Data from: Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies

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关键词：

maximum likelihood;reconstituted DNA;Phrynosomatidae;ddRADseq;conditional likelihood;Phrynosoma

DOI：

doi:10.5061/dryad.t9r3g

摘要：

nt sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy

Data from: The effects of model choice and mitigating bias on the ribosomal tree of life

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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：

r effects on the topological outcome. Our results support a two-domain topology for the tree of life, where Eukarya emerges from within Archaea as sister

Data from: Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial

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关键词：

Placentalia;Bayesian phylogenetics;Zaedyus;evolutionary dynamics;Tertiary;Chaetophractus;Euphractus;Tamandua;Dasypus;Tolypeutes;Mammalia;Armadillos;Priodontes;Xenarthra;Choloepus;Cyclopes;Myrmecophaga;molecular systematics;maximum likelihood;Bradypus;Cenozoic;Cabassous;Mitochondrial and nuclear markers

DOI：

doi:10.5061/dryad.1838

摘要：

Tolypeutinae and Euphractinae. Owing to a greater number of informative sites, the overall concatenation favored the mitochondrial topology

Data from: Analysis of a rapid evolutionary radiation using ultraconserved elements (UCEs): Evidence for a bias in some multi-species coal

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关键词：

Total Evidence;polytomy;Triplec;supermatrix rooted triplets;Galliformes;Phasianidae;gene tree estimation error;supermatrix rooted triples

DOI：

doi:10.5061/dryad.p1m52

摘要：

- Maximum Likelihood (SMRT-ML), a concatenation method that is consistent even when gene trees exhibit topological differences due to the multispecies coal