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Cancer progression is an evolutionary process driven by the selection of cells adapted to gain growth advantage. We present a formal study on the adaptation of gene expression in subclonal evolution. We model evolutionary changes in gene expression as stochastic Ornstein-Uhlenbeck processes, jointly leveraging the evolutionary history of subclones and single-cell expression data. Applying our model to sublines derived from single cells of a mouse melanoma revealed that sublines with distinct phenotypes are underlined by different patterns of gene expression adaptation, indicating non-genetic mechanisms of cancer evolution. Sublines previously observed to be resistant to anti-CTLA4 treatment showed adaptive expression of genes related to invasion and non-canonical Wnt signaling, whereas sublines that responded to treatment showed adaptive expression of genes related to proliferation and canonical Wnt signaling. Our results suggest that clonal phenotypes emerge as the result of specific adaptivity patterns of gene expression. A record of this paper's transparent peer review process is included in the supplemental information., Competing Interests: Declaration of interests The authors declare no competing interests., (Published by Elsevier Inc.)

The advent of long-read sequencing of microbiomes necessitates the development of new taxonomic profilers tailored to long-read shotgun metagenomic datasets. Here, we introduce Lemur and Magnet, a pair of tools optimized for lightweight and accurate taxonomic profiling for long-read shotgun metagenomic datasets. Lemur is a marker-gene-based method that leverages an EM algorithm to reduce false positive calls while preserving true positives; Magnet is a whole-genome read-mapping-based method that provides detailed presence and absence calls for bacterial genomes. We demonstrate that Lemur and Magnet can run in minutes to hours on a laptop with 32 GB of RAM, even for large inputs, a crucial feature given the portability of long-read sequencing machines. Furthermore, the marker gene database used by Lemur is only 4 GB and contains information from over 300,000 RefSeq genomes. Lemur and Magnet are open-source and available at https://github.com/treangenlab/lemur and https://github.com/treangenlab/magnet., Competing Interests: 6Competing interests The authors declare that they have no competing interests.

Efficiency of mosquito-borne disease transmission is dependent upon both the preference and fidelity of mosquitoes as they seek the blood of vertebrate hosts. While mosquitoes select their blood hosts through multi-modal integration of sensory cues, host-seeking is primarily an odor-guided behavior. Differences in mosquito responses to hosts and their odors have been demonstrated to have a genetic component, but the underlying genomic architecture of these responses has yet to be fully resolved. Here, we provide the first characterization of the genomic architecture of host preference in the polymorphic mosquito species, Culex pipiens. The species exists as two morphologically identical bioforms, each with distinct avian and mammalian host preferences. Cx. pipiens females with empirically measured host responses were prepared into reduced representation DNA libraries and sequenced to identify genomic regions associated with host preference. Multiple genomic regions associated with host preference were identified on all 3 Culex chromosomes, and these genomic regions contained clusters of chemosensory genes, as expected based on work in Anopheles gambiae complex mosquitoes and in Aedes aegypti. One odorant receptor and one odorant binding protein gene showed one-to-one orthologous relationships to differentially expressed genes in A. gambiae complex members with divergent host preferences. Overall, our work identifies a distinct set of odorant receptors and odorant binding proteins that may enable Cx. pipiens females to distinguish between their vertebrate blood host species, and opens avenues for future functional studies that could measure the unique contributions of each gene to host preference phenotypes., (© 2024. The Author(s), under exclusive licence to The Genetics Society.)

The last decade of phylogenetics has seen the development of many methods that leverage constraints plus dynamic programming. The goal of this algorithmic technique is to produce a phylogeny that is optimal with respect to some objective function and that lies within a constrained version of tree space. The popular species tree estimation method ASTRAL, for example, returns a tree that (1) maximizes the quartet score computed with respect to the input gene trees and that (2) draws its branches (bipartitions) from the input constraint set. This technique has yet to be used for parsimony problems where the input are binary characters, sometimes with missing values. Here, we introduce the clade-constrained character parsimony problem and present an algorithm that solves this problem for the Dollo criterion score in [Formula: see text] time, where n is the number of leaves, k is the number of characters, and [Formula: see text] is the set of clades used as constraints. Dollo parsimony, which requires traits/mutations to be gained at most once but allows them to be lost any number of times, is widely used for tumor phylogenetics as well as species phylogenetics, for example analyses of low-homoplasy retroelement insertions across the vertebrate tree of life. This motivated us to implement our algorithm in a software package, called Dollo-CDP, and evaluate its utility for analyzing retroelement insertion presence / absence patterns for bats, birds, toothed whales as well as simulated data. Our results show that Dollo-CDP can improve upon heuristic search from a single starting tree, often recovering a better scoring tree. Moreover, Dollo-CDP scales to data sets with much larger numbers of taxa than branch-and-bound while still having an optimality guarantee, albeit a more restricted one. Lastly, we show that our algorithm for Dollo parsimony can easily be adapted to Camin-Sokal parsimony but not Fitch parsimony., (© 2023. The Author(s).)

Cancer progression and treatment can be informed by reconstructing its evolutionary history from tumor cells. Although many methods exist to estimate evolutionary trees (called phylogenies) from molecular sequences, traditional approaches assume the input data are error-free and the output tree is fully resolved. These assumptions are challenged in tumor phylogenetics because single-cell sequencing produces sparse, error-ridden data and because tumors evolve clonally. Here, we study the theoretical utility of methods based on quartets (four-leaf, unrooted phylogenetic trees) in light of these barriers. We consider a popular tumor phylogenetics model, in which mutations arise on a (highly unresolved) tree and then (unbiased) errors and missing values are introduced. Quartets are then implied by mutations present in two cells and absent from two cells. Our main result is that the most probable quartet identifies the unrooted model tree on four cells. This motivates seeking a tree such that the number of quartets shared between it and the input mutations is maximized. We prove an optimal solution to this problem is a consistent estimator of the unrooted cell lineage tree; this guarantee includes the case where the model tree is highly unresolved, with error defined as the number of false negative branches. Lastly, we outline how quartet-based methods might be employed when there are copy number aberrations and other challenges specific to tumor phylogenetics., (© 2023. The Author(s).)

methods are widely used to estimate species trees from genome-scale data. However, they can fail to produce accurate species trees when the input gene trees are highly discordant because of estimation error and biological processes, such as incomplete lineage sorting. Here, we introduce TREE-QMC, a new summary method that offers accuracy and scalability under these challenging scenarios. TREE-QMC builds upon weighted Quartet Max Cut, which takes weighted quartets as input and then constructs a species tree in a divide-and-conquer fashion, at each step forming a graph and seeking its max cut. The wQMC method has been successfully leveraged in the context of species tree estimation by weighting quartets by their frequencies in the gene trees; we improve upon this approach in two ways. First, we address accuracy by normalizing the quartet weights to account for "artificial taxa" introduced during the divide phase so subproblem solutions can be combined during the conquer phase. Second, we address scalability by introducing an algorithm to construct the graph directly from the gene trees; this gives TREE-QMC a time complexity of [Formula: see text], where n is the number of species and k is the number of gene trees, assuming the subproblem decomposition is perfectly balanced. These contributions enable TREE-QMC to be highly competitive in terms of species tree accuracy and empirical runtime with the leading quartet-based methods, even outperforming them on some model conditions explored in our simulation study. We also present the application of these methods to an avian phylogenomics data set., (© 2023 Han and Molloy; Published by Cold Spring Harbor Laboratory Press.)

Recent studies exploring the impact of methylation in tumor evolution suggest that although the methylation status of many of the CpG sites are preserved across distinct lineages, others are altered as the cancer progresses. Because changes in methylation status of a CpG site may be retained in mitosis, they could be used to infer the progression history of a tumor via single-cell lineage tree reconstruction. In this work, we introduce the first principled distance-based computational method, Sgootr, for inferring a tumor's single-cell methylation lineage tree and for jointly identifying lineage-informative CpG sites that harbor changes in methylation status that are retained along the lineage. We apply Sgootr on single-cell bisulfite-treated whole-genome sequencing data of multiregionally sampled tumor cells from nine metastatic colorectal cancer patients, as well as multiregionally sampled single-cell reduced-representation bisulfite sequencing data from a glioblastoma patient. We show that the tumor lineages constructed reveal a simple model underlying tumor progression and metastatic seeding. A comparison of Sgootr against alternative approaches shows that Sgootr can construct lineage trees with fewer migration events and with more in concordance with the sequential-progression model of tumor evolution, with a running time a fraction of that used in prior studies. Lineage-informative CpG sites identified by Sgootr are in inter-CpG island (CGI) regions, as opposed to intra-CGIs, which have been the main regions of interest in genomic methylation-related analyses., (© 2023 Liu et al.; Published by Cold Spring Harbor Laboratory Press.)

Background: The Salmonella enterica serovar Newport red onion outbreak of 2020 was the largest foodborne outbreak of Salmonella in over a decade. The epidemiological investigation suggested two farms as the likely source of contamination. However, single nucleotide polymorphism (SNP) analysis of the whole genome sequencing data showed that none of the Salmonella isolates collected from the farm regions were linked to the clinical isolates-preventing the use of phylogenetics in source identification. Here, we explored an alternative method for analyzing the whole genome sequencing data driven by the hypothesis that if the outbreak strain had come from the farm regions, then the clinical isolates would disproportionately contain plasmids found in isolates from the farm regions due to horizontal transfer., Results: SNP analysis confirmed that the clinical isolates formed a single, nearly-clonal clade with evidence for ancestry in California going back a decade. The clinical clade had a large core genome (4,399 genes) and a large and sparsely distributed accessory genome (2,577 genes, at least 64% on plasmids). At least 20 plasmid types occurred in the clinical clade, more than were found in the literature for Salmonella Newport. A small number of plasmids, 14 from 13 clinical isolates and 17 from 8 farm isolates, were found to be highly similar (> 95% identical)-indicating they might be related by horizontal transfer. Phylogenetic analysis was unable to determine the geographic origin, isolation source, or time of transfer of the plasmids, likely due to their promiscuous and transient nature. However, our resampling analysis suggested that observing a similar number and combination of highly similar plasmids in random samples of environmental Salmonella enterica within the NCBI Pathogen Detection database was unlikely, supporting a connection between the outbreak strain and the farms implicated by the epidemiological investigation., Conclusion: Horizontally transferred plasmids provided evidence for a connection between clinical isolates and the farms implicated as the source of the outbreak. Our case study suggests that such analyses might add a new dimension to source tracking investigations, but highlights the need for detailed and accurate metadata, more extensive environmental sampling, and a better understanding of plasmid molecular evolution., (© 2023. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

A potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescent methods, retroelement insertions (RIs) have emerged as powerful phylogenomic markers for species tree estimation. Here, we show that two recently proposed quartet-based methods, SDPquartets and ASTRAL_BP, are statistically consistent estimators of the unrooted species tree topology under the coalescent when RIs follow a neutral infinite-sites model of mutation and the expected number of new RIs per generation is constant across the species tree. The accuracy of these (and other) methods for inferring species trees from RIs has yet to be assessed on simulated data sets, where the true species tree topology is known. Therefore, we evaluated eight methods given RIs simulated from four model species trees, all of which have short branches and at least three of which are in the anomaly zone. In our simulation study, ASTRAL_BP and SDPquartets always recovered the correct species tree topology when given a sufficiently large number of RIs, as predicted. A distance-based method (ASTRID_BP) and Dollo parsimony also performed well in recovering the species tree topology. In contrast, unordered, polymorphism, and Camin-Sokal parsimony (as well as an approach based on MDC) typically fail to recover the correct species tree topology in anomaly zone situations with more than four ingroup taxa. Of the methods studied, only ASTRAL_BP automatically estimates internal branch lengths (in coalescent units) and support values (i.e., local posterior probabilities). We examined the accuracy of branch length estimation, finding that estimated lengths were accurate for short branches but upwardly biased otherwise. This led us to derive the maximum likelihood (branch length) estimate for when RIs are given as input instead of binary gene trees; this corrected formula produced accurate estimates of branch lengths in our simulation study provided that a sufficiently large number of RIs were given as input. Lastly, we evaluated the impact of data quantity on species tree estimation by repeating the above experiments with input sizes varying from 100 to 100,000 parsimony-informative RIs. We found that, when given just 1000 parsimony-informative RIs as input, ASTRAL_BP successfully reconstructed major clades (i.e., clades separated by branches $>0.3$ coalescent units) with high support and identified rapid radiations (i.e., shorter connected branches), although not their precise branching order. The local posterior probability was effective for controlling false positive branches in these scenarios. [Coalescence; incomplete lineage sorting; Laurasiatheria; Palaeognathae; parsimony; polymorphism parsimony; retroelement insertions; species trees; transposon.]., (© The Author(s) 2021. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Inferring the structure of human populations from genetic variation data is a key task in population and medical genomic studies. Although a number of methods for population structure inference have been proposed, current methods are impractical to run on biobank-scale genomic datasets containing millions of individuals and genetic variants. We introduce SCOPE, a method for population structure inference that is orders of magnitude faster than existing methods while achieving comparable accuracy. SCOPE infers population structure in about a day on a dataset containing one million individuals and variants as well as on the UK Biobank dataset containing 488,363 individuals and 569,346 variants. Furthermore, SCOPE can leverage allele frequencies from previous studies to improve the interpretability of population structure estimates., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Motivation: Metagenomics has revolutionized microbiome research by enabling researchers to characterize the composition of complex microbial communities. Taxonomic profiling is one of the critical steps in metagenomic analyses. Marker genes, which are single-copy and universally found across Bacteria and Archaea, can provide accurate estimates of taxon abundances in the sample., Results: We present TIPP2, a marker gene-based abundance profiling method, which combines phylogenetic placement with statistical techniques to control classification precision and recall. TIPP2 includes an updated set of reference packages and several algorithmic improvements over the original TIPP method. We find that TIPP2 provides comparable or better estimates of abundance than other profiling methods (including Bracken, mOTUsv2 and MetaPhlAn2), and strictly dominates other methods when there are under-represented (novel) genomes present in the dataset., Availability and Implementation: The code for our method is freely available in open-source form at https://github.com/smirarab/sepp/blob/tipp2/README.TIPP.md. The code and procedure to create new reference packages for TIPP2 are available at https://github.com/shahnidhi/TIPP_reference_package., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2021. Published by Oxford University Press.)

Background: Face-to-face feedback plays an important role in health professionals' workplace learning. The literature describes guiding principles regarding effective feedback but it is not clear how to enact these. We aimed to create a Feedback Quality Instrument (FQI), underpinned by a social constructivist perspective, to assist educators in collaborating with learners to support learner-centred feedback interactions. In earlier research, we developed a set of observable educator behaviours designed to promote beneficial learner outcomes, supported by published research and expert consensus. This research focused on analysing and refining this provisional instrument, to create the FQI ready-to-use., Methods: We collected videos of authentic face-to-face feedback discussions, involving educators (senior clinicians) and learners (clinicians or students), during routine clinical practice across a major metropolitan hospital network. Quantitative and qualitative analyses of the video data were used to refine the provisional instrument. Raters administered the provisional instrument to systematically analyse educators' feedback practice seen in the videos. This enabled usability testing and resulted in ratings data for psychometric analysis involving multifaceted Rasch model analysis and exploratory factor analysis. Parallel qualitative research of the video transcripts focused on two under-researched areas, psychological safety and evaluative judgement, to provide practical insights for item refinement. The provisional instrument was revised, using an iterative process, incorporating findings from usability testing, psychometric testing and parallel qualitative research and foundational research., Results: Thirty-six videos involved diverse health professionals across medicine, nursing and physiotherapy. Administering the provisional instrument generated 174 data sets. Following refinements, the FQI contained 25 items, clustered into five domains characterising core concepts underpinning quality feedback: set the scene, analyse performance, plan improvements, foster learner agency, and foster psychological safety., Conclusions: The FQI describes practical, empirically-informed ways for educators to foster quality, learner-centred feedback discussions. The explicit descriptions offer guidance for educators and provide a foundation for the systematic analysis of the influence of specific educator behaviours on learner outcomes., (© 2021. The Author(s).)

Motivation: Admixture, the interbreeding between previously distinct populations, is a pervasive force in evolution. The evolutionary history of populations in the presence of admixture can be modeled by augmenting phylogenetic trees with additional nodes that represent admixture events. While enabling a more faithful representation of evolutionary history, admixture graphs present formidable inferential challenges, and there is an increasing need for methods that are accurate, fully automated and computationally efficient. One key challenge arises from the size of the space of admixture graphs. Given that exhaustively evaluating all admixture graphs can be prohibitively expensive, heuristics have been developed to enable efficient search over this space. One heuristic, implemented in the popular method TreeMix, consists of adding edges to a starting tree while optimizing a suitable objective function., Results: Here, we present a demographic model (with one admixed population incident to a leaf) where TreeMix and any other starting-tree-based maximum likelihood heuristic using its likelihood function is guaranteed to get stuck in a local optimum and return an incorrect network topology. To address this issue, we propose a new search strategy that we term maximum likelihood network orientation (MLNO). We augment TreeMix with an exhaustive search for an MLNO, referring to this approach as OrientAGraph. In evaluations including previously published admixture graphs, OrientAGraph outperformed TreeMix on 4/8 models (there are no differences in the other cases). Overall, OrientAGraph found graphs with higher likelihood scores and topological accuracy while remaining computationally efficient. Lastly, our study reveals several directions for improving maximum likelihood admixture graph estimation., Availability and Implementation: OrientAGraph is available on Github (https://github.com/sriramlab/OrientAGraph) under the GNU General Public License v3.0., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2021. Published by Oxford University Press.)

One of the Grand Challenges in Science is the construction of the Tree of Life, an evolutionary tree containing several million species, spanning all life on earth. However, the construction of the Tree of Life is enormously computationally challenging, as all the current most accurate methods are either heuristics for NP-hard optimization problems or Bayesian MCMC methods that sample from tree space. One of the most promising approaches for improving scalability and accuracy for phylogeny estimation uses divide-and-conquer: a set of species is divided into overlapping subsets, trees are constructed on the subsets, and then merged together using a "supertree method". Here, we present Exact-RFS-2, the first polynomial-time algorithm to find an optimal supertree of two trees, using the Robinson-Foulds Supertree (RFS) criterion (a major approach in supertree estimation that is related to maximum likelihood supertrees), and we prove that finding the RFS of three input trees is NP-hard. Exact-RFS-2 is available in open source form on Github at https://github.com/yuxilin51/GreedyRFS .

Phylogenomics-the estimation of species trees from multilocus data sets-is a common step in many biological studies. However, this estimation is challenged by the fact that genes can evolve under processes, including incomplete lineage sorting (ILS) and gene duplication and loss (GDL), that make their trees different from the species tree. In this article, we address the challenge of estimating the species tree under GDL. We show that species trees are identifiable under a standard stochastic model for GDL, and that the polynomial-time algorithm ASTRAL-multi, a recent development in the ASTRAL suite of methods, is statistically consistent under this GDL model. We also provide a simulation study evaluating ASTRAL-multi for species tree estimation under GDL.

Incremental tree building (INC) is a new phylogeny estimation method that has been proven to be absolute fast converging under standard sequence evolution models. A variant of INC, called Constrained-INC, is designed for use in divide-and-conquer pipelines for phylogeny estimation where a set of species is divided into disjoint subsets, trees are computed on the subsets using a selected base method, and then the subset trees are combined together. We evaluate the accuracy of INC and Constrained-INC for gene tree and species tree estimation on simulated datasets, and compare it to similar pipelines using NJMerge (another method that merges disjoint trees). For gene tree estimation, we find that INC has very poor accuracy in comparison to standard methods, and even Constrained-INC(using maximum likelihood methods to compute constraint trees) does not match the accuracy of the better maximum likelihood methods. Results for species trees are somewhat different, with Constrained-INC coming close to the accuracy of the best species tree estimation methods, while being much faster; furthermore, using Constrained-INC allows species tree estimation methods to scale to large datasets within limited computational resources. Overall, this study exposes the benefits and limitations of divide-and-conquer strategies for large-scale phylogenetic tree estimation.

Phylogenetic inference from genome-wide data (phylogenomics) has revolutionized the study of evolution because it enables accounting for discordance among evolutionary histories across the genome. To this end, summary methods have been developed to allow accurate and scalable inference of species trees from gene trees. However, most of these methods, including the widely used ASTRAL, can only handle single-copy gene trees and do not attempt to model gene duplication and gene loss. As a result, most phylogenomic studies have focused on single-copy genes and have discarded large parts of the data. Here, we first propose a measure of quartet similarity between single-copy and multicopy trees that accounts for orthology and paralogy. We then introduce a method called ASTRAL-Pro (ASTRAL for PaRalogs and Orthologs) to find the species tree that optimizes our quartet similarity measure using dynamic programing. By studying its performance on an extensive collection of simulated data sets and on real data sets, we show that ASTRAL-Pro is more accurate than alternative methods., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Motivation: Species tree estimation is a basic part of biological research but can be challenging because of gene duplication and loss (GDL), which results in genes that can appear more than once in a given genome. All common approaches in phylogenomic studies either reduce available data or are error-prone, and thus, scalable methods that do not discard data and have high accuracy on large heterogeneous datasets are needed., Results: We present FastMulRFS, a polynomial-time method for estimating species trees without knowledge of orthology. We prove that FastMulRFS is statistically consistent under a generic model of GDL when adversarial GDL does not occur. Our extensive simulation study shows that FastMulRFS matches the accuracy of MulRF (which tries to solve the same optimization problem) and has better accuracy than prior methods, including ASTRAL-multi (the only method to date that has been proven statistically consistent under GDL), while being much faster than both methods., Availability and Impementation: FastMulRFS is available on Github (https://github.com/ekmolloy/fastmulrfs)., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2020. Published by Oxford University Press.)

Context: Feedback conversations play a central role in health professions workplace learning. However, learners face a dilemma: if they engage in productive learning behaviours (such as asking questions, raising difficulties, offering opinions or contesting ideas), they risk exposing their limitations or offending the educator. This highlights the importance of psychological safety in encouraging learners to candidly engage in interactive dialogue and the co-construction of knowledge. Previous research has recommended that building safety, trust or an educational alliance is key to productive feedback encounters. Yet it is unclear how to translate this into practice. Hence our research question was: What does psychological safety look like in workplace feedback and how can educators work with learners to foster it?, Methods: We analysed 36 videos of routine formal feedback episodes in clinical practice involving diverse health professionals. A psychologically safe learning environment was inferred when learners progressively disclosed information and engaged in productive learning behaviours during the conversation. We used thematic analysis to identify associated educator strategies, which seemed to promote psychological safety., Results: Four themes were identified: (a) setting the scene for dialogue and candour; (b) educator as ally; (c) a continuing improvement orientation, and (d) encouraging interactive dialogue. Educators approaches captured within these themes, seemed to foster a psychologically safe environment by conveying a focus on learning, and demonstrating respect and support to learners., Conclusions: This study builds on claims regarding the importance of psychological safety in feedback by clarifying what psychological safety in workplace feedback conversations might look like and identifying associated educator approaches. The results may offer educators practical ways they could work with learners to encourage candid dialogue focused on improving performance., (© 2020 John Wiley & Sons Ltd and The Association for the Study of Medical Education.)

DNA sequence alignments have provided the majority of data for inferring phylogenetic relationships with both concatenation and coalescent methods. However, DNA sequences are susceptible to extensive homoplasy, especially for deep divergences in the Tree of Life. Retroelement insertions have emerged as a powerful alternative to sequences for deciphering evolutionary relationships because these data are nearly homoplasy-free. In addition, retroelement insertions satisfy the "no intralocus-recombination" assumption of summary coalescent methods because they are singular events and better approximate neutrality relative to DNA loci commonly sampled in phylogenomic studies. Retroelements have traditionally been analyzed with parsimony, distance, and network methods. Here, we analyze retroelement data sets for vertebrate clades (Placentalia, Laurasiatheria, Balaenopteroidea, Palaeognathae) with 2 ILS-aware methods that operate by extracting, weighting, and then assembling unrooted quartets into a species tree. The first approach constructs a species tree from retroelement bipartitions with ASTRAL, and the second method is based on split-decomposition with parsimony. We also develop a Quartet-Asymmetry test to detect hybridization using retroelements. Both ILS-aware methods recovered the same species-tree topology for each data set. The ASTRAL species trees for Laurasiatheria have consecutive short branch lengths in the anomaly zone whereas Palaeognathae is outside of this zone. For the Balaenopteroidea data set, which includes rorquals (Balaenopteridae) and gray whale (Eschrichtiidae), both ILS-aware methods resolved balaeonopterids as paraphyletic. Application of the Quartet-Asymmetry test to this data set detected 19 different quartets of species for which historical introgression may be inferred. Evidence for introgression was not detected in the other data sets., (© The American Genetic Association 2019. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

After publication of [1], the authors were informed by John A. Rhodes of a counterexample to Theorem 11 of [1].

Motivation: Estimated gene trees are often inaccurate, due to insufficient phylogenetic signal in the single gene alignment, among other causes. Gene tree correction aims to improve the accuracy of an estimated gene tree by using computational techniques along with auxiliary information, such as a reference species tree or sequencing data. However, gene trees and species trees can differ as a result of gene duplication and loss (GDL), incomplete lineage sorting (ILS), and other biological processes. Thus gene tree correction methods need to take estimation error as well as gene tree heterogeneity into account. Many prior gene tree correction methods have been developed for the case where GDL is present., Results: Here, we study the problem of gene tree correction where gene tree heterogeneity is instead due to ILS and/or HGT. We introduce TRACTION, a simple polynomial time method that provably finds an optimal solution to the RF-optimal tree refinement and completion (RF-OTRC) Problem, which seeks a refinement and completion of a singly-labeled gene tree with respect to a given singly-labeled species tree so as to minimize the Robinson-Foulds (RF) distance. Our extensive simulation study on 68,000 estimated gene trees shows that TRACTION matches or improves on the accuracy of well-established methods from the GDL literature when HGT and ILS are both present, and ties for best under the ILS-only conditions. Furthermore, TRACTION ties for fastest on these datasets. We also show that a naive generalization of the RF-OTRC problem to multi-labeled trees is possible, but can produce misleading results where gene tree heterogeneity is due to GDL., Competing Interests: Competing interestsThe authors declare that they have no competing interests., (© The Author(s) 2020.)

Background: Divide-and-conquer methods, which divide the species set into overlapping subsets, construct a tree on each subset, and then combine the subset trees using a supertree method, provide a key algorithmic framework for boosting the scalability of phylogeny estimation methods to large datasets. Yet the use of supertree methods, which typically attempt to solve NP-hard optimization problems, limits the scalability of such approaches., Results: In this paper, we introduce a divide-and-conquer approach that does not require supertree estimation: we divide the species set into pairwise disjoint subsets, construct a tree on each subset using a base method, and then combine the subset trees using a distance matrix. For this merger step, we present a new method, called NJMerge, which is a polynomial-time extension of Neighbor Joining (NJ); thus, NJMerge can be viewed either as a method for improving traditional NJ or as a method for scaling the base method to larger datasets. We prove that NJMerge can be used to create divide-and-conquer pipelines that are statistically consistent under some models of evolution. We also report the results of an extensive simulation study evaluating NJMerge on multi-locus datasets with up to 1000 species. We found that NJMerge sometimes improved the accuracy of traditional NJ and substantially reduced the running time of three popular species tree methods (ASTRAL-III, SVDquartets, and "concatenation" using RAxML) without sacrificing accuracy. Finally, although NJMerge can fail to return a tree, in our experiments, NJMerge failed on only 11 out of 2560 test cases., Conclusions: Theoretical and empirical results suggest that NJMerge is a valuable technique for large-scale phylogeny estimation, especially when computational resources are limited. NJMerge is freely available on Github (http://github.com/ekmolloy/njmerge)., Competing Interests: Competing interestsThe authors declare that they have no competing interests.

Motivation: At RECOMB-CG 2018, we presented NJMerge and showed that it could be used within a divide-and-conquer framework to scale computationally intensive methods for species tree estimation to larger datasets. However, NJMerge has two significant limitations: it can fail to return a tree and, when used within the proposed divide-and-conquer framework, has O(n5) running time for datasets with n species., Results: Here we present a new method called 'TreeMerge' that improves on NJMerge in two ways: it is guaranteed to return a tree and it has dramatically faster running time within the same divide-and-conquer framework-only O(n2) time. We use a simulation study to evaluate TreeMerge in the context of multi-locus species tree estimation with two leading methods, ASTRAL-III and RAxML. We find that the divide-and-conquer framework using TreeMerge has a minor impact on species tree accuracy, dramatically reduces running time, and enables both ASTRAL-III and RAxML to complete on datasets (that they would otherwise fail on), when given 64 GB of memory and 48 h maximum running time. Thus, TreeMerge is a step toward a larger vision of enabling researchers with limited computational resources to perform large-scale species tree estimation, which we call Phylogenomics for All., Availability and Implementation: TreeMerge is publicly available on Github (http://github.com/ekmolloy/treemerge)., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2019. Published by Oxford University Press.)

Background: Verbal feedback plays a critical role in health professions education but it is not clear which components of effective feedback have been successfully translated from the literature into supervisory practice in the workplace, and which have not. The purpose of this study was to observe and systematically analyse educators' behaviours during authentic feedback episodes in contemporary clinical practice., Methods: Educators and learners videoed themselves during formal feedback sessions in routine hospital training. Researchers compared educators' practice to a published set of 25 educator behaviours recommended for quality feedback. Individual educator behaviours were rated 0 = not seen, 1 = done somewhat, 2 = consistently done. To characterise individual educator's practice, their behaviour scores were summed. To describe how commonly each behaviour was observed across all the videos, mean scores were calculated., Results: Researchers analysed 36 videos involving 34 educators (26 medical, 4 nursing, 4 physiotherapy professionals) and 35 learners across different health professions, specialties, levels of experience and gender. There was considerable variation in both educators' feedback practices, indicated by total scores for individual educators ranging from 5.7 to 34.2 (maximum possible 48), and how frequently specific feedback behaviours were seen across all the videos, indicated by mean scores for each behaviour ranging from 0.1 to 1.75 (maximum possible 2). Educators commonly provided performance analysis, described how the task should be performed, and were respectful and supportive. However a number of recommended feedback behaviours were rarely seen, such as clarifying the session purpose and expectations, promoting learner involvement, creating an action plan or arranging a subsequent review., Conclusions: These findings clarify contemporary feedback practice and inform the design of educational initiatives to help health professional educators and learners to better realise the potential of feedback.

Objectives: The literature focuses on teaching communication skills in the 'classroom', with less focus on how such skills are informally learnt in the healthcare workplace. We grouped healthcare work based on the cure:care continuum to explore communication approaches based on work activities. This study asks: 1) How do healthcare professionals believe they learn communication in the workplace? 2) What are the differences (if any) across the 'type of work' as represented by the cure:care continuum?, Design: This qualitative study used semi-structured individual interviews., Setting: Community care and acute hospitals in Australia (Victoria and New South Wales)., Participants: Twenty qualified healthcare professionals (medicine n=4, nursing n=3, allied health n=13) from various clinical specialties (eg, acute, rehabilitation, surgery, palliative care) participated., Methods: Data were analysed using framework analysis, which involved the development of a thematic coding framework. Findings were mapped to participants' descriptions of work using the cure:care continuum., Results: Three themes were identified that varied across the cure:care continuum: professional discourse-tying communication approaches to work activities; personal identities-the influence of personal identities on healthcare communication and role modelling-the influence of others in the socially bound context of healthcare work., Conclusions: This study highlights the influence of professional, personal and social factors on the learning of healthcare communication in the workplace. Our study illuminates differences in communication practice related to work activities, as conceptualised by the cure:care continuum. The results call for further examination of the 'nature' of work activities and the concomitant influence on developing healthcare communication., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2019. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Humans make moral judgments every day, and research demonstrates that these evaluations are based on a host of related event features (e.g., harm, legality). In order to acquire systematic data on how moral judgments are made, our assessments need to be expanded to include real-life, ecologically valid stimuli that take into account the numerous event features that are known to influence moral judgment. To facilitate this, Knutson et al. (in Social Cognitive and Affective Neuroscience, 5(4), 378-384, 2010) developed vignettes based on real-life episodic memories rated concurrently on key moral features; however, the method is time intensive (~1.4-3.4 h) and the stimuli and ratings require further validation and characterization. The present study addresses these limitations by: (i) validating three short subsets of these vignettes (39 per subset) that are time-efficient (10-25 min per subset) yet representative of the ratings and factor structure of the full set, (ii) norming ratings of moral features in a larger sample (total N = 661, each subset N = ~220 vs. Knutson et al. N = 30), (iii) examining the generalizability of the original factor structure by replicating it in a larger sample across vignette subsets, sex, and political ideology, and (iv) using latent profile analysis to empirically characterize vignette groupings based on event feature ratings profiles and vignette content. This study therefore provides researchers with a core battery of well-characterized and realistic vignettes, concurrently rated on key moral features that can be administered in a brief, time-efficient manner to advance research on the nature of moral judgment.

Background: Estimation of species trees from multiple genes is complicated by processes such as incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer, that result in gene trees that differ from each other and from the species phylogeny. Methods to estimate species trees in the presence of gene tree discord due to incomplete lineage sorting have been developed and proved to be statistically consistent when gene tree discord is due only to incomplete lineage sorting and every gene tree includes the full set of species., Results: We establish statistical consistency of certain coalescent-based species tree estimation methods under some models of taxon deletion from genes. We also evaluate the impact of missing data on four species tree estimation methods (ASTRAL-II, ASTRID, MP-EST, and SVDquartets) using simulated datasets with varying levels of incomplete lineage sorting, gene tree estimation error, and degrees/patterns of missing data., Conclusions: All the species tree estimation methods improved in accuracy as the number of genes increased and often produced highly accurate species trees even when the amount of missing data was large. These results together indicate that accurate species tree estimation is possible under a variety of conditions, even when there are substantial amounts of missing data.

Background: For a combination of reasons (including data generation protocols, approaches to taxon and gene sampling, and gene birth and loss), estimated gene trees are often incomplete, meaning that they do not contain all of the species of interest. As incomplete gene trees can impact downstream analyses, accurate completion of gene trees is desirable., Results: We introduce the Optimal Tree Completion problem , a general optimization problem that involves completing an unrooted binary tree (i.e., adding missing leaves) so as to minimize its distance from a reference tree on a superset of the leaves. We present OCTAL , an algorithm that finds an optimal solution to this problem when the distance between trees is defined using the Robinson-Foulds (RF) distance, and we prove that OCTAL runs in [Formula: see text] time, where n is the total number of species. We report on a simulation study in which gene trees can differ from the species tree due to incomplete lineage sorting, and estimated gene trees are completed using OCTAL with a reference tree based on a species tree estimated from the multi-locus dataset. OCTAL produces completed gene trees that are closer to the true gene trees than an existing heuristic approach in ASTRAL-II, but the accuracy of a completed gene tree computed by OCTAL depends on how topologically similar the reference tree (typically an estimated species tree) is to the true gene tree., Conclusions: OCTAL is a useful technique for adding missing taxa to incomplete gene trees and provides good accuracy under a wide range of model conditions. However, results show that OCTAL's accuracy can be reduced when incomplete lineage sorting is high, as the reference tree can be far from the true gene tree. Hence, this study suggests that OCTAL would benefit from using other types of reference trees instead of species trees when there are large topological distances between true gene trees and species trees.

With the increasing availability of whole genome data, many species trees are being constructed from hundreds to thousands of loci. Although concatenation analysis using maximum likelihood is a standard approach for estimating species trees, it does not account for gene tree heterogeneity, which can occur due to many biological processes, such as incomplete lineage sorting. Coalescent species tree estimation methods, many of which are statistically consistent in the presence of incomplete lineage sorting, include Bayesian methods that coestimate the gene trees and the species tree, summary methods that compute the species tree by combining estimated gene trees, and site-based methods that infer the species tree from site patterns in the alignments of different loci. Due to concerns that poor quality loci will reduce the accuracy of estimated species trees, many recent phylogenomic studies have removed or filtered genes on the basis of phylogenetic signal and/or missing data prior to inferring species trees; little is known about the performance of species tree estimation methods when gene filtering is performed. We examine how incomplete lineage sorting, phylogenetic signal of individual loci, and missing data affect the absolute and the relative accuracy of species tree estimation methods and show how these properties affect methods' responses to gene filtering strategies. In particular, summary methods (ASTRAL-II, ASTRID, and MP-EST), a site-based coalescent method (SVDquartets within PAUP*), and an unpartitioned concatenation analysis using maximum likelihood (RAxML) were evaluated on a heterogeneous collection of simulated multilocus data sets, and the following trends were observed. Filtering genes based on gene tree estimation error improved the accuracy of the summary methods when levels of incomplete lineage sorting were low to moderate but did not benefit the summary methods under higher levels of incomplete lineage sorting, unless gene tree estimation error was also extremely high (a model condition with few replicates). Neither SVDquartets nor concatenation analysis using RAxML benefited from filtering genes on the basis of gene tree estimation error. Finally, filtering genes based on missing data was either neutral (i.e., did not impact accuracy) or else reduced the accuracy of all five methods. By providing insight into the consequences of gene filtering, we offer recommendations for estimating species tree in the presence of incomplete lineage sorting and reconcile seemingly conflicting observations made in prior studies regarding the impact of gene filtering.

Context: The accreditation of undergraduate medical education is a universal undertaking. Despite the widespread adoption of accreditation processes and an increasing focus on accreditation as a mechanism to ensure minimum standards are met in various fields, there is little evidence to support the effectiveness of accreditation. Traditionally, accreditation has worked toward achieving two ends: assuring and improving quality. Many recent articles emphasize the need for continuous quality improvement mechanisms to work, as well as the quality assurance role of accreditation., Methods: The aim of the study was to examine the purposes and outcomes of accreditation, and stakeholders' experience of accreditation in Saudi Arabia. Triangulation of data was achieved through literature review, analysis of accreditation documents, examined the outcome of accreditation process (pre and post) through stakeholders' experience of accreditation (learner, teacher, and academic leader perspectives). Data were interrogated using thematic analysis approach involving identifying, analyzing, and reporting repeated patterns (themes) of meaning within data., Results: Three themes emerged from the three phase study: "Passing the exam" versus long-term benefit, generic versus specialized accreditation standards, and internal quality assurance and self-evaluation. The data revealed a number of strategies that stakeholders can employ to achieve a balance between an "accreditation threat" and a quality improvement approach that is likely to have a lasting effect on educational outcomes., Discussion: This empirical study revealed strong parallels between assessment and accreditation purpose, engagement, and outcomes. Like an increasing number of commentaries in the literature, this study suggests that accreditation bodies would do well to shift toward a holistic approach to quality management in medical education; implementation of quality improvement by an external "other"-described by some participants as the "policeman approach"-is not ideal for promoting sustainable quality education. Sustainable accreditation for long-term education improvement is not presented as a method, but as a way of thinking about important, and often overlooked, aspects of accreditation practice. Sustainable accreditation means that there is a need to meet both the immediate accreditation standards ("the exam") as well as establishing a basis for continuing quality improvement.

Phenomenon: Peer learning has many benefits and can assist students in gaining the educational skills required in future years when they become teachers themselves. Peer learning may be particularly useful in clinical learning environments, where students report feeling marginalized, overwhelmed, and unsupported. Educational interventions often fail in the workplace environment, as they are often conceived in the "ideal" rather than the complex, messy real world. This work sought to explore barriers and facilitators to implementing peer learning activities in a clinical curriculum., Approach: Previous peer learning research results and a matrix of empirically derived peer learning activities were presented to local clinical education experts to generate discussion around the realities of implementing such activities. Potential barriers and limitations of and strategies for implementing peer learning in clinical education were the focus of the individual interviews., Findings: Thematic analysis of the data identified three key considerations for real-world implementation of peer learning: culture, epistemic authority, and the primacy of patient-centered care. Strategies for peer learning implementation were also developed from themes within the data, focusing on developing a culture of safety in which peer learning could be undertaken, engaging both educators and students, and establishing expectations for the use of peer learning. Insights: This study identified considerations and strategies for the implementation of peer learning activities, which took into account both educator and student roles. Reported challenges were reflective of those identified within the literature. The resultant framework may aid others in anticipating implementation challenges. Further work is required to test the framework's application in other contexts and its effect on learner outcomes.

Phenomenon: Peer assisted learning (PAL) is frequently employed and researched in preclinical medical education. Fewer studies have examined PAL in the clinical context: These have focused mainly on the accuracy of peer assessment and potential benefits to learner communication and teamwork skills. Research has also examined the positive and negative effects of formal, structured PAL activities in the clinical setting. Given the prevalence of PAL activities during preclinical years, and the unstructured nature of clinical placements, it is likely that nonformal PAL activities are also undertaken. How PAL happens formally and informally and why students find PAL useful in this clinical setting remain poorly understood., Approach: This study aimed to describe PAL activities within the context of clinical placement learning and to explore students' perceptions of these activities. An ethnographic study was conducted to gather empirical data on engagement in clinical placement learning activities, including observations and interviews with students in their 1st clinical year, along with their supervising clinicians. Thematic analysis was used to interrogate the data., Findings: On average, students used PAL for 5.19 hours per week in a range of activities, of a total of 29.29 hours undertaking placements. PAL was recognized as a means of vicarious learning and had greater perceived value when an educator was present to guide or moderate the learning. Trust between students was seen as a requirement for PAL to be effective. Students found passive observation a barrier to PAL and were able to identify ways to adopt an active stance when observing peers interacting with patients. For example, learners reported that the expectation that they had to provide feedback to peers after task observation, resulted in them taking on a more critical gaze where they were encouraged to consider notions of good practice. Insights: Students use PAL in formal (i.e., tutorial) and nonformal (e.g., peer observation and feedback on the ward; discussion during lunch) situations in clinical education and find it useful. The educator is crucial in fostering PAL through providing opportunities for learners to practice together and in helping to moderate discussions about quality of performance. Student engagement in PAL may reduce passivity commonly reported in clinical rotations. Further directions for research into PAL in clinical education are identified along with potential strategies that may maximize the benefits of peer to peer learning.

This study explored the contribution of peer-assisted learning (PAL) in the development of evaluative judgement capacity; the ability to understand work quality and apply those standards to appraising performance. The study employed a mixed methods approach, collecting self-reported survey data, observations of, and reflective interviews with, the medical students observed. Participants were in their first year of clinical placements. Data were thematically analysed. Students indicated that PAL contributed to both the comprehension of notions of quality, and the practice of making comparisons between a given performance and the standards. Emergent themes included peer story-telling, direct observation of performance, and peer-based feedback, all of which helped students to define 'work quality'. By participating in PAL, students were required to make comparisons, therefore using the standards of practice and gaining a deeper understanding of them. The data revealed tensions in that peers were seen as less threatening than supervisors with the advantage of increasing learners' appetites for thoughtful 'intellectual risk taking'. Despite this reported advantage of peer engagement, learners still expressed a preference for feedback from senior teachers as more trusted sources of clinical knowledge. While this study suggests that PAL already contributes to the development of evaluative judgement, further steps could be taken to formalise PAL in clinical placements to improve learners' capacity to make accurate judgements on the performance of self and others. Further experimental studies are necessary to confirm the best methods of using PAL to develop evaluative judgement. This may include both students and educators as instigators of PAL in the workplace.

Background: Health professions education is characterised by work-based learning and relies on effective verbal feedback. However the literature reports problems in feedback practice, including lack of both learner engagement and explicit strategies for improving performance. It is not clear what constitutes high quality, learner-centred feedback or how educators can promote it. We hoped to enhance feedback in clinical practice by distinguishing the elements of an educator's role in feedback considered to influence learner outcomes, then develop descriptions of observable educator behaviours that exemplify them., Methods: An extensive literature review was conducted to identify i) information substantiating specific components of an educator's role in feedback asserted to have an important influence on learner outcomes and ii) verbal feedback instruments in health professions education, that may describe important educator activities in effective feedback. This information was used to construct a list of elements thought to be important in effective feedback. Based on these elements, descriptions of observable educator behaviours that represent effective feedback were developed and refined during three rounds of a Delphi process and a face-to-face meeting with experts across the health professions and education., Results: The review identified more than 170 relevant articles (involving health professions, education, psychology and business literature) and ten verbal feedback instruments in health professions education (plus modified versions). Eighteen distinct elements of an educator's role in effective feedback were delineated. Twenty five descriptions of educator behaviours that align with the elements were ratified by the expert panel., Conclusions: This research clarifies the distinct elements of an educator's role in feedback considered to enhance learner outcomes. The corresponding set of observable educator behaviours aim to describe how an educator could engage, motivate and enable a learner to improve. This creates the foundation for developing a method to systematically evaluate the impact of verbal feedback on learner performance.

Recent fMRI studies have outlined the critical impact of in-scanner head motion, particularly on estimates of functional connectivity. Common strategies to reduce the influence of motion include realignment as well as the inclusion of nuisance regressors, such as the 6 realignment parameters, their first derivatives, time-shifted versions of the realignment parameters, and the squared parameters. However, these regressors have limited success at noise reduction. We hypothesized that using nuisance regressors consisting of the principal components (PCs) of edge voxel time series would be better able to capture slice-specific and nonlinear signal changes, thus explaining more variance, improving data quality (i.e., lower DVARS and temporal SNR), and reducing the effect of motion on default-mode network connectivity. Functional MRI data from 22 healthy adult subjects were preprocessed using typical motion regression approaches as well as nuisance regression derived from edge voxel time courses. Results were evaluated in the presence and absence of both global signal regression and motion censoring. Nuisance regressors derived from signal intensity time courses at the edge of the brain significantly improved motion correction compared to using only the realignment parameters and their derivatives. Of the models tested, only the edge voxel regression models were able to eliminate significant differences in default-mode network connectivity between high- and low-motion subjects regardless of the use of global signal regression or censoring.