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To address unresolved issues with respect to the evolutionary relationships among certain species or genera, we produced novel RNA-Seq data sets for nine different <jats:italic>Ixodes<\/jats:italic> species. We combined this new data with 18 data sets obtained from public databases, both for <jats:italic>Ixodes<\/jats:italic> and non-<jats:italic>Ixodes<\/jats:italic> hard tick species, using soft ticks as an outgroup. We assembled transcriptomes (for 27 species in total), predicted coding sequences and identified single copy orthologues (SCO). Using Maximum-likelihood and Bayesian frameworks, we reconstructed a hard tick phylogeny for the nuclear genome. We also obtained a mitochondrial DNA-based phylogeny using published genome sequences and mitochondrial sequences derived from the new transcriptomes. Our results confirm previous studies showing that the <jats:italic>Ixodes<\/jats:italic> genus is monophyletic and clarify the relationships among <jats:italic>Ixodes<\/jats:italic> sub-genera. This work provides a baseline for studying the evolutionary history of ticks: we indeed found an unexpected acceleration of substitutions for mitochondrial sequences of Prostriata, and for nuclear and mitochondrial genes of two species of <jats:italic>Rhipicephalus<\/jats:italic>, which we relate with patterns of genome architecture and changes of life-cycle, respectively.<\/jats:p>","DOI":"10.1038\/s41598-019-49641-9","type":"journal-article","created":{"date-parts":[[2019,9,9]],"date-time":"2019-09-09T10:03:08Z","timestamp":1568023388000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":43,"title":["A transcriptome-based phylogenetic study of hard ticks (Ixodidae)"],"prefix":"10.1038","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5681-0091","authenticated-orcid":false,"given":"N. 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