summary.csv

,name,Total_matrix_cells,Undetermined_characters,Missing_percent,No_variable_sites,Proportion_variable_sites,Parsimony_informative_sites,Proportion_parsimony_informative,AT_content,GC_content,dataset.DOI,dataset.alignment.datatype,dataset.alignment.nchar,dataset.alignment.ntax,dataset.alignment.partitions,dataset.genomes.bacterial,dataset.genomes.chloroplast,dataset.genomes.dsDNA,dataset.genomes.dsRNA,dataset.genomes.mitochondrial,dataset.genomes.nuclear,dataset.genomes.ssDNA,dataset.genomes.ssRNA,dataset.license,dataset.notes,dataset.study clade.english,dataset.study clade.latin,dataset.study clade.taxon ID,dataset.study root age,dataset.timetree root age,dataset.used for tree inference,study.DOI,study.reference,study.year
0,Varga_2019,30314308,23594271,77.832,4236,0.738,3186,0.555,0.506,0.494,dx.doi.org/10.5061/dryad.gc2k9r9,nucleotide,5737,5285,3,False,False,False,False,False,True,False,False,CC0,"This is the dataset with excluded sites removed. The alignment file is ""5284taxa_ML_alignment_exclude.txt"" from this download https://datadryad.org/bitstream/handle/10255/dryad.203726/Varga_2019_NEE_5284taxa_MaximumLikelihood_analysis.zip?sequence=1. Illegal nexus characters in the alignment (e.g. '/') were replaced with underscores. It was not possible to identify all outgroup species from the published manuscript.",Mushrooms,Basidiomycota,5204,NA,NA,True,dx.doi.org/10.1038/s41559-019-0834-1,"Varga, T., Krizsán, K., Földi, C., Dima, B., Sánchez-García, M., Sánchez-Ramírez, S., et al. (2019). Megaphylogeny resolves global patterns of mushroom evolution. Nature Ecology and Evolution.",2019
1,Wu_2018_dna,823553730,127939673,15.535,6715135,0.7340000000000001,5359146,0.586,0.508,0.49200000000000005,dx.doi.org/10.6084/m9.figshare.6031190.v2,nucleotide,9150597,90,15486,False,False,False,False,False,True,False,False,CCBY,"This is the cds_5162.zip dataset, loci were in frame and codon positions were annotated as such.",mammals,mammalia,40674,NA,177 mya,False,dx.doi.org/10.1016/j.dib.2018.04.094,"Wu, S., Edwards, S., & Liu, L. (2018). Genome-scale DNA sequence data and the evolutionary history of placental mammals. Data in brief, 18, 1972-1975.",2018
2,Wainwright_2012,1586532,171228,10.793,4468,0.529,3805,0.451,0.45399999999999996,0.546,dx.doi.org/10.5061/dryad.5h951h04,nucleotide,8439,188,30,False,False,False,False,False,True,False,False,CC0,NA,Acanthomorph fishes,Acanthomorpha,123368,NA,144.4 mya,True,dx.doi.org/10.1093/sysbio/sys060,"Wainwright PC, Smith WL, Price SA, Tang KL, Sparks JS, Ferry LA, Kuhn KL, Eytan RI, Near TJ. The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond. Systematic Biology. 2012 Dec 1;61(6):1001-27.",2012
3,Branstetter_2017,34360689,7137124,20.771,145271,0.7909999999999999,129078,0.7020000000000001,0.5379999999999999,0.462,dx.doi.org/10.5061/dryad.r8d4q,nucleotide,183747,187,807,False,False,False,False,False,True,False,False,CC0,"This is the dataset Hym-187T-F75, which is the dataset used for the main figure in the paper. One of many datasets available from the link under ""Alignment supermatrices"" on Dryad.",Stinging wasps,Aculeata,7434,170 mya,169 mya,True,dx.doi.org/10.1016/j.cub.2017.03.027,"Branstetter MG, Danforth BN, Pitts JP, Faircloth BC, Ward PS, Buffington ML, Gates MW, Kula RR, Brady SG (2017) Phylogenomic Insights into the Evolution of Stinging Wasps and the Origins of Ants and Bees. Current Biology 27(7): 1019-1025.",2017
4,Seago_2011,218541,52235,23.901999999999997,1313,0.583,1115,0.495,0.607,0.39299999999999996,dx.doi.org/10.5061/dryad.dc1r2,nucleotide,2253,97,7,False,False,False,False,True,True,False,False,CC0,alignment was edited to remove morphological data and taxa with no nucleotide data. Reduced taxa from 116 to 97,ladybirds,Coccinellidae,7080,NA,NA,True,dx.doi.org/10.1016/j.ympev.2011.03.015,"Seago AE, Giorgi JA, Li J, Ślipiński A. Phylogeny, classification and evolution of ladybird beetles (Coleoptera: Coccinellidae) based on simultaneous analysis of molecular and morphological data. Molecular Phylogenetics and Evolution. 2011 Jul 31;60(1):137-51.",2011
5,Fong_2012,2851090,1594272,55.918,12133,0.46799999999999997,9712,0.375,0.532,0.46799999999999997,dx.doi.org/10.5061/dryad.25j6h,nucleotide,25919,110,168,False,False,False,False,False,True,False,False,CC0,This is the SlowGenes dataset from Dryad,vertebrates,Vertebrata,7742,NA,NA,True,dx.doi.org/10.1371/journal.pone.0048990,"Fong JJ, Brown JM, Fujita MK, Boussau B. A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia. PLoS One. 2012 Nov 7;7(11):e48990.",2012
6,McCormack_2013,17804358,3232508,18.156,88014,0.163,24703,0.046,0.63,0.37,dx.doi.org/10.5061/dryad.sd080,nucleotide,539526,33,1541,False,False,False,False,False,True,False,False,CC0,Thanks to Brant Faircloth for providing additional data on the locations of the UCEs,birds,Neoaves,8782,NA,82.8 mya,True,dx.doi.org/10.1371/journal.pone.0054848,"McCormack JE, Harvey MG, Faircloth BC, Crawford NG, Glenn TC, Brumfield RT. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS One. 2013 Jan 29;8(1):e54848.",2013
7,Irisarri_2017,196443900,62866306,32.001999999999995,1285039,0.654,1069208,0.544,,,dx.doi.org/10.5061/dryad.r2n70,protein,1964439,100,4593,False,False,False,False,False,True,False,False,CC0,"This is the 0DP-4593_single_genes dataset, which was used to create the main figure in the paper. Charsets are named according to the original files, but with non-alphanumeric characters removed.",Jawed vertebrates,Gnathostomata,7776,458 mya,473 mya,True,dx.doi.org/10.1038/s41559-017-0240-5,"Irisarri I, Baurain D, Brinkmann H, Delsuc F, Sire J, Kupfer A, Petersen J, Jarek M, Meyer A, Vences M, Philippe H (2017) Phylotranscriptomic consolidation of the jawed vertebrate timetree. Nature Ecology & Evolution 1(9): 1370-1378. https://doi.org/10.1038/s41559-017-0240-5",2017
8,Chen_2015,104750030,22063606,21.063000000000002,1195041,0.662,876162,0.485,,,dx.doi.org/10.5061/dryad.47v40,protein,1806035,58,4682,False,False,False,False,False,True,False,False,CC0,"This is the dataset named ""total_evidence_4682gene_Pro.nex"" from the repository. The original paper filtered this data in many interesting ways.",Jawed vertebrates,Gnathostomata,7776,NA,473 mya,True,dx.doi.org/10.1093/sysbio/syv059,"Chen MY, Liang D, Zhang P (2015) Selecting question-specific genes to reduce incongruence in phylogenomics: a case study of jawed vertebrate backbone phylogeny. Systematic Biology 64(6): 1104-1120.",2015
9,Murray_2013,737307,281539,38.185,1183,0.38,948,0.305,0.555,0.445,dx.doi.org/10.5061/dryad.qn57t,nucleotide,3111,237,9,False,False,False,False,True,True,False,False,CC0,NA,eucharitid wasps,Eucharitidae,216140,NA,NA,True,dx.doi.org/10.1098/rspb.2013.0495,"Murray EA, Carmichael AE, Heraty JM. Ancient host shifts followed by host conservatism in a group of ant parasitoids. Proceedings of the Royal Society of London B: Biological Sciences. 2013 May 22;280(1759):20130495.",2013
10,Unmack_2013,948953,115678,12.19,3607,0.528,3185,0.467,0.54,0.46,dx.doi.org/10.5061/dryad.qq846,nucleotide,6827,139,25,False,False,False,False,True,True,False,False,CC0,NA,rainbowfish,Melanotaeniidae,30700,75 mya,NA,True,dx.doi.org/10.1016/j.ympev.2012.12.019,"Unmack PJ, Allen GR, Johnson JB. Phylogeny and biogeography of rainbowfishes (Melanotaeniidae) from Australia and New Guinea. Molecular Phylogenetics and Evolution. 2013 Apr 30;67(1):15-27.",2013
11,Wood_2012,191845,84470,44.03,2690,0.519,1792,0.34600000000000003,0.426,0.574,dx.doi.org/10.5061/dryad.7231d,nucleotide,5185,37,8,False,False,False,False,True,True,False,False,CC0,"I removed the morphological data and adjusted the partition definitions accordingly. The original file contained two partitions for 28S, but nothing in the dryad package or the manuscript explained what these were. As a result, I joined these two partitions together here.",pelican spiders,Archaeidae,336678,276.5 mya,NA,True,dx.doi.org/10.1093/sysbio/sys092,"Wood HM, Matzke NJ, Gillespie RG, Griswold CE. Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders. Systematic Biology. 2012 Nov 28:sys092.",2012
12,Day_2013,545072,99875,18.323,1343,0.375,999,0.27899999999999997,0.53,0.47,dx.doi.org/10.5061/dryad.b6225,nucleotide,3586,152,11,False,False,False,False,True,True,False,False,CC0,NA,African catfish,Synodontis,42509,NA,18.5 mya,True,dx.doi.org/10.1093/sysbio/syt001,"Day JJ, Peart CR, Brown KJ, Friel JP, Bills R, Moritz T. Continental diversification of an African catfish radiation (Mochokidae: Synodontis). Systematic biology. 2013 Jan 9:syt001.",2013
13,Reddy_2017,32271140,24383025,75.557,56001,0.408,43010,0.313,0.5529999999999999,0.447,dx.doi.org/10.5061/dryad.6536v,nucleotide,137324,235,88,False,False,False,False,False,False,False,False,CC0,"this is the dataset Reddy_sup_fileS5_EB2taxset.nex, which was used to produce figure 3 in the paper from this link https://datadryad.org/bitstream/handle/10255/dryad.141055/Reddy_sup_fileS5_alignments.tar.gz?sequence=1. The charsets in this repository are the main charsets derived from that file (88 in total).",Birds,Aves,8782,NA,111 mya,True,dx.doi.org/10.1093/sysbio/syx041,"Reddy S, Kimball RT, Pandey A, Hosner PA, Braun MJ, Hackett SJ, Han K, Harshman J, Huddleston CJ, Kingston S, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Witt CC, Yuri T, Braun EL (2017) Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling. Systematic Biology 66(5): 857-879.",2017
14,Kawahara_2013,156660,16718,10.672,771,0.345,567,0.253,0.614,0.386,dx.doi.org/10.5061/dryad.gh895,nucleotide,2238,70,9,False,False,False,False,True,True,False,False,CC0,Species names can be resolved using the supp info of the paper itself,Hawaiian fancy cased caterpillars,Hyposmocoma,545366,NA,NA,True,dx.doi.org/10.1111/jeb.12176,"Kawahara AY, Rubinoff D. Convergent evolution of morphology and habitat use in the explosive Hawaiian fancy case caterpillar radiation. Journal of evolutionary biology. 2013 Aug 1;26(8):1763-73.",2013
15,Bergsten_2013,80218,1555,1.9380000000000002,553,0.262,443,0.21,0.606,0.39399999999999996,dx.doi.org/10.5061/dryad.s631d,nucleotide,2111,38,8,False,False,False,False,True,True,False,False,CC0,NA,diving beetles,Dytiscidae,50515,NA,NA,True,dx.doi.org/10.1093/sysbio/syt029,"Bergsten J, Nilsson AN, Ronquist F. Bayesian tests of topology hypotheses with an example from diving beetles. Systematic biology. 2013 Sep 1;62(5):660-73.",2013
16,Whelan_2017,3753488,1982113,52.806999999999995,42240,0.855,35590,0.721,,,dx.doi.org/10.6084/m9.figshare.4484138.v1,protein,49388,76,127,False,False,False,False,False,True,False,False,CCBY,"No study root age is given, becuase the root of the ingroup was used as a calibration. Thanks to Nathan V Whelan for confirming the gene boundaries in the dataset.",Animals,Metazoa,33208,NA,NA,True,dx.doi.org/10.1038/s41559-017-0381-6,"Whelan, N.V., Kocot, K.M., Moroz, T.P., Mukherjee, K., Williams, P., Paulay, G., Moroz, L.L. and Halanych, K.M., 2017. Ctenophore relationships and their placement as the sister group to all other animals. Nature ecology & evolution, 1(11), p.1737.",2017
17,Ran_2018_dna,49249596,1063459,2.1590000000000003,881125,0.68,777882,0.6,0.557,0.44299999999999995,dx.doi.org/10.5061/dryad.f7f57,nucleotide,1296042,38,3924,False,False,False,False,False,True,False,False,CC0,"This is the codon dataset described in the paper, that contains all three codon positions, in frame for each locus",Seed Plants,Spermatophyta,58024,377 mya,313 mya,True,dx.doi.org/10.1098/rspb.2018.1012,"Ran J-H, Shen T-T, Wang M-M, Wang X-Q (2018) Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms. Proceedings of the Royal Society B 285(1881): 20181012.",2018
18,Shen_2018,398842115,59645433,14.955,1084538,0.9329999999999999,1049263,0.902,,,dx.doi.org/10.6084/m9.figshare.5854692,protein,1162805,343,2407,False,False,False,False,False,True,False,False,CCBY,"This alignment is that used to infer the tree in Figure 1, which is named '343_2408OGs.fasta' in the FigShare repository",budding yeasts,Saccharomycotina,147537,404 mya,NA,True,dx.doi.org/10.1016/j.cell.2018.10.023,"Shen, X. X., Opulente, D. A., Kominek, J., Zhou, X., Steenwyk, J. L., Buh, K. V., ... & Boudouris, J. T. (2018). Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum. Cell, 175(6), 1533-1545.",2018
19,Smith_2014,6606432,879391,13.311,4489,0.005,1669,0.002,0.6,0.4,dx.doi.org/10.5061/dryad.qm4j1.3,nucleotide,825804,8,1366,False,False,False,False,False,True,False,False,CC0,"This is one of the five within-species datasets collected for the above study, and comprises the UCEs from that study. In the original study the data were analysed with species-tree methods, and not concatenated.",Plain xenops,Xenops minutus,255386,2.75 mya,NA,True,dx.doi.org/10.1093/sysbio/syt061,"Smith BT, Harvey MG, Faircloth BC, Glenn TC, Brumfield RT (2013) Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales. Systematic Biology 63(1): 83-95.",2013
20,Broughton_2013,1219817,501485,41.111000000000004,12159,0.608,10492,0.525,0.474,0.526,dx.doi.org/10.5061/dryad.f1t15,nucleotide,19997,61,61,False,False,False,False,True,True,False,False,CC0,NA,bony fishes,Osteichthyes,117571,427 mya,436.8 mya,True,dx.doi.org/10.1371/currents.tol.2ca8041495ffafd0c92756e75247483e,"Broughton RE, Betancur RR, Li C, Arratia G, Ortí G. Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution. PLoS Curr. 2013 Apr 16;5(5).",2013
21,Nguyen_2016b,21080,1116,5.294,233,0.34299999999999997,181,0.266,,,dx.doi.org/10.5061/dryad.8vj6j,protein,680,31,1,False,False,False,False,False,True,False,False,CC0,"This is the hsc70-4 dataset from the repository. Root ages are not determined because these are trees of duplicated genes, not just taxa.","sawflies, wasps, bees, and ants",Hymenoptera,7399,NA,NA,True,dx.doi.org/10.1186/s12862-015-0573-0,"Nguyen AD, Gotelli NJ, Helms Cahan S (2016) The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera. BMC Evolutionary Biology 16: 15.",2016
22,Nguyen_2016e,6545,732,11.184000000000001,213,0.5529999999999999,133,0.345,,,dx.doi.org/10.5061/dryad.8vj6j,protein,385,17,1,False,False,False,False,False,True,False,False,CC0,"This is the hsp40 dataset from the repository. Root ages are not determined because these are trees of duplicated genes, not just taxa.","sawflies, wasps, bees, and ants",Hymenoptera,7399,NA,NA,True,dx.doi.org/10.1186/s12862-015-0573-0,"Nguyen AD, Gotelli NJ, Helms Cahan S (2016) The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera. BMC Evolutionary Biology 16: 15.",2016
23,Worobey_2014h,800280,27,0.003,1390,0.61,1250,0.5479999999999999,0.56,0.44,dx.doi.org/10.5061/dryad.m04j9,nucleotide,2280,351,3,False,False,False,False,False,False,False,True,CC0,"This is the PB2 gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details.",Influenza A virus,Influenzavirus A,197911,0.000393 mya,NA,True,dx.doi.org/10.1038/nature13016,"Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257.",2014
24,Worobey_2014a,250536,4688,1.871,959,0.5589999999999999,824,0.48,0.573,0.42700000000000005,dx.doi.org/10.5061/dryad.m04j9,nucleotide,1716,146,3,False,False,False,False,False,False,False,True,CC0,"This is the H7 gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details.",Influenza A virus,Influenzavirus A,197911,0.000156 mya,NA,True,dx.doi.org/10.1038/nature13016,"Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257.",2014
25,Worobey_2014f,714132,54,0.008,1248,0.58,1124,0.523,0.5670000000000001,0.433,dx.doi.org/10.5061/dryad.m04j9,nucleotide,2151,332,3,False,False,False,False,False,False,False,True,CC0,"This is the PA1/2 gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details.",Influenza A virus,Influenzavirus A,197911,0.000403 mya,NA,True,dx.doi.org/10.1038/nature13016,"Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257.",2014
26,Siler_2013,164517,53816,32.711999999999996,792,0.294,665,0.247,0.593,0.40700000000000003,dx.doi.org/10.5061/dryad.cp6gg,nucleotide,2697,61,7,False,False,False,False,True,True,False,False,CC0,NA,wolf snakes,Lycodon,39095,NA,40.2 mya,True,dx.doi.org/10.1111/zsc.12007,"Siler CD, Oliveros CH, Santanen A, Brown RM. Multilocus phylogeny reveals unexpected diversification patterns in Asian wolf snakes (genus Lycodon). Zoologica Scripta. 2013 May 1;42(3):262-77.",2013
27,Misof_2014,85684752,30989469,36.167,525304,0.883,453730,0.763,,,dx.doi.org/10.5061/dryad.3c0f1,protein,595033,144,2868,False,False,False,False,False,True,False,False,CC0,"This is the largest dataset in the supplementary files, specifically, it is supermatrix A in supplementary archive 8. The partitions are from the file supermatrix_A.domains_partitions",insects,Insecta,50557,479 mya,495.1 mya,True,dx.doi.org/10.1126/science.1257570,"Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, Frandsen PB, Ware J, Flouri T, Beutel RG, Niehuis O. Phylogenomics resolves the timing and pattern of insect evolution. Science. 2014 Nov 7;346(6210):763-7.",2014
28,Cannon_2016_dna,7003776,2177442,31.09,61944,0.69,47729,0.532,0.575,0.425,dx.doi.org/10.5061/dryad.493b7,nucleotide,89792,78,424,False,False,False,False,False,True,False,False,CC0,"This dataset (78 taxa, 212 loci) is referred to as the 'primary' dataset in the ms, and forms the basis of Figure 2 in the ms. This is the nucleotide dataset (212_78_MB_nuc.nex) taken from the 'supplementary mrbayes files' link in the Dryad repository (http://datadryad.org/bitstream/handle/10255/dryad.107232/supplementarymrbayesfiles.zip?sequence=1). CHARSETS were added according to the CHARSETS from the protein version of this dataset, which is stored in this repository as Cannon_2016b.",Animals,Metazoa,33208,NA,952 mya,True,dx.doi.org/10.1038/nature16520,"Cannon JT, Vellutini BC, Smith J, Ronquist F, Jondelius U, Hejnol A (2016) Xenacoelomorpha is the sister group to Nephrozoa. Nature 530(7588): 89–93. http://dx.doi.org/10.1038/nature16520",2016
29,Cognato_2001,83468,8996,10.777999999999999,758,0.4,648,0.342,0.6609999999999999,0.33899999999999997,dx.doi.org/10.5061/dryad.678,nucleotide,1897,44,7,False,False,False,False,True,True,False,False,CC0,Morphological characters were removed from the alignment,Bark beetles,Coleoptera: Scolytinae,55867,NA,NA,True,dx.doi.org/10.1080/106351501753462803,"Cognato AI, Vogler AP. Exploring data interaction and nucleotide alignment in a multiple gene analysis of Ips (Coleoptera: Scolytinae). Systematic Biology. 2001 Nov 1;50(6):758-80.",2001
30,Looney_2016,4598517,3639215,79.139,1967,0.501,1617,0.41200000000000003,0.51,0.49,dx.doi.org/10.5061/dryad.gn4p4,nucleotide,3927,1171,4,False,True,False,False,False,True,False,False,CC0,"There is some uncertainty about the outgroups in this dataset. The paper lists them as ""Lactifluus deceptivus, Lactarius lignyotus and Multifurca zonaria"", but the first outgroup does not exist in the alignment - it seems to be listed as ""Lactarius deceptivus"".",Russula,Russula,5402,44 mya,NA,True,dx.doi.org/10.1111/mec.13506,"Looney BP, Ryberg M, Hampe F, Sánchez-García M, Matheny PB (2016) Into and out of the tropics: global diversification patterns in a hyper-diverse clade of ectomycorrhizal fungi. Molecular Ecology 25(2): 630–647.",2016
31,Horn_2014,2282639,343789,15.061,5177,0.447,3525,0.304,0.593,0.40700000000000003,dx.doi.org/10.5061/dryad.sb1j1,nucleotide,11587,197,28,False,True,False,False,True,True,False,False,CC0,NA,spurge,Euphorbia,3990,47.8 mya,61.8 mya,True,dx.doi.org/10.1111/evo.12534,"Horn JW, Xi Z, Riina R, Peirson JA, Yang Y, Dorsey BL, Berry PE, Davis CC, Wurdack KJ (2014) Evolutionary bursts in Euphorbia (Euphorbiaceae) are linked with photosynthetic pathway. Evolution 68(12): 3485-3504.",2014
32,Worobey_2014g,741324,13,0.002,1210,0.532,1096,0.48200000000000004,0.573,0.42700000000000005,dx.doi.org/10.5061/dryad.m04j9,nucleotide,2274,326,3,False,False,False,False,False,False,False,True,CC0,"This is the PB1 gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details.",Influenza A virus,Influenzavirus A,197911,0.000289 mya,NA,True,dx.doi.org/10.1038/nature13016,"Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257.",2014
33,Nguyen_2016d,11968,606,5.064,331,0.47,165,0.23399999999999999,,,dx.doi.org/10.5061/dryad.8vj6j,protein,704,17,1,False,False,False,False,False,True,False,False,CC0,"This is the hsc70-5 dataset from the repository. Root ages are not determined because these are trees of duplicated genes, not just taxa.","sawflies, wasps, bees, and ants",Hymenoptera,7399,NA,NA,True,dx.doi.org/10.1186/s12862-015-0573-0,"Nguyen AD, Gotelli NJ, Helms Cahan S (2016) The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera. BMC Evolutionary Biology 16: 15.",2016
34,Wu_2018_aa,274517910,42704015,15.556,2203490,0.722,1474177,0.483,,,dx.doi.org/10.6084/m9.figshare.6031190.v2,protein,3050199,90,5162,False,False,False,False,False,True,False,False,CCBY,This is the cds_5162.zip dataset. The amino acid dataset was produced by translating each locus.,mammals,mammalia,40674,NA,177 mya,False,dx.doi.org/10.1016/j.dib.2018.04.094,"Wu, S., Edwards, S., & Liu, L. (2018). Genome-scale DNA sequence data and the evolutionary history of placental mammals. Data in brief, 18, 1972-1975.",2018
35,Meiklejohn_2016,11054862,908973,8.222000000000001,44898,0.073,12149,0.02,0.574,0.426,dx.doi.org/10.5061/dryad.p1m52,nucleotide,614159,18,1501,False,False,False,False,True,True,False,False,CC0,Thanks to Brant Faircloth for providing additional data,Gallopheasants,Phasianidae,9005,NA,48.2 mya,True,dx.doi.org/10.1093/sysbio/syw014,"Meiklejohn, K. A., Faircloth, B. C., Glenn, T. C., Kimball, R. T., & Braun, E. L. (2016). Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods. Systematic biology, syw014.",2016
36,Nguyen_2016c,20275,2284,11.265,296,0.365,217,0.268,,,dx.doi.org/10.5061/dryad.8vj6j,protein,811,25,1,False,False,False,False,False,True,False,False,CC0,"This is the hsp83 dataset from the repository. Root ages are not determined because these are trees of duplicated genes, not just taxa.","sawflies, wasps, bees, and ants",Hymenoptera,7399,NA,NA,True,dx.doi.org/10.1186/s12862-015-0573-0,"Nguyen AD, Gotelli NJ, Helms Cahan S (2016) The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera. BMC Evolutionary Biology 16: 15.",2016
37,Jarvis_2015,234990132,39109330,16.643,2000240,0.44299999999999995,1124066,0.249,,,dx.doi.org/10.5524/101041,protein,4519041,52,8295,False,False,False,False,False,True,False,False,CC0,"This dataset is 8295 exons in amino acids from this download 'ftp://parrot.genomics.cn/gigadb/pub/10.5524/101001_102000/101041/FASTA_files_of_loci_datasets.tar.gz' and is in the following path '8295_Amino_Acids/pep-filtered-sate-alignments-original.zip'. The study root age comes from the study paired with this dataset, published in science. This study may also be worth citing when using this dataset dx.doi.org/10.1126/science.1253451",birds,Aves,8782,102 mya,111 mya,True,dx.doi.org/10.1186/s13742-014-0038-1,"Erich D Jarvis, Siavash Mirarab, Andre J Aberer, Bo Li, Peter Houde, Cai Li, Simon Y W Ho, Brant C Faircloth, Benoit Nabholz, Jason T Howard, Alexander Suh, Claudia C Weber, Rute R da Fonseca, Alonzo Alfaro-Núñez, Nitish Narula, Liang Liu, Dave Burt, Hans Ellegren, Scott V Edwards, Alexandros Stamatakis, David P Mindell, Joel Cracraft, Edward L Braun, Tandy Warnow, Wang Jun, M Thomas Pius Gilbert, Guojie Zhang, The Avian Phylogenomics Consortium, Phylogenomic analyses data of the avian phylogenomics project, GigaScience, Volume 4, Issue 1, December 2015, s13742–014–0038–1",2015
38,Brown_2012,68265,7519,11.014000000000001,1028,0.617,891,0.535,0.5710000000000001,0.429,dx.doi.org/10.5061/dryad.7bn0fr99,nucleotide,1665,41,7,False,False,False,False,True,True,False,False,CC0,NA,Asian geckos,Ptychozoon,1118401,NA,84.7 mya,True,dx.doi.org/10.1016/j.ympev.2012.02.019,"Brown RM, Siler CD, Das I, Min Y. Testing the phylogenetic affinities of Southeast Asia’s rarest geckos: Flap-legged geckos (Luperosaurus), Flying geckos (Ptychozoon) and their relationship to the pan-Asian genus Gekko. Molecular phylogenetics and evolution. 2012 Jun 30;63(3):915-21.",2012
39,Pyron_2011,36508864,29152570,79.851,9018,0.7090000000000001,7856,0.618,0.569,0.431,dx.doi.org/10.5061/dryad.vd0m7,nucleotide,12712,2872,34,False,False,False,False,True,True,False,False,CC0,NA,amphibians,Amphibia,8292,NA,321.1 mya,True,dx.doi.org/10.1016/j.ympev.2011.06.012,"Pyron RA, Wiens JJ. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Molecular Phylogenetics and Evolution. 2011 Nov 30;61(2):543-83.",2011
40,Tolley_2013,1025962,237339,23.133000000000003,3846,0.7609999999999999,3358,0.664,0.5770000000000001,0.423,dx.doi.org/10.5061/dryad.11350,nucleotide,5054,203,16,False,False,False,False,True,True,False,False,CC0,NA,chameleons,Chamaeleonidae,40248,65 mya,56.7 mya,True,dx.doi.org/10.1098/rspb.2013.0184,"Tolley KA, Townsend TM, Vences M. Large-scale phylogeny of chameleons suggests African origins and Eocene diversification. Proceedings of the Royal Society of London B: Biological Sciences. 2013 May 22;280(1759):20130184.",2013
41,Borowiec_2015,13859316,3347123,24.151,351953,0.914,302196,0.785,,,dx.doi.org/10.5061/dryad.k6tq2,protein,384981,36,1080,False,False,False,False,False,True,False,False,CC0,The timetree root age is for Porifera vs. other deuterostomes.,metazoans,Metazoa,33208,NA,936.0 mya,True,dx.doi.org/10.1186/s12864-015-2146-4,"Borowiec, M. L., Lee, E. K., Chiu, J. C., & Plachetzki, D. C. (2015). Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa. BMC genomics, 16(1), 1.",2015
42,Lartillot_2012,1179126,212861,18.052,10561,0.6990000000000001,9047,0.598,0.49200000000000005,0.508,dx.doi.org/10.5061/dryad.tt28qk6f,nucleotide,15117,78,51,False,False,False,False,False,True,False,False,CC0,NA,placental mammals,Eutheria,9347,100 mya,105 mya,True,dx.doi.org/10.1111/j.1558-5646.2011.01558.x,"Lartillot N, Delsuc F. Joint reconstruction of divergence times and life‐history evolution in placental mammals using a phylogenetic covariance model. Evolution. 2012 Jun 1;66(6):1773-87.",2012
43,Moyle_2016,39768232,2592269,6.518,139441,0.37200000000000005,78546,0.209,0.6,0.4,dx.doi.org/10.5061/dryad.nf01p,nucleotide,375172,106,515,False,False,False,False,False,True,False,False,CC0,additional information on UCE boundaries was kindly provided by Rob Moyle,songbirds,Oscines,6615,32 mya,53.8 mya,True,dx.doi.org/10.1038/ncomms12709,"Moyle RG, Oliveros CH, Andersen MJ, Hosner PA, Benz BW, Manthey JD, Travers SL, Brown RM, Faircloth BC. Tectonic collision and uplift of Wallacea triggered the global songbird radiation. Nature Communications. 2016 Aug 30;7.",2016
44,Sauquet_2011,277644,97101,34.973,1497,0.275,840,0.154,0.589,0.41100000000000003,dx.doi.org/10.5061/dryad.qq106tm4,nucleotide,5444,51,10,False,True,False,False,False,True,False,False,CC0,NA,southern beeches,Nothofagus,26779,72 mya,79 mya,True,dx.doi.org/10.1093/sysbio/syr116,"Sauquet H, Ho SY, Gandolfo MA, Jordan GJ, Wilf P, Cantrill DJ, Bayly MJ, Bromham L, Brown GK, Carpenter RJ, Lee DM. Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales). Systematic Biology. 2012 Mar 1;61(2):289-313.",2012
45,Ballesteros_2019,78662918,43706563,55.562,1153004,0.777,895536,0.603,,,dx.doi.org/10.5061/dryad.2g1f4n5,protein,1484206,53,3534,False,False,False,False,False,True,False,False,CC0,NA,"Sea spiders, arachnids, and others",Chelicerata,6843,NA,530 mya,True,dx.doi.org/10.1093/sysbio/syz011,"Ballesteros JA, Sharma PP (2019) A critical appraisal of the placement of Xiphosura (Chelicerata) with account of known sources of phylogenetic error. Systematic Biology, online in advance of print.",2019
46,Ran_2018_aa,16416532,355136,2.1630000000000003,281961,0.653,228338,0.529,,,dx.doi.org/10.5061/dryad.f7f57,protein,432014,38,1308,False,False,False,False,False,True,False,False,CC0,This is the amino acid dataset described in the paper. It was generated by translating the codon dataset in this repository Ran_2018_dna,Seed Plants,Spermatophyta,58024,377 mya,313 mya,True,dx.doi.org/10.1098/rspb.2018.1012,"Ran J-H, Shen T-T, Wang M-M, Wang X-Q (2018) Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms. Proceedings of the Royal Society B 285(1881): 20181012.",2018
47,Crawford_2012,4652410,474908,10.208,86887,0.187,27844,0.06,0.618,0.382,dx.doi.org/10.5061/dryad.75nv22qj,nucleotide,465241,10,1145,False,False,False,False,False,True,False,False,CC0,NA,Diapsids,Sauria,32561,NA,277.8 mya,True,dx.doi.org/10.1098/rsbl.2012.0331,"Crawford, N. G., Faircloth, B. C., McCormack, J. E., Brumfield, R. T., Winker, K., & Glenn, T. C. (2012). More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biology Letters, 8(5), 783-786.",2012
48,Anderson_2013,440365,258529,58.708,1077,0.355,643,0.212,0.6829999999999999,0.317,dx.doi.org/10.5061/dryad.93s3n,nucleotide,3037,145,4,False,False,False,False,True,False,False,False,CC0,NA,pencil squids,Loliginidae,6615,NA,NA,True,dx.doi.org/10.1007/s10750-013-1599-1,"Anderson FE, Bergman A, Cheng SH, Pankey MS, Valinassab T. Lights out: the evolution of bacterial bioluminescence in Loliginidae. Hydrobiologia. 2014 Mar 1;725(1):189-203.",2014
49,Devitt_2013,56787,77,0.136,103,0.125,65,0.079,0.662,0.33799999999999997,dx.doi.org/10.5061/dryad.k9g50,nucleotide,823,69,4,False,False,False,False,True,False,False,False,CC0,NA,Large-blotched Ensatina salamander,Ensatina eschscholtzii klauberi,58674,NA,NA,True,dx.doi.org/10.1111/mec.12196,"Devitt TJ, Devitt SE, Hollingsworth BD, McGuire JA, Moritz C. Montane refugia predict population genetic structure in the Large‐blotched Ensatina salamander. Molecular ecology. 2013 Mar 1;22(6):1650-65.",2013
50,Faircloth_2013,4032882,1501649,37.235,57607,0.386,29564,0.198,0.5579999999999999,0.442,dx.doi.org/10.5061/dryad.j015n,nucleotide,149366,27,491,False,False,False,False,False,True,False,False,CC0,"The individual UCEs in the file ""fish-nexus-files-with-gaps-from-uce-alignment.tar.gz"" were concatenated into a single .nex file",Ray-finned fishes,Actinopterygii,7898,NA,386.7 mya,True,dx.doi.org/10.1371/journal.pone.0065923,"Faircloth BC, Sorenson L, Santini F, Alfaro ME (2013) A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS ONE 8(6): e65923",2013
51,Prebus_2017,78079050,5800673,7.428999999999999,702480,0.45,404463,0.259,0.562,0.43799999999999994,dx.doi.org/10.5061/dryad.b464m,nucleotide,1561581,50,2098,False,False,False,False,False,True,False,False,CC0,This is the tmno_50t_min90 dataset from Dryad. The UCE positions were inferred from the rcluster_50t_min90_part.txt file.,Acorn ants,Temnothorax,300110,35 mya,NA,True,dx.doi.org/10.1186/s12862-017-1095-8,"Prebus M (2017) Insights into the evolution, biogeography and natural history of the acorn ants, genus Temnothorax Mayr (hymenoptera: Formicidae). BMC Evolutionary Biology 17: 250. https://doi.org/10.1186/s12862-017-1095-8",2017
52,Oaks_2011,575278,36778,6.393,2366,0.325,2184,0.3,0.523,0.47700000000000004,dx.doi.org/10.5061/dryad.5k9s0,nucleotide,7282,79,50,False,False,False,False,True,True,False,False,CC0,"The original dataset specified each exon for each of the nuclear coding genes. But many of these exons are very short, making it impractical to divide them up into codon positions, so I made the pragmatic decision to lump exons together.",Crocodilians,Crocodylia,1294634,NA,NA,True,dx.doi.org/10.1111/j.1558-5646.2011.01373.x,Oaks JR. A time-calibrated species tree of Crocodylia reveals a recent radiation of the true crocodiles. Evolution. 2011 Nov 1;65(11):3285-97.,2011
53,Becker_2016,36890,2420,6.56,215,0.991,210,0.968,,,dx.doi.org/10.5061/dryad.963hr,protein,217,170,1,True,False,False,False,False,False,False,False,CC0,NA,halophytic bacteria,Halobacteriacea,2236,NA,NA,True,dx.doi.org/10.1371/journal.pone.0156543,"Becker EA, Yao AI, Seitzer PM, Kind T, Wang T, Eigenheer R, Shao KSY, Yarov-Yarovoy V, Facciotti MT (2016) A large and phylogenetically diverse class of type 1 opsins lacking a canonical retinal binding site. PLOS ONE 11(6): e0156543.",2016
54,Dornburg_2012,260436,56891,21.845,1560,0.264,896,0.151,0.48200000000000004,0.518,dx.doi.org/10.5061/dryad.3t19n,nucleotide,5919,44,21,False,False,False,False,True,True,False,False,CC0,NA,Squirrel Fishes,Teleostei: Beryciformes: Holocentridae,47697,NA,144.4 mya,True,dx.doi.org/10.1016/j.ympev.2012.07.020,"Dornburg A, Moore JA, Webster R, Warren DL, Brandley MC, Iglesias TL, Wainwright PC, Near TJ. Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): Reconciling more than 100 years of taxonomic confusion. Molecular phylogenetics and Evolution. 2012 Nov 30;65(2):727-38.",2013
55,Nguyen_2016f,9911,220,2.22,209,0.358,114,0.196,,,dx.doi.org/10.5061/dryad.8vj6j,protein,583,17,1,False,False,False,False,False,True,False,False,CC0,"This is the hsp60 dataset from the repository. Root ages are not determined because these are trees of duplicated genes, not just taxa.","sawflies, wasps, bees, and ants",Hymenoptera,7399,NA,NA,True,dx.doi.org/10.1186/s12862-015-0573-0,"Nguyen AD, Gotelli NJ, Helms Cahan S (2016) The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera. BMC Evolutionary Biology 16: 15.",2016
56,Nguyen_2016a,11696,593,5.07,171,0.249,100,0.145,,,dx.doi.org/10.5061/dryad.8vj6j,protein,688,17,1,False,False,False,False,False,True,False,False,CC0,"This is the hsc70-3 dataset from the repository. Root ages are not determined because these are trees of duplicated genes, not just taxa.","sawflies, wasps, bees, and ants",Hymenoptera,7399,NA,NA,True,dx.doi.org/10.1186/s12862-015-0573-0,"Nguyen AD, Gotelli NJ, Helms Cahan S (2016) The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera. BMC Evolutionary Biology 16: 15.",2016
57,Worobey_2014e,237660,3209,1.35,504,0.721,461,0.66,0.542,0.45799999999999996,dx.doi.org/10.5061/dryad.m04j9,nucleotide,699,340,3,False,False,False,False,False,False,False,True,CC0,"This is the NS gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details.",Influenza A virus,Influenzavirus A,197911,0.000281 mya,NA,True,dx.doi.org/10.1038/nature13016,"Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257.",2014
58,Worobey_2014b,248193,1,0.0,389,0.513,361,0.47600000000000003,0.504,0.496,dx.doi.org/10.5061/dryad.m04j9,nucleotide,759,327,3,False,False,False,False,False,False,False,True,CC0,"This is the MP gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details.",Influenza A virus,Influenzavirus A,197911,0.000163 mya,NA,True,dx.doi.org/10.1038/nature13016,"Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257.",2014
59,Leache_2015,3941993,399584,10.137,40413,0.113,11850,0.033,0.617,0.38299999999999995,dx.doi.org/10.5061/dryad.4vt08,nucleotide,358363,11,583,False,False,False,False,False,True,False,False,CC0,NA,Iguanian lizards,Phrynosomatinae,6615,54 mya,50.6 mya,True,dx.doi.org/10.1093/gbe/evv026,"Leaché, A. D., Chavez, A. S., Jones, L. N., Grummer, J. A., Gottscho, A. D., & Linkem, C. W. (2015). Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing. Genome biology and evolution, 7(3), 706-719.",2015
60,Worobey_2014c,130272,613,0.47100000000000003,684,0.483,618,0.436,0.5720000000000001,0.428,dx.doi.org/10.5061/dryad.m04j9,nucleotide,1416,92,3,False,False,False,False,False,False,False,True,CC0,"This is the N7 gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details.",Influenza A virus,Influenzavirus A,197911,0.000175 mya,NA,True,dx.doi.org/10.1038/nature13016,"Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257.",2014
61,Worobey_2014d,531435,112,0.021,863,0.5760000000000001,784,0.524,0.531,0.469,dx.doi.org/10.5061/dryad.m04j9,nucleotide,1497,355,3,False,False,False,False,False,False,False,True,CC0,"This is the NP gene from figure 2 in the ms. Root age is the oldest node in the tree, taken from the MCC trees on Dryad. Note that the dates of the names represent sampling dates that can be used for tip dating analyses. See original paper and repository for details.",Influenza A virus,Influenzavirus A,197911,0.000245 mya,NA,True,dx.doi.org/10.1038/nature13016,"Worobey M, Han G, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508(7495): 254–257.",2014
62,Cannon_2016_aa,3501888,1088721,31.09,37164,0.828,30646,0.6829999999999999,,,dx.doi.org/10.5061/dryad.493b7,protein,44896,78,212,False,False,False,False,False,True,False,False,CC0,"This dataset (78 taxa, 212 loci) is referred to as the 'primary' dataset in the ms, and forms the basis of Figure 2 in the ms. This is the amino acid dataset (212_78_MB_aa.nex) taken from the 'supplementary mrbayes files' link in the Dryad repository (http://datadryad.org/bitstream/handle/10255/dryad.107232/supplementarymrbayesfiles.zip?sequence=1). There is a nucleotide (1st and 2nd positions only) version of this dataset stored in this repository as Cannon_2016a.",Animals,Metazoa,33208,NA,952 mya,True,dx.doi.org/10.1038/nature16520,"Cannon JT, Vellutini BC, Smith J, Ronquist F, Jondelius U, Hejnol A (2016) Xenacoelomorpha is the sister group to Nephrozoa. Nature 530(7588): 89–93. http://dx.doi.org/10.1038/nature16520",2016
63,Sharanowski_2011,553498,102685,18.552,2166,0.544,1674,0.42,0.539,0.461,dx.doi.org/10.5061/dryad.1688p,nucleotide,3982,139,11,False,False,False,False,False,True,False,False,CC0,NA,parasitoid wasps,Braconidae,7402,NA,NA,True,dx.doi.org/10.1111/j.1365-3113.2011.00580.x,"Sharanowski BJ, Dowling AP, Sharkey MJ. Molecular phylogenetics of Braconidae (Hymenoptera: Ichneumonoidea), based on multiple nuclear genes, and implications for classification. Systematic Entomology. 2011 Jul 1;36(3):549-72.",2011
64,Rightmyer_2013,347048,55246,15.919,1431,0.38799999999999996,1044,0.28300000000000003,0.588,0.41200000000000003,dx.doi.org/10.5061/dryad.jd5ff,nucleotide,3692,94,25,False,False,False,False,True,True,False,False,CC0,NA,bee,Hymenoptera: Megachilidae,124286,NA,NA,True,dx.doi.org/10.1111/syen.12013,"Rightmyer MG, Griswold T, Brady SG. Phylogeny and systematics of the bee genus Osmia (Hymenoptera: Megachilidae) with emphasis on North American Melanosmia: subgenera, synonymies and nesting biology revisited. Systematic Entomology. 2013 Jul 1;38(3):561-76.",2013
65,Richart_2015,3216744,571048,17.752,231761,0.43200000000000005,104700,0.195,0.565,0.435,dx.doi.org/10.5061/dryad.3mr26,nucleotide,536124,6,2016,False,False,False,False,False,True,False,False,CC0,NA,harvestmen or daddy longlegs,Ischyropsalidoidea,101157,NA,258.8 mya,True,dx.doi.org/10.1016/j.ympev.2015.11.010,"Richart C, Hayashi C, Marshal H (2015) Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies. Molecular Phylogenetics and Evolution 95: 171–182",2015
66,Near_2013,5214816,1091376,20.928,5645,0.6579999999999999,4780,0.557,0.45299999999999996,0.547,dx.doi.org/10.5061/dryad.d3mb4,nucleotide,8577,608,30,False,False,False,False,False,True,False,False,CC0,"There were a few issues with capitalisations in the species names, which I fixed",spiny-rayed fishes,Acanthomorpha,123368,NA,NA,True,dx.doi.org/10.1073/pnas.1304661110,"Near TJ, Dornburg A, Eytan RI, Keck BP, Smith WL, Kuhn KL, Moore JA, Price SA, Burbrink FT, Friedman M, Wainwright PC. Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes. Proceedings of the National Academy of Sciences. 2013 Jul 30;110(31):12738-43.",2013