TY - JOUR AU - McCormack, J. E. AU - Faircloth, B. C. AU - Crawford, N. G. AU - Gowaty, P. A. AU - Brumfield, R. T. AU - Glenn, T. C. PY - 2012 DA - 2012// TI - Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis JO - Gen Res VL - 22 UR - https://doi.org/10.1101/gr.125864.111 DO - 10.1101/gr.125864.111 ID - McCormack2012 ER - TY - JOUR AU - Lemmon, E. M. AU - Lemmon, A. R. PY - 2013 DA - 2013// TI - High-throughput genomic data in systematics and phylogenetics JO - Annu Rev Ecol Syst VL - 44 UR - https://doi.org/10.1146/annurev-ecolsys-110512-135822 DO - 10.1146/annurev-ecolsys-110512-135822 ID - Lemmon2013 ER - TY - JOUR AU - Smith, B. T. AU - Harvey, M. G. AU - Faircloth, B. C. AU - Glenn, T. C. AU - Brumfield, R. T. PY - 2013 DA - 2013// TI - Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales JO - Syst Biol VL - 63 UR - https://doi.org/10.1093/sysbio/syt061 DO - 10.1093/sysbio/syt061 ID - Smith2013 ER - TY - JOUR AU - Smith, B. T. AU - McCormack, J. E. AU - Cuervo, A. M. AU - Hickerson, M. J. AU - Aleixo, A. AU - Cadena, C. D. AU - Perez-Eman, J. AU - Burney, C. W. AU - Xie, X. AU - Harvey, M. G. PY - 2014 DA - 2014// TI - The drivers of tropical speciation JO - Nature VL - 515 UR - https://doi.org/10.1038/nature13687 DO - 10.1038/nature13687 ID - Smith2014 ER - TY - JOUR AU - Crawford, N. G. AU - Faircloth, B. C. AU - McCormack, J. E. AU - Brumfield, R. T. AU - Winker, K. AU - Glenn, T. C. PY - 2012 DA - 2012// TI - More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs JO - Biol Lett VL - 8 UR - https://doi.org/10.1098/rsbl.2012.0331 DO - 10.1098/rsbl.2012.0331 ID - Crawford2012 ER - TY - JOUR AU - Faircloth, B. C. AU - McCormack, J. E. AU - Crawford, N. G. AU - Harvey, M. G. AU - Brumfield, R. T. AU - Glenn, T. C. PY - 2012 DA - 2012// TI - Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales JO - Syst Biol VL - 61 UR - https://doi.org/10.1093/sysbio/sys004 DO - 10.1093/sysbio/sys004 ID - Faircloth2012 ER - TY - JOUR AU - Faircloth, B. C. AU - Branstetter, M. G. AU - White, N. D. AU - Brady, S. G. PY - 2015 DA - 2015// TI - Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera JO - Mol Ecol Res VL - 15 UR - https://doi.org/10.1111/1755-0998.12328 DO - 10.1111/1755-0998.12328 ID - Faircloth2015 ER - TY - JOUR AU - Gilbert, P. S. AU - Chang, J. AU - Pan, C. AU - Sobel, E. M. AU - Sinsheimer, J. S. AU - Faircloth, B. C. AU - Alfaro, M. E. PY - 2015 DA - 2015// TI - Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes JO - Mol Phylogenet Evol VL - 92 UR - https://doi.org/10.1016/j.ympev.2015.05.027 DO - 10.1016/j.ympev.2015.05.027 ID - Gilbert2015 ER - TY - JOUR AU - Brady, S. G. AU - Schultz, T. R. AU - Fisher, B. L. AU - Ward, P. S. PY - 2006 DA - 2006// TI - Evaluating alternative hypotheses for the early evolution and diversification of ants JO - Proc Natl Acad Sci VL - 103 UR - https://doi.org/10.1073/pnas.0605858103 DO - 10.1073/pnas.0605858103 ID - Brady2006 ER - TY - JOUR AU - Moreau, C. S. AU - Bell, C. D. AU - Vila, R. AU - Archibald, S. B. AU - Pierce, N. E. PY - 2006 DA - 2006// TI - Phylogeny of the ants: Diversification in the age of angiosperms JO - Science VL - 312 UR - https://doi.org/10.1126/science.1124891 DO - 10.1126/science.1124891 ID - Moreau2006 ER - TY - JOUR AU - Ward, P. S. AU - Brady, S. G. AU - Fisher, B. L. AU - Schultz, T. R. PY - 2010 DA - 2010// TI - Phylogeny and biogeography of dolichoderine ants: effects of data partitioning and relict taxa on historical inference JO - Syst Biol VL - 59 UR - https://doi.org/10.1093/sysbio/syq012 DO - 10.1093/sysbio/syq012 ID - Ward2010 ER - TY - JOUR AU - Brady, S. G. AU - Fisher, B. L. AU - Schultz, T. R. AU - Ward, P. S. PY - 2014 DA - 2014// TI - The rise of army ants and their relatives: diversification of specialized predatory doryline ants JO - BMC Evol Biol VL - 14 UR - https://doi.org/10.1186/1471-2148-14-93 DO - 10.1186/1471-2148-14-93 ID - Brady2014 ER - TY - JOUR AU - Schmidt, C. A. AU - Shattuck, S. O. PY - 2014 DA - 2014// TI - The higher classification of the ant subfamily Ponerinae (Hymenoptera: Formicidae), with a review of ponerine ecology and behavior JO - Zootaxa VL - 3817 UR - https://doi.org/10.11646/zootaxa.3817.1.1 DO - 10.11646/zootaxa.3817.1.1 ID - Schmidt2014 ER - TY - JOUR AU - Ward, P. S. AU - Brady, S. G. AU - Fisher, B. L. AU - Schultz, T. R. PY - 2015 DA - 2015// TI - The evolution of myrmicine ants: phylogeny and biogeography of a hyperdiverse ant clade (Hymenoptera: Formicidae) JO - Syst Ent VL - 40 UR - https://doi.org/10.1111/syen.12090 DO - 10.1111/syen.12090 ID - Ward2015 ER - TY - JOUR AU - Lucky, A. AU - Trautwein, M. D. AU - Guenard, B. S. AU - Weiser, M. D. AU - Dunn, R. R. PY - 2013 DA - 2013// TI - Tracing the rise of ants-out of the ground JO - PLoS ONE VL - 8 UR - https://doi.org/10.1371/journal.pone.0084012 DO - 10.1371/journal.pone.0084012 ID - Lucky2013 ER - TY - JOUR AU - Moreau, C. S. AU - Bell, C. D. PY - 2013 DA - 2013// TI - Testing the museum versus cradle tropical biological diversity hypothesis: phylogeny, diversification, and ancestral biogeographic range evolution of the ants JO - Evolution VL - 67 UR - https://doi.org/10.1111/evo.12105 DO - 10.1111/evo.12105 ID - Moreau2013 ER - TY - JOUR AU - Blaimer, B. B. AU - Brady, S. G. AU - Schultz, T. R. AU - Fisher, B. L. PY - 2015 DA - 2015// TI - Functional and phylogenetic approaches reveal the evolution of diversity in a hyper diverse biota JO - Ecography VL - 38 UR - https://doi.org/10.1111/ecog.01370 DO - 10.1111/ecog.01370 ID - Blaimer2015 ER - TY - JOUR AU - Schultz, T. R. AU - Brady, S. G. PY - 2008 DA - 2008// TI - Major evolutionary transitions in ant agriculture JO - Proc Natl Acad Sci VL - 105 UR - https://doi.org/10.1073/pnas.0711024105 DO - 10.1073/pnas.0711024105 ID - Schultz2008 ER - TY - JOUR AU - Price, S. L. AU - Powell, S. AU - Kronauer, D. J. C. AU - Tran, L. A. P. AU - Pierce, N. E. AU - Wayne, R. K. PY - 2014 DA - 2014// TI - Renewed diversification is associated with new ecological opportunity in the Neotropical turtle ants JO - J Evol Biol VL - 27 UR - https://doi.org/10.1111/jeb.12300 DO - 10.1111/jeb.12300 ID - Price2014 ER - TY - JOUR AU - Ward, P. S. PY - 2014 DA - 2014// TI - The phylogeny and evolution of ants JO - Annu Rev Ecol Syst VL - 45 UR - https://doi.org/10.1146/annurev-ecolsys-120213-091824 DO - 10.1146/annurev-ecolsys-120213-091824 ID - Ward2014 ER - TY - STD TI - Schmidt JO. Chemistry, pharmacology, and chemical ecology of ant venoms. In: Piek T, editor. Venoms of the Hymenoptera. London: Academic Press; 1986: 425–508 ID - ref21 ER - TY - JOUR AU - Saporito, R. A. AU - Garraffo, H. M. AU - Donnelly, M. A. AU - Edwards, A. L. AU - Longino, J. T. AU - Daly, J. W. PY - 2004 DA - 2004// TI - Formicine ants: An arthropod source for the pumiliotoxin alkaloids of dendrobatid poison frogs JO - Proc Natl Acad Sci VL - 101 UR - https://doi.org/10.1073/pnas.0402365101 DO - 10.1073/pnas.0402365101 ID - Saporito2004 ER - TY - JOUR AU - Buschinger, A. PY - 2009 DA - 2009// TI - Social parasitism among ants: a review (Hymenoptera: Formicidae) JO - Myrmecol News VL - 12 ID - Buschinger2009 ER - TY - JOUR AU - LaPolla, J. S. AU - Brady, S. G. AU - Shattuck, S. O. PY - 2010 DA - 2010// TI - Phylogeny and taxonomy of the Prenolepis genus-group of ants (Hymenoptera: Formicidae) JO - Syst Ent VL - 35 UR - https://doi.org/10.1111/j.1365-3113.2009.00492.x DO - 10.1111/j.1365-3113.2009.00492.x ID - LaPolla2010 ER - TY - JOUR AU - Lapolla, J. S. AU - Kallal, R. J. AU - Brady, S. G. PY - 2012 DA - 2012// TI - A new ant genus from the Greater Antilles and Central America, Zatania (Hymenoptera: Formicidae), exemplifies the utility of male and molecular character systems JO - Syst Ent VL - 37 UR - https://doi.org/10.1111/j.1365-3113.2011.00605.x DO - 10.1111/j.1365-3113.2011.00605.x ID - Lapolla2012 ER - TY - STD TI - Blumenstiel B, Cibulskis K, Fisher S, DeFelice M, Barry A, Fennell T, et al. Targeted exon sequencing by in-solution hybrid selection. Curr Protoc Hum Genet. 2010;Unit 18.4.1–18.4.24, Supplement 66. ID - ref26 ER - TY - JOUR AU - Ward, P. S. AU - Downie, D. A. PY - 2005 DA - 2005// TI - The ant subfamily Pseudomyrmecinae (Hymenoptera: Formicidae): phylogeny and evolution of big-eyed arboreal ants JO - Syst Ent VL - 30 UR - https://doi.org/10.1111/j.1365-3113.2004.00281.x DO - 10.1111/j.1365-3113.2004.00281.x ID - Ward2005 ER - TY - JOUR AU - Ward, P. S. AU - Sumnicht, T. P. PY - 2012 DA - 2012// TI - Molecular and morphological evidence for three sympatric species of Leptanilla (Hymenoptera: Formicidae) on the Greek island of Rhodes JO - Myrmecol News VL - 17 ID - Ward2012 ER - TY - STD TI - Katoh K, Asimenos G, Toh H. Multiple alignment of DNA sequences with MAFFT. In: Bioinformatics for DNA sequence analysis. Humana Press, New York City; 2009: 39–64 ID - ref29 ER - TY - STD TI - Faircloth B. Illumiprocessor: a trimmomatic wrapper for parallel adapter and quality trimming. 2013. doi: 10.6079/J9ILL ID - ref30 ER - TY - STD TI - Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; btu170:1–7. ID - ref31 ER - TY - STD TI - Faircloth B. PHYLUCE is a software package for the analysis of conserved genomic loci. 2015. doi:10.6079/J9PHYL ID - ref32 ER - TY - JOUR AU - Grabherr, M. G. AU - Haas, B. J. AU - Yassour, M. AU - Levin, J. Z. AU - Thompson, D. A. AU - Amit, I. AU - Adiconis, X. AU - Fan, L. AU - Raychowdhury, R. AU - Zeng, Q. PY - 2011 DA - 2011// TI - Full-length transcriptome assembly from RNA-Seq data without a reference genome JO - Nat Biotech VL - 29 UR - https://doi.org/10.1038/nbt.1883 DO - 10.1038/nbt.1883 ID - Grabherr2011 ER - TY - JOUR AU - Castresana, J. PY - 2000 DA - 2000// TI - Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026334 DO - 10.1093/oxfordjournals.molbev.a026334 ID - Castresana2000 ER - TY - JOUR AU - Lanfear, R. AU - Calcott, B. AU - Ho, S. Y. W. AU - Guindon, S. PY - 2012 DA - 2012// TI - PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses JO - Mol Biol Evol VL - 29 UR - https://doi.org/10.1093/molbev/mss020 DO - 10.1093/molbev/mss020 ID - Lanfear2012 ER - TY - JOUR AU - Stamatakis, A. PY - 2006 DA - 2006// TI - RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl446 DO - 10.1093/bioinformatics/btl446 ID - Stamatakis2006 ER - TY - STD TI - Zwickl DJ. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. The University of Texas at Austin; 2006; accessible at: https://repositories.lib.utexas.edu/handle/2152/2666 UR - https://repositories.lib.utexas.edu/handle/2152/2666 ID - ref37 ER - TY - JOUR AU - Ronquist, F. AU - Teslenko, M. AU - Mark, P. AU - Ayres, D. L. AU - Darling, A. AU - Höhna, S. AU - Larget, B. AU - Liu, L. AU - Suchard, M. A. AU - Huelsenbeck, J. P. PY - 2012 DA - 2012// TI - MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space JO - Syst Biol VL - 61 UR - https://doi.org/10.1093/sysbio/sys029 DO - 10.1093/sysbio/sys029 ID - Ronquist2012 ER - TY - JOUR AU - Frandsen, P. B. AU - Calcott, B. AU - Mayer, C. AU - Lanfear, R. PY - 2015 DA - 2015// TI - Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates JO - BMC Evol Biol VL - 15 UR - https://doi.org/10.1186/s12862-015-0283-7 DO - 10.1186/s12862-015-0283-7 ID - Frandsen2015 ER - TY - JOUR AU - Townsend, J. P. PY - 2007 DA - 2007// TI - Profiling Phylogenetic Informativeness JO - Syst Biol VL - 56 UR - https://doi.org/10.1080/10635150701311362 DO - 10.1080/10635150701311362 ID - Townsend2007 ER - TY - STD TI - Faircloth BC, Chang J, Alfaro ME. TAPIR enables high-throughput estimation and comparison of phylogenetic informativeness using locus-specific substitution models. 2012. arXiv preprint arXiv:12021215. ID - ref41 ER - TY - JOUR AU - López-Giráldez, F. AU - Townsend, J. P. PY - 2011 DA - 2011// TI - PhyDesign: an online application for profiling phylogenetic informativeness JO - BMC Evol Biol VL - 11 UR - https://doi.org/10.1186/1471-2148-11-152 DO - 10.1186/1471-2148-11-152 ID - López-Giráldez2011 ER - TY - JOUR AU - Drummond, A. J. AU - Suchard, M. A. AU - Xie, D. AU - Rambaut, A. PY - 2012 DA - 2012// TI - Bayesian Phylogenetics with BEAUti and the BEAST 1.7 JO - Mol Biol Evol VL - 29 UR - https://doi.org/10.1093/molbev/mss075 DO - 10.1093/molbev/mss075 ID - Drummond2012 ER - TY - JOUR AU - Ree, R. H. AU - Smith, S. A. PY - 2008 DA - 2008// TI - Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis JO - Syst Biol VL - 57 UR - https://doi.org/10.1080/10635150701883881 DO - 10.1080/10635150701883881 ID - Ree2008 ER - TY - JOUR AU - Beaulieu, J. M. AU - Tank, D. C. AU - Donoghue, M. J. PY - 2013 DA - 2013// TI - A Southern Hemisphere origin for campanulid angiosperms, with traces of the break-up of Gondwana JO - BMC Evol Biol VL - 13 UR - https://doi.org/10.1186/1471-2148-13-80 DO - 10.1186/1471-2148-13-80 ID - Beaulieu2013 ER - TY - JOUR AU - Yu, Y. AU - Harris, A. J. AU - Blair, C. AU - He, X. PY - 2015 DA - 2015// TI - RASP (Reconstruct Ancestral State in Phylogenies): a tool for historical biogeography JO - Mol Phylogen Evol VL - 87 UR - https://doi.org/10.1016/j.ympev.2015.03.008 DO - 10.1016/j.ympev.2015.03.008 ID - Yu2015 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 - Makunin, I. V. AU - Shloma, V. V. AU - Stephen, S. J. AU - Pheasant, M. AU - Belyakin, S. N. PY - 2013 DA - 2013// TI - Comparison of ultra-conserved elements in Drosophilids and Vertebrates JO - PLoS ONE VL - 8 UR - https://doi.org/10.1371/journal.pone.0082362 DO - 10.1371/journal.pone.0082362 ID - Makunin2013 ER - TY - JOUR AU - Bolton, B. PY - 2003 DA - 2003// TI - Synopsis and classification of Formicidae JO - Mem Am Entomol Inst VL - 71 ID - Bolton2003 ER - TY - JOUR AU - Whitfield, J. B. AU - Kjer, K. M. PY - 2008 DA - 2008// TI - Ancient rapid radiations of insects: challenges for phylogenetic analysis JO - Ann Rev Ent VL - 53 UR - https://doi.org/10.1146/annurev.ento.53.103106.093304 DO - 10.1146/annurev.ento.53.103106.093304 ID - Whitfield2008 ER - TY - JOUR AU - Wiegmann, B. M. AU - Trautwein, M. D. AU - Winkler, I. S. AU - Barr, N. B. AU - Kim, J. -. W. AU - Lambkin, C. AU - Bertone, M. A. AU - Cassel, B. K. AU - Bayless, K. M. AU - Heimberg, A. M. PY - 2011 DA - 2011// TI - Episodic radiations in the fly tree of life JO - Proc Natl Acad Sci VL - 108 UR - https://doi.org/10.1073/pnas.1012675108 DO - 10.1073/pnas.1012675108 ID - Wiegmann2011 ER - TY - STD TI - Bazinet AL, Cummings MP, Mitter KT, Mitter CW. Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study. PLoS ONE. 2013; 8(12):e82615. ID - ref52 ER - TY - JOUR AU - Johnson, B. R. AU - Borowiec, M. L. AU - Chiu, J. C. AU - Lee, E. K. AU - Atallah, J. AU - Ward, P. S. PY - 2013 DA - 2013// TI - Phylogenomics resolves evolutionary relationships among ants, bees, and wasps JO - Curr Biol VL - 23 UR - https://doi.org/10.1016/j.cub.2013.08.050 DO - 10.1016/j.cub.2013.08.050 ID - Johnson2013 ER - TY - CHAP AU - Brady, S. G. AU - Gadau, J. AU - Ward, P. S. ED - Austin, A. D. ED - Dowton, M. PY - 2000 DA - 2000// TI - Systematics of the ant genus Camponotus (Hymenoptera: Formicidae): a preliminary analysis using data from the mitochondrial gene cytochrome oxidase I BT - Hymenoptera: evolution, biodiversity and biological control PB - Fourth International Hymenoptera Conference CY - Canberra ID - Brady2000 ER - TY - JOUR AU - Chen, Z. AU - Zhou, S. AU - Ye, D. AU - Chen, Y. AU - Lu, C. PY - 2013 DA - 2013// TI - Molecular phylogeny of the ant subfamily Formicinae (Hymenoptera, Formicidae) from China based on mitochondrial genes JO - Sociobiology VL - 60 UR - https://doi.org/10.13102/sociobiology.v60i2.135-144 DO - 10.13102/sociobiology.v60i2.135-144 ID - Chen2013 ER - TY - JOUR AU - Williams, L. E. AU - Wernegreen, J. J. PY - 2015 DA - 2015// TI - Genome evolution in an ancient bacteria-ant symbiosis: parallel gene loss among Blochmannia spanning the origin of the ant tribe Camponotini JO - PeerJ VL - 3 UR - https://doi.org/10.7717/peerj.881 DO - 10.7717/peerj.881 ID - Williams2015 ER - TY - JOUR AU - Wernegreen, J. J. AU - Kauppinen, S. N. AU - Brady, S. G. AU - Ward, P. S. PY - 2009 DA - 2009// TI - One nutritional symbiosis begat another: phylogenetic evidence that the ant tribe Camponotini acquired Blochmannia by tending sap-feeding insects JO - BMC Evol Biol VL - 9 UR - https://doi.org/10.1186/1471-2148-9-292 DO - 10.1186/1471-2148-9-292 ID - Wernegreen2009 ER - TY - JOUR AU - Near, T. J. AU - Sanderson, M. J. PY - 2004 DA - 2004// TI - Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selection JO - Philos Trans R Soc Lond B Biol Sci VL - 359 UR - https://doi.org/10.1098/rstb.2004.1523 DO - 10.1098/rstb.2004.1523 ID - Near2004 ER - TY - JOUR AU - Ho, S. Y. W. AU - Phillips, M. J. PY - 2009 DA - 2009// TI - Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times JO - Syst Biol VL - 58 UR - https://doi.org/10.1093/sysbio/syp035 DO - 10.1093/sysbio/syp035 ID - Ho2009 ER - TY - JOUR AU - Brady, S. G. PY - 2011 DA - 2011// TI - Effects of fossil calibration-uncertainty on divergence dating in ants and bees JO - Am Ent VL - 57 UR - https://doi.org/10.1093/ae/57.1.56 DO - 10.1093/ae/57.1.56 ID - Brady2011 ER -