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A considerable level of genetic variation among isolates of different intermediate hosts and locations has been documented. Generally, data on the genetic population structure of<jats:italic>T. hydatigena<\/jats:italic>is scanty and lacking in Nigeria. Meanwhile, similar findings in other cestodes like<jats:italic>Echinococcus<\/jats:italic>spp. have been found to be of epidemiological importance. Our aim, therefore, was to characterize and compare the genetic diversity of<jats:italic>T. hydatigena<\/jats:italic>population in Nigeria based on three mitochondrial DNA markers as well as to assess the phylogenetic relationship with populations from other geographical regions.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>In the present study, we described the genetic variation and diversity of<jats:italic>T. hydatigena<\/jats:italic>isolates from Nigerian sheep and goats using three full-length mitochondrial genes: the cytochrome<jats:italic>c<\/jats:italic>oxidase subunit 1 (<jats:italic>cox<\/jats:italic>1), NADH dehydrogenase subunit 1 (<jats:italic>nad<\/jats:italic>1), and NADH dehydrogenase subunit 5 (<jats:italic>nad<\/jats:italic>5).<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The median-joining network of concatenated<jats:italic>cox<\/jats:italic>1-<jats:italic>nad<\/jats:italic>1-<jats:italic>nad<\/jats:italic>5 sequences indicated that<jats:italic>T. hydatigena<\/jats:italic>metacestodes of sheep origin were genetically distinct from those obtained in goats and this was supported by high F<jats:sub>ST<\/jats:sub>values of<jats:italic>nad<\/jats:italic>1,<jats:italic>cox<\/jats:italic>1, and concatenated<jats:italic>cox<\/jats:italic>1-<jats:italic>nad<\/jats:italic>1-<jats:italic>nad<\/jats:italic>5 sequences. Genetic variation was also found to be higher in isolates from goats than from sheep.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>To the best of our knowledge, the present study described the genetic variation of<jats:italic>T. hydatigena<\/jats:italic>population for the first time in Nigeria using full-length mitochondrial genes and suggests the existence of host-specific variants. The population indices of the different DNA markers suggest that analysis of long mitochondrial DNA fragments may provide more information on the molecular ecology of<jats:italic>T<\/jats:italic>.<jats:italic>hydatigena.<\/jats:italic>We recommend that future studies employ long mitochondrial DNA sequence in order to provide reliable data that would\u00a0explain the extent of genetic variation in different hosts\/locations and the biological and epidemiological significance.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s13071-019-3780-5","type":"journal-article","created":{"date-parts":[[2019,11,5]],"date-time":"2019-11-05T16:03:18Z","timestamp":1572969798000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["First molecular description, phylogeny and genetic variation of Taenia hydatigena from Nigerian sheep and goats based on three mitochondrial genes"],"prefix":"10.1186","volume":"12","author":[{"given":"John A.","family":"Ohiolei","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua","family":"Luka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guo-Qiang","family":"Zhu","sequence":"additional","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":"Abdullahi A.","family":"Magaji","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mughees A.","family":"Alvi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan-Tao","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian-Qiu","family":"Li","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":[[2019,11,5]]},"reference":[{"key":"3780_CR1","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1017\/S0022149X14000601","volume":"90","author":"A Scala","year":"2016","unstructured":"Scala A, Urrai G, Varcasia A, Nicolussi P, Mulas M, Goddi L, et al. 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