant differences between growth and biometrics of fish fed different diets (p>0.05). At the end of trial twelve fish from each treatment were collected. Fillets of fish fed organic selenium had selenium concentrations of 0.55 ± 0.01 μg g-1 which were significantly (p<0.05) higher than fish fed inorganic selenium at levels of 0.22 ± 0.008 μg g-1 or fish samples from the marketplace with a selenium level of 0.2 ± 0.03 μg g-1. Fish fed organic selenium also had significantly higher (p<0.05) plasma and kidney selenium in comparison to fish fed inorganic selenium. No significant differences (p>0.05) were observed in glutathione peroxidase activities in either the plasma or liver of Nile tilapia in the different treatment groups. This study shows that organic selenium is a better option for production of Nile tilapia fillets rich in selenium.

Surgical technique for developing a rabbit model of congenital diaphragmatic hernia and tracheal occlusion

The surgical model of congenital diaphragmatic hernia (CDH) has been utilized in exploring treatments and innovative therapies, such as tracheal occlusion (TO). The rabbit is an excellent surgical model compared to others due to lower cost, ease of care, short gestational period, and large litter size. This model is also ideal in studying lung hypoplasia of CDH because rabbit lung development is most similar to humans as alveolarization begins prior to birth and continues post-natally. However, the surgical technique in creating a rabbit model of CDH is quite difficult and information is lacking on how to establish this model. Therefore, the aim of this paper is to describe:

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Surgical technique in establishing a rabbit model of CDH and TO

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Perioperative care for pregnant rabbit does

Bayesian and likelihood phylogenetic reconstructions of morphological traits are not discordant when taking uncertainty into consideration: a comment on Puttick et al

Puttick et al. (2017 Proc. R. Soc. B284, 20162290 (doi:10.1098/rspb.2016.2290)) performed a simulation study to compare accuracy among methods of inferring phylogeny from discrete morphological characters. They report that a Bayesian implementation of the Mk model (Lewis 2001 Syst. Biol.50, 913-925 (doi:10.1080/106351501753462876)) was most accurate (but with low resolution), while a maximum-likelihood (ML) implementation of the same model was least accurate. They conclude by strongly advocating that Bayesian implementations of the Mk model should be the default method of analysis for such data. While we appreciate the authors' attempt to investigate the accuracy of alternative methods of analysis, their conclusion is based on an inappropriate comparison of the ML point estimate, which does not consider confidence, with the Bayesian consensus, which incorporates estimation credibility into the summary tree. Using simulation, we demonstrate that ML and Bayesian estimates are concordant when confidence and credibility are comparably reflected in summary trees, a result expected from statistical theory. We therefore disagree with the conclusions of Puttick et al. and consider their prescription of any default method to be poorly founded. Instead, we recommend caution and thoughtful consideration of the model or method being applied to a morphological dataset.

Modulation of innate immunity in Nile tilapia (Oreochromis niloticus) by dietary supplementation of Bacillus subtilis endospores

Dietary supplementation of probiotics is growing as a scientifically valid alternative to antibiotics for enhancement of overall animal health and productivity in aquaculture. Strains of Bacillus subtilis are regarded as attractive probiotic candidates to the fish farming industry; however, there is a limited number of studies focused on the use of specific strains probiotics in tilapia, and therefore complicating replication. The objective of this study was to examine the effect of the strains NZ86 (NRRL B-50136) and O14VRQ (NRRL B-67221) of B. subtilis on various parameters of the innate immunity in Nile tilapia (Oreochromis niloticus) in a 51-day feeding trial. Supplementation of tilapia with either strain resulted in significant increases (p < 0.05) in plasma lysozyme concentration of varying degrees throughout the trial. Meanwhile, alternative complement activity was significantly elevated (p < 0.05) only after feeding of the NZ86 strain after 14 and 51 days. Conversely, supplementation with O14VRQ resulted in a significant increase (p < 0.05) in the percent of neutrophils in the peripheral blood of tilapia by day 28. At the end of the trial, there was a trend towards increased phagocytic and respiratory burst activities observed in immune organ derived leukocytes. Feeding with either probiotic appeared to have an up-regulation on the gene expression of both pro-inflammatory cytokines in the intestine, yet only O14VRQ was significantly different than the control. Moreover, the occurrence of these results could be associated with supplementation of the probiotic strains, given that Bacillus bacteria were observed to populate the intestines of the dietary treatment groups. These results suggest the potential roles of these B. subtilis probiotic candidates to stimulate immune responses both locally and systemically in tilapia.

Analyzing Contentious Relationships and Outlier Genes in Phylogenomics

Recent studies have demonstrated that conflict is common among gene trees in phylogenomic studies, and that less than one percent of genes may ultimately drive species tree inference in supermatrix analyses. Herein, we examined two data sets where supermatrix and coalescent-based species trees conflict. We identified two highly influential "outlier" genes in each data set. When removed from each data set, the inferred supermatrix trees matched the topologies obtained from coalescent analyses. We also demonstrate that, while the outlier genes in the vertebrate data set have been shown in a previous study to be the result of errors in orthology detection, the outlier genes from a plant data set did not exhibit any obvious systematic error, and therefore, may be the result of some biological process yet to be determined. While topological comparisons among a small set of alternate topologies can be helpful in discovering outlier genes, they can be limited in several ways, such as assuming all genes share the same topology. Coalescent species tree methods relax this assumption but do not explicitly facilitate the examination of specific edges. Coalescent methods often also assume that conflict is the result of incomplete lineage sorting. Herein, we explored a framework that allows for quickly examining alternative edges and support for large phylogenomic data sets that does not assume a single topology for all genes. For both data sets, these analyses provided detailed results confirming the support for coalescent-based topologies. This framework suggests that we can improve our understanding of the underlying signal in phylogenomic data sets by asking more targeted edge-based questions.

Characterization of the histologic appearance of normal gill tissue using special staining techniques

Anatomic pathologists are familiar with stains used in light microscopy to identify cells, storage products, tissue deposits, and pathogens. Assessment of the surrounding tissue with special stains may reveal aspects of interest for the tissue or the species. We illustrate the expected staining characteristics of normal rainbow trout gill tissue with routine hematoxylin and eosin and 18 other histochemical stains.

Predisposing Genes in Breast and Ovarian Cancer: An Overview

The isolation of genes that predispose to familial disease is an important goal in cancer research. The identification of such genes « opens up » the possibility of genetic diagnosis in families so that individuals who are at risk of cancer through inheriting a predisposing mutation can be Identified. Genes that are involved in familial cancer syndromes may also be important in the pathogenesis of sporadic forms of the disease, which are often more common. In the search for genes that predispose to familial breast and ovarian cancer much recent progress has been made. A locus on the long arm of chromosome 17, in the interval 17q12-21, has been identified by genetic linkage, and appears to be responsible for disease in approximately 40 % of breast cancer families and most families that contain breast and ovarian cancer. The region containing this locus, which has been called BRCA1, has been narrowed to a 3-4 cM interval defined by THRA1, the thyroid hormone receptor locus alpha, and D17S183, an anonymous microsatellite polymorphism. Loci other than BRCA1 that have been identified appear not only to predispose to breast and/or ovarian tumors, but to tumors at other sites too. A new locus has been identified on chromosome 2 which is linked to hereditary non-polyposis colorectal cancer (HNPCC). Families with HNPCC are also at risk of endometrial cancer and tumors of the ovary, amongst other cancer sites. Finally, mutations in the p53 gene are inherited in families with Li-Fraumeni syndrome, a rare cancer syndrome predisposing to breast tumors, sarcomas, leukemia and other cancers. Li-Fraumeni syndrome is also the only inherited cancer syndrome that predisposes at least in part to breast cancer where the actual predisposing gene is known. For the other cancer syndromes, the cloning of the predisposing genes is eagerly awaited.