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  • 1. Aberer, André
    et al.
    Stamatakis, Alexis
    Ronquist, Fredrik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    An efficient independence sampler for updating branches in Bayesian Markov chain Monte Carlo sampling of phylogenetic trees2016Inngår i: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, nr 1, s. 161-176Artikkel i tidsskrift (Fagfellevurdert)
  • 2.
    Cannon, Johanna
    et al.
    Naturhistoriska riksmuseet, Enheten för zoologi. Auburn University.
    Vellutini, Bruno
    Sars International Centre for Marine Molecular Biology.
    Smith, Julian
    Winthrop University.
    Ronquist, Fredrik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Jondelius, Ulf
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Hejnol, Andreas
    Sars International Centre for Marine Molecular Biology.
    Xenacoelomorpha is the sister group to Nephrozoa2016Inngår i: Nature, ISSN ISSN: 0028-0836, Vol. 530, s. 89-93Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The position of Xenacoelomorpha in the tree of life remains a major unresolved question in the study of deep animal relationships1. Xenacoelomorpha, comprising Acoela, Nemertodermatida, and Xenoturbella, are bilaterally symmetrical marine worms that lack several features common to most other bilaterians, for example an anus, nephridia, and a circulatory system. Two conflicting hypotheses are under debate: Xenacoelomorpha is the sister group to all remaining Bilateria (= Nephrozoa, namely protostomes and deuterostomes)2,3 or is a clade inside Deuterostomia4. Thus, determining the phylogenetic position of this clade is pivotal for understanding the early evolution of bilaterian features, or as a case of drastic secondary loss of complexity. Here we show robust phylogenomic support for Xenacoelomorpha as the sister taxon of Nephrozoa. Our phylogenetic analyses, based on 11 novel xenacoelomorph transcriptomes and using different models of evolution under maximum likelihood and Bayesian inference analyses, strongly corroborate this result. Rigorous testing of 25 experimental data sets designed to exclude data partitions and taxa potentially prone to reconstruction biases indicates that long- branch attraction, saturation, and missing data do not influence these results. The sister group relationship between Nephrozoa and Xenacoelomorpha supported by our phylogenomic analyses implies that the last common ancestor of bilaterians was probably a benthic, ciliated acoelomate worm with a single opening into an epithelial gut, and that excretory organs, coelomic cavities, and nerve cords evolved after xenacoelomorphs separated from the stem lineage of Nephrozoa. 

    Fulltekst (pdf)
    fulltext
  • 3.
    Häggqvist, Sibylle
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Ulefors, Sven Olof
    Ronquist, Fredrik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    A new species group in Megaselia, the lucifrons group, with description of a new species (Diptera, Phoridae)2015Inngår i: ZooKeys, ISSN 1313-2989, E-ISSN 1313-2970, Vol. 512, s. 89-108Artikkel i tidsskrift (Fagfellevurdert)
    Fulltekst (pdf)
    fulltext
  • 4.
    Höhna, Sebastian
    et al.
    Stockholms universitet.
    Heath, Tracy A.
    Boussau, Bastien
    Landis, Michael J.
    Ronquist, Fredrik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Huelsenbeck, John P.
    Probabilistic graphical model representation in phylogenetics2014Inngår i: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 63, nr 5, s. 753-771Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis–Hastings or Gibbs sampling of the posterior distribution.

  • 5. Höhna, Sebastian
    et al.
    Landis, Michael J.
    Heath, Tracy A.
    Boussau, Bastien
    Lartillot, Nicolas
    Moore, Brian R.
    Huelsenbeck, John P.
    Ronquist, Fredrik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language2016Inngår i: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, nr 4, s. 726-736Artikkel i tidsskrift (Fagfellevurdert)
  • 6. Klopfstein, Seraina
    et al.
    Vilhelmsen, Lars
    Ronquist, Fredrik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    A Nonstationary Markov Model Detects Directional Evolution in Hymenopteran Morphology2015Inngår i: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, nr 6, s. 1089-1103Artikkel i tidsskrift (Fagfellevurdert)
    Fulltekst (pdf)
    fulltext
  • 7. Lartillot, Nicolas
    et al.
    Phillips, Matthew J.
    Ronquist, Fredrik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    A mixed relaxed clock model2016Inngår i: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 371, artikkel-id 20150132Artikkel i tidsskrift (Fagfellevurdert)
  • 8.
    Ronquist, Fredrik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Systematics: Charting the tree of life2014Inngår i: The Tree of Life / [ed] Vargas, P. & Zardoya, R., Sunderland, MA: Sinauer Associates, Inc. , 2014, s. 1-11Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    Biological systematics has undergone dramatic changes in the last 60 years. Darwin had already used the tree of life metaphor to describe evolution in On the Origin of Species, but it was not until the first rigorous tree reconstruction techniques were introduced in the 1950s and 1960s that biologists accepted the idea of basing classification strictly on “phylogenetic relationship,” the branching of evolutionary lineages. This was followed by a series of groundbreaking advances in DNA sequencing and computational methods for phylogeny reconstruction in the 1980s and 1990s, spurring a flood of empirical studies of the tree of life. At the same time, the power of phylogenies in addressing questions in comparative biology was discovered in a wide range of disciplines, making phylogenetic inference an essential tool across the life sciences. A lot of empirical work still remains in most organism groups before the major branches in the tree of life are accurately characterized, but in the more well-studied groups, biologists are now shifting their focus from phylogenetic relationships to the dating of the splits in the tree. Computational approaches are also developing rapidly, allowing the mining of huge genomic data sets in the quest for more accurate evolutionary reconstructions. In parallel with these developments, some systematists are preparing for yet another transformational change, shifting their attention from the major branches in the tree of life (the major lineages) to the charting of the finest twigs and leaves (the species). Advances in both information technology and DNA sequencing are explored in attempts to accelerate the inventory of life on the planet, with the hope of completing our chart of the tree of life in time to save biological diversity for the future. Increasingly, people are becoming aware that this is not merely a question of ethics but that, ultimately, the survival of mankind may be on the line.

    Fulltekst (pdf)
    Manuscript
  • 9.
    Ronquist, Fredrik
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Lartillot, Nicolas
    Phillips, Matthew J.
    Closing the gap between rocks and clocks using total-evidence dating2016Inngår i: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 371, artikkel-id 20150136Artikkel i tidsskrift (Fagfellevurdert)
  • 10.
    Ronquist, Fredrik
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Nieves-Aldrey, José-Luis
    Buffington, Matthew L
    Liu, Zhiwei
    Liljeblad, Johan
    Nylander, Johan A A
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik. BILS.
    Phylogeny, evolution and classification of gall wasps: the plot thickens.2015Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, nr 5Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Gall wasps (Cynipidae) represent the most spectacular radiation of gall-inducing insects. In addition to true gall formers, gall wasps also include phytophagous inquilines, which live inside the galls induced by gall wasps or other insects. Here we present the first comprehensive molecular and total-evidence analyses of higher-level gall wasp relationships. We studied more than 100 taxa representing a rich selection of outgroups and the majority of described cynipid genera outside the diverse oak gall wasps (Cynipini), which were more sparsely sampled. About 5 kb of nucleotide data from one mitochondrial (COI) and four nuclear (28S, LWRh, EF1alpha F1, and EF1alpha F2) markers were analyzed separately and in combination with morphological and life-history data. According to previous morphology-based studies, gall wasps evolved in the Northern Hemisphere and were initially herb gallers. Inquilines originated once from gall inducers that lost the ability to initiate galls. Our results, albeit not conclusive, suggest a different scenario. The first gall wasps were more likely associated with woody host plants, and there must have been multiple origins of gall inducers, inquilines or both. One possibility is that gall inducers arose independently from inquilines in several lineages. Except for these surprising results, our analyses are largely consistent with previous studies. They confirm that gall wasps are conservative in their host-plant preferences, and that herb-galling lineages have radiated repeatedly onto the same set of unrelated host plants. We propose a revised classification of the family into twelve tribes, which are strongly supported as monophyletic across independent datasets. Four are new: Aulacideini, Phanacidini, Diastrophini and Ceroptresini. We present a key to the tribes and discuss their morphological and biological diversity. Until the relationships among the tribes are resolved, the origin and early evolution of gall wasps will remain elusive.

    Fulltekst (pdf)
    fulltext
  • 11.
    Ronquist, Fredrik
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Skyttner, Markus
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Kõljalg, Urmas
    Röppert, Dominik
    Penev, Lyubomir
    Stoev, Pavel
    Peer, Israel
    Stein, Martin
    Calabuig, Isabel
    Agosti, Donat
    Kempa, Matus
    EU-BON Deliverable 1.3. Systems for mobilizing and managing collection-based data (specimen + DNA-data) fully integrated2016Rapport (Annet vitenskapelig)
    Abstract [en]

    Introduction. A large portion of the biodiversity data in natural history collections is still not available digitally. Increasingly, innovative high-throughput methods are being applied to digitize this backlog in bulk, generating large amounts of data. In parallel, natural history museums are becoming increasingly involved in the generation of large amounts of molecular biodiversity data using new massively parallel sequencing platforms. Against this backdrop, the goal of EU BON Task 1.4 has been to support data mobilization efforts targeting collection-based and molecular data, mainly through the development and integration of innovative open-source tools and services.

    Progress towards objectives. The activities have involved work within the context of three major projects: i) DINA, an open-source, modular, web-based collection management system for natural history specimen data. ii) JACQ an open-access system for botanical (herbarium) data. iii) PlutoF, a web platform for working with traditional and molecular biodiversity research data. The task has also involved work on a number of other EU BON partner systems and services, as well as integration across internal EU BON and external biodiversity informatics resources. Finally, these systems have been used for targeted data mobilization efforts.

    Achievements and current status. Within DINA, the focus has been on supporting the engineering of sophisticated biodiversity information systems through the exploration of tools supporting distributed development and a modular plug-and-play design based on services-oriented architectures. This has involved the testing and adoption of tools like Apiary for the design of Application Programming Interfaces (APIs) and Docker for systems integration and deployment tasks. A Python library for data migration to DINA was also developed and tested. Within JACQ, a number of tools were developed to facilitate deployment and data migration to the system, and the AnnoSys tool for annotation of data has been integrated. Within PlutoF, EU BON efforts focused on the development of a citizen-science module and improved functionality for the mobilization of collection (living) specimen data. A number of innovative tools were developed by Pensoft to help mobilize biodiversity data published in the scientific literature, including semantic mark-up of species conservation papers, direct import of data from a range of biodiversity platforms into manuscripts, and a mechanism for providing stable links from publications to global biodiversity repositories. Plazi implemented an automated workflow mining published scientific papers for taxonomic data, currently mobilizing 25 % of all published new names as they become available. GlueCad developed apps allowing citizen scientists reporting spontaneous observations or systematic inventory data to select target taxa and preferred data mobilization platform. IBSAS and UCPH have focused on national data mobilization efforts targeting Slovakia and Denmark, respectively.

    Future developments. Although the development is clearly towards increased integration of biodiversity informatics tools into larger and more sophisticated systems, it is clear that there is no one size that fits all. Nevertheless, the increasingly widespread adoption of community standards, open-source development practises and service-oriented architectures are pushing the capability of current systems forward and facilitating tighter integration across systems. This trend is supported by the appearance of sophisticated tools enabling the design and deployment of complex modular systems. The adoption of the Docker approach is one example of how the biodiversity informatics community may benefit from this.

    Fulltekst (pdf)
    fulltext
  • 12.
    Stigenberg, Julia
    et al.
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Ronquist, Fredrik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Boring, Charles, Andrew
    Phylogeny of the parasitic wasp subfamily Euphorinae (Braconidae) and evolution of its host preferemces2015Inngår i: Systematic Entomology, ISSN 0307-6970, E-ISSN 1365-3113, Vol. 40, nr 3, s. 570-591Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The braconid subfamily Euphorinae is a large, cosmopolitan group of endoparasitoid wasps. The majority of species attack adult hosts, a strategy that is rare among parasitic wasps, but there are also many species that attack nymphs and larval stages. Euphorine hosts may belong to a variety of insect orders (Coleoptera, Hemiptera, Hymenoptera, Neuroptera, Psocoptera, Orthoptera and Lepidoptera) although most euphorine tribes are confined to Coleoptera. Here we investigate the phylogenetic relationships of the Euphorinae based on molecular data (3 kb of nucleotide data from four markers: 18S, 28S, CAD and COI) and propose a higher-level classification based upon the resulting phylogeny. We also infer the evolution of host associations and discuss the diversification of the Euphorinae. Results from both Bayesian inference and maximum-likelihood analysis show that the subfamily, as previously circumscribed, is paraphyletic. We propose that the subfamily be expanded to include the tribes Meteorini and Planitorini (Mannokeraia + Planitorus), so that it corresponds to a clade that is strongly supported as monophyletic in our analyses. Based on our results, a revised higher classification of the Euphorinae is proposed, in which 52 extant genera and 14 tribes are recognized. We reinstate the genus Microctonus belonging to the tribe Perilitini, and synonymize Ussuraridelus with Holdawayella, Sinuatophorus with Eucosmophorus. Furthermore, we propose the following tribal rearrangements: Spathicopis and Stenothremma are transferred to Perilitini; Tuberidelus, Eucosmopho- rus and Plynops to Cosmophorini; Ecclitura to Dinocampini; Chrysopophthorus, Holdawayella and Wesmaelia to Helorimorphini; Proclithroporus and Heia to Towne- silitini. The monotypic tribe Cryptoxilonini is synonymized with Cosmophorini. The genera Pygostolus and Litostolus are placed in a separate tribe, Pygostolini, previously recognized as a subtribe among the Centistini. Parsimony-based ancestral state recon- structions suggest that the ancestor of Euphorinae was a parasitoid of lepidopteran larvae, and that a host shift to larval Coleoptera occurred only in one clade of the Meteorini, some members of which secondarily shifted back to larval lepidopteran hosts. In the remainder of the subfamily, there was an initial shift from larval to adult coleopterans, followed by subsequent shifts to adults or larvae of Hemiptera, Hymenoptera, Neuroptera, Orthoptera and Psocoptera. 

  • 13. Zhang, Chi
    et al.
    Stadler, Tanja
    Klopfstein, Seraina
    Heath, Tracy A.
    Ronquist, Fredrik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Total-evidence dating under the fossilized birth–death process2016Inngår i: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, nr 2, s. 228-249Artikkel i tidsskrift (Fagfellevurdert)
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