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Information on its genetic and evolutionary diversity is scanty. The aim of this study was to investigate the prevalence of <jats:italic>E. shiquicus<\/jats:italic> in plateau pikas (<jats:italic>Ochotona curzoniae<\/jats:italic>), a known intermediate host, and to determine the genetic variation and phylogenetic relationship of the <jats:italic>E. shiquicus<\/jats:italic> population in the Tibet region of China based on mitochondrial DNA.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p><jats:italic>Echinococcus shiquicus<\/jats:italic> samples were collected from Damxung and Ny\u00eamo counties (located in Tibet Autonomous Region, China). The mitochondrial <jats:italic>cox<\/jats:italic>1 and <jats:italic>nad<\/jats:italic>1 gene sequences were analyzed, and the genetic diversity and epidemiology of <jats:italic>E. shiquicus<\/jats:italic> in the region were discussed based on the results.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The prevalence of <jats:italic>E. shiquicus<\/jats:italic> in pikas in Damxung and Ny\u00eamo counties was 3.95% (6\/152) and 6.98% (9\/129), respectively. In combination with previous public sequence data, the haplotype analysis revealed 12 haplotypes (H) characterized by two distinct clusters (I and II), and a sequence distance of 99.1\u201399.9% from the reference haplotype (H1). The diversity and neutrality indices for the entire <jats:italic>E. shiquicus<\/jats:italic> populations were: haplotype diversity (Hd) \u00b1 standard deviation (SD) 0.862\u2009\u00b1\u20090.035; nucleotide diversity (Hd \u00b1 SD) 0.0056 \u00b1 0.0003; Tajima's<jats:italic> D<\/jats:italic> 0.876 (<jats:italic>P<\/jats:italic> &gt; 0.05); and Fu\u2019s<jats:italic> F<\/jats:italic> 6.000 (<jats:italic>P<\/jats:italic> &gt; 0.05).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>This was the first analysis of the newly discovered <jats:italic>E. shiquicus<\/jats:italic> in plateau pikas in the Tibet Autonomous Region of China. The neutrality indices suggest a deficiency of alleles, indicative of a recent population bottleneck.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Graphical Abstract<\/jats:title>\n                \n              <\/jats:sec>","DOI":"10.1186\/s13071-020-04456-w","type":"journal-article","created":{"date-parts":[[2020,11,23]],"date-time":"2020-11-23T14:05:23Z","timestamp":1606140323000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["First report on the phylogenetic relationship, genetic variation of Echinococcus shiquicus isolates in Tibet Autonomous Region, China"],"prefix":"10.1186","volume":"13","author":[{"given":"Guo-Qiang","family":"Zhu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong-Bin","family":"Yan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John Asekhaen","family":"Ohiolei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan-Tao","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wen-Hui","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nian-Zhang","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bao-Quan","family":"Fu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wan-Zhong","family":"Jia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,11,23]]},"reference":[{"issue":"6","key":"4456_CR1","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1016\/j.pt.2012.03.004","volume":"28","author":"RK Davidson","year":"2012","unstructured":"Davidson RK, Romig T, Jenkins E, Tryland M, Robertson LJ. 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The collection and autopsy of the plateau pikas were handled in strict accordance with good animal practice according to the animal ethics procedures and guidelines for animal husbandry and wildlife protection.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"590"}}