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.

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.

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.

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.

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.

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.

IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes.

The Integrated Microbial Genome/Virus (IMG/VR) system v.2.0 (https://img.jgi.doe.gov/vr/) is the largest publicly available data management and analysis platform dedicated to viral genomics. Since the last report published in the 2016, NAR Database Issue, the data has tripled in size and currently contains genomes of 8389 cultivated reference viruses, 12 498 previously published curated prophages derived from cultivated microbial isolates, and 735 112 viral genomic fragments computationally predicted from assembled shotgun metagenomes. Nearly 60% of the viral genomes and genome fragments are clustered into 110 384 viral Operational Taxonomic Units (vOTUs) with two or more members. To improve data quality and predictions of host specificity, IMG/VR v.2.0 now separates prokaryotic and eukaryotic viruses, utilizes known prophage sequences to improve taxonomic assignments, and provides viral genome quality scores based on the estimated genome completeness. New features also include enhanced BLAST search capabilities for external queries. Finally, geographic map visualization to locate user-selected viral genomes or genome fragments has been implemented and download options have been extended. All of these features make IMG/VR v.2.0 a key resource for the study of viruses.

Generation of Binary Tree-Child phylogenetic networks.

Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary tree-child networks is one of the most studied ones. However, very little is known about the combinatorial structure of these networks. In this paper we address the problem of generating all possible binary tree-child (BTC) networks with a given number of leaves in an efficient way via reduction/augmentation operations that extend and generalize analogous operations for phylogenetic trees, and are biologically relevant. Since our solution is recursive, this also provides us with a recurrence relation giving an upper bound on the number of such networks. We also show how the operations introduced in this paper can be employed to extend the evolutive history of a set of sequences, represented by a BTC network, to include a new sequence. An implementation in python of the algorithms described in this paper, along with some computational experiments, can be downloaded from https://github.com/bielcardona/TCGenerators.

Correction: Generation of Binary Tree-Child phylogenetic networks.

[This corrects the article DOI: 10.1371/journal.pcbi.1007347.].

Arm-less mitochondrial tRNAs conserved for over 30 millions of years in spiders.

BACKGROUND: In recent years, Next Generation Sequencing (NGS) has accelerated the generation of full mitogenomes, providing abundant material for studying different aspects of molecular evolution. Some mitogenomes have been observed to harbor atypical sequences with bizarre secondary structures, which origins and significance could only be fully understood in an evolutionary framework. RESULTS: Here we report and analyze the mitochondrial sequences and gene arrangements of six closely related spiders in the sister genera Parachtes and Harpactocrates, which belong to the nocturnal, ground dwelling family Dysderidae. Species of both genera have compacted mitogenomes with many overlapping genes and strikingly reduced tRNAs that are among the shortest described within metazoans. Thanks to the conservation of the gene order and the nucleotide identity across close relatives, we were able to predict the secondary structures even on arm-less tRNAs, which would be otherwise unattainable for a single species. They exhibit aberrant secondary structures with the lack of either DHU or TΨC arms and many miss-pairings in the acceptor arm but this degeneracy trend goes even further since at least four tRNAs are arm-less in the six spider species studied. CONCLUSIONS: The conservation of at least four arm-less tRNA genes in two sister spider genera for about 30 myr suggest that these genes are still encoding fully functional tRNAs though they may be post-transcriptionally edited to be fully functional as previously described in other species. We suggest that the presence of overlapping and truncated tRNA genes may be related and explains why spider mitogenomes are smaller than those of other invertebrates.

The age and diversification of metacrangonyctid subterranean amphipod crustaceans revisited.

The Metacrangonyctidae are a small family of amphipod crustaceans of marine origin found only in subterranean continental waters. They display a broad but punctuated distribution between the Caribbean and the Arabian Peninsula, with major disjunctions either due to vicariance by plate tectonics or to occurrence of recent episodes of long-distance transoceanic dispersal. We re-examine the phylogeny of the family and the time frame for its diversification using mitochondrial genomes in the light of two key taxa recently discovered, from Oman (Arabian Peninsula) and the Rif area of Morocco, respectively. We also use a novel fossil calibration scheme of the mitogenome phylogeny. Results of previous analyses based on palaeogeographic calibrations are not contradicted by the new approach, with vicariance by plate tectonics remaining as the main explanatory factor for the amphi-Atlantic distribution displayed by this ancient group of subterranean amphipods.

Tree-based networks: characterisations, metrics, and support trees.

Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer. One way to obtain such a network is by starting with a (rooted) phylogenetic tree T, called a base tree, and adding arcs between arcs of T. The class of phylogenetic networks that can be obtained in this way is called tree-based networks and includes the prominent classes of tree-child and reticulation-visible networks. Initially defined for binary phylogenetic networks, tree-based networks naturally extend to arbitrary phylogenetic networks. In this paper, we generalise recent tree-based characterisations and associated proximity measures for binary phylogenetic networks to arbitrary phylogenetic networks. These characterisations are in terms of matchings in bipartite graphs, path partitions, and antichains. Some of the generalisations are straightforward to establish using the original approach, while others require a very different approach. Furthermore, for an arbitrary tree-based network N, we characterise the support trees of N, that is, the tree-based embeddings of N. We use this characterisation to give an explicit formula for the number of support trees of N when N is binary. This formula is written in terms of the components of a bipartite graph.

Viral encephalopathy and retinopathy (VER) disease in Epinephelus marginatus from the Balearic Islands marine protected areas.

This is the first description of a betanodavirus infection in the dusky grouper Epinephelus marginatus within the marine protected areas (MPAs) of the Balearic Islands. Histopathology techniques were employed to describe neurological lesions in infected fish. Abnormal swimming, mortality, and neurological lesions were detected in all analysed grouper individuals. Virus particles were observed by means of transmission electron microscopy. Reverse transcription of RNA1 and RNA2 followed by cDNA amplification and sequencing allowed viral classification. Phylogenetic analysis showed the isolates from wild E. marginatus of the Balearic Islands MPAs to be closely related to Dicentrarchus labrax and Mullus barbatus strains from Cyprus and Italy. Although vertical transmission from infected spawners has been described as the major route for nodavirus infection, we point out in this work that horizontal transmission among sub-clinical fishes after migration or commercial import for aquaculture production could play a major role in the spreading of the disease in MPAs.

Molecular resolution to a morphological controversy: The case of North American fossil muskoxen Bootherium and Symbos.

The musk ox (Ovibos moschatus) is the only surviving member of a group of Pleistocene North American musk ox genera (Praeovibos, Ovibos, Bootherium, Euceratherium, and Soergelia) whose taxonomy is uncertain. The helmeted musk ox (Bootherium bombifrons) and the woodland musk ox (Symbos cavifrons) have been synonymised as male and female forms of a single Nearctic species found from Alaska, in the north, to Texas, in the south. However, this reclassification has not been tested using molecular data, despite the potential to use ancient DNA to examine these late Pleistocene taxa. In the present study, we sequenced mitochondrial genomes from seven subfossil musk ox specimens (originally identified as Bootherium and/or Symbos), allowing us to evaluate the identity of these muskoxen, explore their phylogeography, and estimate the timeline for their evolution. We also used nuclear genomic data to determine the sex of six of our seven samples. Ultimately, our molecular data support the synonymisation of the North American muskoxen Bootherium and Symbos.

Species delimitation and mitogenome phylogenetics in the subterranean genus Pseudoniphargus (Crustacea: Amphipoda).

The amphi-Atlantic distributions exhibited by many thalassoid stygobiont (obligate subterranean) crustaceans have been explained by fragmentation by plate tectonics of ancestral shallow water marine populations. The amphipod stygobiont genus Pseudoniphargus is distributed across the Mediterranean region but also in the North Atlantic archipelagos of Bermuda, Azores, Madeira and the Canaries. We used species delimitation methods and mitogenome phylogenetic analyses to clarify the species diversity and evolutionary relationships within the genus and timing their diversification. Analyses included samples from the Iberian Peninsula, northern Morocco, the Balearic, Canarian, Azores and Madeira archipelagoes plus Bermuda. In most instances, morphological and molecular-based species delimitation analyses yielded consistent results. Notwithstanding, in a few cases either incipient speciation with no involvement of detectable morphological divergence or species crypticism were the most plausible explanations for the disagreement found between morphological and molecular species delimitations. Phylogenetic analyses based on a robust calibrated mitochondrial tree suggested that Pseudoniphargus lineages have a younger age than for other thalassoid amphipods displaying a disjunct distribution embracing both sides of the Atlantic Ocean. A major split within the family was estimated to occur at the Paleocene, when a lineage from Northern Iberian Peninsula diverged from the rest of pseudoniphargids. Species diversification in the peri-Mediterranean area was deduced to occur in early Miocene to Tortonian times, while in the Atlantic islands it started in the Pliocene. Our results show that the current distribution pattern of Pseudoniphargus resulted from a complex admix of relatively ancient vicariance events and several episodes of long- distance dispersal.

Molecular phylogenetics supports the origin of an endemic Balearic shrew lineage (Nesiotites) coincident with the Messinian Salinity Crisis.

The red-toothed shrews (Soricinae) are the most widespread subfamily of shrews, distributed from northern South America to North America and Eurasia. Within this subfamily, the tribe Nectogalini includes the fossil species Nesiotites hidalgo recorded from the Late Pleistocene to Holocene of the Balearic Islands (Western Mediterranean). Although there is a consensus about the close relationship between the extinct red-toothed shrew genera Nesiotites and Asoriculus based on morphology, molecular data are necessary to further evaluate the phylogenetic relationships of the Balearic fossils. We obtained a near complete mitochondrial genome of N. hidalgo, allowing the first molecular phylogenetic analysis of this species. Analyses based on 15,167 bp of the mitochondrial genome placed N. hidalgo as close relative to the extant Himalayan shrew (Soriculus nigrescens), and a combined analysis using molecular and morphological data confirm that N. hidalgo and Asoriculus gibberodon are sister-taxa with S. nigrescens as the immediate outgroup. Molecular clock and divergence estimates suggest that the split between N. hidalgo and its closest living relative occurred around 6.44 Ma, which is in agreement with the previously proposed colonisation of the Balearic Islands from mainland Europe by nectogaline shrews during the Messinian Salinity Crisis (5.97-5.33 My ago). Our results highlight that it is possible to retrieve genetic data from extinct small mammals from marginal environments for DNA preservation. Additional finds from the fossil record of Soricinae from the Eurasian Late Miocene/Early Pliocene are needed to shed further light on the still confusing taxonomy and paleobiogeography of this clade.

Reconstruction of LGT networks from tri-LGT-nets.

Phylogenetic networks have gained attention from the scientific community due to the evidence of the existence of evolutionary events that cannot be represented using trees. A variant of phylogenetic networks, called LGT networks, models specifically lateral gene transfer events, which cannot be properly represented with generic phylogenetic networks. In this paper we treat the problem of the reconstruction of LGT networks from substructures induced by three leaves, which we call tri-LGT-nets. We first restrict ourselves to a class of LGT networks that are both mathematically treatable and biologically significant, called BAN-LGT networks. Then, we study the decomposition of such networks in subnetworks with three leaves and ask whether or not this decomposition determines the network. The answer to this question is negative, but if we further impose time-consistency (species involved in a later gene transfer must coexist) the answer is affirmative, up to some redundancy that can never be recovered but is fully characterized.

Towards the centralization of digestive oncologic surgery: changes in activity, techniques and outcome.

AIM: The objective of the present study was to examine changes in the activity, surgical techniques and results from the process of centralization of complex digestive oncologic surgery in 2005-2012 as compared to 1996-2000. MATERIAL AND METHODS: A retrospective cohort study employing the minimum basic data set of hospital discharge (MBDSHD 1996-2012) from public centers in Catalonia (Spain) was performed. The population consisted of individuals aged > 18 who underwent digestive oncologic surgery (esophagus, pancreas, liver, stomach or rectum). Medical centers were divided into low, medium, and high-volume centers (≤ 5, 6-10, and > 10 interventions/year, respectively). The tendency Chi-squared test was used to assess the centralization of patients in high-volume centers and hospital mortality evolution during the study period. Logistic regression was performed to assess the relationship between volume and outcome. RESULTS: A centralization of complex oncologic digestive surgery between 10% (liver) and 46% (esophagus) was obtained by means of a reduction in the number of hospitals that perform these interventions and a significant rise in the number of patients operated in high-volume centers (all types p ≤ 0.0001, except for esophagus). A significant decrease in mortality was observed, especially in esophagus (from 15% in 1996/2000 to 7% in 2009/12, p = 0.003) and pancreas (from 12% in 1996/2000 to 6% in 2009/12, p trend < 0.0001). CONCLUSIONS: A centralization of oncologic digestive surgery in high-volume centers and a reduction of hospital mortality in Catalonia were reported among esophageal and pancreatic cancers. However, no significant changes were found for others cancer types.

Next-generation sequencing, phylogenetic signal and comparative mitogenomic analyses in Metacrangonyctidae (Amphipoda: Crustacea).

BACKGROUND: Comparative mitochondrial genomic analyses are rare among crustaceans below the family or genus level. The obliged subterranean crustacean amphipods of the family Metacrangonyctidae, found from the Hispaniola (Antilles) to the Middle East, including the Canary Islands and the peri-Mediterranean region, have an evolutionary history and peculiar biogeography that can respond to Tethyan vicariance. Indeed, recent phylogenetic analysis using all protein-coding mitochondrial sequences and one nuclear ribosomal gene have lent support to this hypothesis (Bauzà-Ribot et al. 2012). RESULTS: We present the analyses of mitochondrial genome sequences of 21 metacrangonyctids in the genera Metacrangonyx and Longipodacrangonyx, covering the entire geographical range of the family. Most mitogenomes were attained by next-generation sequencing techniques using long-PCR fragments sequenced by Roche FLX/454 or GS Junior pyro-sequencing, obtaining a coverage depth per nucleotide of up to 281×. All mitogenomes were AT-rich and included the usual 37 genes of the metazoan mitochondrial genome, but showed a unique derived gene order not matched in any other amphipod mitogenome. We compare and discuss features such as strand bias, phylogenetic informativeness, non-synonymous/synonymous substitution rates and other mitogenomic characteristics, including ribosomal and transfer RNAs annotation and structure. CONCLUSIONS: Next-generation sequencing of pooled long-PCR amplicons can help to rapidly generate mitogenomic information of a high number of related species to be used in phylogenetic and genomic evolutionary studies. The mitogenomes of the Metacrangonyctidae have the usual characteristics of the metazoan mitogenomes (circular molecules of 15,000-16,000 bp, coding for 13 protein genes, 22 tRNAs and two ribosomal genes) and show a conserved gene order with several rearrangements with respect to the presumed Pancrustacean ground pattern. Strand nucleotide bias appears to be reversed with respect to the condition displayed in the majority of crustacean mitogenomes since metacrangonyctids show a GC-skew at the (+) and (-) strands; this feature has been reported also in the few mitogenomes of Isopoda (Peracarida) known thus far. The features of the rRNAs, tRNAs and sequence motifs of the control region of the Metacrangonyctidae are similar to those of the few crustaceans studied at present.

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.