Early Bird Publications

Website designed by Sushma Reddy and Edward Braun. Updated by Edward Braun on 10 August 2013

Early Bird has produced a number of publications that can be divided into three major categories. The primary focus of the Early Bird project was deep avian phylogenetics and the related resource development, and we have have written a number of paper describing the evolution of birds as a whole or relationships within specific orders.

Early Bird also included studies of comparative molecular and organismal evolution and a number of additional publications focused on a variety of topics including phylogenomics and more recent evolutionary divergences. In addition to the alphabetical lists within these categories we also provide a complete chronological list of Early Bird publications.

Early Bird publication woordle

Word cloud summarizing a subset of Early Bird publications focused on deep avian phylogentics. The word cloud was produced using wordle.

Deep Avian Phylogenetics

Amaral, F.S.R., F.H. Sheldon, A. Gamauf, E. Haring, M.J. Riesing, L.F. Silveira, and A. Wajntal.  2009. Patterns and processes of diversification in a widespread and ecologically diverse avian group, the buteonine hawks (Aves, Accipitridae). Molecular Phylogenetics and Evolution, 53:  703-715.

Amaral, F.S.R., F.H. Sheldon, and A. Wajntal.  2010.  Towards an assessment of character interdependence in avian RNA phylogenetics: a general secondary structure model for the avian mitochondrial 16S rRNA.  Molecular Phylogenetics and Evolution, 56: 498-506.

Bonilla, A.J., E.L. Braun, and R.T. Kimball. 2010. Comparative molecular evolution and phylogenetic utility of 3'-UTRs and introns in Galliformes. Molecular Phylogenetics and Evolution, 56: 536-542. [full text]

Chojnowski, J.L., R.T. Kimball, and E.L. Braun. 2008. Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes. Gene, 410: 89-96. [full text]

Cox, W.A., R.T. Kimball, and E.L. Braun. 2007. Phylogenetic position of the New World quail (Odontophoridae): Eight nuclear loci and three mitochondrial regions contradict morphology and the Sibley-Ahlquist tapestry. The Auk, 124: 71-84. [full text]

Gibb, G.C., O. Kardailsky, R.T. Kimball, E.L. Braun, and D. Penny. 2007. Mitochondrial genomes and avian phylogeny: Complex characters and resolvability without explosive radiations. Molecular Biology and Evolution, 24: 269-280. [full text]

Hackett, S.J., R.T. Kimball, S. Reddy, R.C.K. Bowie, E.L. Braun, M.J. Braun, J.L. Chojnowski, W.A. Cox, K.-L. Han, J. Harshman, C. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, F.H. Sheldon, D.W. Steadman, C.C. Witt and T. Yuri. 2008. A phylogenomic study of birds reveals their evolutionary history. Science, 320: 1763-1768. [full text] [supplementary information]
    Science podcast by R.T. Kimball
    Featured as a News Focus [Pennisi 2008 Science, 320: 1716-7]

Han, K.-L., M.B. Robbins, and M.J. Braun. 2010. A multi-gene estimate of phylogeny in the nightjars and nighthawks (Caprimulgidae). Molecular Phylogenetics and Evolution, 55: 443-453.

Harshman, J., E.L. Braun, M.J. Braun, C.J. Huddleston, R.C.K. Bowie, J.L. Chojnowski, S.J. Hackett, K-L. Han, R.T. Kimball, B.D. Marks, K.J. Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, S.J. Steppan, C.C. Witt, and T. Yuri. 2008. Phylogenomic evidence for multiple losses of flight in ratite birds. Proceedings of the National Academy of Sciences, 105:13462-13467. [full text] [supplementary information]

Kimball, R.T. and E.L. Braun. 2008. A multigene phylogeny of Galliformes supports a single origin of erectile ability in non-feathered facial traits. Journal of Avian Biology, 39: 438-445. [full text]

Kimball, R.T., E.L. Braun, R.C.K. Bowie, M.J. Braun, J.L. Chojnowski, S.J. Hackett, K.-L. Han, J. Harshman, V. Heimer-Torres, W. Holznagel, C.J. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, J.V. Smith, C.C. Witt, and T. Yuri. 2009. A set of resources to amplify nuclear regions across the avian genome. Molecular Phylogenetics and Evolution, 50: 654-660. [full text]

Kimball, R.T, C.M. St. Mary, and E.L. Braun. 2011. A macroevolutionary perspective on multiple sexual traits in the Phasianidae (Galliformes). International Journal of Evolutionary Biology, Article ID 423938. [full text with corrigendum]
NOTE: After publication we noticed that bootstrap support had been inadvertently omitted from the final tree figure. We have appended a corrected figure as a corrigendum.

Kimball, R.T., N. Wang, V. Heimer-McGinn, C. Ferguson, and E.L. Braun. 2013. Identifying localized biases in large datasets: A case study using the avian tree of life. Molecular Phylogenetics and Evolution, 69:1021-1032. [full text] (link to doi: http://dx.doi.org/10.1016/j.ympev.2013.05.029).

Smith, J.V., E.L. Braun, R.T. Kimball. 2013. Ratite nonmonophyly: independent evidence from 40 novel loci. Systematic Biology, 62: 35-49. [full text]

Steadman, D.W. 2008. Doves (Columbidae) and cuckoos (Cuclidae) from the early Miocene of Florida. Bulletin of the Florida Museum of Natural History, 48: 1-16.

Wang, N., E.L. Braun, R.T. Kimball. 2012. Testing hypotheses about the sister group of the passeriformes using an independent 30-locus data set. Molecular Biology and Evolution, 29: 737-750. [full text] [supplementary information]

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Comparative Molecular and Organismal Evolution

Braun, E.L., R.T. Kimball, K.-L. Han, N.R. Iuhasz-Velez, A.J. Bonilla, J.L. Chojnowski, J.V. Smith, R.C.K. Bowie, M.J. Braun, S.J. Hackett, J. Harshman, C.J. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, C.C. Witt, and T. Yuri. 2011. Homoplastic microinversions and the avian tree of life. BMC Evolutionary Biology, 11:141. [full text] [additional files]

Franklin, J. and D.W. Steadman. 2008 Prehistoric species richness of birds on oceanic islands. Oikos 117: 1885-1891.

Han, K.-L., E.L. Braun, R.T. Kimball, S. Reddy, R.C.K. Bowie, M.J. Braun, J.L. Chojnowski, S.J. Hackett, J. Harshman, C.J. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, F.H. Sheldon, D.W. Steadman, C.C. Witt, and T. Yuri. 2011. Are transposable element insertions homoplasy free?: An examination using the avian tree of life. Systematic Biology, 60: 375-386.

Steadman, D.W. 2005. The paleoecology and fossil history of migratory landbirds. pp. 5-17 in R.S. Greenberg and P.P. Marra, eds. Birds of Two Worlds. Johns Hopkins University Press, Baltimore, MD

Steadman, D. W. 2006. Extinction and Biogeography of Tropical Pacific Birds. University of Chicago Press, Chicago, IL. 577 pp. + index. [see at Amazon]

Steadman, D.W. and Ó. Carranza-Castañeda. 2006. Early Pliocene to early Pleistocene birds from central México. Pp. 61-71 in Ó. Carranza-Castañeda & E.H. Lindsay, eds. Advances in Late Tertiary Vertebrate Paleontology in México. Universidad Nacional Autónoma de México, Instituto de Geología y Centro de Geociencias, Publicación Especial No. 4.

Yuri, T., M.J. Braun, R.T. Kimball, and E.L. Braun. 2008. Duplication and accelerated evolution of growth hormone gene in passerine birds. Molecular Biology and Evolution 25: 352-361. [full text][supplementary figure S1] [excel file for supplementary data 1[excel file for supplementary data 1]
NOTE: The originally published title was an error (the published erratum is included in the pdf available here)

Yuri, T., R.T. Kimball, J. Harshman, R.C.K. Bowie, M.J. Braun, J.L. Chojnowski, K.-L. Han, S.J. Hackett, C.J. Huddleston, W.S. Moore, S. Reddy, F.H. Sheldon, C.C. Witt, and E.L. Braun. 2013. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. Biology, 2:419-444. [full text] [a version with supplementary data describing revised taxonomy information relevant to this study is available in a pdf]

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Other Papers Facilitated by Early Bird

Chojnowski, J.L. and E.L. Braun. 2008. Turtle isochore structure is intermediate between amphibians and other amniotes. Integrative and Comparative Biology, 48: 454-462.

Cleere, N., A.W. Kratter, D.W. Steadman, M.J. Braun, C.J. Huddleston, C.E. Filardi and G. Dutson. 2007. A new genus of frogmouth (Podargidae) from the Solomon Islands – results from a taxonomic review of Podargus ocellatus inexpectatus Hartert 1901. Ibis, 149:271-286.

Katsu Y, E.L. Braun, L.J. Guillette Jr., and T. Iguchi. 2009. From reptilian phylogenomics to reptilian genomes: analyses of c-Jun and DJ-1 proto-oncogenes. Cytogenetic and Genome Research, 127: 79-93.

Kirchman, J.J. and D.W. Steadman. 2005. Rails (Aves: Rallidae: Gallirallus) from prehistoric sites in the Kingdom of Tonga, including description of a new species. Proceedings of the Biological Society of Washington, 118:465-477.

Kirchman, J.J. and D.W. Steadman. 2006. Rails (Rallidae: Gallirallus) from prehistoric archaeological sites in Western Oceania. Zootaxa, 1316:1-31.

Marks, B. D. 2010. Are lowland rainforests really evolutionary museums? Phylogeography of the green hylia (Hylia prasina) in the Afrotropics. Molecular Phylogenetics and Evolution, 55: 178-184.

Marks, B.D., J.D. Weckstein, and R.G. Moyle. 2007. Molecular phylogenetics of the bee-eaters (Aves: Meropidae) based on nuclear and mitochondrial DNA sequence data. Molecular Phylogenetics and Evolution, 45: 23-32.

Moyle, R.G, J. Cracraft, M. Lakim, J. Nais, and F.H. Sheldon. 2006. Reconsideration of the phylogenetic relationships of the enigmatic Bornean Bristlehead (Pityriasis gymnocephala). Molecular Phylogenetics and Evolution, 39: 893-898.

Moyle, R.G., J. Fuchs, E. Pasquet, and B.D. Marks. 2007. Feeding behavior, toe count, and the phylogenetic relationships among alcedinine kingfishers. Journal of Avian Biology, 38: 317-326.

Moyle, R. G. and B. D. Marks. 2006. Phylogenetic relationships of the bulbuls (Aves: Pycnonotidae) based on mitochondrial and nuclear DNA sequence data. Molecular Phylogenetics and Evolution, 40: 687-695.

Sheldon, F.H., D. J. Lohman, H.C. Lim, F. Zou, S.M. Goodman, D.M. Prawiradilaga, K. Winker, T.M. Braile, and R.G. Moyle. 2009. Phylogeography of the magpie-robin species complex (Aves: Turdidae: Copsychus) reveals a Philippine species, an interesting isolating barrier, and unusual dispersal patterns in the Indian Ocean and Southeast Asia. Journal of Biogeography 36:1070-1083.

Steadman, D.W. 2006. A new species of extinct tooth-billed pigeon (Didunculus) from the Kingdom of Tonga, and the concept of endemism in insular landbirds. Journal of Zoology, 268: 233-241.

Whiteman, N.K., R.T. Kimball, and P.G. Parker. 2007. Co-phylogeography and comparative population genetics of the threatened Galápagos hawk and three ectoparasite species: ecology shapes population histories within parasite communities. Molecular Ecology, 16: 4759-4773.

Zou, F.S., H.C. Lim, B. Marks, R.G. Moyle, and F.H. Sheldon. 2007. Molecular phylogenetic analysis of the Grey-cheeked Fulvetta (Alcippe morrisonia) of China and Indochina: A case of remarkable genetic divergence in a “species."  Molecular Phylogenetics and Evolution, 44: 165-174.118:465-477.

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Chronological List

2014:

Kimball, R.T. and E.L. Braun. 2014 Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix. PeerJ, 2:e361. [full text] link to the full text at PeerJ.

Meiklejohn, K.A., M.J. Danielson, B.C. Faircloth, T.C. Glenn, E.L. Braun, and R.T. Kimball. 2014. Incongruence among different mitochondrial regions: A case study using complete mitogenomes. Molecular Phylogenetics and Evolution, 78:314-323. [full text] (doi: 10.1016/j.ympev.2014.06.003)

2013:

Kimballl, R.T., N. Wang, V. Heimer-McGinn, C. Ferguson, and E.L. Braun. 2013. Identifying localized biases in large datasets: A case study using the avian tree of life. Molecular Phylogenetics and Evolution, 69:1021-1032. [full text] (doi: 10.1016/j.ympev.2013.05.029).

Smith, J.V., E.L. Braun, R.T. Kimball. 2013. Ratite nonmonophyly: independent evidence from 40 novel loci. Systematic Biology, 62: 35-49. [full text]

Yuri, T., R.T. Kimball, J. Harshman, R.C.K. Bowie, M.J. Braun, J.L. Chojnowski, K.-L. Han, S.J. Hackett, C.J. Huddleston, W.S. Moore, S. Reddy, F.H. Sheldon, C.C. Witt, and E.L. Braun. 2013. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. Biology, 2:419-444. [full text] [a version with supplementary data describing revised taxonomy information relevant to this study is available in a pdf]

2012:

Wang, N., E.L. Braun, R.T. Kimball. 2012. Testing hypotheses about the sister group of the passeriformes using an independent 30-locus data set. Molecular Biology and Evolution, 29: 737-750. [full text] [supplementary information]

2011:

Braun, E.L., R.T. Kimball, K.-L. Han, N.R. Iuhasz-Velez, A.J. Bonilla, J.L. Chojnowski, J.V. Smith, R.C.K. Bowie, M.J. Braun, S.J. Hackett, J. Harshman, C.J. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, C.C. Witt, and T. Yuri. 2011. Homoplastic microinversions and the avian tree of life. BMC Evolutionary Biology, 11:141. [full text] [additional files]

Han, K.-L., E.L. Braun, R.T. Kimball, S. Reddy, R.C.K. Bowie, M.J. Braun, J.L. Chojnowski, S.J. Hackett, J. Harshman, C.J. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, F.H. Sheldon, D.W. Steadman, C.C. Witt, and T. Yuri. 2011. Are transposable element insertions homoplasy free?: An examination using the avian tree of life. Systematic Biology, 60: 375-386.

Kimball, R.T, C.M. St. Mary, and E.L. Braun. 2011. A Macroevolutionary Perspective on Multiple Sexual Traits in the Phasianidae (Galliformes). International Journal of Evolutionary Biology, Article ID 423938.  [full text with corrigendum]

2010:

Amaral, F.S.R., F.H. Sheldon, and A. Wajntal.  2010.  Towards an assessment of character interdependence in avian RNA phylogenetics: a general secondary structure model for the avian mitochondrial 16S rRNA.  Molecular Phylogenetics and Evolution, 56: 498-506.

Bonilla, A.J., E.L. Braun, and R.T. Kimball. 2010. Comparative molecular evolution and phylogenetic utility of 3'-UTRs and introns in Galliformes. Molecular Phylogenetics and Evolution, 56: 536-542. [full text]

Han, K.-L., M.B. Robbins, and M.J. Braun. 2010. A multi-gene estimate of phylogeny in the nightjars and nighthawks (Caprimulgidae). Molecular Phylogenetics and Evolution, 55: 443-453. 

Marks, B. D. 2010. Are lowland rainforests really evolutionary museums? Phylogeography of the green hylia (Hylia prasina) in the Afrotropics. Molecular Phylogenetics and Evolution, 55: 178-184.

2009:

Amaral, F.S.R., F.H. Sheldon, A. Gamauf, E. Haring, M.J. Riesing, L.F. Silveira, and A. Wajntal.  2009. Patterns and processes of diversification in a widespread and ecologically diverse avian group, the buteonine hawks (Aves, Accipitridae). Molecular Phylogenetics and Evolution, 53:  703-715.

Katsu Y, E.L. Braun, L.J. Guillette Jr., and T. Iguchi. 2009. From reptilian phylogenomics to reptilian genomes: analyses of c-Jun and DJ-1 proto-oncogenes. Cytogenetic and Genome Research, 127: 79-93.

Kimball, R.T., E.L. Braun, R.C.K. Bowie, M.J. Braun, J.L. Chojnowski, S.J. Hackett, K.-L. Han, J. Harshman, V. Heimer-Torres, W. Holznagel, C.J. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, J.V. Smith, C.C. Witt, and T. Yuri. 2009. A set of resources to amplify nuclear regions across the avian genome. Molecular Phylogenetics and Evolution, 50: 654-660. [full text]

Sheldon, F.H., D. J. Lohman, H.C. Lim, F. Zou, S.M. Goodman, D.M. Prawiradilaga, K. Winker, T.M. Braile, and R.G. Moyle. 2009. Phylogeography of the magpie-robin species complex (Aves: Turdidae: Copsychus) reveals a Philippine species, an interesting isolating barrier, and unusual dispersal patterns in the Indian Ocean and Southeast Asia. Journal of Biogeography 36:1070-1083.

2008:

Chojnowski, J.L., R.T. Kimball, and E.L. Braun. 2008. Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes. Gene, 410: 89-96. [full text]

Chojnowski, J.L. and E.L. Braun. 2008. Turtle isochore structure is intermediate between amphibians and other amniotes. Integrative and Comparative Biology, 48: 454-462.

Franklin, J. and D.W. Steadman. 2008 Prehistoric species richness of birds on oceanic islands. Oikos 117: 1885-1891.

Hackett, S.J., R.T. Kimball, S. Reddy, R.C.K. Bowie, E.L. Braun, M.J. Braun, J.L. Chojnowski, W.A. Cox, K.-L. Han, J. Harshman, C. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, F.H. Sheldon, D.W. Steadman, C.C. Witt and T. Yuri. 2008. A phylogenomic study of birds reveals their evolutionary history. Science, 320: 1763-1768. [full text] [supplementary information]
    Science podcast by R.T. Kimball
    Featured as a News Focus [Pennisi 2008 Science, 320: 1716-7]

Harshman, J., E.L. Braun, M.J. Braun, C.J. Huddleston, R.C.K. Bowie, J.L. Chojnowski, S.J. Hackett, K-L. Han, R.T. Kimball, B.D. Marks, K.J. Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, S.J. Steppan, C.C. Witt, and T. Yuri. 2008. Phylogenomic evidence for multiple losses of flight in ratite birds. Proceedings of the National Academy of Sciences, 105:13462-13467. [full text] [supplementary information]

Kimball, R.T. and E.L. Braun. 2008.A multigene phylogeny of Galliformes supports a single origin of erectile ability in non-feathered facial traits. Journal of Avian Biology, 39: 438-445. [full text]

Steadman, D.W. 2008. Doves (Columbidae) and cuckoos (Cuclidae) from the early Miocene of Florida. Bulletin of the Florida Museum of Natural History, 48: 1-16.

Yuri, T., M.J. Braun, R.T. Kimball, and E.L. Braun. 2008. Duplication and accelerated evolution of growth hormone gene in passerine birds. Molecular Biology and Evolution 25: 352-361. [full text][supplementary figure S1] [excel file for supplementary data 1[excel file for supplementary data 1]
NOTE: The originally published title was an error (the published erratum is included in the pdf available here)

2007:

Cleere, N., A.W. Kratter, D.W. Steadman, M.J. Braun, C.J. Huddleston, C.E. Filardi and G. Dutson. 2007. A new genus of frogmouth (Podargidae) from the Solomon Islands – results from a taxonomic review of Podargus ocellatus inexpectatus Hartert 1901. Ibis, 149:271-286.

Cox, W.A., R.T. Kimball, and E.L. Braun. 2007. Phylogenetic position of the New World quail (Odontophoridae): Eight nuclear loci and three mitochondrial regions contradict morphology and the Sibley-Ahlquist tapestry. The Auk, 124: 71-84. [full text]

Gibb, G.C., O. Kardailsky, R.T. Kimball, E.L. Braun, and D. Penny. 2007. Mitochondrial genomes and avian phylogeny: Complex characters and resolvability without explosive radiations. Molecular Biology and Evolution, 24: 269-280. [full text]

Marks, B.D., J.D. Weckstein, and R.G. Moyle. 2007. Molecular phylogenetics of the bee-eaters (Aves: Meropidae) based on nuclear and mitochondrial DNA sequence data. Molecular Phylogenetics and Evolution, 45: 23-32.

Moyle, R.G., J. Fuchs, E. Pasquet, and B.D. Marks. 2007. Feeding behavior, toe count, and the phylogenetic relationships among alcedinine kingfishers. Journal of Avian Biology, 38: 317-326.

Whiteman, N.K., R.T. Kimball, and P.G. Parker. 2007. Co-phylogeography and comparative population genetics of the threatened Galápagos hawk and three ectoparasite species: ecology shapes population histories within parasite communities. Molecular Ecology, 16: 4759-4773.

Zou, F.S., H.C. Lim, B. Marks, R.G. Moyle, and F.H. Sheldon. 2007. Molecular phylogenetic analysis of the Grey-cheeked Fulvetta (Alcippe morrisonia) of China and Indochina: A case of remarkable genetic divergence in a “species."  Molecular Phylogenetics and Evolution, 44: 165-174.

2006:

Kirchman, J.J. and D.W. Steadman. 2006. Rails (Rallidae: Gallirallus) from prehistoric archaeological sites in Western Oceania. Zootaxa, 1316:1-31.

Moyle, R.G, J. Cracraft, M. Lakim, J. Nais, and F.H. Sheldon. 2006. Reconsideration of the phylogenetic relationships of the enigmatic Bornean Bristlehead (Pityriasis gymnocephala). Molecular Phylogenetics and Evolution,39: 893-898.

Moyle, R. G. and B. D. Marks. 2006. Phylogenetic relationships of the bulbuls (Aves: Pycnonotidae) based on mitochondrial and nuclear DNA sequence data. Molecular Phylogenetics and Evolution, 40: 687-695.

Steadman, D.W. 2006. A new species of extinct tooth-billed pigeon (Didunculus) from the Kingdom of Tonga, and the concept of endemism in insular landbirds. Journal of Zoology, 268: 233-241.

Steadman, D. W. 2006. Extinction and Biogeography of Tropical Pacific Birds. University of Chicago Press, Chicago, IL. 577 pp. + index.[see at Amazon]

Steadman, D.W. and Ó. Carranza-Castañeda. 2006. Early Pliocene to early Pleistocene birds from central México. Pp. 61-71 in Ó. Carranza-Castañeda & E.H. Lindsay, eds. Advances in Late Tertiary Vertebrate Paleontology in México. Universidad Nacional Autónoma de México, Instituto de Geología y Centro de Geociencias, Publicación Especial No. 4.

2005:

Kirchman, J.J. and D.W. Steadman. 2005. Rails (Aves: Rallidae: Gallirallus) from prehistoric sites in the Kingdom of Tonga, including description of a new species. Proceedings of the Biological Society of Washington, 118:465-477.

Steadman, D. W. 2005. The paleoecology and fossil history of migratory landbirds. pp. 5-17 in R.S. Greenberg and P.P. Marra, eds. Birds of Two Worlds. Johns Hopkins University Press, Baltimore, MD

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