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genes in the pathogenic genus Treponema","volume":"23","author":"R Gray","year":"2006","journal-title":"Molecular biology and evolution"},{"key":"ref9","first-page":"99","article-title":"A treponematosis dated from the Late Roman Empire in Normandie, France","volume":"1493","author":"J Blondiaux","year":"1994","journal-title":"L\u2019Origine de la syphilis en Europe: Avant ou apr\u00e9s"},{"issue":"4","key":"ref10","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1002\/ajpa.20335","article-title":"Histological identification of syphilis in pre-Columbian England","volume":"129","author":"TE von Hunnius","year":"2006","journal-title":"American Journal of Physical Anthropology"},{"issue":"5","key":"ref11","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1086\/203691","article-title":"The origin and antiquity of syphilis: paleopathological diagnosis and interpretation","volume":"29","author":"B Baker","year":"1988","journal-title":"Current anthropology"},{"issue":"Suppl 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Microbiology and Infectious Diseases"},{"key":"ref18","first-page":"89","article-title":"S\u00edfilis en la Ciudad de M\u00e9xico: an\u00e1lisis osteopatol\u00f3gico","volume":"22","author":"L M\u00e1rquez Morf\u00edn","year":"2015","journal-title":"Cuicuilco"},{"key":"ref19","unstructured":"Escobedo Ram\u00edrez DAR, M.; Berdeja Mart\u00ednez, J. A.; G\u00f3mez Mart\u00ednez, A. E. Reporte General del Proyecto Arqueologico Santa Isabel. Estacionamiento Bellas Artes. Subbdireccion de Salvamento Arqueologico, INAH, Mexico City. 1995."},{"key":"ref20","author":"L Scheuer","year":"2000"},{"key":"ref21","article-title":"Excavation, Analysis, Interpretation","author":"D Ubelaker","year":"1978"},{"key":"ref22","author":"M Massler","year":"1958"},{"issue":"1","key":"ref23","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1002\/oa.1390040107","article-title":"Accuracy of age estimation from developing teeth of a population of known age (0\u20135.4 years)","volume":"4","author":"HM Liversidge","year":"1994","journal-title":"International Journal of Osteoarchaeology"},{"key":"ref24","unstructured":"Jeanty P, Romero R. Normal values for the leg. In: R Romero, G Pilu, P Jeanty, A Ghidini, J C Hobbins (eds) Prenatal Diagnosis of Congenital Anomalies Appleton and Lange: Norwalk. 1983:324."},{"key":"ref25","unstructured":"Buikstra JE, Ubelaker DH. Standards for data collection from human skeletal remains: Proceedings of a seminar at the Field Museum of Natural History (Arkansas Archaeology Research Series 44). Fayetteville Arkansas Archaeological Survey. 1994."},{"key":"ref26","author":"DJ Ortner","year":"2003"},{"key":"ref27","author":"ML Powell","year":"2005"},{"issue":"5","key":"ref28","doi-asserted-by":"crossref","first-page":"1402","DOI":"10.1093\/clinids\/20.5.1402","article-title":"Treponemal disease revisited: Skeletal discriminators for Yaws, Bejel, and venereal syphilis","volume":"20","author":"BM Rothschild","year":"1995","journal-title":"Clinical Infectious Diseases"},{"issue":"509","key":"ref29","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1259\/0007-1285-43-509-333","article-title":"The lesions of congenital syphilis","volume":"43","author":"B Cremin","year":"1970","journal-title":"The British journal of radiology"},{"key":"ref30","first-page":"2448","article-title":"Diagnosis of bone and joint disorders","author":"D Resnick","year":"1995"},{"key":"ref31","author":"AC Aufderheide","year":"1998"},{"key":"ref32","first-page":"66","article-title":"S\u00edfilis cong\u00e9nita: Presentaci\u00f3n de un caso radiol\u00f3gico","volume":"51","author":"J Chungara","year":"2006","journal-title":"Cuadernos"},{"issue":"10","key":"ref33","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1016\/S1473-3099(15)00136-X","article-title":"Challenges and key research questions for yaws eradication","volume":"15","author":"M Marks","year":"2015","journal-title":"The Lancet Infectious diseases"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.24201\/hm.v64i3.3000","article-title":"La s\u00edfilis y su car\u00e1cter end\u00e9mico en la Ciudad de M\u00e9xico","volume":"64","author":"L M\u00e1rquez Morf\u00edn","year":"2015","journal-title":"Historia Mexicana"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"177","DOI":"10.24201\/edu.v31i1.1507","article-title":"Mortalidad de ni\u00f1os y s\u00edfilis cong\u00e9nita en la Ciudad de M\u00e9xico en 1915","volume":"31","author":"L M\u00e1rquez 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Picard Tools version 1.140 2016."},{"key":"ref82","first-page":"btt193","article-title":"mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters","author":"H J\u00f3nsson","year":"2013","journal-title":"Bioinformatics"},{"issue":"5","key":"ref83","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"MA DePristo","year":"2011","journal-title":"Nat Genet"},{"issue":"2","key":"ref84","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"P Cingolani","year":"2012","journal-title":"Fly"},{"issue":"W1","key":"ref85","doi-asserted-by":"crossref","first-page":"W58","DOI":"10.1093\/nar\/gkw233","article-title":"HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing","volume":"44","author":"H Weissensteiner","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"ref86","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"A Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"issue":"7","key":"ref87","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets","volume":"33","author":"S Kumar","year":"2016","journal-title":"Molecular biology and evolution"},{"key":"ref88","unstructured":"Rambaut AS, M.A.; Xie, D.; Drummond, A.J. Tracer v1.6, Available from <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/beast.bio.ed.ac.uk\/Tracer\" xlink:type=\"simple\">http:\/\/beast.bio.ed.ac.uk\/Tracer<\/ext-link>. 2014."},{"issue":"6","key":"ref89","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"AR Quinlan","year":"2010","journal-title":"Bioinformatics"},{"issue":"9","key":"ref90","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"M Krzywinski","year":"2009","journal-title":"Genome research"}],"container-title":["PLOS Neglected Tropical Diseases"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pntd.0006447","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,3]],"date-time":"2023-09-03T08:46:10Z","timestamp":1693730770000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0006447"}},"subtitle":[],"editor":[{"given":"Steven J.","family":"Norris","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,6,21]]},"references-count":90,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2018,6,21]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pntd.0006447","relation":{},"ISSN":["1935-2735"],"issn-type":[{"value":"1935-2735","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,6,21]]}}}