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  • 1.
    Cannon, Johanna
    et al.
    Swedish Museum of Natural History, Department of Zoology. Auburn University.
    Kocot, Kevin
    University of Alabama.
    Phylogenomic approaches using transcriptome data.2016In: Marine Genomics: Methods and Protocols / [ed] Sarah Bourlat, New York: Humana Press, 2016, p. 65-80Chapter in book (Other academic)
  • 2.
    Cannon, Johanna
    et al.
    Swedish Museum of Natural History, Department of Zoology. Auburn University.
    Kocot, Kevin
    University of Queensland.
    Waits, Damien
    Auburn University.
    Weese, David
    Georgia College and State University.
    Swalla, Billie
    University of Washington.
    Santos, Scott
    Auburn University.
    Halanych, Kenneth
    Auburn University.
    Phylogenomic Resolution of the Hemichordate and Echinoderm Clade2014In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 24, p. 2827-2832Article in journal (Refereed)
    Abstract [en]

    Ambulacraria, comprising Hemichordata and Echinodermata, is closely related to Chordata, making it integral to understanding chordate origins and polarizing chordate molecular and morphological characters. Unfortunately, relationships within Hemichordata and Echinoder- mata have remained unresolved, compromising our ability to extrapolate findings from the most closely related molecular and developmental models outside of Chordata (e.g., the acorn worms Saccoglossus kowalevskii and Ptychodera flava and the sea urchin Strongylocentrotus purpuratus). To resolve long-standing phylogenetic issues within Ambulacraria, we sequenced transcriptomes for 14 hemichordates as well as 8 echinoderms and complemented these with existing data for a total of 33 ambulacrarian operational taxonomic units (OTUs). Examination of leaf stability values revealed rhabdopleurid pterobranchs and the enteropneust Stereobalanus canadensis were unstable in placement; therefore, analyses were also run without these taxa. Analyses of 185 genes resulted in reciprocal monophyly of Enteropneusta and Pterobranchia, placed the deep-sea family Torquaratoridae within Ptychoderidae, and confirmed the position of ophiuroid brittle stars as sister to asteroid sea stars (the Asterozoa hypothesis). These results are consistent with earlier perspectives concerning plesiomorphies of Ambulacraria, including pharyngeal gill slits, a single axocoel, and paired hydrocoels and somatocoels. The resolved ambulacrarian phylogeny will help clarify the early evolution of chordate characteristics and has implications for our understanding of major fossil groups, including graptolites and somasteroideans. 

  • 3.
    Cannon, Johanna
    et al.
    Swedish Museum of Natural History, Department of Zoology. Auburn University.
    Vellutini, Bruno
    Sars International Centre for Marine Molecular Biology.
    Smith, Julian
    Winthrop University.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Jondelius, Ulf
    Swedish Museum of Natural History, Department of Zoology.
    Hejnol, Andreas
    Sars International Centre for Marine Molecular Biology.
    Xenacoelomorpha is the sister group to Nephrozoa2016In: Nature, ISSN ISSN: 0028-0836, Vol. 530, p. 89-93Article in journal (Refereed)
    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. 

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  • 4.
    D'Aniello, Salvatore
    et al.
    Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn.
    Delroisse, Jérôme
    Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences, University of Mons.
    Valero-Garcia, Alberto
    Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn.
    Lowe, Elijah
    Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn.
    Byrne, Maria
    Schools of Medical and Biological Sciences, The University of Sydney.
    Cannon, Johanna
    Swedish Museum of Natural History, Department of Zoology.
    Halanych, Kenneth
    Auburn University, Department of Biological Sciences.
    Elphick, Maurice
    School of Biological & Chemical Sciences, Queen Mary University of London.
    Mallefet, Jerome
    Laboratory of Marine Biology, Earth and Life Institute, Université Catholique de Louvain.
    Kaul-Strehlow, Sabrina
    Department of Molecular Evolution and Development, University of Vienna.
    Lowe, Christopher
    Hopkins Marine Station of Stanford University.
    Flammang, Patrick
    Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences, University of Mons.
    Ullrich-Lutter, Esther
    Museum fuer Naturkunde Berlin.
    Wanniger, Andreas
    Department of Integrative Zoology, University of Vienna.
    Arnone, Maria Ina
    Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn.
    Opsin evolution in the AmbulacrariaIn: Marine Genomics, ISSN 1874-7787, E-ISSN 1876-7478Article in journal (Refereed)
    Abstract [en]

    Opsins — G-protein coupled receptors involved in photoreception — have been extensively studied in the animal kingdom. The present work provides new insights into opsin-based photoreception and photoreceptor cell evo- lution with a first analysis of opsin sequence data for a major deuterostome clade, the Ambulacraria. Systematic data analysis, including for the first time hemichordate opsin sequences and an expanded echinoderm dataset, led to a robust opsin phylogeny for this cornerstone superphylum. Multiple genomic and transcriptomic resources were surveyed to cover each class of Hemichordata and Echinodermata. In total, 119 ambulacrarian opsin sequences were found, 22 new sequences in hemichordates and 97 in echinoderms (including 67 new sequences). We framed the ambulacrarian opsin repertoire within eumetazoan diversity by including selected reference opsins from non-ambulacrarians. Our findings corroborate the presence of all major ancestral bilaterian opsin groups in Ambulacraria. Furthermore, we identified two opsin groups specific to echinoderms. In conclu- sion, a molecular phylogenetic framework for investigating light-perception and photobiological behaviors in marine deuterostomes has been obtained. 

  • 5.
    Kocot, Kevin
    et al.
    University of Alabama.
    Struck, Torsten
    Natural History Museum, Department of Research and Collections, University of Oslo.
    Merkel, Julia
    Johannes Gutenberg University.
    Waits, Damien
    Auburn University.
    Todt, Christiane
    University Museum of Bergen.
    Brannock, Pamela
    Auburn University.
    Weese, David
    Auburn University.
    Cannon, Johanna
    Swedish Museum of Natural History, Department of Zoology. Auburn University.
    Moroz, Leonid
    The Whitney Laboratory for Marine Bioscience.
    Lieb, Bernhard
    Johannes Gutenberg University.
    Halanych, Kenneth
    Auburn University.
    Phylogenomics of Lophotrochozoa with consideration of systematic error2017In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 66, no 2, p. 256-282Article in journal (Refereed)
    Abstract [en]

    Phylogenomic studies have improved understanding of deep metazoan phylogeny and show promise for resolving incongruences among analyses based on limited numbers of loci. One region of the animal tree that has been especially difficult to resolve, even with phylogenomic approaches, is relationships within Lophotrochozoa (the animal clade that includes molluscs, annelids, and flatworms among others). Lack of resolution in phylogenomic analyses could be due to insufficient phylogenetic signal, limitations in taxon and/or gene sampling, or systematic error. Here, we investigated why lophotrochozoan phylogeny has been such a difficult question to answer by identifying and reducing sources of systematic error. We supplemented existing data with 32 new transcriptomes spanning the diversity of Lophotrochozoa and constructed a new set of Lophotrochozoa-specific core orthologs. Of these, 638 orthologous groups (OGs) passed strict screening for paralogy using a tree-based approach. In order to reduce possible sources of systematic error, we calculated branch-length heterogeneity, evolutionary rate, percent missing data, compositional bias, and saturation for each OG and analyzed increasingly stricter subsets of only the most stringent (best) OGs for these five variables. Principal component analysis of the values for each factor examined for each OG revealed that compositional heterogeneity and average patristic distance contributed most to the variance observed along the first principal component while branch-length heterogeneity and, to a lesser extent, saturation contributed most to the variance observed along the second. Missing data did not strongly contribute to either. Additional sensitivity analyses examined effects of removing taxa with heterogeneous branch lengths, large amounts of missing data, and compositional heterogeneity. Although our analyses do not unambiguously resolve lophotrochozoan phylogeny, we advance the field by reducing the list of viable hypotheses. Moreover, our systematic approach for dissection of phylogenomic data can be applied to explore sources of incongruence and poor support in any phylogenomic dataset. 

  • 6.
    Tassia, Michael
    et al.
    Auburn University.
    Cannon, Johanna
    Swedish Museum of Natural History, Department of Zoology. Auburn University.
    Konikoff, Charlotte
    University of Washington.
    Shenkar, Noa
    University of Washington.
    Halanych, Kenneth
    Auburn University.
    Swalla, Billie
    The Global Diversity of Hemichordata2016In: PLOS ONE, E-ISSN 1932-6203, Vol. 11, no 10, article id e0162564Article in journal (Refereed)
    Abstract [en]

    Phylum Hemichordata, composed of worm-like Enteropneusta and colonial Pterobranchia, has been reported to only contain about 100 species. However, recent studies of hemichordate phylogeny and taxonomy suggest the species number has been largely underestimated. One issue is that species must be described by experts, and historically few taxonomists have studied this group of marine invertebrates. Despite this previous lack of coverage, interest in hemichordates has piqued in the past couple of decades, as they are critical to understanding the evolution of chordates–as acorn worms likely resemble the deuterostome ancestor more closely than any other extant animal. This review provides an overview of our current knowledge of hemichordates, focusing specifically on their global biodiversity, geographic distribution, and taxonomy. Using information available in the World Register of Marine Species and published literature, we assembled a list of 130 described, extant species. The majority (83%) of these species are enteropneusts, and more taxonomic descriptions are forthcoming. Ptychoderidae contained the greatest number of species (41 species), closely followed by Harrimaniidae (40 species), of the recognized hemichordate families. Hemichordates are found throughout the world’s oceans, with the highest reported numbers by regions with marine labs and diligent taxonomic efforts (e.g. North Pacific and North Atlantic). Pterobranchs are abundant in Antarctica, but have also been found at lower latitudes. We consider this a baseline report and expect new species of Hemichordata will continue to be discovered and described as new marine habitats are characterized and explored.

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1 - 6 of 6
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