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ABSTRACTIn the present study, we applied our ‘precise annotation’ to the mitochondrial (mt) genomes of human, chimpanzee, rhesus macaque and mouse using 5′ and 3′ end small RNAs. Our new annotations updated previous annotations. In particular, our new annotations led to two important novel findings: (1) the identification of five Conserved Sequence Blocks (CSB1, CSB2, CSB3, LSP and HSP) in the control regions; and (2) the annotation of Transcription Initiation and novel Transcription Termination Sites. Based on these annotations, we proposed a novel model of mt transcription which can account for the mt transcription and its regulation in mammals. According to our model, Transcription Termination Sites function as switches to regulate the production of short, long primary transcripts and uninterrupted transcription, rather than simply terminate the mt transcription. Moreover, the expression levels of mitochondrial transcription termination factors control the proportions of rRNAs, mRNAs and lncRNAs in total mt RNA. Our findings point to the existence of many other, as yet unidentified, Transcription Termination Sites in mammals.

•The subgenus Alloceraeamay be the sister to the other subgenera of the genus Haemaphysalis.•Haemaphysalis(Al.) inermisand H. (Al.) kitaokaiwere well removed from the rest of the Haemaphysalisspecies in our phylogenies.•Haemaphysalis(Al.) inermishad an insertion of 132-bp in the mt genome between the tRNA-Glu (E) gene and the nad1protein-coding gene.•Either Africaniella transversaleor Robertsicus elaphensis, or perhaps Africaniella transversaleplus Ro. elaphensis, are the sister-group to the rest of the metastriate Ixodida.•The “structurally primitive”, “structurally intermediate” and “structurally advanced” Haemaphysalisgroups of Hoogstraal and Kim (1985) do not appear to be monophyletic.•Our amino-acid dataset had Archaeocroton sphenodontias the sister to Ha. (Al.) inermisand Ha. (Alloceraea) kitaokai.•Alectorobius capensisfrom Japan had a higher pairwise (%) genetic-identity to A. sawaiithan to the other A. capensisticks from South Africa; the A. capensisspecimens we sequenced from Japan may be from a cryptic species with respect to the Alectorobius capensisfrom South Africa.

The genus-level classification of soft ticks (Argasidae) is controversial. A previous phylogenetic analysis of morphological and developmental characters found that the genus Ornithodoroswas paraphyletic and raised a new genus, Carios, for species previously in the genera Antricola, Argas, Ornithodoros, and Nothoaspis(Klompen and Oliver, 1993). Genetic analyses of soft ticks to date have been limited to 16S rRNA, which is not highly phylogenetically informative for this group. We sequenced the entire mitochondrial genomes of 7 species of soft ticks, and the partial mitochondrial genomes of a further 5 species of soft ticks. We used these sequences to test the genus-level classification of soft ticks. Our analyses strongly support a clade of Neotropical species (mostly bat-associated) within the subfamily Ornithodorinae. This clade, which we call Neotropical Ornithodorinae, has species from 2 genera, Antricolaand Nothoaspis, and 2 subgenera, Ornithodoros(Alectorobius) and Ornithodoros(Subparmatus). We also addressed the phylogenetic position of Ornithodoros savignyi, the type species of the genus Ornithodoros. Our analysis strongly supports a clade consisting of Ornithodoros savignyiand 4 other Ornithodorosspecies: Or. brasiliensis, Or. moubata, Or. porcinus, and Or. rostratus. This clade, Ornithodorossensu stricto, did not contain the Alectorobiusand Subparmatusspecies, Or.(Alectorobius) fonsecai, Or.(Alectorobius) capensis, and Or.(Subparmatus) marinkellei, which in traditional classification schemes have been placed in the genus Ornithodoros. Our comparison of mitochondrial rRNA, nuclear rRNA, and mitochondrial genome analyses show that only mitochondrial genome sequences have the potential to resolve the controversial phylogenetic relationships within the major soft tick lineages, such as the taxonomic status of Cariossensu Klompen and Oliver (1993).

We sequenced the entire mitochondrial genomes of 3 species of metastriate ticks: Haemaphysalis formosensis, H. parva, and Amblyomma cajennense. We also sequenced two thirds (ca. 9500bp) of the mitochondrial genomes of H. humerosaand H. hystricis. We used these 5 mitochondrial genome sequences together with the 13 tick mitochondrial genomes we sequenced previously and the 2 tick mitochondrial genomes sequenced by Black and Roehrdanz (1998), as well as the nuclear rRNA genes from 84 ticks and mites, in phylogenetic analyses. Our analyses reveal deep phylogenetic structure within the genus Haemaphysalis, with at least 2 species, H. parvaand H. inermisthat are highly divergent from the rest of the genus Haemaphysalis. We identify a region of the 18S rRNA gene which correlates with this division of the genus Haemaphysalisas well as a novel insertion in the mitochondrial genome of H. parva. We reject the hypotheses of Hoogstraal and Aeschlimann (1982) and Barker and Murrell (2004) on the relationships among metastriate genera. Instead, our analysis provides further evidence for the division of the Metastriata into 2 major lineages: (i) Amblyommas.s. plus Rhipicephalinae (i.e. Rhipicephalus, Hyalomma, Rhipicentor, and Dermacentor); and (ii) Haemaphysalisplus Bothriocrotonplus Amblyomma sphenodonti. We also provide further evidence for the polyphyly of the genus Amblyommawith respect to A. sphenodontiand A. elaphense.The most likely position of A. elaphenseis sister to the rest of the Metastriata; the most likely position of A. sphenodontiis sister to the genus Bothriocroton. These 2 species do not belong in the genus Amblyomma, and we propose that new genera are required for A. sphenodontiand A. elaphense.

We inferred phylogeny among the three major lineages of the Acari (mites) from the small subunit rRNA gene. Our phylogeny indicates that the Opilioacariformes is the sister-group to the Ixodida+Holothyrida, not the Ixodida+Mesostigmata+Holothyrida, as previously thought. Support for this relationship increased when sites with the highest rates of nucleotide substitution, and thus the greatest potential for saturation with nucleotide substitutions, were removed. Indeed, the increase in support (and resolution) was despite a 70% reduction in the number of parsimony-informative sites from 408 to 115. This shows that rather than ?noisy' sites having no impact on resolution of deep branches, ?noisy' sites have the potential to obscure phylogenetic relationships. The arrangement, Ixodida+Holothyrida+Opilioacariformes, however, may be an artefact of long-branch attraction since relative-rate tests showed that the Mesostigmata have significantly faster rates of nucleotide substitution than other parasitiform mites. Thus, the fast rates of nucleotide substitution of the Mesostigmata might have caused the Mesostigmata to be attracted to the outgroup in our trees. We tested the hypothesis that the high rate of nucleotide substitution in some mites was related to their short generation times. The Acari species that have high nucleotide substitution rates usually have short generation times; these mites also tend to be more active and thus have higher metabolic rates than other mites. Therefore, more than one factor may affect the rate of nucleotide substitution in these mites.

Abstract. We isolated bacteria from ticks, lice and fleas. Partial small subunit rRNA sequences were obtained for each isolate and the closest matches in the FastA database were determined. These bacteria were mostly Gram-positive (Firmicutes), although representatives from the Proteobacteria (α, β, γ subdivisions) and CFB group were also isolated. Most of the isolates we found were from genera that were present in most of the ectoparasites studied, but a few genera were restricted to one species of ectoparasite. The most commonly isolated genera were Stenotrophomonas, Staphylococcus, Pseudomonas, Acinetobacter and Bacillus. Species of Bacillus and Proteus, which have biopesticide potential, were found in some of these ectoparasites. Overall, the communities of bacteria were similar to those found in other studies of parasitic arthropods.

The number of repeats in repetitive DNA like micro- and minisatellites is often determined by polymerase chain reaction (PCR). When we counted repeats in an array of mitochondrial repeats in the cattle tick (Boophilus microplus) we found that the number of repeats increased during PCR. Multiplication of the repeats was independent of the primers used to amplify the region, the PCR annealing temperature and the length of the PCR product. The use of PCR to determine the number of repeats in arrays needs to be reassessed. For long repeats, a subset of samples should always be analysed by Southern blot hybridization to confirm the PCR results.

We inferred the phylogeny of 33 species of ticks from the subfamilies Rhipicephalinae and Hyalomminae from analyses of nuclear and mitochondrial DNA and morphology. We used nucleotide sequences from 12S rRNA, cytochrome c oxidase I, internal transcribed spacer 2 of the nuclear rRNA, and 18S rRNA. Nucleotide sequences and morphology were analyzed separately and together in a total-evidence analysis. Analyses of the five partitions together (3303 characters) gave the best-resolved and the best-supported hypothesis so far for the phylogeny of ticks in the Rhipicephalinae and Hyalomminae, despite the fact that some partitions did not have data for some taxa. However, most of the hidden conflict (lower support in the total-evidence analyses compared to that in the individual analyses) was found in those partitions that had taxa without data. The partitions with complete taxonomic sampling had more hidden support (higher support in the total-evidence analyses compared to that in the separate-partition analyses) than hidden conflict. Mapping of geographic origins of ticks onto our phylogeny indicates an African origin for the Rhipicephalinae sensu lato (i.e., including Hyalomma spp.), the Rhipicephalus–Boophilus lineage, the Dermacentor–Anocentor lineage, and the Rhipicephalus–Booophilus–Nosomma–Hyalomma–Rhipicentor lineage. The Nosomma–Hyalomma lineage appears to have evolved in Asia. Our total-evidence phylogeny indicates that (i) the genus Rhipicephalus is paraphyletic with respect to the genus Boophilus, (ii) the genus Dermacentor is paraphyletic with respect to the genus Anocentor, and (iii) some subgenera of the genera Hyalomma and Rhipicephalus are paraphyletic with respect to other subgenera in these genera. Study of the Rhipicephalinae and Hyalomminae over the last 7 years has shown that analyses of individual datasets (e.g., one gene or morphology) seldom resolve many phylogenetic relationships, but analyses of more than one dataset can generate well-resolved phylogenies for these ticks.

We inferred the phylogeny of 21 species and subspecies of ticks from the subfamilies Rhipicephalinae and Hyalomminae using cytochrome coxidase subunit I (COI) and 12S rRNA mitochondrial gene sequences. Two members of the subfamily Haemaphysalinae were used for outgroup reference. The largest rhipicephaline genus, Rhipicephalus, was represented by ticks from six of the species groups, the second largest genus, Dermacentor,by species from two of three of its subgenera, and the genus Boophilusby 3 of its 5 species. We analyzed the 12S and COI sequences separately and together; statistically significant incongruence between the 12S rDNA and the COI sequences was not detected in the combined dataset using the incongruence length difference test. The combined dataset provided greater phylogenetic resolution than the individual datasets, and although the 12S rDNA data had only 25% of the parsimony-informative characters, it provided half of the total partitioned Bremer support for the combined dataset. We present the first hypothesis of phylogenetic relationships among some species groups of Rhipicephalusbut our most controversial result was that the genus Rhipicephalusis apparently paraphyletic, unless species of Boophilusare included in it. The species of Rhipicephalusmost closely related to Boophilusspp. were from the R. pravusand R. evertsispecies groups, which may implicate an African origin for this important group of ticks.

The southern paralysis tick, Ixodes cornuatus, is a tick of veterinary and medical importance in Australia. We use two methods, CLIMEX, and an envelope-model approach which we name the ‘climatic-range method’ to study the climatic requirements of I. cornuatusand thus to attempt to account for the geographic distribution of I. cornuatus. CLIMEX and our climatic-range method allowed us to account for 94% and 97% of the records of I. cornuatusrespectively. We also studied the host preferences of I. cornuatuswhich we subsequently used in conjunction with our species distribution methods to account for the presence and the absences of I. cornuatusacross Australia. Our findings indicate that the actual geographic distribution of I. cornuatusis smaller than the potential geographic range of this tick, and thus, that there are regions in Australia which may be suitable for I. cornuatuswhere this tick has not been recorded. Although our findings indicate that I. cornuatusmight be able to persist in these currently unoccupied regions, our findings also indicate that the potential geographic range of I. cornuatusmay shrink by 51 to 76% by 2090, depending on which climate change scenario comes to pass.

We examined the phylogeny of ticks (Acari:Parasitiformes:Ixodida) and their closest known mite relatives (Acari:Parasitiformes:Mesostigmata and Holothyrida) using 18S rRNA sequences. In our analyses, we included sequences from 36 taxa. Sequences for 13 hard ticks (Family Ixodidae), 5 soft ticks (Family Argasidae), and 2 mesostigmatid mites were obtained from the GenBank database and we generated sequences for 15 hard ticks and 1 holothyrid mite. Ten of these tick species were endemic to Australia. Our analyses indicated that the suborder Holothyrida is more closely related to Ixodida than to Mesostigmata, the group used as outgroup in earlier molecular studies. This finding is consistent with Lehtinen's (1991) hypothesis that the Holothyrida rather than the Mesostigmata is the sister-group to the Ixodida. Within the hard ticks the genusAponommaand thus the family Amblyomminae were paraphyletic. Taxonomic revision of these taxa is needed. The genusAmblyommawas paraphyletic without the inclusion of “typical”Aponommaspecies (Ap. latumandAp. fimbriatum). There was a basal divergence between endemic Australian and other species in both the Metastriata and the Prostriata divisions of the hard ticks.

Nocardia pinensisand N. amaraeare nocardioform actinomycetes that predominate in and stabilize biological foams on the surface of aeration tanks in activated sludge sewage treatment processes. Their taxonomy is confused since it is difficult to align them with known nocardioform actinomycete genera based upon chemotaxonomic, numerical taxonomic or phenetic information. A review of this information is provided to demonstrate the difficulties. We have sequenced the 16S rRNA gene (16S rDNA) of the type strains of N. pinensisand N. amaraeand compared these with representative nocardioform actinomycete sequences. N. amaraewas most closely related to and had the highest sequence similarity with Gordona terrae. The support in our phylogenetic analysis for this was significant (bootstrap values of 99-100%). This is consistent with recent publications placing N. amaraeinto the genus Gordona. N. pinensiswas most closely related to G. terraeand N. amaraeand was an outlier to the Gordonagroup. However, further analyses which included Gordona bronchialisindicated that N. pinensismay not be firmly related to the genus Gordona.

Phylogenies of trematodes based on characters derived from morphology and life cycles have been controversial. Here, we add molecular data to the phylogenetic study of a group of trematodes, members of the superfamily Hemiuroidea Looss, 1899. DNA sequences from the V4 domain of the nuclear small subunit (18S) rRNA gene and a matrix of morphological characters modified from a previous study were used. There was no significant incongruence between the molecular and the morphological data. However, this was probably due largely to the limited resolving power of the morphological data. Analyses support a monophyletic Hemiuroidea containing at least the families Accacoeliidae, Derogenidae, Didymozoidae, Hirudinellidae, Sclerodistomidae, Syncoeliidae, Isoparorchiidae, Lecithasteridae, and Hemiuridae. These families fall into two principal clades. One contains the first six families and the other the Hemiuridae and lecithasterine lecithasterids. The positions of the hysterolecithine lecithasterids and the Isoparorchiidae were poorly resolved. The Ptychogonimidae may be the sister group of the remaining Hemiuroidea, but there was no support from the molecular data for the placement of the Azygiidae within the superfamily.

The following species are described, figured and/or recorded from the Great Barrier Reef at Heron Island or Lizard Island, Queensland, with comparative material reported from other areas of the ocean around Australia or New Guinea: Dinurus longisinus(new synonym: D. hippuri) from Seriola lalandi, Heron Island and Coryphaena hippurus, Papua New Guinea; Ectenurus trachurifrom Caranx sexfasciatus, Diploprion bifasciatus, Pterocaesio marri, Seriola lalandiand Atherinomorus capricorniensis, Heron Island; Erilepturus hamati(with 25 new synonyms) from Lutjanus carponotatus, Lizard Island, Platycephalus bassensis, Coff's Harbour, NSW, P. fuscus, Coff's Harbour, NSW and Moreton Bay, Queensland, P. endrachtensis, Sillago analis, S. maculata, S. ciliata, Pseudorhombus arsiusand Polydactylussp. from Moreton Bay, Queensland and Lates calcarifer, Darwin, Northern Territory; Tubulovesicula angusticaudafrom Echeneis naucratesand Lethrinus miniatus, Heron Island and Anguilla reinhardtii, Moreton Bay and Bribie Island, Queensland; Elytrophalloides humerusfrom Trachinotus botlaand T. coppingeri, Heron Island; Lecithochirium kawakawafrom Euthynnus affinisHeron Island and Lizard Island: Lecithochirium cirrhiti(new synonyms: L. sammarae, L. nohu) from Sargocentron rubrum, Heron Island; Lecithochirium caesionisfrom Pterocaesio marri, heron Island; Plerurus digitatus(new synonyms: P. cynoglossi, P. atulis, P. scomberomori) from Plectropomus leopardus, Heron Island, Lutjanus erythropterus, Variola louti, Scomberomorus semifasciatus, Grammatorcynus bicarinatusand Carangoides embureyi, C. gymnostethoides, Lizard Island, Scomberomorus commerson, Heron Island, Lizard Island, New Britain, Papua New Guinea, Point Lookout, Queensland and Moreton Bay, Queensland, Euthynnus affinisHeron Island, Lizard Island and New Britain, Papua New Guinea, Sphyraena barracuda, Heron Island and Lizard Island, Scomberomorus munroi, S. queenslandicusand Saurida undosquamis, Moreton Bay, Queensland and Chirocentrus dorab, Bundaberg, Queensland. The Lecithochiriumspecies-group ‘Cirrhiti’ is considered indistiguishable from the species-group ‘Lotellae’.

Argasid systematics remains controversial with widespread adherence to the Hoogstraal (1985) classification scheme, even though it does not reflect evolutionary relationships and results in paraphyly for the main genera of soft ticks (Argasidae), namely Argasand Ornithodoros. The alternative classification scheme, proposed by Klompen and Oliver (1993), has problems of its own: most notably paraphyly of the subgenus Pavlovskyellaand the controversial grouping together of the subgenera Alectorobius, Antricola, Carios, Chiropterargas, Nothoaspis, Parantricola, Reticulinasusand Subparmatusinto the genus Carios. Recent phylogenetic analyses of 18S/28S rRNA sequences and mitochondrial genomes agree with the scheme of Klompen and Oliver (1993), with regard to the paraphyly of Pavlovskyella, placement of Alveonasus, Ogadenus, Proknekaliaand Secretargasin the Argasinae and placement of Cariosand Chiropterargasin the Ornithodorinae (Mans et al., 2019). The Cariosclade and its constituent subgenera remain controversial, since the phylogenetic position of its type species Carios(Carios) vespertilionisLatreille, 1796 (formerly Argas vespertilionis) has not been determined with confidence. The current study aimed to resolve Cariossensu lato Klompen and Oliver, 1993, and Cariossensu stricto Hoogstraal, 1985, by determining and analysing phylogenetic nuclear and mitochondrial markers for C.(C.) vespertilionis. Both the nuclear and mitochondrial markers support placement of Carioss.s. within the subfamily Ornithodorinae, but to the exclusion of the clade that includes the 6 other subgenera that are part of Carioss.l. Klompen and Oliver (1993), namely Alectorobius, Antricola, Nothoaspis, Parantricola, Reticulinasusand Subparmatus.These 6 subgenera form a monophyletic clade that might be placed as new subgenera within the genus Alectorobius, or elevated to genera. Given the substantial differences in biology among these subgenera, we propose that these 6 subgenera be elevated to genera. Thus, we propose to modify the classification scheme of Mans et al. (2019) so that the subfamily Argasinae now has six genera, Alveonasus, Argas(subgenera Argasand Persicargas), Navis, Ogadenus, Proknekaliaand Secretargas, and the subfamily Ornithodorinae has nine genera, Alectorobius, Antricola(subgenera Antricolaand Parantricola), Carios, Chiropterargas, Nothoaspis, Ornithodoros(subgenera Microargas, Ornamentum, Ornithodoros, Pavlovskyellaand Theriodoros), Otobius, Reticulinasusand Subparmatus(genera indicated in bold).

High-throughput sequencing (HTS) technology has profoundly been involved in sequencing whole genomes of several organisms in a fast and cost-effective manner. Although HTS provides an alternative biomonitoring method to the time-consuming and taxonomy-expertise dependent morphological approach, still we cannot rule out the possibility of the impediment and misidentification biases. In this article we aim to retrieve whole mitochondrial genome (mitogenome) sequences from publicly available raw sequencing data for phylogenetic comparison of Ixodes persulcatus. For this comparison, we sequenced whole mitogenomes of four I. persulcatusticks from Japan and constructed mitogenomes from raw sequencing data of 74 I. persulcatusticks from China. Bayesian phylogenetic trees were inferred by the concatenated fifteen mitochondrial genes. We further tested our results by the phylogenetic analysis of cytochrome c oxidase subunit 1 (cox1) gene and internal transcribed spacer 2 (ITS2) sequences. Our findings showed that 70 constructed mitogenomes from China were clustered with the sequenced four mitogenomes of I. persulcatusfrom Japan. We also revealed that mitogenome sequences retrieved from two data sets CRR142297 and CRR142298 were clustered with Ixodes nipponensis. Moreover, other two mitogenome sequences from CRR142310 and CRR142311 formed a clade with Ixodes pavlovskyi.The phylogenetic analysis of cox1gene and ITS2 sequences confirmed the identification errors of these four samples. The overall phylogenetics in our study concluded that accurate morphological identification is necessary before implementing HTS to avoid any misidentification biases.

Mutations associated with pyrethroid resistance were found in Mexican strains of Rhipicephalus microplus (Canestrini). A mutation in the sodium channel gene was reported in strains highly resistant to permethrin and another mutation in an esterase gene in a strain that shows moderate resistance to the same pesticide. Methods based on the melting temperature difference of amplified allele-specific DNA fragments were developed that can detect these mutations rapidly in individual larvae. When these methods were applied to ticks from various strains of R. microplus from Australia, neither of these mutations could be demonstrated. Different resistance mechanisms have apparently developed independently between Australian and Mexican strains of R. microplus.

The southern cattle tick, Boophilus microplus (Canestrini), causes annual economic losses in the hundreds of millions of dollars to cattle producers throughout the world, and ranks as the most economically important tick from a global perspective. Control failures attributable to the development of pesticide resistance have become commonplace, and novel control technologies are needed. The availability of the genome sequence will facilitate the development of these new technologies, and we are proposing sequencing to a 4–6X draft coverage. Many existing biological resources are available to facilitate a genome sequencing project, including several inbred laboratory tick strains, a database of ≈45,000 expressed sequence tags compiled into a B. microplus Gene Index, a bacterial artificial chromosome (BAC) library, an established B. microplus cell line, and genomic DNA suitable for library synthesis. Collaborative projects are underway to map BACs and cDNAs to specific chromosomes and to sequence selected BAC clones. When completed, the genome sequences from the cow, B. microplus, and the B. microplus-borne pathogens Babesia bovis and Anaplasma marginale will enhance studies of host-vector-pathogen systems. Genes involved in the regeneration of amputated tick limbs and transitions through developmental stages are largely unknown. Studies of these and other interesting biological questions will be advanced by tick genome sequence data. Comparative genomics offers the prospect of new insight into many, perhaps all, aspects of the biology of ticks and the pathogens they transmit to farm animals and people. The B. microplus genome sequence will fill a major gap in comparative genomics: a sequence from the Metastriata lineage of ticks. The purpose of the article is to synergize interest in and provide rationales for sequencing the genome of B. microplus and for publicizing currently available genomic resources for this tick.