Seventy-eight entire mitochondrial genomes and nuclear rRNA genes provide insight into the phylogeny of the hard ticks, particularly the Haemaphysalis species, Africaniella transversale and Robertsicus elaphensis

• Published in: Ticks and tick-borne diseases 2023-03, Vol.14 (2), p.102070-102070, Article 102070
• Main Authors: Kelava, Samuel, Mans, Ben J., Shao, Renfu, Barker, Dayana, Teo, Ernest J.M., Chatanga, Elisha, Gofton, Alexander W., Moustafa, Mohamed Abdallah Mohamed, Nakao, Ryo, Barker, Stephen C.
• Format: Article
• Language: English
• Subjects: Acari; Amblyomma - genetics; Animals; Genes, rRNA; Genome, Mitochondrial; Ixodida; Ixodidae; Ixodidae - genetics; Phylogeny; Rhipicephalus - genetics
• ISSN: 1877-959X; 1877-9603
• DOI: 10.1016/j.ttbdis.2022.102070

•The subgenus Alloceraea may be the sister to the other subgenera of the genus Haemaphysalis.•Haemaphysalis (Al.) inermis and H. (Al.) kitaokai were well removed from the rest of the Haemaphysalis species in our phylogenies.•Haemaphysalis (Al.) inermis had an insertion of 132-bp in the mt genome between the tRNA-Glu (E) gene and the nad1 protein-coding gene.•Either Africaniella transversale or Robertsicus elaphensis, or perhaps Africaniella transversale plus Ro. elaphensis, are the sister-group to the rest of the metastriate Ixodida.•The “structurally primitive”, “structurally intermediate” and “structurally advanced” Haemaphysalis groups of Hoogstraal and Kim (1985) do not appear to be monophyletic.•Our amino-acid dataset had Archaeocroton sphenodonti as the sister to Ha. (Al.) inermis and Ha. (Alloceraea) kitaokai.•Alectorobius capensis from Japan had a higher pairwise (%) genetic-identity to A. sawaii than to the other A. capensis ticks from South Africa; the A. capensis specimens we sequenced from Japan may be from a cryptic species with respect to the Alectorobius capensis from South Africa. Hoogstraal and Kim (1985) proposed from morphology, three groups of Haemaphysalis subgenera: (i) the “structurally advanced”; (ii) the “structurally intermediate”; and (iii) the “structurally primitive” subgenera. Nuclear gene phylogenies, however, did not indicate monophyly of these morphological groups but alas, only two mitochondrial (mt) genomes from the “structurally intermediate” subgenera had been sequenced. The phylogeny of Haemaphysalis has not yet been resolved. We aimed to resolve the phylogeny of the genus Haemaphysalis, with respect to the subgenus Alloceraea. We presented 15 newly sequenced and annotated mt genomes from 15 species of ticks, five species of which have not been sequenced before, and four new 18S rRNA and 28S rRNA nuclear gene sequences. Our datasets were constructed from 10 mt protein-coding genes, cox1, and the 18S and 28S nuclear rRNA genes. We found a 132-bp insertion between tRNA-Glu (E) gene and the nad1 gene in the mt genome of Haemaphysalis (Alloceraea) inermis that resembles insertions in H. (Alloceraea) kitaokai and Rhipicephalus (Boophilus) geigyi. Our mt phylogenies had the three species of Amblyomma (Aponomma) we sequenced embedded in the main clade of Amblyomma: Am. (Aponomma) fimbriatum, Am. (Aponomma) gervaisi and Am. (Aponomma) latum. This is further support for the hypothesis that the evolution of eyes appears to have