BACKGROUND: Phylogenies play a crucial role in biological research. Unfortunately, the search for the optimal phylogenetic tree incurs significant computational costs, and most of the existing state-of-the-art tools cannot deal with extremely large datasets in reasonable times.
RESULTS: In this work, we introduce the new VeryFastTree code (version 4.0), which is able to construct a tree on 1 server using single-precision arithmetic from a massive 1 million alignment dataset in only 36 hours, which is 3 times and 3.2 times faster than its previous version and FastTree-2, respectively. This new version further boosts performance by parallelizing all tree traversal operations during the tree construction process, including subtree pruning and regrafting moves. Additionally, it introduces significant new features such as support for new and compressed file formats, enhanced compatibility across a broader range of operating systems, and the integration of disk computing functionality. The latter feature is particularly advantageous for users without access to high-end servers, as it allows them to manage very large datasets, albeit with an increase in computing time.
CONCLUSIONS: Experimental results establish VeryFastTree as the fastest tool in the state-of-the-art for maximum likelihood phylogeny estimation. It is publicly available at https://github.com/citiususc/veryfasttree. In addition, VeryFastTree is included as a package in Bioconda, MacPorts, and all Debian-based Linux distributions.

Constraints on phenotypic evolution can lead to patterns of convergent evolution, by limiting the \'pool\' of potential phenotypes in the face of endogenous (functional, developmental) or exogenous (competition, predation) selective pressures. Evaluation of convergence depends on integrating ecological and morphological data within a robust, comparative phylogenetic context. The staggering diversity of teleost fishes offers a multitude of lineages adapted for similar ecological roles, and therefore, offers numerous replicated evolutionary experiments for exploring phenotypic convergence. However, our understanding of fish feeding systems has been primarily shaped by marine species, with the monolithic exception of freshwater cichlids. Here we use piranhas and pacus (Serrasalmidae) to explore the evolution of different feeding ecologies and their morphological proxies in Neotropical freshwater environments. Specifically, we explore whether convergence is more widespread among plant-eating fishes, arising from strong constraints on phenotypic evolution in herbivores. Using osteological micro-computed tomographic imaging (μCT), we describe the major axes of morphological variation in pacus and piranhas, regarding their diet and feeding behaviors. Next, we evaluated whether herbivorous niches are less labile than other dietary guilds and whether herbivorous species\' phenotypes evolve at a slower evolutionary rate than other taxa. We then assess how convergent herbivorous taxa are, using three different suites of morphological characters (dental, jaw, and abdominal morphometrics). Ecologically, herbivory is not a dead end, exhibiting similar observed transition rates as those between carnivores and omnivores. However, we documented widespread convergence in herbivores and that herbivores have slower rates of phenotypic evolution than carnivores. Most instances of convergence are found in herbivorous taxa, specifically in frugivores and folivores. Moreover, instances of \'complete\' convergence, indicated by positive convergence metrics observed in more than one morphometric dataset, were only found in herbivores. Herbivores do appear to evolve under constrained circumstances, but this has not limited their ecological lability.

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Introduction The goal of total knee arthroplasty is to replace diseased cartilage and bone with an artificial implant to improve the patient\'s quality of life. The knee has historically been reconstructed to the patient\'s mechanical axis (MA). However, kinematically aligned techniques have been increasingly used. Kinematic alignment requires less soft-tissue resection and aligns the knee with what is anatomically natural to the patient, while there is concern that kinematically aligned knees will lead to earlier failure due to potential unequal weight distribution on the implant. The purpose of this study is to compare the parallelism from the floor of the joint-line cuts using kinematic and mechanical alignment and understand if the MA is a proper estimation of the tibial-ankle axis (TA). Methods A retrospective study was conducted by recruiting all high tibial osteotomy and distal femoral osteotomy recipients operated on by two surgeons in two MedStar Health hospitals from 01/2013 to 07/2020 with full-length films in preparation for restorative procedures. Baseline osteoarthritis was graded using the Kellgren-Lawrence classification system with all patients presenting as Grade 0. The TA and the joint-line orientations of the MA and kinematic axis (KA) were measured on 66 legs. The average distance from parallelism to the ground was compared between the MA and the KA and between the MA and the TA using a paired t-test. Results KA joint-line orientation (1.705° deviation) was more parallel to the floor in the bipedal stance phase than the MA (2.316° deviation, p=0.0156). The MA (2.316° deviation) was not a proper estimation of the TA (4.278° deviation, p=0.0001). Conclusion By utilizing the KA technique, the restoration of the natural joint line, as well as a joint that is more parallel to the floor in the stance phase compared to the MA, is achieved. The parallelism to the ground of the KA during the bipedal stance phase suggests an even load distribution across the knee. In addition, due to its similarity to the KA and anatomical significance in weight-bearing distribution, further investigation into the hip-to-calcaneal axis as an approximation of the joint line is warranted.

Graphics processing units (GPUs) facilitate massive parallelism and high-capacity storage, and thus are suitable for the iterative reconstruction of ultrahigh-resolution micro computed tomography (CT) scans by on-the-fly system matrix (OTFSM) calculation using ordered subsets expectation maximization (OSEM). We propose a finite state automaton (FSA) method that facilitates iterative reconstruction using a heterogeneous multi-GPU platform through parallelizing the matrix calculations derived from a ray tracing system of ordered subsets. The FSAs perform flow control for parallel threading of the heterogeneous GPUs, which minimizes the latency of launching ordered-subsets tasks, reduces the data transfer between the main system memory and local GPU memory, and solves the memory-bound of a single GPU. In the experiments, we compared the operation efficiency of OS-MLTR for three reconstruction environments. The heterogeneous multiple GPUs with job queues for high throughput calculation speed is up to five times faster than the single GPU environment, and that speed up is nine times faster than the heterogeneous multiple GPUs with the FIFO queues of the device scheduling control. Eventually, we proposed an event-triggered FSA method for iterative reconstruction using multiple heterogeneous GPUs that solves the memory-bound issue of a single GPU at ultrahigh resolutions, and the routines of the proposed method were successfully executed on each GPU simultaneously.

Diabetic nephropathy (DN) and diabetic retinopathy (DR), as microvascular complications of diabetes mellitus, are currently the leading causes of end-stage renal disease (ESRD) and blindness, respectively, in the adult working population, and they are major public health problems with social and economic burdens. The parallelism between the two in the process of occurrence and development manifests in the high overlap of disease-causing risk factors and pathogenesis, high rates of comorbidity, mutually predictive effects, and partial concordance in the clinical use of medications. However, since the two organs, the eye and the kidney, have their unique internal environment and physiological processes, each with specific influencing molecules, and the target organs have non-parallelism due to different pathological changes and responses to various influencing factors, this article provides an overview of the parallelism and non-parallelism between DN and DR to further recognize the commonalities and differences between the two diseases and provide references for early diagnosis, clinical guidance on the use of medication, and the development of new drugs.

To meet the demand for the track\'s geometric parameter detection equipment for train speed and high-speed aerodynamics tests, a zero-calibration gauge device is designed with the centering limit, height adjustment and horizontal display function in this paper. The bending situation of the zero-calibration gauge is analyzed and the processing technology is studied, which ensures the rationality and realizability of the design of zero-calibration gauge. Then the gauge zero value and the parallelism of the working surface of zero-calibration gauge have been experimentally tested. The experimental results show that the parameter of gauge zero value is 1434.829 mm with a standard deviation of 1.4 μm. The parallelism of the two upper working surfaces is 1.1 μm, and the parallelism of the two inner working surfaces is 4 μm. Finally, the uncertainty evaluation of zero-calibration gauge is completed. The measurement uncertainty of gauge zero value is 12 μm and the measurement uncertainty of height difference is 6 μm.

Poetic diction routinely involves two complementary classes of features: (i) parallelisms, i.e. repetitive patterns (rhyme, metre, alliteration, etc.) that enhance the predictability of upcoming words, and (ii) poetic deviations that challenge standard expectations/predictions regarding regular word form and order. The present study investigated how these two prediction-modulating fundamentals of poetic diction affect the cognitive processing and aesthetic evaluation of poems, humoristic couplets and proverbs. We developed quantitative measures of these two groups of text features. Across the three text genres, higher deviation scores reduced both comprehensibility and aesthetic liking whereas higher parallelism scores enhanced these. The positive effects of parallelism are significantly stronger than the concurrent negative effects of the features of deviation. These results are in accord with the hypothesis that art reception involves an interplay of prediction errors and prediction error minimization, with the latter paving the way for processing fluency and aesthetic liking. This article is part of the theme issue \'Art, aesthetics and predictive processing: theoretical and empirical perspectives\'.

Parallel clines across environmental gradients can be strong evidence of adaptation. House mice (Mus musculus domesticus) were introduced to the Americas by European colonizers and are now widely distributed from Tierra del Fuego to Alaska. Multiple aspects of climate, such as temperature, vary predictably across latitude in the Americas. Past studies of North American populations across latitudinal gradients provided evidence of environmental adaptation in traits related to body size, metabolism, and behavior and identified candidate genes using selection scans. Here, we investigate genomic signals of environmental adaptation on a second continent, South America, and ask whether there is evidence of parallel adaptation across multiple latitudinal transects in the Americas. We first identified loci across the genome showing signatures of selection related to climatic variation in mice sampled across a latitudinal transect in South America, accounting for neutral population structure. Consistent with previous results, most candidate SNPs were in regulatory regions. Genes containing the most extreme outliers relate to traits such as body weight or size, metabolism, immunity, fat, and development or function of the eye as well as traits associated with the cardiovascular and renal systems. We then combined these results with published results from two transects in North America. While most candidate genes were unique to individual transects, we found significant overlap among candidate genes identified independently in the three transects, providing strong evidence of parallel adaptation and identifying genes that likely underlie recent environmental adaptation in house mice across North and South America.

A general view in the study of pollination syndromes is that floral traits usually represent convergent floral adaptations to specific functional pollinator groups. However, the definition of convergence is elusive and contradictory in the literature. Is convergence the independent evolution of either the same trait or similar traits with the same function? A review of the concept of convergence in developmental biology and phylogenetic systematics may shed new light in studies of pollination syndromes.
The aims of this article are (1) to explore the notion of convergence and other concepts (analogy, homoplasy and parallelism) within the theory and practice of developmental evolution and phylogenetic systematics; (2) to modify the definitions of syndromes in order to embrace the concepts of analogy and convergence; (3) to revisit the bat pollination syndrome in the context of angiosperm phylogeny, with focus on the showy \'petaloid\' organs associated with the syndrome; (4) to revisit the genetic-developmental basis of flower colour; (5) to raise evolutionary hypotheses of floral evolution associated with the bat pollination syndrome; and (6) to highlight some of the current frontiers of research on the origin and evolution of flowers and its impact on pollination syndrome studies in the 21st century.
The inclusion of the concepts of analogy and convergence within the concept of syndromes will constitute a new agenda of inquiry that integrates floral biology, phylogenetic systematics and developmental biology. Phyllostomid and pteropodid bat pollination syndrome traits in eudicots and monocots represent cases of analogous and convergent evolution. Pollination syndromes are a multivariate concept intrinsically related to the understanding of flower organogenesis and evolution. The formulation of hypotheses of pollination syndromes must consider the phylogenetic levels of universality for both plant and animal taxa, flower development, genetics, homology and evolution, and a clear definition of evolutionary concepts, including analogy, convergence, homoplasy and parallelism.