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Data from: Phylogenomics of Lophotrochozoa with consideration of systematic error
负责人:
关键词:
Trochozoa Spiralia Mollusca Nemertea Annelida Brachiopoda Phoronida Entoprocta Bryozoa Platyzoa
DOI:
doi:10.5061/dryad.30k4v.1
摘要:
ssed strict screening for paralogy using a tree-based approach. In order to reduce possible sources of systematic error, we calculated branch-length
Data from: Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing tra
负责人:
关键词:
Leucadendron spissifolium subsp. spissifolium;Leucadendron chamelaea;Leucadendron burchelli;Leucadendron rubrum;Leucadendron flexuosum;Leucadendron lanigerum var. laevigatum;Leucadendron dubium;Leucadendron sericeum;RNA-seq;Leucadendron brunioides var. brunioides;phylogenetic markers;Leucadendron roodii;Leucadendron elimense subsp. salteri;Leucadendron elimense subsps. alteri;Leucadendron meridianum;Proteaceae;Leucadendron sessile;Leucadendron muirii;Mimetes cucullatus;Leucadendron spissifolium subsp. fragrans;Leucadendron stellare;Leucadendron osbornei;Leucadendron dregei;Leucadendron platyspermum;Leucadendron conicum;Leucadendron discolor;Leucadendron laureolum;Leucadendron singulare;Leucadendron elimense subsp. vyeboomense;Leucadendron meyerianum;Leucadendron nervosum;Leucadendron barkerae;Leucadendron ericifolium;Leucadendron floridum;3'-UTR;Non-models groups;Leucadendron loeriense;Leucadendron microcephalum;Leucospermum erubescens;Leucadendron verticillatum;orthology;Leucadendron album;Leucadendron thymifolium;Leucadendron modestum;Leucadendron corymbosum;Paranomus spathulatus;Leucadendron nitidum;Leucadendron glaberrimum subsp. glaberrimum;Leucadendron loranthifolium
DOI:
doi:10.5061/dryad.tp5g2
摘要:
), we adopted a framework aimed at minimizing the probability of paralogy and maximizing polymorphism. We anchored when possible the right-hand primer int
Data from: Phylogenomics of Lophotrochozoa with consideration of systematic error
负责人:
关键词:
Rhyssoplax olivaceus;Lineus lacteus;Novocrania anomala;Boccardia proboscidea;Clymenella torquata;Glottidia pyramidata;Phascolosoma agassizii;saturation;Patella vulgata;Adineta vaga;Leptochiton asellus;Megadasys sp.;Spathoderma clenchi;Schistosoma mansoni;Platyzoa;Brachionus plicatilis;Loxosoma pectinaricola;Paranemertes peregrina;Phenacolepas pulchella;Taenia pisiformis;Ruditapes philippinarum;Sepioteuthis lessoniana;Macellomenia schanderi;Capitella teleta;Phoronis vancouverensis;Pomatoceros lamarckii;Alexandromenia crassa;Prochaetoderma californicum;Entalina tetragona;Symbion americanus;Spiralia;Neomenia carinata;Dosidicus gigas;Alitta virens;Tubulanus polymorphus-Halanych;Nemertea;Cephalothrix linearis;Mollusca;drosophila melanogaster;Laqueus californicus;Crassostrea gigas;Laevipilina hyalina;Macrodasys sp.;Phoronida;Aplysia californica;Mytilus edulis;Hemithiris psittacea;Bryozoa;Pectinaria gouldii;Octopus vulgaris;Brachiopoda;Compositional heterogeneity;Lineus longissimus;Gnathostomula paradoxa;Leptochiton rugatus;Graptacme eborea;Cephalothrix hongkongensis;Lottia gigantea;Nuculana pernula;Helobdella robusta;Priapulus caudatus;Daphnia pulex;Barentsia gracilis;Trochozoa;Malacobdella grossa;Enucula tenuis;Loxosomella cf. vivipara;Crepidula fornicata;Haliotis rufescens;Polyzoa;Nucella lapillus;Pedicellina cernua;Sagitta sp.;Tubulanus polymorphus-Struck;Annelida;Gadila tolmiei;Cerebratulus marginatus;Entoprocta;Villosa lienosa;Bugula neritina;Glycera dibranchiata;Lineus ruber;Sepia esculenta;Solemya velum;Long branch attraction;Schmidtea mediterranea;Pinctada fucata;Phoronis psammophila
DOI:
doi:10.5061/dryad.30k4v
摘要:
ssed strict screening for paralogy using a tree-based approach. In order to reduce possible sources of systematic error, we calculated branch-length
Data from: An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae
负责人:
关键词:
Lactuca quercina L.;Antennaria geyeri A. Gray;Picris amalecitana (Boiss.) Eig;Cousinia pusilla C. Winkl.;Compositae;Pericallis murrayi (Bornm.) B.Nord;Leontodon tingitanus Boiss. & Reut. Ball;Echinops strigosus L.;Syncarpha sp. DC.;Moquinia racemosa (Spreng.) DC.;Vernonia missurica Raf.;Sonchus radicatus Aiton;Helianthus annuus L.;Stokesia laevis (Hill) Greene;Luciliocline subspicata (Wedd.) Anderb. & S.E. Freire;Pseudognaphalium obtusifolium (L. Hilliard & B.L. Burtt);Sobral & J.N.Nakaj.;Senecio flavus L.;Senecio involucratus (Kunth) DC.;Sonchus pinnatus Aiton;Centrapalus pauciflorus (Willd.) H. Rob.;Cousinia macroptera C.A. Mey.;Minasia pereirae H.Rob.;Senecio lingulatus Franch.;Tithonia rotundifolia (Mill.) S.F.Blake;Lepidaploa opposita A.M.Teles;Lychnophora granmogolensis (Duarte) D.J.N. Hind;Lactuca palmensis Bolle;Verbesina alternifolia (L.) Britton ex Kearney;Cousinia alberto regelia C. Winkl.;J.N. Nakaj. & H. Rob.;phylogenetics.;Carlina vulgaris L.;Lychnophora brunioides Mart.;Sonchus ustulatus subsp maderensis Aldridge;Helianthus argophyllus Torr. & A. Gray;Cousinia spryginii Kult.;Chronopappus bifrons (DC.) ex Pers. DC.;Antennaria corymbosa E.E. Nelson;Pericallis webbii (Sch.Bip.) Bolle;Senecio patens (Kunth) DC.;Picris hieracioides subsp. umbellata (Schrank) Ces.;Stilpnopappus tomentosus Mart. ex DC.;Lychnophora hatschbachii H.Rob.;Allocephalus gamolepis Bringel;Lipochaeta lobata (Gaud.) DC.;Lactuca serriola L.;Oedera squarrosa (L.) Anderb. & K.Bremer;Cynara cardunculus L.;Lactuca perennis L.;Carthamus tinctorius L;Pericallis echinata (L'Hér.) B.Nord.;Facelis lasiocarpa (Griseb.) Cabrera;Chresta angustifolia Gardner;Picris japonica Thunb.;Culticum canescens;Picris hieracioides subsp. hispidissima (Bartl.) Slovák & Ku?era;Antennaria flagellaris (A. Gray) A. Gray;Vernoniastrum ambiguum (Kotschy & Peyr.) H. Rob.;non-paralogy;Hyb-Seq;Lipochaeta micrantha (Nutt.) A.Gray;Rojasianthe superba Standl. & Steyerm.;Picris hieracioides subsp. hieracioides L.;Pericallis lanata (L'Hér.) B.Nord.;Piptolepis ericoides (Lam.) Sch. Bip.;Picris olympica Boiss.;Chresta plantaginifolia (Less.) Gardner;Xenophyllum lycopodioides (S.F.Blake) V.A.Funk;Lactuca orientalis Boiss.;Picris nuristanica Bornm.;Wollastonia biflora (L.) DC.;Helianthus verticillatus Small;Vernonanthura patens (Kunth) H.Rob.;Montanoa tomentosa Cerv.;Chresta harleyi H. Rob.;Antennaria anaphaloides Rydb.;Senecio nivalis (Kunth) Cuatrec.;Pericallis papyracea (DC.) B.Nord.;Cousinia strobilocephala Tscherneva & Vved.;Werneria aretioides Wedd.;Phoebanthus tenuifolius (Torr. & A.Gray) S.F.Blake;Hieracium alpinum L.;Nabalus albus (L.) Hook.;Senecio subinvolucratus Cuatrec.;Gundelia tournefortii L.;Lactuca tatarica (L.) C. A. Mey.;Taraxacum kok-saghyz L.E. Rodin;Vernonia gigantea (Walter) Trel. ex Branner & Coville;Lipochaeta subcordata A.Gray;Helianthus porteri (A. Gray) Pruski;Brachyglottis repanda J.R. Forst & G. Forst;long branches;Sonchus tuberifer Svent.;Disparago sp. Gaertn.;Chresta pacourinoides (Mart. ex DC.) Siniscalchi & Loeuille;Pericallis aurita (L'Hér.) B.Nord.;Lychnophora santosii H.Rob.;Lychnophora haplopappa sp. ined.;Chresta curumbensis (Philipson) H.Rob.;Hololepis pedunculata DC. ex Pers. DC.;Gamochaetopsis alpina (Poepp.) Anderb. & S.E. Freire;Lychnophora morii H.Rob.;Paralychnophora harleyi (H. Rob.) D.J.N. Hind;Chresta sphaerocephala DC.;hybrid capture;Asteraceae
DOI:
doi:10.5061/dryad.60vb576
摘要:
were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, datasets of non-paralogous loci were built
Data from: The effects of model choice and mitigating bias on the ribosomal tree of life
负责人:
关键词:
Trichoplax adhaerens;Cyanophora paradoxa;Desulfurispirillum indicum;Chlamydomonas reinhardtii;Bigelowiella natans;Cenarchaeum symbiosum;Cryptosporidium muris;Zymomonas mobilis;Nitrosoarchaeum limnia;Lactobacillus fermentum;Aspergillus flavus;Oscillibacter valericigenes;Arachnula sp;Archaeoglobus fulgidus;single-matrix model;Thermoplasma acidophilum;Paenibacillus sp;Perkinsus marinus;Corynebacterium pseudotuberculosis;Natromonas pharaonis;Staphylothermus marinus;two-domain tree;Diplonema sp;Prevotella denticola;Cyanothece sp;Ribosomal tree of life;Candida albicans;Anaerolinea thermophila;Methanocaldococcus jannaschii;Phaeodactylum tricornutum;Methylacidiphilum infernorum;Methanosarcina mazei;Dictyostelium discoideum;Chlorobium limicola;Thermotoga maritima;Methanosphaera stadtmanae;Babesia bovis;Thermodesulfatator indicus;Thermovibrio ammonificans;Flamella sp;Korarchaeum cryptofilum;Syntrophus aciditrophicus;Methanobrevibacter smithii;Deinococcus deserti;Gemmatimonas aurantiaca;Dyadobacter fermentans;Methanococcus aeolicus;Tribonema sp;Toxoplasma gondii;Acetobacter pasteurianus;Methanococcoides burtonii;Leishmania major;Thalassiosira pseudonana;Aeropyrum pernix;Nitrosomonas europaea;mixture model;Thermococcus kodakarensis;Arabidopsis thaliana;Apis mellifera;Nitrosopumilis sp;Halobacterium salinarum;Acidilobus saccharovorans;Pyrobaculum aerophilium;Fibrobacter succinogenes;Acanthamoeba sp;Idiomarina loihiensis;Ciona intestinalis;Meiothermus silvanus;Thermocrinis albus;Neisseria meningitidis;Spirochaeta coccoides;Methanopyrus kandleri;Xylella fastidiosa;Bodo sp;Ignicoccus hospitalis;Physarum polycephalum;Desulfurococcus mucosus;Danio rerio;Compositional heterogeneity;Treponema brennaborense;Sulfolobus solfataricus;Hypterthermus butylicus;Picrophilus torridus;Plasmodium vivax;Denitrovibrio acetiphilus;Haloarcula marismortui;three-domain tree;Metallosphaera sedula;Phytophthora infestans;Planctomyces brasiliensis;Thermovirga lienii;Trypanosoma brucei;Dictyoglomus thermophilum;Cryptobacterium curtum;Trimastix pyriformis;Cryptococcus gattii;Dehalococcoides ethenogenes;Pyrolobus fumarii;Guillardia theta;Methanoculleus marisingri;Thermus scotoductus;Syntrophothermus lipocalidus;Coraliomargarita akajimensis;Desulfobacca acetoxidans;Nitrosospira multiformis;Heterosigma sp;Prochlorococcus marinus;Fusobacterium nucleatum;Rhodopirellula baltica;Emiliana huxleyi;Nanoarchaeum equitans;Pyrococcus horikoshii;Ostreococcus tauri;Euglena sp
DOI:
doi:10.5061/dryad.7785h
摘要:
conflicting phylogenetic signals from HGT and/or paralogy. Thus, we tested several models of varying sophistication on three different datasets, performed

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