{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T12:29:45Z","timestamp":1790425785535,"version":"4.1.0"},"reference-count":95,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2025,6,10]],"date-time":"2025-06-10T00:00:00Z","timestamp":1749513600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000155","name":"Social Sciences and Humanities Research Council of Canada","doi-asserted-by":"publisher","award":["752-2016-2085"],"award-info":[{"award-number":["752-2016-2085"]}],"id":[{"id":"10.13039\/501100000155","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Cambridge Commonwealth, European and International Trust and Trinity Hall College"},{"DOI":"10.13039\/501100000713","name":"Society for the Promotion of Roman Studies","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000713","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CANA Foundation grant"},{"DOI":"10.13039\/501100000243","name":"W. Garfield Weston Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000243","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000155","name":"Social Sciences and Humanities Research Council of Canada","doi-asserted-by":"publisher","award":["767-2016-2288"],"award-info":[{"award-number":["767-2016-2288"]}],"id":[{"id":"10.13039\/501100000155","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007631","name":"Canadian Institute for Advanced Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007631","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:p>The detection of parasite infections in past populations has classically relied on microscopic analysis of sediment samples and coprolites. In recent years, additional methods have been integrated into paleoparasitology such as enzyme-linked immunosorbent assay (ELISA) and ancient DNA (aDNA). The aim of this study was to evaluate a multimethod approach for paleoparasitology using microscopy, ELISA, and sedimentary ancient DNA (sedaDNA) with a parasite-specific targeted capture approach and high-throughput sequencing. Using 26 samples dating from c. 6400 BCE to 1500 CE that were previously analyzed with microscopy and ELISA, we aimed to more accurately detect and reconstruct parasite diversity in the Roman Empire and compare this diversity to earlier and later time periods to explore temporal changes in parasite diversity. Microscopy was found to be the most effective technique for identifying the eggs of helminths, with 8 taxa identified. ELISA was the most sensitive for detecting protozoa that cause diarrhea (notably <jats:italic>Giardia duodenalis<\/jats:italic>). Parasite DNA was recovered from 9 samples, with no parasite DNA recovered from any pre-Roman sites. Sedimentary DNA analysis identified whipworm at a site where only roundworm was visible on microscopy, and also revealed that the whipworm eggs at another site came from two different species (<jats:italic>Trichuris trichiura<\/jats:italic> and <jats:italic>Trichuris muris<\/jats:italic>). Our results show that a multimethod approach provides the most comprehensive reconstruction of parasite diversity in past populations. In the pre-Roman period, taxonomic diversity included a mixed spectrum of zoonotic parasites, together with whipworm, which is spread by ineffective sanitation. We see a marked change during the Roman and medieval periods with an increasing dominance of parasites transmitted by ineffective sanitation, especially roundworm, whipworm and protozoa that cause diarrheal illness.<\/jats:p>","DOI":"10.1371\/journal.pntd.0013135","type":"journal-article","created":{"date-parts":[[2025,6,10]],"date-time":"2025-06-10T17:47:17Z","timestamp":1749577637000},"page":"e0013135","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":12,"title":["Sedimentary ancient DNA as part of a multimethod paleoparasitology approach reveals temporal trends in human parasitic burden in the Roman period"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5501-6590","authenticated-orcid":true,"given":"Marissa L.","family":"Ledger","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tyler J.","family":"Murchie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachery","family":"Dickson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melanie","family":"Kuch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott D.","family":"Haddow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher J.","family":"Kn\u00fcsel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gil J.","family":"Stein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mike Parker","family":"Pearson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Ballantyne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Knight","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Koen","family":"Deforce","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maureen","family":"Carroll","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Candace","family":"Rice","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tyler","family":"Franconi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nata\u0161a","family":"\u0160arki\u0107","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sa\u0161a","family":"Red\u017ei\u010d","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erica","family":"Rowan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas","family":"Cahill","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeroen","family":"Poblome","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria de F\u00e1tima","family":"Palma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helmut","family":"Br\u00fcckner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Piers D.","family":"Mitchell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hendrik","family":"Poinar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,6,10]]},"reference":[{"key":"pntd.0013135.ref001","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1146\/annurev-micro-090817-062436","article-title":"Paleomicrobiology: diagnosis and evolution of ancient pathogens","volume":"73","author":"KI Bos","year":"2019","journal-title":"Annu Rev Microbiol"},{"key":"pntd.0013135.ref002","doi-asserted-by":"crossref","DOI":"10.3389\/fevo.2020.00040","article-title":"Palaeomicrobiology: application of ancient DNA sequencing to better understand bacterial genome evolution and adaptation","volume":"8","author":"LA Arriola","year":"2020","journal-title":"Front Ecol Evol"},{"issue":"19","key":"pntd.0013135.ref003","doi-asserted-by":"crossref","DOI":"10.1016\/j.cub.2020.08.081","article-title":"The recovery, interpretation and use of ancient pathogen genomes","volume":"30","author":"S Duch\u00eane","year":"2020","journal-title":"Curr Biol"},{"issue":"4","key":"pntd.0013135.ref004","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2209476119","article-title":"Ancient pathogens provide a window into health and well-being","volume":"120","author":"CM Lewis","year":"2023","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"pntd.0013135.ref005","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1016\/S1473-3099(13)70323-2","article-title":"Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis","volume":"14","author":"DM Wagner","year":"2014","journal-title":"Lancet Infect Dis"},{"issue":"3","key":"pntd.0013135.ref006","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1038\/s41559-020-1106-9","article-title":"Emergence of human-adapted Salmonella enterica is linked to the Neolithization process","volume":"4","author":"FM Key","year":"2020","journal-title":"Nat Ecol Evol"},{"issue":"7705","key":"pntd.0013135.ref007","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1038\/s41586-018-0097-z","article-title":"Ancient hepatitis B viruses from the bronze age to the medieval period","volume":"557","author":"B M\u00fchlemann","year":"2018","journal-title":"Nature"},{"key":"pntd.0013135.ref008","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/j.cell.2018.11.005","article-title":"Emergence and spread of basal lineages of Yersinia pestis during the Neolithic decline","volume":"176","author":"N Rascovan","year":"2019","journal-title":"Cell"},{"key":"pntd.0013135.ref009","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/s41576-019-0119-1","article-title":"Ancient pathogen genomics as an emerging tool for infectious disease research","volume":"20","author":"MA Spyrou","year":"2019","journal-title":"Nat Rev Genet"},{"issue":"1","key":"pntd.0013135.ref010","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1038\/s42003-022-04394-6","article-title":"Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis","volume":"6","author":"K Eaton","year":"2023","journal-title":"Commun Biol"},{"issue":"2","key":"pntd.0013135.ref011","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1002\/ajpa.23978","article-title":"Comparison of extraction methods for recovering ancient microbial DNA from paleofeces","volume":"171","author":"RW Hagan","year":"2020","journal-title":"Am J Phys Anthropol"},{"issue":"1812","key":"pntd.0013135.ref012","doi-asserted-by":"crossref","first-page":"20190576","DOI":"10.1098\/rstb.2019.0576","article-title":"Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities","volume":"375","author":"S Sabin","year":"2020","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"issue":"1888","key":"pntd.0013135.ref013","first-page":"20180991","article-title":"Molecular archaeoparasitology identifies cultural changes in the Medieval Hanseatic trading centre of L\u00fcbeck","volume":"285","author":"K Roche","year":"2018","journal-title":"Proc Biol Sci"},{"issue":"4","key":"pntd.0013135.ref014","article-title":"Ancient DNA from latrines in Northern Europe and the Middle East (500 BC-1700 AD) reveals past parasites and diet","volume":"13","author":"MJ S\u00f8e","year":"2018","journal-title":"PLoS One"},{"issue":"8","key":"pntd.0013135.ref015","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0008600","article-title":"Epidemiological insights from a large-scale investigation of intestinal helminths in Medieval Europe","volume":"14","author":"PG Flammer","year":"2020","journal-title":"PLoS Negl Trop Dis"},{"issue":"9","key":"pntd.0013135.ref016","doi-asserted-by":"crossref","first-page":"2648","DOI":"10.1128\/AEM.03242-13","article-title":"Viruses in a 14th-century coprolite","volume":"80","author":"S Appelt","year":"2014","journal-title":"Appl Environ Microbiol"},{"issue":"47","key":"pntd.0013135.ref017","doi-asserted-by":"crossref","first-page":"16842","DOI":"10.1073\/pnas.1410429111","article-title":"Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch","volume":"111","author":"TFF Ng","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pntd.0013135.ref018","first-page":"27","article-title":"An introduction to paleoparasitology.","volume-title":"Foundations of paleoparasitology","author":"LF. Ferreira","year":"2014"},{"issue":"5","key":"pntd.0013135.ref019","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1017\/S003118201700141X","article-title":"Palaeoparasitology and palaeogenetics: review and perspectives for the study of ancient human parasites","volume":"145","author":"NM-L C\u00f4t\u00e9","year":"2018","journal-title":"Parasitology"},{"issue":"11","key":"pntd.0013135.ref020","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.1017\/S0031182019000726","article-title":"Parasitological research in the molecular age","volume":"146","author":"C Selbach","year":"2019","journal-title":"Parasitology"},{"issue":"6","key":"pntd.0013135.ref021","article-title":"Parasitic infections and resource economy of Danish iron age settlement through ancient DNA sequencing","volume":"13","author":"KW Tams","year":"2018","journal-title":"PLoS One"},{"issue":"1","key":"pntd.0013135.ref022","doi-asserted-by":"crossref","first-page":"12656","DOI":"10.1038\/s41598-020-69497-8","article-title":"Metagenomics and microscope revealed T. trichiura and other intestinal parasites in a cesspit of an Italian nineteenth century aristocratic palace","volume":"10","author":"D Chessa","year":"2020","journal-title":"Sci Rep"},{"key":"pntd.0013135.ref023","doi-asserted-by":"crossref","first-page":"105399","DOI":"10.1016\/j.actatropica.2020.105399","article-title":"African helminth infection out of Africa: paleoparasitological and paleogenetic investigations in Pretos Novos cemetery, Rio de Janeiro, Brazil (1769-1830)","volume":"205","author":"L Guedes","year":"2020","journal-title":"Acta Trop"},{"issue":"3","key":"pntd.0013135.ref024","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1017\/S0031182019001719","article-title":"First report of pre-Hispanic Fasciola hepatica from South America revealed by ancient DNA","volume":"147","author":"MO Beltrame","year":"2020","journal-title":"Parasitology"},{"issue":"1","key":"pntd.0013135.ref025","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0227810","article-title":"Pre-Columbian zoonotic enteric parasites: an insight into Puerto Rican indigenous culture diets and life styles","volume":"15","author":"R Wiscovitch-Russo","year":"2020","journal-title":"PLoS One"},{"key":"pntd.0013135.ref026","doi-asserted-by":"crossref","first-page":"104713","DOI":"10.1016\/j.meegid.2021.104713","article-title":"Gastrointestinal parasite burden in 4th-5th c. CE Florence highlighted by microscopy and paleogenetics","volume":"90","author":"R K\u00e9vin","year":"2021","journal-title":"Infect Genet Evol"},{"issue":"1","key":"pntd.0013135.ref027","doi-asserted-by":"crossref","first-page":"12045","DOI":"10.1038\/s41598-022-10690-2","article-title":"Genomic palaeoparasitology traced the occurrence of Taenia asiatica in ancient Iran (Sassanid Empire, 2th cent. CE-6th cent. CE)","volume":"12","author":"Z Askari","year":"2022","journal-title":"Sci Rep"},{"issue":"1","key":"pntd.0013135.ref028","doi-asserted-by":"crossref","first-page":"3888","DOI":"10.1038\/s41467-022-31487-x","article-title":"Population genomics of ancient and modern Trichuris trichiura","volume":"13","author":"SR Doyle","year":"2022","journal-title":"Nat Commun"},{"issue":"3","key":"pntd.0013135.ref029","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1177\/09596836211060490","article-title":"Helminth infection and human mobility in sambaquis: paleoparasitological, paleogenetic, and microremains investigations in Jabuticabeira II, Brazil (2890\u2009\u00b1\u200955 to 1805\u2009\u00b1\u200965 BP)","volume":"32","author":"AM I\u00f1iguez","year":"2021","journal-title":"Holocene"},{"issue":"1","key":"pntd.0013135.ref030","first-page":"70","article-title":"Genetic analysis of ancient Clonorchis sinensis eggs attained from Goryeong mummy of Joseon dynasty period","volume":"108","author":"CS Oh","year":"2022","journal-title":"J Parasitol"},{"key":"pntd.0013135.ref031","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1017\/qua.2020.59","article-title":"Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set","volume":"99","author":"TJ Murchie","year":"2020","journal-title":"Quat res"},{"issue":"3","key":"pntd.0013135.ref032","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1016\/j.ijpp.2013.04.004","article-title":"Simplifying the process of extracting intestinal parasite eggs from archaeological sediment samples: a comparative study of the efficacy of widely-used disaggregation techniques","volume":"3","author":"E Anastasiou","year":"2013","journal-title":"Int J Paleopathol"},{"key":"pntd.0013135.ref033","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.ijpp.2021.03.001","article-title":"Gastrointestinal infection in Italy during the Roman imperial and longobard periods: a paleoparasitological analysis of sediment from skeletal remains and sewer drains","volume":"33","author":"ML Ledger","year":"2021","journal-title":"Int J Paleopathol"},{"issue":"7","key":"pntd.0013135.ref034","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1016\/S1473-3099(14)70794-7","article-title":"Prehistoric schistosomiasis parasite found in the Middle East","volume":"14","author":"E Anastasiou","year":"2014","journal-title":"Lancet Infect Dis"},{"key":"pntd.0013135.ref035","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.ijpp.2015.02.003","article-title":"Human intestinal parasites from a Mamluk period cesspool in the Christian quarter of Jerusalem: potential indicators of long distance travel in the 15th century AD","volume":"9","author":"H-Y Yeh","year":"2015","journal-title":"Int J Paleopathol"},{"key":"pntd.0013135.ref036","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.ijpp.2017.09.002","article-title":"Intestinal parasites from the 2nd-5th century AD latrine in the Roman baths at Sagalassos (Turkey)","volume":"19","author":"FS Williams","year":"2017","journal-title":"Int J Paleopathol"},{"key":"pntd.0013135.ref037","first-page":"289","article-title":"Intestinal parasites from public and private latrines and the harbour canal in Roman period Ephesus, Turkey (1st c. BCE to 6th c. CE)","volume":"21","author":"ML Ledger","year":"2018","journal-title":"J Arch Sci Rep"},{"issue":"369","key":"pntd.0013135.ref038","doi-asserted-by":"crossref","first-page":"573","DOI":"10.15184\/aqy.2019.61","article-title":"Parasite infection at the early farming community of \u00c7atalh\u00f6y\u00fck","volume":"93","author":"ML Ledger","year":"2019","journal-title":"Antiquity"},{"issue":"12","key":"pntd.0013135.ref039","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1017\/S0031182019001021","article-title":"Intestinal parasites at the Late Bronze Age settlement of must farm, in the fens of East Anglia, UK (9th century B.C.E.)","volume":"146","author":"ML Ledger","year":"2019","journal-title":"Parasitology"},{"key":"pntd.0013135.ref040","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.ijpp.2019.06.004","article-title":"Intestinal parasites in six Islamic medieval period latrines from 10th-11th century C\u00f3rdoba (Spain) and 12th-13th century M\u00e9rtola (Portugal)","volume":"26","author":"DA Knorr","year":"2019","journal-title":"Int J Paleopathol"},{"issue":"4","key":"pntd.0013135.ref041","doi-asserted-by":"crossref","first-page":"631","DOI":"10.3764\/aja.124.4.0631","article-title":"Intestinal parasitic infection in the eastern roman empire during the imperial period and late antiquity","volume":"124","author":"ML Ledger","year":"2020","journal-title":"Am J Archaeol"},{"key":"pntd.0013135.ref042","first-page":"102761","article-title":"Diet, hygiene and health in Roman period northern Gaul: a multidisciplinary study of a latrine from an artisan household in the vicus Orolaunum (Arlon, southern Belgium, c. 250\u2013280 CE)","volume":"35","author":"K Deforce","year":"2021","journal-title":"J Archaeol Sci Rep"},{"issue":"8","key":"pntd.0013135.ref043","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1017\/S0031182022000476","article-title":"Intestinal parasites in the Neolithic population who built Stonehenge (Durrington Walls, 2500 BCE)","volume":"149","author":"PD Mitchell","year":"2022","journal-title":"Parasitology"},{"issue":"2","key":"pntd.0013135.ref044","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/S0035-9203(03)00011-7","article-title":"Amoebiasis distribution in the past: first steps using an immunoassay technique","volume":"98","author":"MLC Goncalves","year":"2004","journal-title":"Trans R Soc Trop Med Hyg"},{"key":"pntd.0013135.ref045","doi-asserted-by":"crossref","first-page":"129","DOI":"10.4000\/archeosciences.281","article-title":"Pal\u00e9oparasitologie et immunologie. L\u2019exemple d\u2019Entamoeba histolytica","volume":"30","author":"M Le Bailly","year":"2006","journal-title":"ArcheoSci"},{"issue":"7","key":"pntd.0013135.ref046","doi-asserted-by":"crossref","first-page":"1849","DOI":"10.1016\/j.jas.2007.11.017","article-title":"Dysentery in the crusader kingdom of Jerusalem: an ELISA analysis of two medieval latrines in the City of Acre (Israel)","volume":"35","author":"PD Mitchell","year":"2008","journal-title":"J Archaeol Sci"},{"key":"pntd.0013135.ref047","first-page":"219","article-title":"A first attempt to retrace the history of dysentery caused by Entamoeba histolytica.","volume-title":"Sanitation, latrines and intestinal parasites in past populations","author":"M Le Bailly","year":"2015"},{"issue":"1","key":"pntd.0013135.ref048","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1645\/14-650.1","article-title":"DNA typing of ancient parasite eggs from environmental samples identifies human and animal worm infections in Viking-age settlement","volume":"101","author":"MJ S\u00f8e","year":"2015","journal-title":"J Parasitol"},{"issue":"7","key":"pntd.0013135.ref049","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1017\/S0031182017000129","article-title":"Improved diagnosis of Trichuris trichiura by using a bead-beating procedure on ethanol preserved stool samples prior to DNA isolation and the performance of multiplex real-time PCR for intestinal parasites","volume":"144","author":"MMM Kaisar","year":"2017","journal-title":"Parasitology"},{"issue":"39","key":"pntd.0013135.ref050","doi-asserted-by":"crossref","first-page":"15758","DOI":"10.1073\/pnas.1314445110","article-title":"Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments","volume":"110","author":"J Dabney","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"6","key":"pntd.0013135.ref051","doi-asserted-by":"crossref","DOI":"10.1101\/pdb.prot5448","article-title":"Illumina sequencing library preparation for highly multiplexed target capture and sequencing","volume":"2010","author":"M Meyer","year":"2010","journal-title":"Cold Spring Harb Protoc"},{"issue":"1","key":"pntd.0013135.ref052","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkr771","article-title":"Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform","volume":"40","author":"M Kircher","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"pntd.0013135.ref053","article-title":"GenBank","volume":"41","author":"DA Benson","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"pntd.0013135.ref054","article-title":"Database resources of the National Center for biotechnology information","volume":"44","author":"NCBI Resource Coordinators","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"18","key":"pntd.0013135.ref055","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gku699","article-title":"leeHom: adaptor trimming and merging for Illumina sequencing reads","volume":"42","author":"G Renaud","year":"2014","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"pntd.0013135.ref056","doi-asserted-by":"crossref","first-page":"587","DOI":"10.3347\/kjp.2019.57.6.587","article-title":"Assessing the parasitic burden in a late antique florentine emergency burial site","volume":"57","author":"K Roche","year":"2019","journal-title":"Korean J Parasitol"},{"issue":"9895","key":"pntd.0013135.ref057","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1016\/S0140-6736(13)61757-2","article-title":"The intestinal parasites of King Richard III","volume":"382","author":"PD Mitchell","year":"2013","journal-title":"Lancet"},{"issue":"1","key":"pntd.0013135.ref058","doi-asserted-by":"crossref","first-page":"103","DOI":"10.3347\/kjp.2016.54.1.103","article-title":"Effects of disinfectants on larval development of Ascaris suum Eggs","volume":"54","author":"K-S Oh","year":"2016","journal-title":"Korean J Parasitol"},{"issue":"13","key":"pntd.0013135.ref059","doi-asserted-by":"crossref","first-page":"1554","DOI":"10.1017\/S0031182021001256","article-title":"Ascaris lumbricoides eggs or artefacts? A diagnostic conundrum","volume":"148","author":"MP Maurelli","year":"2021","journal-title":"Parasitology"},{"issue":"13","key":"pntd.0013135.ref060","doi-asserted-by":"crossref","first-page":"1682","DOI":"10.1093\/bioinformatics\/btt193","article-title":"mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters","volume":"29","author":"H J\u00f3nsson","year":"2013","journal-title":"Bioinformatics"},{"key":"pntd.0013135.ref061","doi-asserted-by":"crossref","DOI":"10.1128\/9781555819002","volume-title":"Diagnostic medical parasitology","author":"LS Garcia","year":"2016"},{"issue":"11","key":"pntd.0013135.ref062","doi-asserted-by":"crossref","first-page":"1659","DOI":"10.1177\/0959683617702236","article-title":"Paleoparasitological investigations on the Neolithic lakeside settlement of La Draga (Lake Banyoles, Spain)","volume":"27","author":"C Maicher","year":"2017","journal-title":"Holocene"},{"issue":"1","key":"pntd.0013135.ref063","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.gene.2011.10.043","article-title":"Comparative analyses of the complete mitochondrial genomes of Ascaris lumbricoides and Ascaris suum from humans and pigs","volume":"492","author":"G-H Liu","year":"2012","journal-title":"Gene"},{"issue":"9","key":"pntd.0013135.ref064","article-title":"Ascaris from humans and pigs appear to be reproductively isolated species","volume":"10","author":"MJ S\u00f8e","year":"2016","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"pntd.0013135.ref065","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.parint.2009.10.001","article-title":"ITS1 intra-individual variability of Ascaris isolates from Brazil","volume":"59","author":"D Leles","year":"2010","journal-title":"Parasitol Int"},{"issue":"10","key":"pntd.0013135.ref066","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1016\/j.trstmh.2012.06.009","article-title":"Genetic characterisation and molecular epidemiology of Ascaris spp. from humans and pigs in Brazil","volume":"106","author":"Amazonas Research Group","year":"2012","journal-title":"Trans R Soc Trop Med Hyg"},{"issue":"1626","key":"pntd.0013135.ref067","first-page":"2669","article-title":"Disentangling hybridization and host colonization in parasitic roundworms of humans and pigs","volume":"274","author":"CD Criscione","year":"2007","journal-title":"Proc Biol Sci"},{"issue":"2","key":"pntd.0013135.ref068","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1017\/S0022149X12000193","article-title":"Assessing the zoonotic potential of Ascaris suum and Trichuris suis: looking to the future from an analysis of the past","volume":"86","author":"P Nejsum","year":"2012","journal-title":"J Helminthol"},{"issue":"6","key":"pntd.0013135.ref069","doi-asserted-by":"crossref","first-page":"932","DOI":"10.1093\/infdis\/jiu193","article-title":"Molecular epidemiology of ascariasis: a global perspective on the transmission dynamics of Ascaris in people and pigs","volume":"210","author":"M Betson","year":"2014","journal-title":"J Infect Dis"},{"issue":"8","key":"pntd.0013135.ref070","first-page":"1355","article-title":"Ascaris lumbricoides, Ascaris suum, or \u201cAscaris lumbrisuum\u201d?","volume":"213","author":"EB da Silva Alves","year":"2016","journal-title":"J Infect Dis"},{"issue":"6","key":"pntd.0013135.ref071","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1016\/j.jas.2009.12.029","article-title":"Amplification and sequencing of Trichuris trichiura ancient DNA extracted from archaeological sediments","volume":"37","author":"CS Oh","year":"2010","journal-title":"J Archaeol Sci"},{"issue":"8","key":"pntd.0013135.ref072","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0105910","article-title":"Molecular paleoparasitological hybridization approach as effective tool for diagnosing human intestinal parasites from scarce archaeological remains","volume":"9","author":"LH Jaeger","year":"2014","journal-title":"PLoS One"},{"issue":"1","key":"pntd.0013135.ref073","article-title":"A new high-throughput approach to genotype ancient human gastrointestinal parasites","volume":"11","author":"NML C\u00f4t\u00e9","year":"2016","journal-title":"PLoS One"},{"issue":"6","key":"pntd.0013135.ref074","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1645\/16-102","article-title":"Ancient Ascaris DNA sequences of cytochrome B, cytochrome C oxidase subunit 1, NADH dehydrogenase subunit 1, and internal transcribed spacer 1 genes from Korean Joseon Mummy Feces","volume":"103","author":"JH Hong","year":"2017","journal-title":"J Parasitol"},{"issue":"3","key":"pntd.0013135.ref075","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0034131","article-title":"Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA","volume":"7","author":"S Sawyer","year":"2012","journal-title":"PLoS One"},{"issue":"11","key":"pntd.0013135.ref076","doi-asserted-by":"crossref","first-page":"6310","DOI":"10.1093\/nar\/gkx361","article-title":"A new model for ancient DNA decay based on paleogenomic meta-analysis","volume":"45","author":"L Kistler","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"23","key":"pntd.0013135.ref077","doi-asserted-by":"crossref","DOI":"10.1016\/j.cub.2016.10.016","article-title":"Plasmodium falciparum malaria in 1st-2nd century CE southern Italy","volume":"26","author":"S Marciniak","year":"2016","journal-title":"Curr Biol"},{"key":"pntd.0013135.ref078","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/j.jhevol.2014.11.003","article-title":"Ancient human genomics: the methodology behind reconstructing evolutionary pathways","volume":"79","author":"S Marciniak","year":"2015","journal-title":"J Hum Evol"},{"key":"pntd.0013135.ref079","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.quascirev.2013.06.006","article-title":"A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa","volume":"75","author":"MW Pedersen","year":"2013","journal-title":"Quat Sci Rev"},{"issue":"7","key":"pntd.0013135.ref080","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1002\/jqs.2740","article-title":"Using palaeoenvironmental DNA to reconstruct past environments: progress and prospects","volume":"29","author":"NJ Rawlence","year":"2014","journal-title":"J Quat Sci"},{"issue":"1660","key":"pntd.0013135.ref081","doi-asserted-by":"crossref","first-page":"20130382","DOI":"10.1098\/rstb.2013.0382","article-title":"Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA","volume":"370","author":"L Parducci","year":"2015","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"issue":"1","key":"pntd.0013135.ref082","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1186\/s13071-022-05602-2","article-title":"Transcriptome profiling of male and female Ascaris lumbricoides reproductive tissues","volume":"15","author":"O Phuphisut","year":"2022","journal-title":"Parasit Vectors"},{"issue":"3","key":"pntd.0013135.ref083","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1017\/S0022149X1500019X","article-title":"Faecal egg counts and expulsion dynamics of the whipworm, Trichuris trichiura following self-infection","volume":"90","author":"EP Hansen","year":"2016","journal-title":"J Helminthol"},{"issue":"3","key":"pntd.0013135.ref084","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/j.soilbio.2005.05.019","article-title":"Adsorption of DNA on clay minerals and various colloidal particles from an Alfisol","volume":"38","author":"P Cai","year":"2006","journal-title":"Soil Biol Biochem"},{"issue":"4","key":"pntd.0013135.ref085","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1016\/j.clay.2010.09.015","article-title":"DNA adsorption on synthetic and natural allophanes","volume":"50","author":"K Saeki","year":"2010","journal-title":"Appl Clay Sci"},{"key":"pntd.0013135.ref086","doi-asserted-by":"crossref","first-page":"104728","DOI":"10.1016\/j.apgeochem.2020.104728","article-title":"Geochemical identification of potential DNA-hotspots and DNA-infrared fingerprints in lake sediments","volume":"122","author":"HJ Kanbar","year":"2020","journal-title":"Appl Geochem"},{"issue":"7939","key":"pntd.0013135.ref087","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/s41586-022-05453-y","article-title":"A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA","volume":"612","author":"KH Kj\u00e6r","year":"2022","journal-title":"Nature"},{"key":"pntd.0013135.ref088","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1590\/S0074-02762003000900016","article-title":"Human intestinal parasites in the past: new findings and a review","volume":"98","author":"MLC Gon\u00e7alves","year":"2003","journal-title":"Mem Inst Oswaldo Cruz"},{"issue":"4","key":"pntd.0013135.ref089","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1016\/j.jas.2009.11.018","article-title":"Paleoparasitological results from coprolites dated at the Pleistocene\u2013Holocene transition as source of paleoecological evidence in Patagonia","volume":"37","author":"MH Fugassa","year":"2010","journal-title":"J Archaeol Sci"},{"issue":"3","key":"pntd.0013135.ref090","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/j.actatropica.2010.03.004","article-title":"Ancient dicrocoeliosis: occurrence, distribution and migration","volume":"115","author":"M Le Bailly","year":"2010","journal-title":"Acta Trop"},{"issue":"5","key":"pntd.0013135.ref091","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1179\/1364859411Y.0000000029","article-title":"Dicrocoelium dendriticum: an emerging spurious infection in a geographic area with a high level of immigration","volume":"105","author":"I Cabeza-Barrera","year":"2011","journal-title":"Ann Trop Med Parasitol"},{"key":"pntd.0013135.ref092","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1017\/9780511732386.005","article-title":"The Roman world.","volume-title":"Parasites in past civilizations and their impact upon health","author":"PD. Mitchell","year":"2023"},{"issue":"3","key":"pntd.0013135.ref093","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1002\/oa.2786","article-title":"Tracing zoonotic parasite infections throughout human evolution","volume":"32","author":"ML Ledger","year":"2019","journal-title":"Intl J of Osteoarchaeol"},{"issue":"2","key":"pntd.0013135.ref094","doi-asserted-by":"crossref","first-page":"231","DOI":"10.2307\/280729","article-title":"Parasitology as an interpretive tool in archaeology","volume":"57","author":"KJ Reinhard","year":"1992","journal-title":"Am Antiq"},{"issue":"1","key":"pntd.0013135.ref095","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/s41572-020-0171-3","article-title":"Whipworm and roundworm infections","volume":"6","author":"KJ Else","year":"2020","journal-title":"Nat Rev Dis Primers"}],"container-title":["PLOS Neglected Tropical Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0013135","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,10]],"date-time":"2025-06-10T17:47:43Z","timestamp":1749577663000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0013135"}},"subtitle":[],"editor":[{"given":"Elham","family":"Kazemirad","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,6,10]]},"references-count":95,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2025,6,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pntd.0013135","relation":{},"ISSN":["1935-2735"],"issn-type":[{"value":"1935-2735","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,6,10]]}}}