TY - CHAP AU - Minelli, A. AU - Golovatch, S. ED - SA, L. PY - 2013 DA - 2013// TI - Myriapods BT - Encyclopedia of biodiversity. 5 PB - Academic Press CY - Waltham MA UR - https://doi.org/10.1016/B978-0-12-384719-5.00208-2 DO - 10.1016/B978-0-12-384719-5.00208-2 ID - Minelli2013 ER - TY - STD TI - Fernández R, Edgecombe GD, Giribet G. Phylogenomics illuminates the backbone of the Myriapoda tree of life and reconciles morphological and molecular phylogenies. Sci Rep. 2018;8. https://doi.org/10.1038/s41598-017-18562-w. ID - ref2 ER - TY - CHAP AU - Edgecombe, G. D. PY - 2011 DA - 2011// TI - Phylogenetic relationships of Myriapoda BT - Treatise on Zoology-Anatomy, Taxonomy, Biology The Myriapoda. 1: Brill ID - Edgecombe2011 ER - TY - JOUR AU - Fernández, R. AU - Laumer, C. E. AU - Vahtera, V. AU - Libro, S. AU - Kaluziak, S. AU - Sharma, P. P. PY - 2014 DA - 2014// TI - Evaluating topological conflict in centipede phylogeny using transcriptomic data sets JO - Mol Biol Evol VL - 31 UR - https://doi.org/10.1093/molbev/msu108 DO - 10.1093/molbev/msu108 ID - Fernández2014 ER - TY - JOUR AU - Hill, C. A. AU - Wikel, S. K. PY - 2005 DA - 2005// TI - The Ixodes scapularis genome project: an opportunity for advancing tick research JO - Trends Parasitol VL - 21 UR - https://doi.org/10.1016/j.pt.2005.02.004 DO - 10.1016/j.pt.2005.02.004 ID - Hill2005 ER - TY - JOUR AU - Giraldo-Calderón, G. I. AU - Emrich, S. J. AU - MacCallum, R. M. AU - Maslen, G. AU - Dialynas, E. AU - Topalis, P. PY - 2015 DA - 2015// TI - VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1117 DO - 10.1093/nar/gku1117 ID - Giraldo-Calderón2015 ER - TY - STD TI - Chipman AD, Ferrier DEK, Brena C, Qu J, Hughes DST et al. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima. PLoS Biol 2014, 12:e1002005. doi: https://doi.org/10.1371/journal.pbio.1002005. ID - ref7 ER - TY - STD TI - Stoev P, Komerički MA, Akkari N, Liu MS, Zhou MX, Weigand AM, et al. Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data. Biodivers Data J. 2013:e1013. https://doi.org/10.3897/BJ.1.e1013. ID - ref8 ER - TY - JOUR AU - Colbourne, J. K. AU - Pfrender, M. E. AU - Gilbert, D. AU - Thomas, W. K. AU - Tucker, A. AU - Oakley, T. H. AU - Tokishita, S. AU - Aerts, A. AU - Arnold, G. J. AU - Basu, M. K. PY - 2011 DA - 2011// TI - The ecoresponsive genome of Daphnia pulex JO - Science. VL - 331 UR - https://doi.org/10.1126/science.1197761 DO - 10.1126/science.1197761 ID - Colbourne2011 ER - TY - JOUR AU - Misof, B. AU - Liu, S. AU - Meusemann, K. AU - Peters, R. S. AU - Donath, A. AU - Mayer, C. PY - 2014 DA - 2014// TI - Phylogenomics resolves the timing and pattern of insect evolution JO - Science. VL - 346 UR - https://doi.org/10.1126/science.1257570 DO - 10.1126/science.1257570 ID - Misof2014 ER - TY - JOUR AU - Pauli, T. AU - Vedder, L. AU - Dowling, D. AU - Petersen, M. AU - Meusemann, K. PY - 2016 DA - 2016// TI - Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects JO - BMC Genomics VL - 17 UR - https://doi.org/10.1186/s12864-016-3205-1 DO - 10.1186/s12864-016-3205-1 ID - Pauli2016 ER - TY - JOUR AU - Terrapon, N. AU - Li, C. AU - Robertson, H. M. AU - Ji, L. AU - Meng, X. AU - Booth, W. PY - 2014 DA - 2014// TI - Molecular traces of alternative social organization in a termite genome JO - Nat Commun VL - 5 UR - https://doi.org/10.1038/ncomms4636 DO - 10.1038/ncomms4636 ID - Terrapon2014 ER - TY - JOUR AU - Shimodaira, H. PY - 2002 DA - 2002// TI - An approximately unbiased test of phylogenetic tree selection JO - Syst Biol VL - 51 UR - https://doi.org/10.1080/10635150290069913 DO - 10.1080/10635150290069913 ID - Shimodaira2002 ER - TY - JOUR AU - Strimmer, K. AU - Haeseler, A. PY - 1997 DA - 1997// TI - Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment JO - Proc Natl Acad Sci U S A VL - 94 UR - https://doi.org/10.1073/pnas.94.13.6815 DO - 10.1073/pnas.94.13.6815 ID - Strimmer1997 ER - TY - JOUR AU - Peters, R. S. AU - Krogmann, L. AU - Mayer, C. AU - Donath, A. AU - Gunkel, S. AU - Meusemann, K. PY - 2017 DA - 2017// TI - Evolutionary history of the hymenoptera JO - Curr Biol VL - 27 UR - https://doi.org/10.1016/j.cub.2017.01.027 DO - 10.1016/j.cub.2017.01.027 ID - Peters2017 ER - TY - JOUR AU - Simon, S. AU - Blanke, A. AU - Meusemann, K. PY - 2018 DA - 2018// TI - Reanalyzing the Palaeoptera problem–the origin of insect flight remains obscure JO - Arthropod Struct Dev VL - 47 UR - https://doi.org/10.1016/j.asd.2018.05.002 DO - 10.1016/j.asd.2018.05.002 ID - Simon2018 ER - TY - JOUR AU - Regier, J. C. AU - Shultz, J. W. AU - Ganley, A. R. D. AU - Hussey, A. AU - Shi, D. AU - Ball, B. PY - 2008 DA - 2008// TI - Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence JO - Syst Biol VL - 57 UR - https://doi.org/10.1080/10635150802570791 DO - 10.1080/10635150802570791 ID - Regier2008 ER - TY - JOUR AU - Rehm, P. AU - Meusemann, K. AU - Borner, J. AU - Misof, B. AU - Burmester, T. PY - 2014 DA - 2014// TI - Phylogenetic position of Myriapoda revealed by 454 transcriptome sequencing JO - Mol Phylogenet Evol VL - 77 UR - https://doi.org/10.1016/j.ympev.2014.04.007 DO - 10.1016/j.ympev.2014.04.007 ID - Rehm2014 ER - TY - JOUR AU - Gai, Y. -. H. AU - Song, D. -. X. AU - Sun, H. -. Y. AU - Zhou, K. -. Y. PY - 2006 DA - 2006// TI - Myriapod monophyly and relationships among myriapod classes based on nearly complete 28S and 18S rDNA sequences JO - Zool Sci VL - 23 UR - https://doi.org/10.2108/zsj.23.1101 DO - 10.2108/zsj.23.1101 ID - Gai2006 ER - TY - JOUR AU - Regier, J. C. AU - Shultz, J. W. AU - Zwick, A. AU - Hussey, A. AU - Ball, B. AU - Wetzer, R. PY - 2010 DA - 2010// TI - Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences JO - Nature. VL - 463 UR - https://doi.org/10.1038/nature08742 DO - 10.1038/nature08742 ID - Regier2010 ER - TY - STD TI - Zwick A, Regier JC, Zwickl DJ. Resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics: differentiating serine codons in 21-amino-acid models. PLoS One. 2012;7. https://doi.org/10.1371/journal.pone.0047450. ID - ref21 ER - TY - STD TI - Miyazawa H, Ueda C, Yahata K, Su ZH. Molecular phylogeny of Myriapoda provides insights into evolutionary patterns of the mode in post-embryonic development. Sci Rep. 2014;4. https://doi.org/10.1038/srep04127. ID - ref22 ER - TY - JOUR AU - Jermiin, L. S. AU - Ho, S. Y. W. AU - Ababneh, F. AU - Robinson, J. AU - Larkum, A. W. D. PY - 2004 DA - 2004// TI - The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated JO - Syst Biol VL - 53 UR - https://doi.org/10.1080/10635150490468648 DO - 10.1080/10635150490468648 ID - Jermiin2004 ER - TY - JOUR AU - Ababneh, F. AU - Jermiin, L. S. AU - Ma, C. AU - Robinson, J. PY - 2006 DA - 2006// TI - Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences JO - Bioinformatics. VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl064 DO - 10.1093/bioinformatics/btl064 ID - Ababneh2006 ER - TY - JOUR AU - Quang, L. S. AU - Gascuel, O. AU - Lartillot, N. PY - 2008 DA - 2008// TI - Empirical profile mixture models for phylogenetic reconstruction JO - Bioinformatics. VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn445 DO - 10.1093/bioinformatics/btn445 ID - Quang2008 ER - TY - JOUR AU - Wang, H. -. C. AU - Minh, B. Q. AU - Susko, E. AU - Roger, A. J. PY - 2018 DA - 2018// TI - Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation JO - Syst Biol VL - 67 UR - https://doi.org/10.1093/sysbio/syx068 DO - 10.1093/sysbio/syx068 ID - Wang2018 ER - TY - STD TI - Pattengale ND, Alipour M, Bininda-Emonds OR, Moret BM, Stamatakis A. How many bootstrap replicates are necessary? J Comput Biol. 2010;17:337–54. https://doi.org/10.1089/cmb.2009.0179. ID - ref27 ER - TY - JOUR AU - Aberer, A. J. AU - Krompass, D. AU - Stamatakis, A. PY - 2013 DA - 2013// TI - Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice JO - Syst Biol VL - 62 UR - https://doi.org/10.1093/sysbio/sys078 DO - 10.1093/sysbio/sys078 ID - Aberer2013 ER - TY - JOUR AU - Giribet, G. AU - Edgecombe, G. D. PY - 2019 DA - 2019// TI - The phylogeny and evolutionary history of arthropods JO - Curr Biol VL - 29 UR - https://doi.org/10.1016/j.cub.2019.04.057 DO - 10.1016/j.cub.2019.04.057 ID - Giribet2019 ER - TY - JOUR AU - Lartillot, N. AU - Philippe, H. PY - 2004 DA - 2004// TI - A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process JO - Mol Biol Evol VL - 21 UR - https://doi.org/10.1093/molbev/msh112 DO - 10.1093/molbev/msh112 ID - Lartillot2004 ER - TY - JOUR AU - Schwentner, M. AU - Combosch, D. J. AU - Nelson, J. P. AU - Giribet, G. PY - 2017 DA - 2017// TI - A phylogenomic solution to the origin of insects by resolving crustacean-hexapod relationships JO - Curr Biol VL - 27 UR - https://doi.org/10.1016/j.cub.2017.05.040 DO - 10.1016/j.cub.2017.05.040 ID - Schwentner2017 ER - TY - JOUR AU - Feuda, R. AU - Dohrmann, M. AU - Pett, W. AU - Philippe, H. AU - Rota-Stabelli, O. AU - Lartillot, N. AU - Wörheide, G. AU - Pisani, D. PY - 2017 DA - 2017// TI - Improved modeling of compositional heterogeneity supports sponges as sister to all other animals JO - Curr Biol VL - 27 UR - https://doi.org/10.1038/s41598-017-18562-w DO - 10.1038/s41598-017-18562-w ID - Feuda2017 ER - TY - JOUR AU - Whelan, N. V. AU - Halanych, K. M. PY - 2017 DA - 2017// TI - Who let the CAT out of the bag? Accurately dealing with substitutional heterogeneity in phylogenomic analyses JO - Syst Biol VL - 66 UR - https://doi.org/10.1093/sysbio/syw084 DO - 10.1093/sysbio/syw084 ID - Whelan2017 ER - TY - STD TI - Kück P, Wilkinson M, Groß C, Foster PG, Wägele JW. Can quartet analyses combining maximum likelihood estimation and Hennigian logic overcome long branch attraction in phylogenomic sequence data? PLoS One. 2017;12. https://doi.org/10.1371/journal.pone.0183393. ID - ref34 ER - TY - JOUR AU - Pease, J. B. AU - Brown, J. W. AU - Walker, J. F. AU - Hinchliff, C. E. AU - Smith, S. A. PY - 2018 DA - 2018// TI - Quartet sampling distinguishes lack of support from conflicting support in the green plant tree of life JO - Am J Bot VL - 105 UR - https://doi.org/10.1002/ajb2.1016 DO - 10.1002/ajb2.1016 ID - Pease2018 ER - TY - JOUR AU - Zhou, X. AU - Lutteropp, S. AU - Czech, L. AU - Stamatakis, A. AU - Looz, M. AU - Rokas, A. PY - 2020 DA - 2020// TI - Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence JO - Syst Biol VL - 69 UR - https://doi.org/10.1093/sysbio/syz058 DO - 10.1093/sysbio/syz058 ID - Zhou2020 ER - TY - STD TI - Edgecombe GD, Giribet G. Myriapod phylogeny and the relationships of Chilopoda. In: Llorente Bousquets JE, Morrone JJ, editors. Biodiversidad, Taxonomía y Biogeografía de Artropodos de México: Hacia una Síntesis de su Conocimiento. Universidad Nacional Autonoma de México. III. p. 143–68. https://scholar.harvard.edu/ggs/publications/myriapod-phylogeny-and-relationships-chilopoda. UR - https://scholar.harvard.edu/ggs/publications/myriapod-phylogeny-and-relationships-chilopoda ID - ref37 ER - TY - JOUR AU - Kriventseva, E. V. AU - Tegenfeldt, F. AU - Petty, T. J. AU - Waterhouse, R. M. AU - Simao, F. A. AU - Pozdnyakov, I. A. PY - 2015 DA - 2015// TI - OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1220 DO - 10.1093/nar/gku1220 ID - Kriventseva2015 ER - TY - JOUR AU - Petersen, M. AU - Meusemann, K. AU - Donath, A. AU - Dowling, D. AU - Liu, S. AU - Peters, R. S. PY - 2017 DA - 2017// TI - Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes JO - BMC Bioinformatics. VL - 18 UR - https://doi.org/10.1186/s12859-017-1529-8 DO - 10.1186/s12859-017-1529-8 ID - Petersen2017 ER - TY - JOUR AU - Misof, B. AU - Meyer, B. AU - Reumont, B. M. AU - Kück, P. AU - Misof, K. AU - Meusemann, K. PY - 2013 DA - 2013// TI - Selecting informative subsets of sparse supermatrices increases the chance to find correct trees JO - BMC Bioinformatics VL - 14 UR - https://doi.org/10.1186/1471-2105-14-348 DO - 10.1186/1471-2105-14-348 ID - Misof2013 ER - TY - JOUR AU - Dell’Ampio, E. AU - Meusemann, K. AU - Szucsich, N. U. AU - Peters, R. S. AU - Meyer, B. AU - Borner, J. PY - 2014 DA - 2014// TI - Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects JO - Mol Biol Evol VL - 31 UR - https://doi.org/10.1093/molbev/mst196 DO - 10.1093/molbev/mst196 ID - Dell’Ampio2014 ER - TY - JOUR AU - Lanfear, R. AU - Frandsen, P. B. AU - Wright, A. M. AU - Senfeld, T. AU - Calcott, B. PY - 2017 DA - 2017// TI - PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses JO - Mol Biol Evol VL - 34 UR - https://doi.org/10.1093/molbev/msw260 DO - 10.1093/molbev/msw260 ID - Lanfear2017 ER - TY - JOUR AU - Stamatakis, A. PY - 2014 DA - 2014// TI - RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies JO - Bioinformatics. VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu033 DO - 10.1093/bioinformatics/btu033 ID - Stamatakis2014 ER - TY - JOUR AU - Le, S. Q. AU - Dang, C. C. AU - Gascuel, O. PY - 2012 DA - 2012// TI - Modeling protein evolution with several amino acid replacement matrices depending on site rates JO - Mol Biol Evol VL - 29 UR - https://doi.org/10.1093/molbev/mss112 DO - 10.1093/molbev/mss112 ID - Le2012 ER - TY - JOUR AU - Nguyen, L. -. T. AU - Schmidt, H. A. AU - Haeseler, A. AU - Minh, B. Q. PY - 2015 DA - 2015// TI - IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies JO - Mol Biol Evol VL - 32 UR - https://doi.org/10.1093/molbev/msu300 DO - 10.1093/molbev/msu300 ID - Nguyen2015 ER - TY - JOUR AU - Chernomor, O. AU - Haeseler, A. AU - Minh, B. Q. PY - 2016 DA - 2016// TI - Terrace aware data structure for phylogenomic inference from supermatrices JO - Syst Biol VL - 65 UR - https://doi.org/10.1093/sysbio/syw037 DO - 10.1093/sysbio/syw037 ID - Chernomor2016 ER - TY - STD TI - Junier T, Zdobnov EM. The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. Bioinformatics. 2010:261669–70. https://doi.org/10.1093/bioinformatics/btq243. ID - ref47 ER -