{"id":"https://openalex.org/W2752019144","doi":"https://doi.org/10.1371/journal.pntd.0005887","title":"Temporal phylogeography of Yersinia pestis in Madagascar: Insights into the long-term maintenance of plague","display_name":"Temporal phylogeography of Yersinia pestis in Madagascar: Insights into the long-term maintenance of plague","publication_year":2017,"publication_date":"2017-09-05","ids":{"openalex":"https://openalex.org/W2752019144","doi":"https://doi.org/10.1371/journal.pntd.0005887","mag":"2752019144","pmid":"https://pubmed.ncbi.nlm.nih.gov/28873412","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/5600411"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pntd.0005887","doi":"https://doi.org/10.1371/journal.pntd.0005887","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pntd.0005887","pdf_url":"https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0005887&type=printable","source":{"id":"https://openalex.org/S46544255","display_name":"PLoS neglected tropical diseases","issn_l":"1935-2727","issn":["1935-2727","1935-2735"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-2","ki-jl-1","medline","norway-1","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Neglected Tropical Diseases","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0005887&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109122553","display_name":"Amy J. Vogler","orcid":"https://orcid.org/0009-0008-0209-6209","observed_orcids":["https://orcid.org/0009-0008-0209-6209"]},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amy J. Vogler","raw_affiliation_strings":["The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000242585","display_name":"Voahangy Andrianaivoarimanana","orcid":"https://orcid.org/0000-0003-1550-3869","observed_orcids":["https://orcid.org/0000-0003-1550-3869"]},"institutions":[{"id":"https://openalex.org/I4210133373","display_name":"Institut Pasteur de Madagascar","ror":"https://ror.org/03fkjvy27","country_code":"MG","type":"nonprofit","lineage":["https://openalex.org/I4210133373"]}],"countries":["MG"],"is_corresponding":false,"raw_author_name":"Voahangy Andrianaivoarimanana","raw_affiliation_strings":["Plague Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Plague Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar","institution_ids":["https://openalex.org/I4210133373"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009834561","display_name":"Sandra Telfer","orcid":"https://orcid.org/0000-0002-9596-0711","observed_orcids":["https://orcid.org/0000-0002-9596-0711"]},"institutions":[{"id":"https://openalex.org/I195460627","display_name":"University of Aberdeen","ror":"https://ror.org/016476m91","country_code":"GB","type":"education","lineage":["https://openalex.org/I195460627"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sandra Telfer","raw_affiliation_strings":["School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom","institution_ids":["https://openalex.org/I195460627"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080065322","display_name":"Carina M. Hall","orcid":"https://orcid.org/0000-0001-6941-3207","observed_orcids":["https://orcid.org/0000-0001-6941-3207"]},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carina M. Hall","raw_affiliation_strings":["The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072982028","display_name":"Jason W. Sahl","orcid":"https://orcid.org/0000-0002-2497-0138","observed_orcids":["https://orcid.org/0000-0002-2497-0138","https://orcid.org/0000-0002-1077-7310"]},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason W. Sahl","raw_affiliation_strings":["The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081346172","display_name":"Crystal M. Hepp","orcid":"https://orcid.org/0000-0002-0612-3648","observed_orcids":["https://orcid.org/0000-0002-0612-3648"]},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Crystal M. Hepp","raw_affiliation_strings":["The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029939113","display_name":"Heather Centner","orcid":"https://orcid.org/0000-0001-9537-7094","observed_orcids":["https://orcid.org/0000-0001-9537-7094"]},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Heather Centner","raw_affiliation_strings":["The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018529858","display_name":"Genevieve H.L. Andersen","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Genevieve Andersen","raw_affiliation_strings":["The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089723232","display_name":"Dawn N. Birdsell","orcid":"https://orcid.org/0000-0003-0055-9552","observed_orcids":["https://orcid.org/0000-0003-0055-9552"]},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dawn N. Birdsell","raw_affiliation_strings":["The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049203211","display_name":"Lila Rahalison","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210133373","display_name":"Institut Pasteur de Madagascar","ror":"https://ror.org/03fkjvy27","country_code":"MG","type":"nonprofit","lineage":["https://openalex.org/I4210133373"]}],"countries":["MG"],"is_corresponding":false,"raw_author_name":"Lila Rahalison","raw_affiliation_strings":["Plague Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Plague Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar","institution_ids":["https://openalex.org/I4210133373"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045551446","display_name":"Roxanne D. Nottingham","orcid":"https://orcid.org/0009-0006-2800-6481","observed_orcids":["https://orcid.org/0009-0006-2800-6481"]},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Roxanne Nottingham","raw_affiliation_strings":["The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045601734","display_name":"Paul Keim","orcid":"https://orcid.org/0000-0003-0089-5820","observed_orcids":["https://orcid.org/0000-0003-0089-5820"]},"institutions":[{"id":"https://openalex.org/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]},{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Keim","raw_affiliation_strings":["Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America","The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I1284308235"]},{"raw_affiliation_string":"The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080099109","display_name":"David M. Wagner","orcid":"https://orcid.org/0000-0003-2684-6007","observed_orcids":["https://orcid.org/0000-0003-2684-6007"]},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David M. Wagner","raw_affiliation_strings":["The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-2684-6007","affiliations":[{"raw_affiliation_string":"The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022054893","display_name":"Minoarisoa Esther Rajerison","orcid":"https://orcid.org/0000-0002-0389-9280","observed_orcids":["https://orcid.org/0000-0002-0389-9280"]},"institutions":[{"id":"https://openalex.org/I4210133373","display_name":"Institut Pasteur de Madagascar","ror":"https://ror.org/03fkjvy27","country_code":"MG","type":"nonprofit","lineage":["https://openalex.org/I4210133373"]}],"countries":["MG"],"is_corresponding":true,"raw_author_name":"Minoarisoa Rajerison","raw_affiliation_strings":["Plague Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Plague Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar","institution_ids":["https://openalex.org/I4210133373"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5022054893","https://openalex.org/A5080099109"],"corresponding_institution_ids":["https://openalex.org/I203172682","https://openalex.org/I4210133373"],"apc_list":{"value":2670,"currency":"USD","value_usd":2670},"apc_paid":{"value":2670,"currency":"USD","value_usd":2670},"fwci":3.1805,"has_fulltext":true,"cited_by_count":38,"citation_normalized_percentile":{"value":0.91890548,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"11","issue":"9","first_page":"e0005887","last_page":"e0005887"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12232","display_name":"Yersinia bacterium, plague, ectoparasites research","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T12232","display_name":"Yersinia bacterium, plague, ectoparasites research","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.0019000000320374966,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12492","display_name":"Zoonotic diseases and public health","score":0.0,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/yersinia-pestis","display_name":"Yersinia pestis","score":1.0},{"id":"https://openalex.org/keywords/plague","display_name":"plague","score":0.8980000019073486},{"id":"https://openalex.org/keywords/madagascar","display_name":"Madagascar","score":0.7289999723434448},{"id":"https://openalex.org/keywords/subpopulations","display_name":"subpopulations","score":0.6859999895095825},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"whole genome sequencing","score":0.6819999814033508},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphisms","display_name":"single nucleotide polymorphisms","score":0.621999979019165},{"id":"https://openalex.org/keywords/variable-number-of-tandem-repeats","display_name":"variable number tandem repeats","score":0.9110000133514404},{"id":"https://openalex.org/keywords/dispersal","display_name":"dispersal","score":0.45100000500679016}],"concepts":[{"id":"https://openalex.org/C2778222588","wikidata":"https://www.wikidata.org/wiki/Q153875","display_name":"Yersinia pestis","level":4,"score":0.9083770513534546},{"id":"https://openalex.org/C94043034","wikidata":"https://www.wikidata.org/wiki/Q377756","display_name":"Phylogeography","level":4,"score":0.8061543107032776},{"id":"https://openalex.org/C47559259","wikidata":"https://www.wikidata.org/wiki/Q778143","display_name":"Biological dispersal","level":3,"score":0.7690095901489258},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7373275756835938},{"id":"https://openalex.org/C2778059882","wikidata":"https://www.wikidata.org/wiki/Q133780","display_name":"Plague (disease)","level":2,"score":0.6315476894378662},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4957023859024048},{"id":"https://openalex.org/C189036908","wikidata":"https://www.wikidata.org/wiki/Q2587423","display_name":"Variable number tandem repeat","level":4,"score":0.46552368998527527},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.45043256878852844},{"id":"https://openalex.org/C98722961","wikidata":"https://www.wikidata.org/wiki/Q7189436","display_name":"Phylogenetic diversity","level":4,"score":0.44064319133758545},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.42597946524620056},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4238263964653015},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.37586531043052673},{"id":"https://openalex.org/C90856448","wikidata":"https://www.wikidata.org/wiki/Q431","display_name":"Zoology","level":1,"score":0.349851131439209},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29642370343208313},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.21632730960845947},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.16769170761108398},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.15332281589508057},{"id":"https://openalex.org/C60987743","wikidata":"https://www.wikidata.org/wiki/Q1460232","display_name":"Virulence","level":3,"score":0.11551758646965027},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008270","descriptor_name":"Madagascar","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D010930","descriptor_name":"Plague","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"descriptor_ui":"D010930","descriptor_name":"Plague","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D015010","descriptor_name":"Yersinia pestis","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D015010","descriptor_name":"Yersinia pestis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015010","descriptor_name":"Yersinia pestis","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019353","descriptor_name":"Endemic Diseases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058974","descriptor_name":"Phylogeography","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062211","descriptor_name":"Spatio-Temporal Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pntd.0005887","doi":"https://doi.org/10.1371/journal.pntd.0005887","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pntd.0005887","pdf_url":"https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0005887&type=printable","source":{"id":"https://openalex.org/S46544255","display_name":"PLoS neglected tropical diseases","issn_l":"1935-2727","issn":["1935-2727","1935-2735"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-2","ki-jl-1","medline","norway-1","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Neglected Tropical Diseases","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5600411","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5600411","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Negl Trop Dis","raw_type":"Text"},{"id":"pmid:28873412","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28873412","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS neglected tropical diseases","raw_type":"Journal Article"},{"id":"pmh:oai:aura.abdn.ac.uk:2164/9691","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/2164/9691","pdf_url":"http://hdl.handle.net/2164/9691","source":{"id":"https://openalex.org/S4306400966","display_name":"Aberdeen University Research Archive (Aberdeen University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I195460627","host_organization_name":"University of Aberdeen","host_organization_lineage":["https://openalex.org/I195460627"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal article"},{"id":"pmh:oai:HAL:pasteur-01635032v1","doi":null,"is_oa":true,"landing_page_url":"https://riip.hal.science/pasteur-01635032","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Neglected Tropical Diseases, 2017, 11 (9), &#x27E8;10.1371/journal.pntd.0005887&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:186a17beb1514134b6597038cc59b38c","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/186a17beb1514134b6597038cc59b38c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Neglected Tropical Diseases, Vol 11, Iss 9, p e0005887 (2017)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/5377681","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Temporal_phylogeography_of_i_Yersinia_pestis_i_in_Madagascar_Insights_into_the_long-term_maintenance_of_plague/5377681","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pntd.0005887","doi":"https://doi.org/10.1371/journal.pntd.0005887","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pntd.0005887","pdf_url":"https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0005887&type=printable","source":{"id":"https://openalex.org/S46544255","display_name":"PLoS neglected tropical diseases","issn_l":"1935-2727","issn":["1935-2727","1935-2735"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-2","ki-jl-1","medline","norway-1","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Neglected Tropical Diseases","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3147155732","display_name":"Plague epidemiology and risk in the heterogeneous rural landscapes of Madagascar .","funder_award_id":"081705","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G4566068512","display_name":null,"funder_award_id":"HSHQDC-10-C-00139","funder_id":"https://openalex.org/F4320332664","funder_display_name":"Science and Technology Directorate"},{"id":"https://openalex.org/G4675027466","display_name":"Disease risk in Madagascar.","funder_award_id":"095171/Z/10/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G7727204144","display_name":"Disease risk in Madagascar.","funder_award_id":"095171","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G8479135178","display_name":null,"funder_award_id":"HSHQDC-10-C-00139","funder_id":"https://openalex.org/F4320306110","funder_display_name":"U.S. Department of Homeland Security"}],"funders":[{"id":"https://openalex.org/F4320306110","display_name":"U.S. Department of Homeland Security","ror":"https://ror.org/00jyr0d86"},{"id":"https://openalex.org/F4320310831","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188"},{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320332664","display_name":"Science and Technology Directorate","ror":"https://ror.org/00jyr0d86"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2752019144.pdf","grobid_xml":"https://content.openalex.org/works/W2752019144.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W654784861","https://openalex.org/W1211915768","https://openalex.org/W1506603736","https://openalex.org/W1652308581","https://openalex.org/W1969321150","https://openalex.org/W1970506897","https://openalex.org/W1988411942","https://openalex.org/W1996917290","https://openalex.org/W2013164703","https://openalex.org/W2028031087","https://openalex.org/W2036345955","https://openalex.org/W2054691189","https://openalex.org/W2060329364","https://openalex.org/W2063659768","https://openalex.org/W2066084832","https://openalex.org/W2067424477","https://openalex.org/W2071632015","https://openalex.org/W2075097033","https://openalex.org/W2087928701","https://openalex.org/W2090383417","https://openalex.org/W2092343047","https://openalex.org/W2094939159","https://openalex.org/W2095680943","https://openalex.org/W2098998255","https://openalex.org/W2100303227","https://openalex.org/W2108234281","https://openalex.org/W2114418658","https://openalex.org/W2116513121","https://openalex.org/W2118048521","https://openalex.org/W2119180969","https://openalex.org/W2130362098","https://openalex.org/W2140635656","https://openalex.org/W2142635246","https://openalex.org/W2145912774","https://openalex.org/W2156358357","https://openalex.org/W2156434383","https://openalex.org/W2158196600","https://openalex.org/W2162098634","https://openalex.org/W2164901462","https://openalex.org/W2168133698","https://openalex.org/W2171142493","https://openalex.org/W2171217032","https://openalex.org/W2171929540","https://openalex.org/W2172699566","https://openalex.org/W2255567519","https://openalex.org/W2281699267","https://openalex.org/W2300858882","https://openalex.org/W2322358787","https://openalex.org/W2472226552","https://openalex.org/W2483236535","https://openalex.org/W2509122085","https://openalex.org/W2623178109","https://openalex.org/W3143846784","https://openalex.org/W4394666350","https://openalex.org/W6769428862"],"related_works":["https://openalex.org/W7100265468","https://openalex.org/W1969321150","https://openalex.org/W4416719096","https://openalex.org/W2795462247","https://openalex.org/W7095211008","https://openalex.org/W2066084832","https://openalex.org/W4285309869","https://openalex.org/W4367597701","https://openalex.org/W2809743816","https://openalex.org/W3172839437"],"abstract_inverted_index":{"BACKGROUND:":[0],"Yersinia":[1],"pestis":[2,51,92,184,225,258],"appears":[3],"to":[4,87,96,111,175],"be":[5],"maintained":[6],"in":[7,52,76,133,199,206,239,255,260,292,296],"multiple,":[8],"geographically":[9,120],"separate,":[10],"and":[11,37,69,82,122,129,163,172,283],"phylogenetically":[12,123],"distinct":[13,124],"subpopulations":[14,27,125,171,259,282],"within":[15,227],"the":[16,21,47,100,134,211,233,278,284],"highlands":[17],"of":[18,23,42,49,140,152,160,181,202,223,237,245,270,280,287],"Madagascar.":[19],"However,":[20],"dynamics":[22,279],"these":[24],"locally":[25],"differentiated":[26],"through":[28,115],"time":[29,213],"are":[30,155,230],"mostly":[31],"unknown.":[32],"To":[33],"address":[34],"that":[35,73,126,146,164,194,219],"gap":[36],"further":[38],"inform":[39],"our":[40],"understanding":[41],"plague":[43,238,290],"epidemiology,":[44],"we":[45,74],"investigated":[46],"phylogeography":[48],"Y.":[50,91,183,224,257],"Madagascar":[53],"over":[54,137,188],"an":[55],"18":[56,119],"year":[57,174,295],"period.":[58,214],"METHODOLOGY/PRINCIPAL":[59],"FINDINGS:":[60],"We":[61,98,117,144,177],"generated":[62],"whole":[63],"genome":[64],"sequences":[65],"for":[66,232],"31":[67],"strains":[68],"discovered":[70],"new":[71,208],"SNPs":[72,81],"used":[75],"conjunction":[77],"with":[78,149,157,262,267],"previously":[79],"identified":[80,118],"variable-number":[83],"tandem":[84],"repeats":[85],"(VNTRs)":[86],"genotype":[88,205],"773":[89],"Malagasy":[90],"samples":[93,103],"from":[94,173],"1995":[95],"2012.":[97],"mapped":[99],"locations":[101,136],"where":[102],"were":[104],"obtained":[105],"on":[106],"a":[107,138,203,207,253,293,297],"fine":[108],"geographic":[109,147],"scale":[110,247],"examine":[112],"phylogeographic":[113],"patterns":[114],"time.":[116],"separate":[121],"display":[127],"spatial":[128],"temporal":[130],"stability,":[131],"persisting":[132],"same":[135],"period":[139],"almost":[141],"two":[142],"decades.":[143],"found":[145,179],"areas":[148,229],"higher":[150],"levels":[151,159,269],"topographical":[153,264],"relief":[154,265],"associated":[156,266,285],"greater":[158],"phylogenetic":[161],"diversity":[162],"sampling":[165],"frequency":[166],"can":[167],"vary":[168],"considerably":[169],"among":[170],"year.":[176],"also":[178],"evidence":[180,193],"various":[182],"dispersal":[185,196],"events,":[186],"including":[187],"long":[189,234],"distances,":[190],"but":[191],"no":[192],"any":[195],"events":[197],"resulted":[198],"successful":[200],"establishment":[201],"transferred":[204],"location":[209],"during":[210],"examined":[212],"CONCLUSIONS/SIGNIFICANCE:":[215],"Our":[216],"analysis":[217],"suggests":[218],"persistent":[220],"endemic":[221],"cycles":[222],"transmission":[226],"local":[228],"responsible":[231],"term":[235],"maintenance":[236],"Madagascar,":[240,261],"rather":[241],"than":[242],"repeated":[243],"episodes":[244],"wide":[246],"epidemic":[248],"spread.":[249],"Landscape":[250],"likely":[251,276],"plays":[252],"role":[254],"maintaining":[256],"increased":[263,268],"localized":[271],"differentiation.":[272],"Local":[273],"ecological":[274],"factors":[275],"affect":[277],"individual":[281],"likelihood":[286],"observing":[288],"human":[289],"cases":[291],"given":[294],"particular":[298],"location.":[299]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2017-09-15T00:00:00"}
