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The invariable site plus Γ model (I+Γ) is widely used to model rate heterogeneity among alignment sites in maximum likelihood and Bayesian phylogenetic analyses. The proof that the I+ continuous Γ model is identifiable (model parameters can be inferred correctly given enough data) has increased the creditability of its application to phylogeny reconstruction. However, most phylogenetic software implement the I+ discrete Γ model, whose identifiability is likely but unproven. How well the parameters of the I+ discrete Γ model are estimated is still disputed. Especially the correlation between the fraction of invariable sites and the fractions of sites with a slow evolutionary rate is discussed as being problematic. We show that optimization heuristics as implemented in frequently used phylogenetic software (PhyML, RAxML, IQ-TREE, and MrBayes) cannot always reliably estimate the shape parameter, the proportion of invariable sites, and the tree length. Here, we propose an improved optimization heuristic that accurately estimates the three parameters. While research efforts mainly focus on tree search methods, our results signify the equal importance of verifying and developing effective estimation methods for complex models of sequence evolution. [ABSTRACT FROM AUTHOR]

Ammonia-oxidising archaea (AOA) are ubiquitous and abundant in nature and play a major role in nitrogen cycling. AOA have been studied intensively based on the amoA gene (encoding ammonia monooxygenase subunit A), making it the most sequenced functional marker gene. Here, based on extensive phylogenetic and meta-data analyses of 33,378 curated archaeal amoA sequences, we define a highly resolved taxonomy and uncover global environmental patterns that challenge many earlier generalisations. Particularly, we show: (i) the global frequency of AOA is extremely uneven, with few clades dominating AOA diversity in most ecosystems; (ii) characterised AOA do not represent most predominant clades in nature, including soils and oceans; (iii) the functional role of the most prevalent environmental AOA clade remains unclear; and (iv) AOA harbour molecular signatures that possibly reflect phenotypic traits. Our work synthesises information from a decade of research and provides the first integrative framework to study AOA in a global context. [ABSTRACT FROM AUTHOR]

Proteins have distinct structural and functional constraints at different sites that lead to site-specific preferences for particular amino acid residues as the sequences evolve. Heterogeneity in the amino acid substitution process between sites is not modeled by commonly used empirical amino acid exchange matrices. Such model misspecification can lead to artefacts in phylogenetic estimation such as long-branch attraction. Although sophisticated site-heterogeneous mixture models have been developed to address this problem in both Bayesian and maximum likelihood (ML) frameworks, their formidable computational time and memory usage severely limits their use in large phylogenomic analyses. Here we propose a posterior mean site frequency (PMSF) method as a rapid and efficient approximation to full empirical profile mixture models for ML analysis. The PMSF approach assigns a conditional mean amino acid frequency profile to each site calculated based on amixturemodel fitted to the data using a preliminary guide tree. These PMSF profiles can then be used for in-depth tree-searching in place of the full mixture model. Compared with widely used empirical mixture models with k classes, our implementation of PMSF in IQ-TREE (http://www.iqtree.org) speeds up the computation by approximately k/1.5-fold and requires a small fraction of the RAM. Furthermore, this speedup allows, for the first time, full nonparametric bootstrap analyses to be conducted under complex site-heterogeneous models on large concatenated data matrices. Our simulations and empirical data analyses demonstrate that PMSF can effectively ameliorate long-branch attraction artefacts. In some empirical and simulation settings PMSF provided more accurate estimates of phylogenies than the mixturemodels from which they derive. [ABSTRACT FROM AUTHOR]

In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption of partition models. Under such models each gene, or more generally partition, is allowed to evolve under its own evolutionary model. Although partition models provide a more comprehensive analysis of supermatrices, missing data may hamper the tree search algorithms due to the existence of phylogenetic (partial) terraces. Here, we introduce the phylogenetic terrace aware (PTA) data structure for the efficient analysis under partition models. In the presence of missing data PTA exploits (partial) terraces and induced partition trees to save computation time. We show that an implementation of PTA in IQ-TREE leads to a substantial speedup of up to 4.5 and 8 times compared with the standardIQ-TREEandRAxMLimplementations, respectively.PTAis generally applicable to all types of partition models and common topological rearrangements thus can be employed by all phylogenomic inference software. [ABSTRACT FROM AUTHOR]

Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE is freely available at http://www.cibiv.at/software/ iqtree. [ABSTRACT FROM AUTHOR]

Plants and fungi respond to environmental light stimuli via the action of different photoreceptor modules. One such class, responding to the blue region of light, is constituted by photoreceptors containing so-called light-oxygen-voltage (LOV) domains as sensor modules. Four major LOV families are currently identified in eukaryotes: (i) the plant phototropins, regulating various physiological effects such as phototropism, chloroplast relocation, and stomatal opening; (ii) the aureochromes, mediating photomorphogenesis in photosynthetic stramenopile algae; (iii) the plant circadian photoreceptors of the zeitlupe (ZTL)/adagio (ADO)/flavin-binding Kelch repeat F-box protein 1 (FKF1) family; and (iv) the fungal circadian photoreceptors white-collar 1 (WC-1). Blue-light-sensitive LOV signaling modules are also widespread throughout the prokaryotic world, and physiological responses mediated by bacterial LOV photoreceptors were recently reported. Thus, the question arises as to the evolutionary relationship between the pro- and eukaryotic LOV photoreceptor systems. We used Bayesian and maximum-likelihood tree reconstruction methods to infer evolutionary scenarios that might have led to the widespread appearance of LOV domains among the pro- and eukaryotes. The phylogenetic study presented here suggests a bacterial origin for the LOV domains of the four major eukaryotic LOV photoreceptor families, whereas the LOV sensor domains were most likely recruited from the bacteria in the course of plastid and mitochondrial endosymbiosis. [ABSTRACT FROM AUTHOR]

The “phylogenetic diversity” (PD) measure of biodiversity is evaluated using a phylogenetic tree, usually inferred from morphological or molecular data. Consequently, it is vulnerable to errors in that tree, including those resulting from sampling error, model misspecification, or conflicting signals. To improve the robustness of PD, we can evaluate the measure using either a collection (or distribution) of trees or a phylogenetic network. Recently, it has been shown that these 2 approaches are equivalent but that the problem of maximizing PD in the general concept is NP-hard. In this study, we provide an efficient dynamic programming algorithm for maximizing PD when splits in the trees or network form a circular split system. We illustrate our method using a case study of game birds (“Galliformes”) and discuss the different choices of taxa based on our approach and PD. [ABSTRACT FROM PUBLISHER]

This study aims to identify the occurrence and characteristics of PCDD/Fs in soil and sediment samples from secondary copper and aluminum villages in northern Vietnam using the HRGC/MS system. Additionally, it assesses the impact of PCDD/Fs on human health and the potential ecological risks they pose. The residual concentrations of PCDD/Fs in soil and sediment samples collected from the secondary copper Dai Bai village and secondary aluminum Man Xa village were as follows: 0.37 ± 0.29 ng TEQ/kg d.w. (ranging from 0.06 to 0.63 ng TEQ/kg d.w.); 4.88 ± 0.51 ng TEQ/kg d.w. (ranging from 0.512 to 12.17 ng TEQ/kg d.w.); 11.2 ± 5.31 ng TEQ/kg d.w. (ranging from 5.12 to 15.2 ng TEQ/kg d.w.); and 21 ± 12.7 ng TEQ/kg d.w. (ranging from 0.37 to 31.6 ng TEQ/kg d.w.), respectively. The distribution of PCDD/Fs indicated Octa- and Hepta-CDD/Fs as the dominant congeners with high chlorine content. The TEQ levels of PCDD/Fs in all soil and sediment samples were found to be below the allowable limit according to Vietnamese regulations, with the top contributor being 2,3,4,7,8-PeCDF. Samples collected near the production areas exhibited higher levels of PCDD/Fs compared to those collected farther away. The UNEP toolkit was utilized to determine the permissible dioxin TEQ concentrations suitable for livestock farming. The lifetime average daily doses (LADD) of PCDD/Fs via soil ingestion in Man Xa and Dai Bai were calculated as 0.04 × 10−3 and 1.54 × 10−3 pg TEQ/kg d.w. respectively. The relative cancer risks for humans were estimated at 0.05 × 10−12 and 2.05 × 10−12. Furthermore, the ecological risk assessment method indicates that dioxin in all soil and sediment samples near the aluminum recycling craft village had a negative impact on the ecosystem. In contrast, sediment samples taken away from the aluminum recycling craft village and all sediment soil samples in the bronze casting village did not show negative impacts on the ecosystem. [ABSTRACT FROM AUTHOR]

Eating behaviors, which are shaped during childhood, are one of the important factors influencing children's growth. This study aimed to investigate the variations in eating behaviors among Vietnamese preschool children aged 3 to 6 years using the Children Eating Behavior Questionnaire (CEBQ) and their association with anthropometric Z -scores. A cross-sectional study was conducted on 10 172 children from 36 to 72 months old, recruited from three different socioeconomic regions of Hanoi. Differentiation of eating behaviors between two sexes was observed across all age groups, but most obvious at 36 to 48 months of age. The subscales of emotional overeating (EOE), enjoyment of food (EF), and desire to drink (DD) were higher in 60- to 72-month age groups and vice versa for slowness in eating (SE) and emotional undereating (EUE) subscales. Analyses using the general linear model showed that CEBQ subscales were associated with anthropometric Z -scores in both girls and boys., Competing Interests: Declaration of Conflicting InterestsThe author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

This paper presents a systematic literature review focused on the use of inductively coupled plasma mass spectrometry (ICP-MS) combined with PCA, a multivariate technique, for determining the geographical origin of plant foods. Recent studies selected and applied the ICP-MS analytical method and PCA in plant food geographical traceability. The collected results from many previous studies indicate that ICP-MS with PCA is a useful tool and is widely used for authenticating and certifying the geographic origin of plant food. The review encourages scientists and managers to discuss the possibility of introducing an international standard for plant food traceability using ICP-MS combined with PCA. The use of a standard method will reduce the time and cost of analysis and improve the efficiency of trade and circulation of goods. Furthermore, the main steps needed to establish the standard for this traceability method are reported, including the development of guidelines and quality control measures, which play a pivotal role in providing authentic product information through each stage of production, processing, and distribution for consumers and authority agencies. This might be the basis for establishing the standards for examination and controlling the quality of foods in the markets, ensuring safety for consumers.

Amino acid substitution models play a crucial role in phylogenetic analyses. Maximum likelihood (ML) methods have been proposed to estimate amino acid substitution models; however, they are typically complicated and slow. In this article, we propose QMaker, a new ML method to estimate a general time-reversible $Q$ matrix from a large protein data set consisting of multiple sequence alignments. QMaker combines an efficient ML tree search algorithm, a model selection for handling the model heterogeneity among alignments, and the consideration of rate mixture models among sites. We provide QMaker as a user-friendly function in the IQ-TREE software package (http://www.iqtree.org) supporting the use of multiple CPU cores so that biologists can easily estimate amino acid substitution models from their own protein alignments. We used QMaker to estimate new empirical general amino acid substitution models from the current Pfam database as well as five clade-specific models for mammals, birds, insects, yeasts, and plants. Our results show that the new models considerably improve the fit between model and data and in some cases influence the inference of phylogenetic tree topologies.[Amino acid replacement matrices; amino acid substitution models; maximum likelihood estimation; phylogenetic inferences.]., (© The Author(s) 2021. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.)

Early-onset breast cancer (EOBC) causes substantial loss of life and productivity, creating a major burden among women worldwide. We analyzed 1,265,548 Hapmap3 single-nucleotide polymorphisms (SNP) among a discovery set of 3,523 EOBC incident cases and 2,702 population control women ages ≤ 51 years. The SNPs with smallest P values were examined in a replication set of 3,470 EOBC cases and 5,475 control women. We also tested EOBC association with 19,684 genes by annotating each gene with putative functional SNPs, and then combining their P values to obtain a gene-based P value. We examined the gene with smallest P value for replication in 1,145 breast cancer cases and 1,142 control women. The combined discovery and replication sets identified 72 new SNPs associated with EOBC (P < 4 × 10(-8)) located in six genomic regions previously reported to contain SNPs associated largely with later-onset breast cancer (LOBC). SNP rs2229882 and 10 other SNPs on chromosome 5q11.2 remained associated (P < 6 × 10(-4)) after adjustment for the strongest published SNPs in the region. Thirty-two of the 82 currently known LOBC SNPs were associated with EOBC (P < 0.05). Low power is likely responsible for the remaining 50 unassociated known LOBC SNPs. The gene-based analysis identified an association between breast cancer and the phosphofructokinase-muscle (PFKM) gene on chromosome 12q13.11 that met the genome-wide gene-based threshold of 2.5 × 10(-6). In conclusion, EOBC and LOBC seem to have similar genetic etiologies; the 5q11.2 region may contain multiple distinct breast cancer loci; and the PFKM gene region is worthy of further investigation. These findings should enhance our understanding of the etiology of breast cancer.