{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T01:46:56Z","timestamp":1793238416591,"version":"4.5.0"},"reference-count":129,"publisher":"eLife Sciences Publications, Ltd","license":[{"start":{"date-parts":[[2020,3,25]],"date-time":"2020-03-25T00:00:00Z","timestamp":1585094400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2020,3,25]],"date-time":"2020-03-25T00:00:00Z","timestamp":1585094400000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2020,3,25]],"date-time":"2020-03-25T00:00:00Z","timestamp":1585094400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["Wellcome Sanger Institute core funding, WT098051"],"award-info":[{"award-number":["Wellcome Sanger Institute core funding, WT098051"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["Wellcome Sanger Institute core funding, WT206194"],"award-info":[{"award-number":["Wellcome Sanger Institute core funding, WT206194"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007601","name":"EU Framework Programme for Research and Innovation","doi-asserted-by":"publisher","award":["FP7- 222895"],"award-info":[{"award-number":["FP7- 222895"]}],"id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>Protozoan parasites of the Leishmania donovani complex \u2013 L. donovani and L. infantum \u2013 cause the fatal disease visceral leishmaniasis. We present the first comprehensive genome-wide global study, with 151 cultured field isolates representing most of the geographical distribution. L. donovani isolates separated into five groups that largely coincide with geographical origin but vary greatly in diversity. In contrast, the majority of L. infantum samples fell into one globally-distributed group with little diversity. This picture is complicated by several hybrid lineages. Identified genetic groups vary in heterozygosity and levels of linkage, suggesting different recombination histories. We characterise chromosome-specific patterns of aneuploidy and identified extensive structural variation, including known and suspected drug resistance loci. This study reveals greater genetic diversity than suggested by geographically-focused studies, provides a resource of genomic variation for future work and sets the scene for a new understanding of the evolution and genetics of the Leishmania donovani complex.<\/jats:p>","DOI":"10.7554\/elife.51243","type":"journal-article","created":{"date-parts":[[2020,3,24]],"date-time":"2020-03-24T08:00:15Z","timestamp":1585036815000},"source":"Crossref","is-referenced-by-count":123,"title":["Global genome diversity of the Leishmania donovani complex"],"prefix":"10.7554","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4725-1793","authenticated-orcid":true,"given":"Susanne U","family":"Franssen","sequence":"first","affiliation":[{"name":"Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline","family":"Durrant","sequence":"additional","affiliation":[{"name":"Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivia","family":"Stark","sequence":"additional","affiliation":[{"name":"Charit\u00e9 Universit\u00e4tsmedizin, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bettina","family":"Moser","sequence":"additional","affiliation":[{"name":"Charit\u00e9 Universit\u00e4tsmedizin, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8385-6730","authenticated-orcid":true,"given":"Tim","family":"Downing","sequence":"additional","affiliation":[{"name":"Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom"},{"name":"Dublin City University, Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3282-1319","authenticated-orcid":true,"given":"Hideo","family":"Imamura","sequence":"additional","affiliation":[{"name":"Institute of Tropical Medicine, Antwerp, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9217-5240","authenticated-orcid":true,"given":"Jean-Claude","family":"Dujardin","sequence":"additional","affiliation":[{"name":"Institute of Tropical Medicine, Antwerp, Belgium"},{"name":"Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mandy J","family":"Sanders","sequence":"additional","affiliation":[{"name":"Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabel","family":"Mauricio","sequence":"additional","affiliation":[{"name":"Universidade Nova de Lisboa Instituto de Higiene e Medicina, Lisboa, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael A","family":"Miles","sequence":"additional","affiliation":[{"name":"London School of Hygiene and Tropical Medicine, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lionel F","family":"Schnur","sequence":"additional","affiliation":[{"name":"Kuvin Centre for the Study of Infectious and Tropical Diseases, IMRIC, Hebrew University-Hadassah, Medical School, Jerusalem, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles L","family":"Jaffe","sequence":"additional","affiliation":[{"name":"Kuvin Centre for the Study of Infectious and Tropical Diseases, IMRIC, Hebrew University-Hadassah, Medical School, Jerusalem, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8162-420X","authenticated-orcid":true,"given":"Abdelmajeed","family":"Nasereddin","sequence":"additional","affiliation":[{"name":"Kuvin Centre for the Study of Infectious and Tropical Diseases, IMRIC, Hebrew University-Hadassah, Medical School, Jerusalem, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henk","family":"Schallig","sequence":"additional","affiliation":[{"name":"Amsterdam University Medical Centres \u2013 Academic Medical Centre at the University of Amsterdam, Department of Medical Microbiology \u2013 Experimental Parasitology, Amsterdam, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Yeo","sequence":"additional","affiliation":[{"name":"London School of Hygiene and Tropical Medicine, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tapan","family":"Bhattacharyya","sequence":"additional","affiliation":[{"name":"London School of Hygiene and Tropical Medicine, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad Z","family":"Alam","sequence":"additional","affiliation":[{"name":"Department of Parasitology, Bangladesh Agricultural University, Mymensingh, Bangladesh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9581-0377","authenticated-orcid":true,"given":"Matthew","family":"Berriman","sequence":"additional","affiliation":[{"name":"Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thierry","family":"Wirth","sequence":"additional","affiliation":[{"name":"Institut de Syst\u00e9matique, Evolution, Biodiversit\u00e9, ISYEB, Mus\u00e9um national d'Histoire naturelle, CNRS, Sorbonne Universit\u00e9, EPHE, Universit\u00e9 des Antilles, Paris, France"},{"name":"\u00c9cole Pratique des Hautes \u00c9tudes (EPHE), Paris Sciences & Lettres (PSL), Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriele","family":"Sch\u00f6nian","sequence":"additional","affiliation":[{"name":"Charit\u00e9 Universit\u00e4tsmedizin, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5475-3583","authenticated-orcid":true,"given":"James A","family":"Cotton","sequence":"additional","affiliation":[{"name":"Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"4374","published-online":{"date-parts":[[2020,3,25]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0004349","article-title":"A historical overview of the classification, evolution, and dispersion of\u00a0Leishmania\u00a0parasites and sandflies","volume":"10","author":"Akhoundi","year":"2016","journal-title":"PLOS Neglected Tropical Diseases"},{"key":"bib2","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1126\/science.1169464","article-title":"Demonstration of genetic exchange during cyclical development of\u00a0Leishmania\u00a0in the sand fly vector","volume":"324","author":"Akopyants","year":"2009","journal-title":"Science"},{"key":"bib3","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1016\/j.micinf.2009.04.009","article-title":"The paraphyletic composition of Leishmania donovani zymodeme MON-37 revealed by multilocus microsatellite typing","volume":"11","author":"Alam","year":"2009","journal-title":"Microbes and Infection"},{"key":"bib4","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1016\/j.meegid.2014.01.019","article-title":"Genetic diversity of\u00a0Leishmania\u00a0donovani\/infantum complex in China through microsatellite analysis","volume":"22","author":"Alam","year":"2014","journal-title":"Infection, Genetics and Evolution"},{"key":"bib5","doi-asserted-by":"publisher","DOI":"10.21767\/1791-809X.1000519","article-title":"Leishmaniasis: a review on parasite, vector and reservoir host","volume":"11","author":"Alemayehu","year":"2017","journal-title":"Health Science Journal"},{"key":"bib6","doi-asserted-by":"publisher","first-page":"1600","DOI":"10.1093\/bioinformatics\/btl140","article-title":"Improved scoring of functional groups from gene expression data by decorrelating GO graph structure","volume":"22","author":"Alexa","year":"2006","journal-title":"Bioinformatics"},{"key":"bib7","doi-asserted-by":"publisher","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Research"},{"key":"bib8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0065-308X(04)57001-X","article-title":"Canine Leishmaniasis","volume":"57","author":"Alvar","year":"2004","journal-title":"Advances in Parasitology\u00a0"},{"key":"bib9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0035671","article-title":"Leishmaniasis worldwide and global estimates of its incidence","volume":"7","author":"Alvar","year":"2012","journal-title":"PLOS ONE"},{"key":"bib10","doi-asserted-by":"publisher","first-page":"4482","DOI":"10.1128\/AAC.00768-16","article-title":"Silver and nitrate oppositely modulate antimony susceptibility through aquaglyceroporin 1 in\u00a0Leishmania\u00a0(Viannia) Species","volume":"60","author":"Andrade","year":"2016","journal-title":"Antimicrobial Agents and Chemotherapy"},{"key":"bib11","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1016\/S1473-3099(07)70297-9","article-title":"Leishmania donovani leishmaniasis in Cyprus","volume":"8","author":"Antoniou","year":"2008","journal-title":"The Lancet Infectious Diseases"},{"key":"bib12","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000093","article-title":"Microreact: visualizing and sharing data for genomic epidemiology and phylogeography","volume":"2","author":"Argim\u00f3n","year":"2016","journal-title":"Microbial Genomics"},{"key":"bib13","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1128\/AAC.00736-11","article-title":"Downregulation of Mitogen-Activated protein kinase 1 of Leishmania donovani Field Isolates Is Associated with Antimony Resistance","volume":"56","author":"Ashutosh","year":"2012","journal-title":"Antimicrobial Agents and Chemotherapy"},{"key":"bib14","doi-asserted-by":"publisher","first-page":"D457","DOI":"10.1093\/nar\/gkp851","article-title":"TriTrypDB: a functional genomic resource for the Trypanosomatidae","volume":"38","author":"Aslett","year":"2010","journal-title":"Nucleic Acids Research"},{"key":"bib15","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1093\/genetics\/164.4.1635","article-title":"The population genetics of clonal and partially clonal diploids","volume":"164","author":"Balloux","year":"2003","journal-title":"Genetics"},{"key":"bib16","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1016\/0166-6851(90)90079-2","article-title":"Interclonal variations in molecular karyotype in Leishmania infantum imply a \u2018mosaic\u2019 strain structure","volume":"40","author":"Bastien","year":"1990","journal-title":"Molecular and Biochemical Parasitology"},{"key":"bib17","doi-asserted-by":"publisher","first-page":"231","DOI":"10.3201\/eid1602.090623","article-title":"Domestic Animals and Epidemiology of Visceral Leishmaniasis, Nepal","volume":"16","author":"Bhattarai","year":"2010","journal-title":"Emerging Infectious Diseases"},{"key":"bib18","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"bib19","doi-asserted-by":"publisher","DOI":"10.1002\/0471142905.hg1802s79","article-title":"Improved protocols for illumina sequencing","volume":"80","author":"Bronner","year":"2014","journal-title":"Current Protocols in Human Genetics"},{"key":"bib20","doi-asserted-by":"publisher","first-page":"951","DOI":"10.1016\/S0140-6736(18)31204-2","article-title":"Leishmaniasis","volume":"392","author":"Burza","year":"2018","journal-title":"The Lancet"},{"key":"bib21","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01399-18","article-title":"Leishmania genome dynamics during environmental adaptation reveal Strain-Specific differences in gene copy number variation, karyotype instability, and telomeric amplification","volume":"9","author":"Bussotti","year":"2018","journal-title":"mBio"},{"key":"bib22","doi-asserted-by":"crossref","first-page":"18427","DOI":"10.1016\/S0021-9258(18)55077-8","article-title":"Heavy metal resistance: a new role for P-glycoproteins in\u00a0Leishmania","volume":"266","author":"Callahan","year":"1991","journal-title":"The Journal of Biological Chemistry"},{"key":"bib23","doi-asserted-by":"publisher","first-page":"1231","DOI":"10.1016\/j.micinf.2003.09.005","article-title":"Transcription in kinetoplastid protozoa: why be normal?","volume":"5","author":"Campbell","year":"2003","journal-title":"Microbes and Infection"},{"key":"bib24","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1016\/j.ebiom.2018.09.029","article-title":"A Leishmania\u00a0infantum genetic marker associated with miltefosine treatment failure for visceral leishmaniasis","volume":"36","author":"Carnielli","year":"2018","journal-title":"EBioMedicine"},{"key":"bib25","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly"},{"key":"bib26","doi-asserted-by":"publisher","DOI":"10.1101\/516211","article-title":"Genomic analysis of natural intra-specific hybrids among ethiopian isolates of\u00a0Leishmania\u00a0donovani","volume-title":"bioRxiv","author":"Cotton","year":"2019"},{"key":"bib27","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"bib28","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1016\/j.meegid.2005.02.004","article-title":"Molecular epidemiology of clonal diploids: a quick overview and a short DIY (do it yourself) notice","volume":"6","author":"De Mee\u00fbs","year":"2006","journal-title":"Infection, Genetics and Evolution"},{"key":"bib29","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1005296","article-title":"Amastin knockdown in\u00a0Leishmania\u00a0braziliensis affects Parasite-Macrophage interaction and results in impaired viability of intracellular amastigotes","volume":"11","author":"de Paiva","year":"2015","journal-title":"PLOS Pathogens"},{"key":"bib30","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1046\/j.1365-2958.2002.02740.x","article-title":"Functional analysis of the enteropathogenic Escherichia coli type III secretion system chaperone CesT identifies domains that mediate substrate interactions","volume":"43","author":"Delahay","year":"2002","journal-title":"Molecular Microbiology"},{"key":"bib31","doi-asserted-by":"publisher","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":"DePristo","year":"2011","journal-title":"Nature Genetics"},{"key":"bib32","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0030377","article-title":"Fast computation and applications of genome mappability","volume":"7","author":"Derrien","year":"2012","journal-title":"PLOS ONE"},{"key":"bib33","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1007\/s00436-007-0528-5","article-title":"Organization of H locus conserved repeats in\u00a0Leishmania\u00a0(Viannia) braziliensis correlates with lack of gene amplification and drug resistance","volume":"101","author":"Dias","year":"2007","journal-title":"Parasitology Research"},{"key":"bib34","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1016\/j.vetpar.2014.03.029","article-title":"High rates of\u00a0Leishmania\u00a0infantum and Trypanosoma nabiasi infection in wild rabbits (Oryctolagus cuniculus) in sympatric and syntrophic conditions in an endemic canine leishmaniasis area: epidemiological consequences","volume":"202","author":"D\u00edaz-S\u00e1ez","year":"2014","journal-title":"Veterinary Parasitology"},{"key":"bib35","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0007900","article-title":"Genomes of\u00a0Leishmania\u00a0parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent","volume":"13","author":"Domagalska","year":"2019","journal-title":"PLOS Neglected Tropical Diseases"},{"key":"bib36","doi-asserted-by":"publisher","first-page":"2143","DOI":"10.1101\/gr.123430.111","article-title":"Whole genome sequencing of multiple\u00a0Leishmania\u00a0donovani clinical isolates provides insights into population structure and mechanisms of drug resistance","volume":"21","author":"Downing","year":"2011","journal-title":"Genome Research"},{"key":"bib37","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v022.i04","article-title":"The ade4 package: implementing the duality diagram for ecologists","volume":"22","author":"Dray","year":"2007","journal-title":"Journal of Statistical Software"},{"key":"bib38","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1016\/j.pt.2014.09.004","article-title":"Mosaic aneuploidy in\u00a0Leishmania: the perspective of whole genome sequencing","volume":"30","author":"Dujardin","year":"2014","journal-title":"Trends in Parasitology"},{"key":"bib39","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00599-17","article-title":"Modulation of aneuploidy in Leishmania donovani\u00a0during adaptation to different in Vitro and in Vivo Environments and Its Impact on Gene Expression","volume":"8","author":"Dumetz","year":"2017","journal-title":"mBio"},{"key":"bib40","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00548-17","article-title":"Molecular preadaptation to antimony resistance in\u00a0Leishmania\u00a0donovani on the indian subcontinent","volume":"3","author":"Dumetz","year":"2018","journal-title":"mSphere"},{"key":"bib41","doi-asserted-by":"publisher","first-page":"843","DOI":"10.1016\/0035-9203(88)90013-2","article-title":"Earthquakes, influenza and cycles of indian kala-azar","volume":"82","author":"Dye","year":"1988","journal-title":"Transactions of the Royal Society of Tropical Medicine and Hygiene"},{"key":"bib42","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Research"},{"key":"bib43","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.tpb.2018.06.001","article-title":"The neutral frequency spectrum of linked sites","volume":"123","author":"Ferretti","year":"2018","journal-title":"Theoretical Population Biology"},{"key":"bib44","article-title":"Scripts and data files corresponding to the manuscript \"Global genome diversity of the\u00a0Leishmania donovani\u00a0complex\".","volume-title":"GitHub","author":"Franssen","year":"2020","unstructured":"Franssen SU, Cotton JA. 2020. Scripts and data files corresponding to the manuscript \"Global genome diversity of the\u00a0Leishmania donovani\u00a0complex\". GitHub. 357c713. https:\/\/github.com\/susefranssen\/Global_genome_diversity_Ldonovani_complex."},{"key":"bib45","doi-asserted-by":"publisher","DOI":"10.1186\/1756-3305-3-6","article-title":"Further studies on the phlebotomine sandflies of the kala-azar endemic lowlands of Humera-Metema (north-west Ethiopia) with observations on their natural blood meal sources","volume":"3","author":"Gebre-Michael","year":"2010","journal-title":"Parasites & Vectors"},{"key":"bib46","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1111\/j.1365-2915.1996.tb00082.x","article-title":"The roles of Phlebotomus martini and p.celiae (Diptera: phlebotominae) as vectors of visceral leishmaniasis in the aba roba focus, southern Ethiopia","volume":"10","author":"Gebre-Michael","year":"1996","journal-title":"Medical and Veterinary Entomology"},{"key":"bib47","doi-asserted-by":"publisher","DOI":"10.1590\/0074-02760180438","article-title":"Complete and de novo assembly of the\u00a0Leishmania braziliensis\u00a0(M2904) genome","volume":"114","author":"Gonz\u00e1lez-de la Fuente","year":"2019","journal-title":"Mem\u00f3rias Do Instituto Oswaldo Cruz"},{"key":"bib48","doi-asserted-by":"publisher","first-page":"31010","DOI":"10.1074\/jbc.M403959200","article-title":"Drug uptake and modulation of drug resistance in\u00a0Leishmania\u00a0by an aquaglyceroporin","volume":"279","author":"Gourbal","year":"2004","journal-title":"The Journal of Biological Chemistry"},{"key":"bib49","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0001507","article-title":"Multilocus microsatellite typing (MLMT) of strains from Turkey and Cyprus reveals a novel monophyletic L. donovani sensu lato group","volume":"6","author":"Gouzelou","year":"2012","journal-title":"PLOS Neglected Tropical Diseases"},{"key":"bib50","doi-asserted-by":"publisher","first-page":"1895","DOI":"10.1093\/nar\/21.8.1895","article-title":"Homologous recombination between direct repeat sequences yields P-glycoprotein containing amplicons in arsenite resistant\u00a0Leishmania","volume":"21","author":"Grondin","year":"1993","journal-title":"Nucleic Acids Research"},{"key":"bib51","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/S1567-1348(01)00008-9","article-title":"Genomic polymorphism of\u00a0Leishmania\u00a0infantum: a relationship with clinical pleomorphism?","volume":"1","author":"Guerbouj","year":"2001","journal-title":"Infection, Genetics and Evolution"},{"key":"bib52","doi-asserted-by":"publisher","DOI":"10.1186\/s13071-017-2175-8","article-title":"Evaluation of a multilocus sequence typing (MLST) scheme for\u00a0Leishmania\u00a0(Viannia) braziliensis and\u00a0Leishmania\u00a0(Viannia) panamensis in Colombia","volume":"10","author":"Herrera","year":"2017","journal-title":"Parasites & Vectors"},{"key":"bib53","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.0030187","article-title":"Adaptive gene expression divergence inferred from population genomics","volume":"3","author":"Holloway","year":"2007","journal-title":"PLOS Genetics"},{"key":"bib54","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01393-17","article-title":"Gene expression in Leishmania is regulated predominantly by gene dosage","volume":"8","author":"Iantorno","year":"2017","journal-title":"mBio"},{"key":"bib55","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.12613","article-title":"Evolutionary genomics of epidemic visceral leishmaniasis in the indian subcontinent","volume":"5","author":"Imamura","year":"2016","journal-title":"eLife"},{"key":"bib56","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1003672","article-title":"The mating competence of geographically diverse\u00a0Leishmania\u00a0major strains in their natural and unnatural sand fly vectors","volume":"9","author":"Inbar","year":"2013","journal-title":"PLOS Genetics"},{"key":"bib57","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1008042","article-title":"Whole genome sequencing of experimental hybrids supports meiosis-like sexual recombination in\u00a0Leishmania","volume":"15","author":"Inbar","year":"2019","journal-title":"PLOS Genetics"},{"key":"bib58","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1017\/S0031182004005955","article-title":"Leishmania donovani is the only cause of visceral leishmaniasis in east Africa; previous descriptions of L. infantum and \u201cL. archibaldi\u201d from this region are a consequence of convergent evolution in the isoenzyme data","volume":"129","author":"Jamjoom","year":"1999","journal-title":"Parasitology"},{"key":"bib59","doi-asserted-by":"publisher","first-page":"3435","DOI":"10.1093\/bioinformatics\/btr589","article-title":"PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)","volume":"27","author":"Kofler","year":"2011","journal-title":"Bioinformatics"},{"key":"bib60","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1016\/j.micinf.2006.12.009","article-title":"Multilocus microsatellite typing (MLMT) reveals genetically isolated populations between and within the main endemic regions of visceral leishmaniasis","volume":"9","author":"Kuhls","year":"2007","journal-title":"Microbes and Infection"},{"key":"bib61","doi-asserted-by":"publisher","first-page":"2342","DOI":"10.1093\/emboj\/18.9.2342","article-title":"Increased transport of pteridines compensates for mutations in the high affinity folate transporter and contributes to methotrexate resistance in the protozoan parasite\u00a0Leishmania tarentolae","volume":"18","author":"K\u00fcndig","year":"1999","journal-title":"The EMBO Journal"},{"key":"bib62","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/j.micinf.2013.09.005","article-title":"Constitutive mosaic aneuploidy is a unique genetic feature widespread in the\u00a0Leishmania\u00a0genus","volume":"16","author":"Lachaud","year":"2014","journal-title":"Microbes and Infection"},{"key":"bib63","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1016\/j.meegid.2011.04.004","article-title":"Guns, germs and dogs: on the origin of Leishmania chagasi","volume":"11","author":"Leblois","year":"2011","journal-title":"Infection, Genetics and Evolution"},{"key":"bib64","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/S0166-6851(99)00132-2","article-title":"The\u00a0Leishmania\u00a0donovani LD1 locus gene ORFG encodes a biopterin transporter (BT1)","volume":"104","author":"Lemley","year":"1999","journal-title":"Molecular and Biochemical Parasitology"},{"key":"bib65","doi-asserted-by":"publisher","first-page":"1387","DOI":"10.1093\/nar\/gkn1069","article-title":"Gene expression modulation is associated with gene amplification, supernumerary chromosomes and chromosome loss in antimony-resistant\u00a0Leishmania\u00a0infantum","volume":"37","author":"Leprohon","year":"2009","journal-title":"Nucleic Acids Research"},{"key":"bib66","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"bib67","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"bib68","doi-asserted-by":"publisher","first-page":"9375","DOI":"10.1073\/pnas.0703678104","article-title":"Evolutionary and geographical history of the\u00a0Leishmania donovani\u00a0complex with a revision of current taxonomy","volume":"104","author":"Lukes","year":"2007","journal-title":"PNAS"},{"key":"bib69","doi-asserted-by":"publisher","first-page":"987","DOI":"10.1128\/CMR.00080-14","article-title":"Visceral leishmaniasis in China: an endemic disease under control","volume":"28","author":"Lun","year":"2015","journal-title":"Clinical Microbiology Reviews"},{"key":"bib70","first-page":"515","article-title":"Distribution of leishmaniasis in the old world","volume":"44","author":"Lysenko","year":"1971","journal-title":"Bulletin of the World Health Organization"},{"key":"bib71","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005944","article-title":"MUMmer4: a fast and versatile genome alignment system","volume":"14","author":"Mar\u00e7ais","year":"2018","journal-title":"PLOS Computational Biology"},{"key":"bib72","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/S0166-6851(03)00174-9","article-title":"The H region HTBF gene mediates terbinafine resistance in\u00a0Leishmania\u00a0major","volume":"131","author":"Marchini","year":"2003","journal-title":"Molecular and Biochemical Parasitology"},{"key":"bib73","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003053","article-title":"Determinants for the development of visceral leishmaniasis disease","volume":"9","author":"McCall","year":"2013","journal-title":"PLOS Pathogens"},{"key":"bib74","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0003476","article-title":"Intrachromosomal amplification, locus deletion and point mutation in the aquaglyceroporin AQP1 gene in antimony resistant\u00a0Leishmania\u00a0(Viannia) guyanensis","volume":"9","author":"Monte-Neto","year":"2015","journal-title":"PLOS Neglected Tropical Diseases"},{"key":"bib75","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1111\/j.1600-065X.2010.00983.x","article-title":"Cell biology and immunology of Leishmania","volume":"240","author":"Mougneau","year":"2011","journal-title":"Immunological Reviews"},{"key":"bib76","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1111\/mmi.12178","article-title":"Telomeric gene deletion and intrachromosomal amplification in antimony-resistant\u00a0Leishmania","volume":"88","author":"Mukherjee","year":"2013","journal-title":"Molecular Microbiology"},{"key":"bib77","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0001284","article-title":"Incidence of symptomatic and asymptomatic\u00a0Leishmania\u00a0donovani infections in high-endemic foci in India and Nepal: a prospective study","volume":"5","author":"Ostyn","year":"2011","journal-title":"PLOS Neglected Tropical Diseases"},{"key":"bib78","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1093\/bioinformatics\/btg412","article-title":"APE: analyses of phylogenetics and evolution in R language","volume":"20","author":"Paradis","year":"2004","journal-title":"Bioinformatics"},{"key":"bib79","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1038\/ng2053","article-title":"Comparative genomic analysis of three\u00a0Leishmania\u00a0species that cause diverse human disease","volume":"39","author":"Peacock","year":"2007","journal-title":"Nature Genetics"},{"key":"bib80","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1111\/1755-0998.12129","article-title":"StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations","volume":"13","author":"Pembleton","year":"2013","journal-title":"Molecular Ecology Resources"},{"key":"bib81","doi-asserted-by":"publisher","first-page":"23766","DOI":"10.1074\/jbc.M605214200","article-title":"Phospholipid translocation and miltefosine potency require both L. donovani miltefosine transporter and the new protein LdRos3 in leishmania parasites","volume":"281","author":"P\u00e9rez-Victoria","year":"2006","journal-title":"Journal of Biological Chemistry"},{"key":"bib82","article-title":"SMALT mapper","author":"Ponstingl","year":"2010","unstructured":"Ponstingl H. 2010. SMALT mapper. https:\/\/www.sanger.ac.uk\/science\/tools\/smalt-0."},{"key":"bib83","doi-asserted-by":"publisher","first-page":"4077","DOI":"10.1128\/JCM.42.9.4077-4082.2004","article-title":"Isoenzymatic analysis of 712 strains of\u00a0Leishmania infantum\u00a0in the south of France and relationship of enzymatic polymorphism to clinical and epidemiological features","volume":"42","author":"Pratlong","year":"2004","journal-title":"Journal of Clinical Microbiology"},{"key":"bib84","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1111\/mmi.12383","article-title":"The\u00a0Leishmania\u00a0major\u2005BBSome subunit BBS1 is essential for parasite virulence in the mammalian host","volume":"90","author":"Price","year":"2013","journal-title":"Molecular Microbiology"},{"key":"bib85","doi-asserted-by":"publisher","first-page":"1961","DOI":"10.1038\/s41559-017-0361-x","article-title":"Haplotype selection as an adaptive mechanism in the protozoan pathogen\u00a0Leishmania\u00a0donovani","volume":"1","author":"Prieto Barja","year":"2017","journal-title":"Nature Ecology & Evolution"},{"key":"bib86","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"bib87","doi-asserted-by":"publisher","first-page":"1915","DOI":"10.1017\/S0031182009991156","article-title":"Transmission, reservoir hosts and control of zoonotic visceral leishmaniasis","volume":"136","author":"Quinnell","year":"2009","journal-title":"Parasitology"},{"key":"bib88","article-title":"R: A Language and Environment for Statistical Computing","author":"R Development Core Team","year":"2013","unstructured":"R Development Core Team. 2013. R: A Language and Environment for Statistical Computing. Vienna, Austria. http:\/\/www.r-project.org."},{"key":"bib89","doi-asserted-by":"publisher","first-page":"4195","DOI":"10.1111\/mec.12872","article-title":"Reproductive clonality in protozoan pathogens--truth or artefact?","volume":"23","author":"Ram\u00edrez","year":"2014","journal-title":"Molecular Ecology"},{"key":"bib90","doi-asserted-by":"publisher","first-page":"147","DOI":"10.2147\/CLEP.S44267","article-title":"Epidemiology of visceral leishmaniasis","volume":"6","author":"Ready","year":"2014","journal-title":"Clinical Epidemiology"},{"key":"bib91","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1093\/dnares\/dst031","article-title":"The genome sequence of\u00a0Leishmania\u00a0(Leishmania) amazonensis: functional annotation and extended analysis of gene models","volume":"20","author":"Real","year":"2013","journal-title":"DNA Research"},{"key":"bib92","doi-asserted-by":"publisher","first-page":"1175","DOI":"10.1111\/j.1365-2958.2010.07130.x","article-title":"Overexpression of a single\u00a0Leishmania\u00a0major gene enhances parasite infectivity in vivo and in vitro","volume":"76","author":"Reiling","year":"2010","journal-title":"Molecular Microbiology"},{"key":"bib93","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1051\/parasite\/1990653111","article-title":"Taxonomy of\u00a0Leishmania. Use of isoenzymes. Suggestions for a new classification","volume":"65","author":"Rioux","year":"1990","journal-title":"Annales De Parasitologie Humaine Et Compar\u00e9e"},{"key":"bib94","doi-asserted-by":"publisher","DOI":"10.1186\/s13071-016-1412-x","article-title":"Regulation of immunity during visceral\u00a0Leishmania\u00a0infection","volume":"9","author":"Rodrigues","year":"2016","journal-title":"Parasites & Vectors"},{"key":"bib95","doi-asserted-by":"publisher","first-page":"2129","DOI":"10.1101\/gr.122945.111","article-title":"Chromosome and gene copy number variation allow major structural change between species and strains of\u00a0Leishmania","volume":"21","author":"Rogers","year":"2011","journal-title":"Genome Research"},{"key":"bib96","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004092","article-title":"Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated\u00a0Leishmania\u00a0population","volume":"10","author":"Rogers","year":"2014","journal-title":"PLOS Genetics"},{"key":"bib97","doi-asserted-by":"publisher","first-page":"16808","DOI":"10.1073\/pnas.1415109111","article-title":"Cross-species genetic exchange between visceral and cutaneous strains of\u00a0Leishmania\u00a0in the sand fly vector","volume":"111","author":"Romano","year":"2014","journal-title":"PNAS"},{"key":"bib98","doi-asserted-by":"publisher","first-page":"10224","DOI":"10.1073\/pnas.0904420106","article-title":"Extreme inbreeding in\u00a0Leishmania\u00a0braziliensis","volume":"106","author":"Rougeron","year":"2009","journal-title":"PNAS"},{"key":"bib99","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1093\/oxfordjournals.molbev.a040454","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"Saitou","year":"1987","journal-title":"Molecular Biology and Evolution"},{"key":"bib100","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1016\/j.pt.2007.12.006","article-title":"Leishmaniases in the Mediterranean in the era of molecular epidemiology","volume":"24","author":"Sch\u00f6nian","year":"2008","journal-title":"Trends in Parasitology"},{"key":"bib101","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1017\/S0031182010001538","article-title":"Molecular approaches for a better understanding of the epidemiology and population genetics of\u00a0Leishmania","volume":"138","author":"Sch\u00f6nian","year":"2011","journal-title":"Parasitology"},{"key":"bib102","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1016\/S0169-4758(97)01111-3","article-title":"LD1 amplifications in\u00a0Leishmania","volume":"13","author":"Segovia","year":"1997","journal-title":"Parasitology Today"},{"key":"bib103","doi-asserted-by":"publisher","first-page":"1134","DOI":"10.1111\/mmi.13291","article-title":"In vitro selection of miltefosine resistance in promastigotes of\u00a0Leishmania\u00a0donovani from Nepal: genomic and metabolomic characterization","volume":"99","author":"Shaw","year":"2016","journal-title":"Molecular Microbiology"},{"key":"bib104","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1016\/j.pt.2006.02.006","article-title":"The evolution and diversity of kinetoplastid flagellates","volume":"22","author":"Simpson","year":"2006","journal-title":"Trends in Parasitology"},{"key":"bib105","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1016\/j.ijantimicag.2010.03.012","article-title":"Overexpression of histone H2A modulates drug susceptibility in\u00a0Leishmania\u00a0parasites","volume":"36","author":"Singh","year":"2010","journal-title":"International Journal of Antimicrobial Agents"},{"key":"bib106","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.01279","article-title":"Genome plasticity in cultured Leishmania donovani: Comparison of Early and Late Passages","volume":"9","author":"Sinha","year":"2018","journal-title":"Frontiers in Microbiology"},{"key":"bib107","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1093\/genetics\/137.1.331","article-title":"Linkage disequilibrium in growing and stable populations","volume":"137","author":"Slatkin","year":"1994","journal-title":"Genetics"},{"key":"bib108","doi-asserted-by":"publisher","first-page":"1022","DOI":"10.1038\/4151022a","article-title":"Adaptive protein evolution in Drosophila","volume":"415","author":"Smith","year":"2002","journal-title":"Nature"},{"key":"bib109","doi-asserted-by":"publisher","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","article-title":"RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models","volume":"22","author":"Stamatakis","year":"2006","journal-title":"Bioinformatics"},{"key":"bib110","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1111\/j.1462-5822.2010.01534.x","article-title":"FISH analysis reveals aneuploidy and continual generation of chromosomal mosaicism in\u00a0Leishmania\u00a0major","volume":"13","author":"Sterkers","year":"2011","journal-title":"Cellular Microbiology"},{"key":"bib111","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1016\/j.pt.2014.07.002","article-title":"Parasexuality and mosaic aneuploidy in\u00a0Leishmania: alternative genetics","volume":"30","author":"Sterkers","year":"2014","journal-title":"Trends in Parasitology"},{"key":"bib112","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1093\/molbev\/msq249","article-title":"Estimation of the neutrality index","volume":"28","author":"Stoletzki","year":"2011","journal-title":"Molecular Biology and Evolution"},{"key":"bib113","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1016\/S0166-6851(01)00215-8","article-title":"Conservation of the LD1 region in\u00a0Leishmania\u00a0includes DNA implicated in LD1 amplification","volume":"113","author":"Sunkin","year":"2001","journal-title":"Molecular and Biochemical Parasitology"},{"key":"bib114","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0021800","article-title":"REVIGO summarizes and visualizes long lists of gene ontology terms","volume":"6","author":"Supek","year":"2011","journal-title":"PLOS ONE"},{"key":"bib115","doi-asserted-by":"publisher","first-page":"31120","DOI":"10.1074\/jbc.M110.114462","article-title":"Leishmania subtilisin is a maturase for the trypanothione reductase system and contributes to disease pathology","volume":"285","author":"Swenerton","year":"2010","journal-title":"Journal of Biological Chemistry"},{"key":"bib116","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1016\/j.ijpara.2017.04.004","article-title":"Comparative analyses of whole genome sequences of\u00a0Leishmania\u00a0infantum isolates from humans and dogs in northeastern Brazil","volume":"47","author":"Teixeira","year":"2017","journal-title":"International Journal for Parasitology"},{"key":"bib117","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0006659","article-title":"Atypical leishmaniasis: a global perspective with emphasis on the indian subcontinent","volume":"12","author":"Thakur","year":"2018","journal-title":"PLOS Neglected Tropical Diseases"},{"key":"bib118","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1016\/0166-6851(91)90174-5","article-title":"A DNA sequence (LD1) which occurs in several genomic organizations in\u00a0Leishmania","volume":"47","author":"Tripp","year":"1991","journal-title":"Molecular and Biochemical Parasitology"},{"key":"bib119","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/0166-6851(92)90125-4","article-title":"A multicopy, extrachromosomal DNA in\u00a0Leishmania\u00a0infantum contains two inverted repeats of the 27.5-kilobase LD1 sequence and encodes numerous transcripts","volume":"55","author":"Tripp","year":"1992","journal-title":"Molecular and Biochemical Parasitology"},{"key":"bib120","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1001868","article-title":"Genome-wide stochastic adaptive DNA amplification at direct and inverted DNA repeats in the parasite\u00a0Leishmania","volume":"12","author":"Ubeda","year":"2014","journal-title":"PLOS Biology"},{"key":"bib121","doi-asserted-by":"publisher","first-page":"1477","DOI":"10.1111\/j.1365-2958.2008.06494.x","article-title":"Alteration in glycerol and metalloid permeability by a single mutation in the extracellular C-loop of leishmania major aquaglyceroporin LmAQP1","volume":"70","author":"Uzcategui","year":"2008","journal-title":"Molecular Microbiology"},{"key":"bib122","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi1110s43","article-title":"From FastQ data to high confidence variant calls: the genome analysis toolkit best practices pipeline","volume":"11","author":"Van der Auwera","year":"2013","journal-title":"Curr Protoc Bioinforma Ed Board Andreas Baxevanis Al"},{"key":"bib123","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1042\/bse0510063","article-title":"Folate metabolic pathways in\u00a0Leishmania","volume":"51","author":"Vickers","year":"2011","journal-title":"Essays in Biochemistry"},{"key":"bib124","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.11473","article-title":"Population genomics reveals the origin and asexual evolution of human infective trypanosomes","volume":"5","author":"Weir","year":"2016","journal-title":"eLife"},{"key":"bib125","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1073\/pnas.24.7.253","article-title":"The distribution of gene frequencies under irreversible mutation","volume":"24","author":"Wright","year":"1938","journal-title":"PNAS"},{"key":"bib126","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1007133","article-title":"Genome wide comparison of ethiopian Leishmania donovani strains reveals differences potentially related to parasite survival","volume":"14","author":"Zackay","year":"2018","journal-title":"PLOS Genetics"},{"key":"bib127","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0063124","article-title":"Phylogenetic and evolutionary analysis of chinese\u00a0Leishmania\u00a0isolates based on multilocus sequence typing","volume":"8","author":"Zhang","year":"2013","journal-title":"PLOS ONE"},{"key":"bib128","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1004244","article-title":"Genetic analysis of\u00a0Leishmania\u00a0donovani tropism using a naturally attenuated cutaneous strain","volume":"10","author":"Zhang","year":"2014","journal-title":"PLOS Pathogens"},{"key":"bib129","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1016\/S1473-3099(03)00517-6","article-title":"Post-kala-azar dermal leishmaniasis","volume":"3","author":"Zijlstra","year":"2003","journal-title":"The Lancet Infectious Diseases"}],"container-title":["eLife"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdn.elifesciences.org\/articles\/51243\/elife-51243-v2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/cdn.elifesciences.org\/articles\/51243\/elife-51243-v2.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/elifesciences.org\/articles\/51243","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,11]],"date-time":"2023-10-11T20:57:17Z","timestamp":1697057837000},"score":1,"resource":{"primary":{"URL":"https:\/\/elifesciences.org\/articles\/51243"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,3,25]]},"references-count":129,"alternative-id":["10.7554\/eLife.51243"],"URL":"https:\/\/doi.org\/10.7554\/elife.51243","archive":["CLOCKSS"],"relation":{"references":[{"id-type":"accession","id":"ERP000140","asserted-by":"subject"},{"id-type":"accession","id":"PRJEB2473","asserted-by":"subject"},{"id-type":"accession","id":"PRJEB14372","asserted-by":"subject"},{"id-type":"accession","id":"SRS484824","asserted-by":"subject"},{"id-type":"accession","id":"ERS001832","asserted-by":"subject"},{"id-type":"accession","id":"PRJEB2115","asserted-by":"subject"},{"id-type":"accession","id":"ERS218438","asserted-by":"subject"},{"id-type":"accession","id":"PRJNA494801","asserted-by":"subject"}],"is-supplemented-by":[{"id-type":"accession","id":"PRJEB2600","asserted-by":"subject"},{"id-type":"accession","id":"PRJEB2724","asserted-by":"subject"},{"id-type":"accession","id":"PRJEB8947","asserted-by":"subject"},{"id-type":"accession","id":"ERS001888","asserted-by":"subject"}],"has-review":[{"id-type":"doi","id":"10.7554\/eLife.51243.sa2","asserted-by":"object"},{"id-type":"doi","id":"10.7554\/eLife.51243.sa1","asserted-by":"object"}],"has-preprint":[{"id-type":"doi","id":"10.1101\/710145","asserted-by":"object"}]},"ISSN":["2050-084X"],"issn-type":[{"value":"2050-084X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,3,25]]},"article-number":"e51243"}}