Conservation Genetics

, Volume 19, Issue 1, pp 99–110 | Cite as

Population genetics and distribution data reveal conservation concerns to the sky island endemic Pithecopus megacephalus (Anura, Phyllomedusidae)

  • Elisa Karen Silva Ramos
  • Rafael Félix de Magalhães
  • Eloisa Helena Reis Sari
  • Augusto Henrique Batista Rosa
  • Paulo Christiano Anchietta Garcia
  • Fabrício Rodrigues Santos
Research Article


Pithecopus megacephalus is a reticulated monkey–frog species endemic to the highlands of the Espinhaço Mountain Range in southeastern Brazil, an important centre of endemism in South America. This species has a discontinuous distribution and is considered “data-deficient” by the IUCN Red List, raising concerns about its conservation. Understanding the historical dynamics and connectivity of P. megacephalus populations can provide guidelines for preservation of this species in the wild. To investigate the population dynamics of P. megacephalus, we obtained multilocus DNA data for 55 individuals from different locations along the species’ known distribution. Spatial population structure, genetic diversity and demographic parameters were evaluated using population genetic and phylogeographical tools. We also evaluated its extent of occurrence and area of occupancy to investigate extinction risk of this species. We found genetic structure along P. megacephalus’ spatial distribution in the South Espinhaço Mountain Range corresponding to three population groups: northern, central and southern. Our results could provide important data on geographic distribution and population dynamics for a Data Deficient species. Therefore, we suggest these population data, together with the species’ limited occurrence in sky island environments could be used for a more accurate classification of P. megacephalus in the IUCN list, and conservation strategies for the species should be planned accordingly.


Genetic structure Data deficient species Espinhaço Mountain Range IUCN Red List Protected areas 



We thank Felipe Sá Fortes Leite, Laila Mascarenhas Pimenta, Camila Rabelo Rievers, Francisco Fonseca Ribeiro de Oliveira, and all institutions (cited above) for providing tissues and information for this study. We also thank to Alejandro Moliterno Vanerio and Vincenzo Alexander Ellis for reviewing the English. This research was funded by the Brazilian agencies FAPEMIG (Fundação de Amparo à Pesquisa do Estado de Minas Gerais), Fundação o Boticário de Proteção à Natureza, CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico), and CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) (Grant PROTAX 440665/2015-9). EKSR and RFM acknowledge CAPES for their graduate level fellowships. EHRS was funded by a CAPES-PNPD fellowship. AHBR acknowledges CNPq for post-graduate fellowships (130314/2016-1). FRS and PCAG are supported by CNPq research fellowships. Finally, we thanks two anonymous reviewers for valuable suggestions that improved this manuscript.

Supplementary material

10592_2017_1013_MOESM1_ESM.docx (613 kb)
Supplementary material 1 (DOCX 612 KB)


  1. Alvarado-Serrano DF, Knowles LL (2014) Ecological niche models in phylogeographic studies: applications, advances and precautions. Mol Ecol 14:233–248. doi: 10.1111/1755-0998.12184 CrossRefGoogle Scholar
  2. Angulo A (2008) Phyllomedusa megacephala. The IUCN Red List of Threatened Species.2008:e.T55857A11363174. Accessed 10 Oct 2016
  3. Avise JC (2009) Phylogeography: retrospect and prospect. J Biogeogr 36:3–15. doi: 10.1111/j.1365-2699.2008.02032.x CrossRefGoogle Scholar
  4. Bachman S, Moat J, Hill A, de la Torre J, Scott B (2011) Supporting Red List threat assessments with GeoCAT: geospatial conservation assessment tool. ZooKeys 150:117–126. doi: 10.3897/zookeys.150.2109 CrossRefGoogle Scholar
  5. Bálint M, Domisch S, Engelhardt CH, Haase P, Lehrian S, Sauer J, Theissinger K, Pauls SU, Nowak C (2011) Cryptic biodiversity loss linked to global climate change. Nat Climate Change 1:313–318. doi: 10.1038/nclimate1191 CrossRefGoogle Scholar
  6. Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48CrossRefPubMedGoogle Scholar
  7. Barata IM, Uhlig VM, Silva GH, Ferreira GB (2016) Downscaling the gap: protected areas, scientific knowledge and the conservation of amphibian species in Minas Gerais, Southeastern Brazil. S. Am J Herpetol 11:34–45. doi: 10.2994/SAJH-D-16-00006.1 CrossRefGoogle Scholar
  8. Barbosa AR, Fiorini CF, Silva-Pereira V, Mello-Silva R, Borba EL (2012) Geographical genetic structuring and phenotypic variation in the Vellozia hirsuta (Velloziaceae) ochlospecies complex. Am J Bot 99:1477–1488. doi: 10.3732/ajb.1200070 CrossRefPubMedGoogle Scholar
  9. Becker CG, Fonseca CR, Haddad CF, Batista RF, Prado PI (2007) Habitat split and the global decline of amphibians. Science 318:1775–1777. doi: 10.1126/science.1149374 CrossRefPubMedGoogle Scholar
  10. Beebee TJC (2005) Conservation genetics of amphibians. Heredity 95:423–4277. doi: 10.1038/sj.hdy.6800736 CrossRefPubMedGoogle Scholar
  11. Bonatelli IA, Perez MF, Peterson AT, Taylor NP, Zappi DC, Machado MC, Moraes EM (2014) Interglacial microrefugia and diversification of a cactus species complex: phylogeography and palaeodistributional reconstructions for Pilosocereus aurisetus and allies. Mol Ecol 23:3044–3063. doi: 10.1111/mec.12780 CrossRefPubMedGoogle Scholar
  12. Bouckaert R, Heled J, Kühnert D. Vaughan T, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A Software Platform for Bayesian evolutionary analysis. Plos Comput Biol 10:4 e1003537. doi: 10.1371/journal.pcbi.1003537 CrossRefPubMedGoogle Scholar
  13. Brandão RA, Leite FS, Françoso RD, Faivovich J (2012) Phyllomedusa megacephala (Miranda-Ribeiro 1926) (Amphibia, Anura, Hylidae, Phyllomedusinae): distribution extension, new state record and map. Herpetology Notes 5:535–537Google Scholar
  14. Bryant D, Moulton V (2003) Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 21:255–265. doi: 10.1093/molbev/msh018 CrossRefPubMedGoogle Scholar
  15. Caramaschi U (2006) Redefinição do grupo de Phyllomedusa hypochondrialis, com redescrição de P. megacephala. (Miranda-Ribeiro, 1926), revalidação de P. azurea Cope, 1862 e descrição de uma nova espécie (Amphibia, Anura, Hylidae). Arquivos do Museu Nacional 64:159–179Google Scholar
  16. Chaves AV, Freitas GH, Vasconcelos MF, Santos FR (2015) Biogeographic patterns, origin and speciation of the endemic birds from eastern Brazilian mountaintops: a review. Syst Biodivers 13:1–16. doi: 10.1080/14772000.2014.972477 CrossRefGoogle Scholar
  17. Chemale F Jr, Dussin IA, Martins M, Santos MN (2011) Nova abordagem tectono-estratigráfica do Supergrupo Espinhaço em sua porção meridional (MG). Geonomos 19:173–179. doi: 10.18285/geonomos.v19i2.52 Google Scholar
  18. Collevatti RG, Rabelo SG, Vieira RF (2009) Phylogeography and disjunct distribution in Lychnophora ericoides (Asteraceae), an endangered cerrado shrub species. Ann Bot-London 104:655–664. doi: 10.1093/aob/mcp157 CrossRefGoogle Scholar
  19. Corander J, Marttinen P (2006) Bayesian identification of admixture events using multilocus molecular markers. Mol Ecol 15:2833–2843. doi: 10.1111/j.1365-294X.2006.02994.x CrossRefPubMedGoogle Scholar
  20. Corander J, Waldmann P, Sillanpaa MJ (2003) Bayesian analysis of genetic differentiation between populations. Genetics 163:367–374PubMedPubMedCentralGoogle Scholar
  21. Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772. doi: 10.1038/nmeth.2109 CrossRefPubMedPubMedCentralGoogle Scholar
  22. DeChaine EG, Martin AP (2004) Marked genetic divergence among sky island populations of Sedum lanceolatum (Crassulaceae) in the Rocky Mountains. Am J Bot 92:477–486. doi: 10.3732/ajb.92.3.477 CrossRefGoogle Scholar
  23. Diniz-Filho JAF, Campos Telles MP, Bonatto SL, Eizirik E, Freitas TRO, Marco P Jr, Soares TN (2008) Mapping the evolutionary twilight zone: molecular markers, populations and geography. J Biogeogr 35:753–763. doi: 10.1111/j.1365-2699.2008.01912.x CrossRefGoogle Scholar
  24. Dmitriev DA, Rakitov RA (2008) Decoding of superimposed traces produced by direct sequencing of heterozygous indels. PLOS Comput Biol 4:e1000113. doi: 10.1371/journal.pcbi.1000113 CrossRefPubMedPubMedCentralGoogle Scholar
  25. Drummond AJ, Bouckaert RR (2014) Bayesian evolutionary analysis with BEAST 2. University Press, CambridgeGoogle Scholar
  26. Duellman WE, Marion AB, Hedges SB (2016) Phylogenetics, classification, and biogeography of the treefrogs (Amphibia: Anura: Arboranae). Zootaxa 4104:001–109. doi: 10.11646/zootaxa.4104.1.1 CrossRefGoogle Scholar
  27. Eterovick PC, Barros IS (2003) Niche occupancy in south-eastern Brazilian tadpole communities in montane-meadow streams. J Trop Ecol 19:439–448. doi: 10.1017/S026646740300347X CrossRefGoogle Scholar
  28. Eterovick PC, de Carnaval ACO, Borges-Nojosa DM, Silvano DL, Segalla MV, Sazima I (2005) Amphibian declines in Brazil: an overview. Biotropica 37:166–179. doi: 10.1111/j.1744-7429.2005.00024.x CrossRefGoogle Scholar
  29. Excoffier L, Lischer HE (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resources 10:564–567. doi: 10.1111/j.1755-0998.2010.02847.x CrossRefGoogle Scholar
  30. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50CrossRefGoogle Scholar
  31. Faivovich J, Haddad CF, Baeta D, Jungferd K, Ivarese G, Brandão RA, Sheil C, Barrientos LS, Barrio-Amorós CL, Cruz CA, Wheeler WC (2010) The phylogenetic relationships of the charismatic poster frogs Phyllomedusinae (Anura, Hylidae). Cladistics 25:1–35. doi: 10.1111/j.1096-0031.2009.00287.x Google Scholar
  32. Fernandes GW, Barbosa NP, Negreiros D, Paglia AP (2014) Challenges for the conservation of vanishing megadiverse rupestrian grasslands. Nat Conservação 12:162–165 doi.  10.1016/j.ncon.2014.08.003 CrossRefGoogle Scholar
  33. Flot JF, Couloux A, Tillier S (2010) Haplowebs as a graphical tool for delimiting species: a revival of Doyle’s’ field for recombination’ approach and its application to the coral genus Pocillopora in Clipperton. BMC Evol Biol 10:1–14. doi: 10.1186/1471-2148-10-372 CrossRefGoogle Scholar
  34. Freitas G, Chaves AV, Costa LM, Santos FR, Rodrigues M (2012) A new species of Cinclodes from the Espinhaço Range, southeastern Brazil: insights into the biogeographical history of the South American highlands. Ibis 154:738–755. doi: 10.1111/j.1474-919X.2012.01268.x CrossRefGoogle Scholar
  35. Galbreath KE, Hafner DJ, Zamudio KR (2009) When cold is better: climate-driven elevation shifts yield complex patterns of diversification and demography in an alpine specialist (American pika, Ochotona princeps). Evol Int J org Evolution 63:2848–2863. doi: 10.1111/j.1558-5646.2009.00803.x CrossRefGoogle Scholar
  36. Gibbard P, Kolfschoten TV (2004) The pleistocene and holocene epochs. In: Gradstein FM, Ogg JG, Smith AG (eds) A geologic time scale 2004. Cambridge University Press, Cambridge, pp 441–452Google Scholar
  37. Guillot G, Mortier F, Estoup A (2005) GENELAND: a computer package for landscape genetics. Mol Ecol Notes 5:712–715. doi: 10.1111/j.1471-8286.2005.01031.x CrossRefGoogle Scholar
  38. Hahn MW, Rausher MD, Cunningham CW (2002) Distinguishing between selection and population expansion in an experimental lineage of bacteriophage T7. Genetics 161:11–20PubMedPubMedCentralGoogle Scholar
  39. Hare MP (2001) Prospects for nuclear gene phylogeography. Trends Ecol Evol 16:700–706. doi: 10.1016/S0169-5347(01)02326-6 CrossRefGoogle Scholar
  40. He K, Jiang X (2014) Sky islands of southwest China. I: An overview of phylogeographic patterns. Chin Sci Bull 59:1–13. doi: 10.1007/s11434-013-0089-1 CrossRefGoogle Scholar
  41. Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254–267. doi: 10.1093/molbev/msj030 CrossRefPubMedGoogle Scholar
  42. IUCN (2001) IUCN red list categories and criteria: version 3.1. IUCN Species Survival Commission. IUCN, GlandGoogle Scholar
  43. IUCN (2012) IUCN red list categories and criteria: version 3.1. 2nd edn. IUCN, Gland, Switzerland and Cambridge, UKGoogle Scholar
  44. IUCN (2016) Guidelines for using the IUCN categories and criteria. Version 12. Prepared by the standards and petitions subcommittee of the IUCN Species Survival Commission. Accessed 10 Aug 2016
  45. Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web service. BMC Genet 6:13. doi: 10.1186/1471-2156-6-13 CrossRefPubMedPubMedCentralGoogle Scholar
  46. Joly S, Bryant D, Lockhart PJ (2015) Flexible methods for estimating genetic distances from single nucleotide polymorphisms. Methods Ecol Evol 6:938–948. doi: 10.1111/2041-210X.12343 CrossRefGoogle Scholar
  47. Knowles LL (2000) Tests of Pleistocene speciation in montane grasshoppers (genus Melanoplus) from the sky islands of western North America. Evol Int J org Evol 54:1337–1348. doi: 10.1111/j.0014-3820.2000.tb00566.x CrossRefGoogle Scholar
  48. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. doi: 10.1093/molbev/msw054 CrossRefPubMedGoogle Scholar
  49. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948. doi: 10.1093/bioinformatics/btm404 CrossRefPubMedGoogle Scholar
  50. Leigh JW, Bryant D (2015) POPART: full-feature software for haplotype network construction. Methods Ecol Evol 6:1110–1116. doi: 10.1111/2041-210X.12410 CrossRefGoogle Scholar
  51. Leite FSF (2012) Taxonomia, biogeografia e conservação dos anfíbios da Serra do Espinhaço. Tese, Universidade Federal de Minas GeraisGoogle Scholar
  52. Leite FSF, Juncá FA, Eterovick PC (2008) Status do conhecimento, endemismo e conservação de anfíbios anuros da Cadeia do Espinhaço. Brasil Megadiversidade 4:158–176Google Scholar
  53. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452. doi: 10.1093/bioinformatics/btp187 CrossRefPubMedGoogle Scholar
  54. Lousada JM, Borba EL, Ribeiro KT, Ribeiro LC, Lovato MB (2011) Genetic structure and variability of the endemic and vulnerable Vellozia gigantea (Velloziaceae) associated with the landscape in the Espinhaço Range, in southeastern Brazil: implications for conservation. Genetica 139:431–440. doi: 10.1007/s10709-011-9561-5 CrossRefPubMedGoogle Scholar
  55. Lousada JM, Lovato MB, Borba EL (2013) High genetic divergence and low genetic variability in disjunct populations of the endemic Vellozia compacta (Velloziaceae) occurring in two edaphic environments of Brazilian campos rupestres. Braz J Bot 36:45–53. doi: 10.1007/s40415-013-0001-x CrossRefGoogle Scholar
  56. Moraes EM, Yotoko KSC, Manfrin MH, Solferini VN, Sene FM (2009) Phylogeography of the cactophilic species Drosophila gouveai: demographic events and divergence timing in dry vegetation enclaves in eastern Brazil. J Biogeogr 36:2136–2147. doi: 10.1111/j.1365-2699.2009.02145.x CrossRefGoogle Scholar
  57. Morais AR, Siqueira MN, Lemes P, Maciel NM, De Marco Jr P, Brito D (2013) Unraveling the conservation status of Data Deficient species. Biol Conserv 166:98–102. doi: 10.1016/j.biocon.2013.06.010 CrossRefGoogle Scholar
  58. Myers N, Mittermeier RA, Mittermeier CG, Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403:853–858. doi: 10.1038/35002501 CrossRefPubMedGoogle Scholar
  59. Nabholz B, Glemin S, Galtier N (2007) Strong variations of mitochondrial mutation rate across mammals—the longevity hypothesis. Mol Biol Evol 25:120–130. doi: 10.1093/molbev/msm248 CrossRefPubMedGoogle Scholar
  60. Oliveira FFR, Nogueira PAG, Eterovick PC (2012) Natural history of Phyllomedusa megacephala (Miranda-Ribeiro, 1926) (Anura: Hylidae) in southeastern Brazil, with descriptions of its breeding biology and male territorial behaviour. J Nat Hist 46:117–129. doi: 10.1080/00222933.2011.626127 CrossRefGoogle Scholar
  61. Pauls SU, Nowak C, Bálint M, Pfenninger M (2013) The impact of global climate change on genetic diversity within populations and species. Mol Ecol 22:925–946. doi: 10.1111/mec.12152 CrossRefPubMedGoogle Scholar
  62. Pimm SL, Jenkins CN, Abell R, Brooks TM, Gittleman JL, Joppa LN, Sexton JO (2014) The biodiversity of species and their rates of extinction, distribution, and protection. Science 344:1246752-1–1246752-10. doi: 10.1126/science.1246752 CrossRefGoogle Scholar
  63. Posada D, Crandall KA, Templeton AR (2000) GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Mol Ecol 9:487–488. doi: 10.1046/j.1365-294x.2000.00887.x CrossRefPubMedGoogle Scholar
  64. Pounds AJ, Bustamante MR, Coloma LA, Consuegra AA, Fogden MPL, Foster PN, Young BE (2006) Widespread amphibian extinctions from epidemic disease driven by global warming. Nature 439:161–167. doi: 10.1038/nature04246 CrossRefPubMedGoogle Scholar
  65. Prado CPA, Haddad CFB, Zamudio KR (2012) Cryptic lineages and Pleistocene population expansion in a Brazilian Cerrado frog. Mol Ecol 21:921–941. doi: 10.1111/j.1365-294X.2011.05409.x CrossRefPubMedGoogle Scholar
  66. R Core Team (2016). R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna
  67. Saadi A (1995) A geomorfologia da Serra do Espinhaço em Minas Gerais e de suas margens. Geonomos 3:41–63CrossRefGoogle Scholar
  68. Salerno PE, Señaris JC, Rojas-Runjaic FJM, Cannatella DC (2015) Recent evolutionary history of Lost World endemics: population genetics, species delimitation, and phylogeography of sky-island treefrogs. Mol Phylogenet Evol 82:314–323. doi: 10.1016/j.ympev.2014.10.020 CrossRefPubMedGoogle Scholar
  69. Sambrook J, Russel DW (2001) Molecular cloning: a laboratory manual. CSH Laboratory Press, Cold Spring Harbor, NYGoogle Scholar
  70. Silveira FAO, Negreiros D, Barbosa NPU et al (2016) Ecology and evolution of plant diversity in the endangered campo rupestre: a neglected conservation priority. Plant Soil. doi: 10.1007/s11104-015-2637-8 Google Scholar
  71. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978–989. doi: 10.1086/319501 CrossRefPubMedPubMedCentralGoogle Scholar
  72. Storfer A, Murphy MA, Spear SF, Holderegger R, Waits LP (2010) Landscape genetics: where are we now? Mol Ecol 19:3496–3514. doi: 10.1111/j.1365-294X.2010.04691.x CrossRefPubMedGoogle Scholar
  73. Stuart SN (2008) Threatened amphibians of the world, 1. edn. Lynx, BarcelonaGoogle Scholar
  74. Sunnucks P (2000) Efficient genetic markers for population biology. Trends Ecol Evol 15:376–377. doi: 10.1016/S0169-5347(00)01825-5 Google Scholar
  75. Trovó M, Andrade MG, Sano P, Ribeiro P, Van den Berg C (2013) Molecular phylogeny and biogeography of Neotropical Paepalanthoideae with emphasis on Brazilian Paepalanthus (Eriocaulaceae). Bot J Linn Soc 171:225–243. doi: 10.1111/j.1095-8339.2012.01310.x CrossRefGoogle Scholar
  76. Turchetto-Zolet AC, Pinheiro F, Salgueiro F, Palma-Silva C (2013) Phylogeographical patterns shed light on evolutionary process in South America. Mol Ecol 22:1193–1213. doi: 10.1111/mec.12164 CrossRefPubMedGoogle Scholar
  77. Warshall P (1994) The madrean sky island archipelago: a planetary overview. In: DeBano L, Ffolliott P, Ortega-Rubio A, Gottfried G, Hamre R, Edminster C (eds) Biodiversity and management of the Madrean Archipelago: the Sky Islands of Southwestern United States and Northwestern Mexico. US Department of Agriculture, Forest Service, Fort Collins, pp 6–18Google Scholar
  78. Weeks AR, Sgro CM, Young AG, Frankham R, Mitchell NJ, Miller KA, Hoffmann AA (2011) Assessing the benefits and risks of translocations in changing environments: a genetic perspective. Evol Appl 4:709–725. doi: 10.1111/j.1752-4571.2011.00192.x CrossRefPubMedPubMedCentralGoogle Scholar
  79. Weeks AR, Stoklosa J, Hoffmann AA (2016) Conservation of genetic uniqueness of populations may increase extinction likelihood of endangered species: the case of Australian mammals. Front Zool 13:31. doi: 10.1186/s12983-016-0163-z CrossRefPubMedPubMedCentralGoogle Scholar
  80. Young BE, Stuart SN, Chanson JS, Cox NA, Boucher T M (2004) Disappearing jewels: the status of new world amphibians. NatureServe, ArlingtonGoogle Scholar
  81. Zeisset I, Beebee T J C (2008) Amphibian phylogeography: a model for understanding historical aspects of species distributions. Heredity 101:109–119. doi: 10.1038/hdy.2008.30 CrossRefPubMedGoogle Scholar

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© Springer Science+Business Media B.V. 2017

Authors and Affiliations

  1. 1.Departamento de Biologia Geral, Instituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
  2. 2.Departamento de Zoologia, Instituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil

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