Phylogenetic analyses of ticks (Acari: Ixodida) using mitochondrial genome sequences

Burger, Thomas (2013). Phylogenetic analyses of ticks (Acari: Ixodida) using mitochondrial genome sequences PhD Thesis, School of Chemistry & Molecular Biosciences, The University of Queensland.

       
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Author Burger, Thomas
Thesis Title Phylogenetic analyses of ticks (Acari: Ixodida) using mitochondrial genome sequences
School, Centre or Institute School of Chemistry & Molecular Biosciences
Institution The University of Queensland
Publication date 2013
Thesis type PhD Thesis
Supervisor Stephen C Barker
Renfu Shao
Total pages 215
Total colour pages 73
Total black and white pages 146
Language eng
Subjects 060301 Animal Systematics and Taxonomy
060309 Phylogeny and Comparative Analysis
060409 Molecular Evolution
Formatted abstract
Ticks (Acari: Ixodida) are haematophagous ectoparasites of terrestrial vertebrates. Our understanding of the phylogenetic relationships among tick lineages has been limited by the lack of resolution provided by the most commonly used phylogenetic markers. I used mitochondrial genome sequences and nuclear rRNA genes to infer the phylogenetic relationships among groups of ticks, and resolve long-standing issues in the phylogeny of ticks.

I first attempted to resolve the phylogenetic placement of Amblyomma sphenodonti and Am. elaphense with respect to the rest of the genus Amblyomma. I sequenced the mitochondrial genomes of these two species as well as Am. fimbriatum, Bothriocroton concolor, and Bt. undatum. My analysis of these mitochondrial genome sequences strongly supported paraphyly of the genus Amblyomma with respect to Am. sphenodonti and Am. elaphense. My analysis suggested that Am. sphenodonti and Am. elaphense were the sister groups to two established genera; Bothriocroton in the case of Am. sphenodonti, and Haemaphysalis in the case of Am. elaphense. However, I could not exclude alternative phylogenetic placements of either species. I hypothesised that additional mitochondrial genome sequences from the genera Haemaphysalis and Rhipicephalus may help to more conclusively resolve the phylogenetic positions of Am. sphenodonti and Am. elaphense. I therefore sequenced the mitochondrial genomes of four species of Haemaphysalis as well as Am. cajennense, the type species of the genus Amblyomma. Including these additional species in the analysis yielded increased support for the phylogenetic placement of Am. sphenodonti and Am. elaphense. The most likely phylogenetic placement of Am. elaphense was as the sister group to the rest of the Metastriata, but the phylogenetic placement of Am. sphenodonti was sister to the genera Bothriocroton or Haemaphysalis. Additionally, I found support for a new arrangement of metastriate genera, consisting of two major lineages: Amblyomma s.s. and the subfamily Rhipicephalinae; and Haemaphysalis, Bothriocroton, and Am. sphenodonti. I also discovered a deeply divergent lineage within the genus Haemaphysalis consisting of at least two species: H. parva and H. inermis.

Next, I used mitochondrial genomes, three widely-sequenced partial mitochondrial genes, and one nuclear marker to investigate phylogenetic relationships within the subgenus Rhipicephalus (Boophilus). My analysis revealed that there may be a cryptic species within R. microplus: specimens of R. microplus from several locations in China and India form a clade more closely related to R. annulatus than specimens of R. microplus from Southeast Asia, Africa and South America. My analysis also supported the reinstatement of R. australis for cattle ticks from Australia, Indonesia and New Caledonia previously reported as R. microplus. Indeed, my data showed that the cattle ticks R. microplus (both clades), R. annulatus and R. australis are a species complex, which I called the R. microplus species complex. I investigated the ability of different mitochondrial and nuclear markers to differentiate these clades of the R. microplus species complex and found that cox1 and 16S rRNA sequences were far more informative than 12S rRNA and ITS2.

I then sequenced a further 12 mitochondrial genomes of soft ticks to address the phylogenetic relationships among soft tick genera, and to test the previous phylogenetic relationships of soft ticks inferred from morphology. My analysis had strong support for a clade of six Neotropical species of Antricola, Nothoaspis, Ornithodoros (Alectorobius) and Ornithodoros (Subparmatus), as well as a clade of five species of Ornithodoros (Ornithodoros) and Ornithodoros (Pavlovskyella), including the type species of the genus, Ornithodoros savignyi. The species in my Neotropical clade were all placed in the genus Carios s.l. by Klompen and Oliver (1993), along with the subgenus Argas (Carios), on the basis of morphology. My analysis of mitochondrial genome sequences and nuclear rRNA thus strongly supported the paraphyly of the genus Ornithodoros s.l., as suggested by Klompen and Oliver (1993). My analysis of mitochondrial 12S and 16S rRNA sequences supported the placement of Argas (Carios) vespertilionis (the type species of the subgenus Carios) within the Ornithodorinae, but was unable to resolve the phylogenetic position of Argas (Carios) vespertilionis in relation to my Neotropical clade. Thus, I demonstrated that mitochondrial genome sequences have the phylogenetic resolution to resolve the controversial phylogenetic relationships among soft tick genera.

My work has shown the power of mitochondrial genome sequences in resolving controversial phylogenetic relationships among tick lineages: the polyphyly of the genus Amblyomma with respect to Am. sphenodonti and Am. elaphense; the sister group relationship between the Rhipicephalinae and the genus Amblyomma s.s.; the relationships within the R. microplus complex; and the relationships among soft tick genera. In the future, mitochondrial genome sequences will be useful for resolving the phylogenetic relationship among groups of ticks which have yet to be adequately tested with molecular data: the rhipicephaline genera Anomalohimalaya, Cosmiomma, and Margaropus; and the soft tick subgenera Argas (Carios), Argas (Chiropterargas), and Ornithodoros (Reticulinasus).
Keyword Ticks
Ixodida
Mitochondrial genomes
18S rRNA
Phylogeny
Systematics
Amblyomma

 
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Created: Wed, 19 Feb 2014, 13:12:08 EST by Mr Thomas Burger on behalf of Scholarly Communication and Digitisation Service