Comparison of Orchard Networks Using Their Extended µ-Representation.

Phylogenetic networks generalize phylogenetic trees in order to model reticulation events. Although the comparison of phylogenetic trees is well studied, and there are multiple ways to do it in an efficient way, the situation is much different for phylogenetic networks. Some classes of phylogenetic networks, mainly tree-child networks, are known to be classified efficiently by their µ-representation, which essentially counts, for every node, the number of paths to each leaf. In this article, we introduce the extended µ-representation of networks, where the number of paths to reticulations is also taken into account. This modification allows us to distinguish orchard networks and to define a metric on the space of such networks that can, moreover, be computed efficiently. The class of orchard networks, as well as being one of the classes with biological significance (one such network can be interpreted as a tree with extra arcs involving coexisting organisms), is one of the most generic ones (in mathematical terms) for which such a representation can (conjecturally) exist, since a slight relaxation of the definition leads to a problem that is Graph Isomorphism Complete.

Generation of Orchard and Tree-Child Networks.

Phylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is the class of orchard networks, that generalizes tree-child networks, one of the most studied classes of networks. In this paper we focus on the combinatorial and algorithmic problem of the generation of binary orchard networks, and also of binary tree-child networks. To this end, we use that these networks are defined as those that can be recovered by reversing a certain reduction process. Then, we show how to choose a "minimum" reduction process among all that can be applied to a network, and hence we get a unique representation of the network that, in fact, can be given in terms of sequences of pairs of integers, whose length is related to the number of leaves and reticulations of the network. Therefore, the generation of networks is reduced to the generation of such sequences of pairs. Our main result is a recursive method for the efficient generation of all minimum sequences, and hence of all orchard (or tree-child) networks with a given number of leaves and reticulations. An implementation in C of the algorithms described in this paper, along with some computational experiments, can be downloaded from the public repository  https://github.com/gerardet46/OrchardGenerator . Using this implementation, we have computed the number of binary orchard networks with at most 6 leaves and 8 reticulations.

Chromosome-level assembly and annotation of the Xyrichtys novacula (Linnaeus, 1758) genome.

The pearly razorfish (Xyrichtys novacula), commonly known as raor in the Balearic Islands, is a wrasse within the family Labridae. This fish species has particular biological and socio-cultural characteristics making it an ideal model organism in the fields of behavioural ecology, molecular ecology and conservation biology. In this study, we present the first annotated chromosome-level assembly for this species. Sequencing involved a combination of long reads with Oxford Nanopore Technologies, Illumina paired-end short reads (2 × 151 bp), Hi-C and RNA-seq from different tissues. The nuclear genome assembly has a scaffold N50 of 34.33 Mb, a total assembly span of 775.53 Mb and 99.63% of the sequence assembled into 24 superscaffolds, consistent with its known karyotype. Quality metrics revealed a consensus accuracy (QV) of 42.92 and gene completeness > 98%. The genome annotation resulted in 26,690 protein-coding genes and 12,737 non-coding transcripts. The coding regions encoded 39,613 unique protein products, 93% of them with assigned function. Overall, the publication of the X. novacula's reference genome will broaden the scope and impact of genomic research conducted on this iconic and colourful species.

Factorial validity, predictive validity and measurement invariance of the Danish version of the coach-created Empowering Disempowering Motivational Climate Questionnaire (EDMCQ-C).

PURPOSE: The purpose of this study was to translate and validate a Danish version of the coach-created Empowering and Disempowering Motivational Climate Questionnaire (EDMCQ-C), retest the factor structure and provide further investigation into the psychometric properties in terms of measurement invariance across gender, age and competitive level, reliability and predictive validity. METHODS: The participants were 1719 male and 551 female Danish football players 12-20 years of age (M = 14.81) playing at recreational, medium and elite levels. Participants filled in EDMCQ-C as well as questionnaires measuring psychological needs (BPNESS) and behaviour regulation (BRSQ). Factor structure of the EDMCQ-C was tested using Exploratory Structural Equation Modelling. To test whether the factor structure differed across gender, age group and competitive level, an invariance analysis comparing configurational, metric and scalar models was conducted. RESULTS: EDMCQ-C showed good psychometric properties and measurement invariance across age, gender and competitive level. Both dimensions of EDMCQ-C were associated to needs satisfaction and behaviour regulation in expected directions and had high internal consistency. CONCLUSION: This study provides evidence for the reliability of the two dimensions of EDMCQ-C, their predictive validity and for measurement invariance across age, gender and competitive level and provides a Danish version of the EDMCQ with sound psychometric properties.

Perfectionistic Environments and Irrational Beliefs on the Transition to Elite Athletic Performance: A Longitudinal Study.

This study aimed to longitudinally evaluate talented athletes' levels of perfectionism, irrational beliefs, and motivations with regard to their athletic careers. A total of 390 athletes from U14, U16, and junior categories (MageT1 = 15.42) answered shortened versions of the Sport-MPS2, iPBI, and BRSQ during two consecutive seasons, along with questions referring to their current and predicted prioritization of sports and education. Participants reported high levels of perfectionistic strivings and medium to low levels of socially prescribed perfectionism and concern over mistakes decreasing from T1 to T2. A decrease was also found for demandingness and awfulizing, but increased levels were found for depreciation in T2. Participants report very high intrinsic motivation with low levels of external regulation and amotivation, but intrinsic motivation decreased from season to season. This general profile varied depending upon future expectancies toward dedication to sports and education. Those who foresaw a prioritized dedication to sports presented significantly higher levels of socially prescribed perfectionism, perfectionistic strivings, and intrinsic motivation, while those who considered that sports would not be prioritized in the following 5 years reported higher levels of demandingness, awfulizing, depreciation, and amotivation. Additionally, while current levels of motivation (T2) seemed to be predicted mainly by previous motivation levels (T1), significant predictive capacity was also detected for socially prescribed perfectionism positively predicting external regulations and amotivation, perfectionistic strivings negatively predicting amotivation, and depreciation negatively predicting intrinsic motivation and positively predicting both extrinsic regulation and amotivation. We discuss the potential perils of developing extremely demanding environments, as they could potentially result in poor motivational profiles of athletes in their talent development stage during the junior to senior transition.

Classes of explicit phylogenetic networks and their biological and mathematical significance.

The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately represented by a phylogenetic tree, and rooted phylogenetic networks that describe such complex processes have been introduced as a generalization of rooted phylogenetic trees. In fact, estimating rooted phylogenetic networks from genomic sequence data and analyzing their structural properties is one of the most important tasks in contemporary phylogenetics. Over the last two decades, several subclasses of rooted phylogenetic networks (characterized by certain structural constraints) have been introduced in the literature, either to model specific biological phenomena or to enable tractable mathematical and computational analyses. In the present manuscript, we provide a thorough review of these network classes, as well as provide a biological interpretation of the structural constraints underlying these networks where possible. In addition, we discuss how imposing structural constraints on the network topology can be used to address the scalability and identifiability challenges faced in the estimation of phylogenetic networks from empirical data.

A polynomial invariant for a new class of phylogenetic networks.

Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this paper, we generalize a complete polynomial invariant on trees to a class of phylogenetic networks called separable networks, which will include orchard networks. Networks are becoming increasingly important for their ability to represent reticulation events, such as hybridization, in evolutionary history. We provide a function from the space of internally multi-labelled phylogenetic networks, a more generic graph structure than phylogenetic networks where the reticulations are also labelled, to a polynomial ring. We prove that the separability condition allows us to characterize, via the polynomial, the phylogenetic networks with the same number of leaves and same number of reticulations by considering their internally labelled versions. While the invariant for trees is a polynomial in [Formula: see text] where n is the number of leaves, the invariant for internally multi-labelled phylogenetic networks is an element of [Formula: see text], where r is the number of reticulations in the network. When the networks are considered without leaf labels the number of variables reduces to r + 2.

Trends in global research on industrial parks: A bibliometric analysis from 1996-2019.

Industrial parks have been used to promote the economic development of countries. However, its rapid growth has generated environmental problems related to the depletion of natural resources and pollution. Consequently, the network analysis and the bibliometric analysis applied in this research generated qualitative and quantitative information from a systemic perspective on the thematic and community evolution of research on industrial parks (IP) performed to improve its negative environmental impact and reach sustainability. This study used the Web of Science (WoS) database from 1996 - 2019. The main trends and critical research points were identified in four periods of 6-year each. Social network analysis (SNA) was used to identify the intellectual structure main and the academic collaboration networks established among countries/territories, institutions, and authors. The most productive country in articles is currently China (882), however, when we consider the frequency of articles per million inhabitants, it ranks seventh. The WoS database grouped 63.6 â€‹% of the articles published in the subjects of "Environmental Sciences & Ecology", "Engineering", and "Science & Technology - Other Topics". Industrial Ecology (IE), Industrial Symbiosis (IS), and Circular Economy (CE) were the author keywords with the highest frequency, indicating that IP research has focused from these perspectives to promote the exchange of byproducts and to evaluate the performance and environmental impact of industrial areas through the use of methodologies such as carbon footprints, emergy analysis, and life cycle analysis (LCA). Finally, some themes were identified and proposed for future research based on analyzing research trends and hot spots from the literature review on industrial parks.

Aln2tbl: building a mitochondrial features table from a assembly alignment in fasta format.

The sequencing, annotation and analysis of complete mitochondrial genomes is an important research tool in phylogeny and evolution. Starting with the primary sequence, genes/features are generally annotated automatically to obtain preliminary annotations in the form of a feature table. Further manual curation in a graphic alignment editor is nevertheless necessary to revise annotations. As such, the automatically generated feature table is invalidated and has to be modified manually before submission to data banks. We developed aln2tbl.py, a python script that recreates a feature table from a manually refined alignment of genes mapped on the mitochondrial genome in fasta format. The feature table is populated with notes and annotations specific to mitochondrial genomes. The table can be used to create a sqn file to be submitted directly to data banks. In summary, our scripts fills one gap in the available toolbox and, combined with other software, allows the automation of the entire process, from primary sequence to annotated genome submission, even if a manual curation step is conducted in a visual sequence editor.

EZmito: a simple and fast tool for multiple mitogenome analyses.

Complete mitochondrial genome data are frequently applied to address phylogenetic/phylogeographic issues at different taxonomic levels in ecology and evolution. While sample preparation/sequencing is becoming more and more straightforward thanks to dropping costs for next-generation sequencing (NGS), data preparation and visualization remains a manually intensive step that may lead to errors if improperly conducted. We have elaborated, and here introduce, EZmito, a simple and intuitive, freely accessible Web Server aimed at automating some of these tasks. EZmito is divided into three main tools: EZpipe that assembles DNA matrices for phylo-mitogenomic analyses; EZskew that calculates genome, strand, and codon nucleotide compositional skews and EZcodon which computes Relative Synonymous Codon Usage statistics as well as amino acid usage frequency over multiple mitogenomes. Output is produced in tabular format as well as publication-quality graphics.

PDKit: A data science toolkit for the digital assessment of Parkinson's Disease.

PDkit is an open source software toolkit supporting the collaborative development of novel methods of digital assessment for Parkinson's Disease, using symptom measurements captured continuously by wearables (passive monitoring) or by high-use-frequency smartphone apps (active monitoring). The goal of the toolkit is to help address the current lack of algorithmic and model transparency in this area by facilitating open sharing of standardised methods that allow the comparison of results across multiple centres and hardware variations. PDkit adopts the information-processing pipeline abstraction incorporating stages for data ingestion, quality of information augmentation, feature extraction, biomarker estimation and finally, scoring using standard clinical scales. Additionally, a dataflow programming framework is provided to support high performance computations. The practical use of PDkit is demonstrated in the context of the CUSSP clinical trial in the UK. The toolkit is implemented in the python programming language, the de facto standard for modern data science applications, and is widely available under the MIT license.

Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea).

We present the sequencing and comparative analysis of 17 mitochondrial genomes of Nearctic and Neotropical amphipods of the genus Hyalella, most from the Andean Altiplano. The mitogenomes obtained comprised the usual 37 gene-set of the metazoan mitochondrial genome showing a gene rearrangement (a reverse transposition and a reversal) between the North and South American Hyalella mitogenomes. Hyalella mitochondrial genomes show the typical AT-richness and strong nucleotide bias among codon sites and strands of pancrustaceans. Protein-coding sequences are biased towards AT-rich codons, with a preference for leucine and serine amino acids. Numerous base changes (539) were found in tRNA stems, with 103 classified as fully compensatory, 253 hemi-compensatory and the remaining base mismatches and indels. Most compensatory Watson-Crick switches were AU -> GC linked in the same haplotype, whereas most hemi-compensatory changes resulted in wobble GU and a few AC pairs. These results suggest a pairing fitness increase in tRNAs after crossing low fitness valleys. Branch-site level models detected positive selection for several amino acid positions in up to eight mitochondrial genes, with atp6 and nad5 as the genes displaying more sites under selection.

Another blow to the conserved gene order in Annelida: Evidence from mitochondrial genomes of the calcareous tubeworm genus Hydroides.

Mitochondrial genomes are frequently applied in phylogenetic and evolutionary studies across metazoans, yet they are still poorly represented in many groups of invertebrates, including annelids. Here, we report ten mitochondrial genomes from the annelid genus Hydroides (Serpulidae) and compare them with all available annelid mitogenomes. We detected all 13 protein coding genes in Hydroides spp., including the atp8 which was reported as a missing gene in the Christmas Tree worm Spirobranchus giganteus, another annelid of the family Serpulidae. All available mitochondrial genomes of Hydroides show a highly positive GC skew combined with a highly negative AT skew - a feature consistent with that found only in the mitogenome of S. giganteus. In addition, amino acid sequences of the 13 protein-coding genes showed a high genetic distance between the Hydroides clade and S. giganteus, suggesting a fast rate of mitochondrial sequence evolution in Serpulidae. The gene order of protein-coding genes within Hydroides exhibited extensive rearrangements at species level, and were different from the arrangement patterns of other annelids, including S. giganteus. Phylogenetic analyses based on protein-coding genes recovered Hydroides as a monophyletic group sister to Spirobranchus with a long branch, and sister to the fan worm Sabellidae. Yet the Serpulidae + Sabellidae clade was unexpectedly grouped with Sipuncula, suggesting that mitochondrial genomes alone are insufficient to resolve the phylogenetic position of Serpulidae within Annelida due to its high base substitution rates. Overall, our study revealed a high variability in the gene order arrangement of mitochondrial genomes within Serpulidae, provided evidence to question the conserved pattern of the mitochondrial gene order in Annelida and called for caution when applying mitochondrial genes to infer their phylogenetic relationships.

VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families.

MOTIVATION: Two key steps in the analysis of uncultured viruses recovered from metagenomes are the taxonomic classification of the viral sequences and the identification of putative host(s). Both steps rely mainly on the assignment of viral proteins to orthologs in cultivated viruses. Viral Protein Families (VPFs) can be used for the robust identification of new viral sequences in large metagenomics datasets. Despite the importance of VPF information for viral discovery, VPFs have not yet been explored for determining viral taxonomy and host targets. RESULTS: In this work, we classified the set of VPFs from the IMG/VR database and developed VPF-Class. VPF-Class is a tool that automates the taxonomic classification and host prediction of viral contigs based on the assignment of their proteins to a set of classified VPFs. Applying VPF-Class on 731K uncultivated virus contigs from the IMG/VR database, we were able to classify 363K contigs at the genus level and predict the host of over 461K contigs. In the RefSeq database, VPF-class reported an accuracy of nearly 100% to classify dsDNA, ssDNA and retroviruses, at the genus level, considering a membership ratio and a confidence score of 0.2. The accuracy in host prediction was 86.4%, also at the genus level, considering a membership ratio of 0.3 and a confidence score of 0.5. And, in the prophages dataset, the accuracy in host prediction was 86% considering a membership ratio of 0.6 and a confidence score of 0.8. Moreover, from the Global Ocean Virome dataset, over 817K viral contigs out of 1 million were classified. AVAILABILITY AND IMPLEMENTATION: The implementation of VPF-Class can be downloaded from https://github.com/biocom-uib/vpf-tools. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Phylogenomics of the Hyalella amphipod species-flock of the Andean Altiplano.

Species diversification in ancient lakes has enabled essential insights into evolutionary theory as they embody an evolutionary microcosm compared to continental terrestrial habitats. We have studied the high-altitude amphipods of the Andes Altiplano using mitogenomic, nuclear ribosomal and single-copy nuclear gene sequences obtained from 36 Hyalella genomic libraries, focusing on species of the Lake Titicaca and other water bodies of the Altiplano northern plateau. Results show that early Miocene South American lineages have recently (late Pliocene or early Pleistocene) diversified in the Andes with a striking morphological convergence among lineages. This pattern is consistent with the ecological opportunities (access to unoccupied resources, initial relaxed selection on ecologically-significant traits and low competition) offered by the lacustrine habitats established after the Andean uplift.

Complete mitochondrial genome of the pearly razorfish Xyrichtys novacula: phylogenetic analysis of its placement within the Labridae family.

In this paper, we report the complete mitochondrial genome (17,306 bp) of the pearly razorfish Xyrichtys novacula Linnaeus, 1758, a labrid that inhabits tropical and temperate Atlantic waters and the Mediterranean Sea. The circular double-stranded sequence contains the typical teleost gene order with 13 protein-coding genes, 22 tRNA, 2 rRNA, 1 control region, and 2 intergenic spacers between the rRNAs. Using the sequences of all protein-coding genes, we inferred the phylogeny for the Labriade family using 24 labrids and 3 outgroup species that placed X. novacula in a monophyletic group including species from the Pseudocheilines, Pseudolabrines, and Julidines.

Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils.

Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3' end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in Trigonopterus regarding to A+T frequencies and AT and GC skews that also greatly diverge at the codon site and coding strand levels.

Mitogenome phylogenetics in the genus Palaemon (Crustacea: Decapoda) sheds light on species crypticism in the rockpool shrimp P. elegans.

The genus Palaemon comprises worldwide marine and freshwater shrimps and prawns, and some of them are ecologically or commercially important species. Palaemon is not currently a monophyletic group, so phylogenetics and systematics are constantly changing. Species crypticism has been pointed out in several Palaemon species, being the clearest evidence in the European rockpool shrimp P. elegans. Here we sequenced and described seven European Palaemon mitochondrial genomes. The mitochondrial protein-coding genes were used, along with those of three other Palaemon species, to perform mitogenome phylogenetic analyses to clarify the evolutionary relationships within the genus, and particularly to shed light on the cryptic species found within P. elegans. The Messinian Salinity Crisis (5.3-5.9 Ma, late Miocene) was proposed to be the origin of this cryptic species and it was used as aged constraint for calibration analysis. We provide the largest and the first time-calibrated mitogenome phylogeny of the genus Palaemon and mitogenome substitution rate was estimated (1.59% per million years) in Decapoda for the first time. Our results highlighted the need for future systematics changes in Palaemon and crypticism in P. elegans was confirmed. Mitochondrial genome and cox1 (1.41%) substitution rate estimates matched those published elsewhere, arguing that the Messinian Salinity Crisis was a plausible event driving the split between P. elegans and its cryptic species. Molecular dating suggested that Pleistocene glaciations were likely involved in the differentiation between the Atlantic and Mediterranean populations of P. elegans. On the contrary, the divergence between the Atlantic and Mediterranean populations of the common littoral shrimp P. serratus was greater and dated to be much older (4.5-12.3 Ma, Plio-Miocene), so we considered that they could represent two separated species. Therefore, species crypticism in the genus Palaemon seems to be a common phenomenon.

Generation of Level- k LGT Networks.

Phylogenetic networks provide a mathematical model to represent the evolution of a set of species where, apart from speciation, reticulate evolutionary events have to be taken into account. Among these events, lateral gene transfers need special consideration due to the asymmetry in the roles of the species involved in such an event. To take into account this asymmetry, LGT networks were introduced. Contrarily to the case of phylogenetic trees, the combinatorial structure of phylogenetic networks is much less known and difficult to describe. One of the approaches in the literature is to classify them according to their level and find generators of the given level that can be used to recursively generate all networks. In this paper, we adapt the concept of generators to the case of LGT networks. We show how these generators, classified by their level, give rise to simple LGT networks of the specified level, and how any LGT network can be obtained from these simple networks, that act as building blocks of the generic structure. The stochastic models of evolution of phylogenetic networks are also much less studied than those for phylogenetic trees. In this setting, we introduce a novel two-parameter model that generates LGT networks. Finally, we present some computer simulations using this model in order to investigate the complexity of the generated networks, depending on the parameters of the model.