Phylogenetic analysis of the mitochondrial genomes and nuclear rRNA genes of ticks reveals a deep phylogenetic structure within the genus Haemaphysalis and further elucidates the polyphyly of the genus Amblyomma with respect to Amblyomma sphenodonti and Amblyomma elaphense

Ticks and Tick-borne Diseases

Volumn 4, Issue 4, 2013, Pages 265-274

  Burger, Thomas D ^a   Shao, Renfu ^b   Barker, Stephen C ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b UNIVERSITY OF THE SUNSHINE COAST   (Australia)

Author keywords

18S rRNA; 28S rRNA; Amblyomma; Haemaphysalis; Ixodida; Mitochondrial genomes; Phylogeny

Indexed keywords

NUCLEAR RNA;

AMBLYOMMA; AMBLYOMMA CAJENNENSE; AMBLYOMMA ELAPHENSE; AMBLYOMMA SPHENODONTI; ARTICLE; BOTHRIOCROTON; DERMACENTOR; GENE SEQUENCE; GENETIC CORRELATION; GENUS; HAEMAPHYSALIS; HAEMAPHYSALIS FORMOSENSIPARVA; HAEMAPHYSALIS FORMOSENSIS; HAEMAPHYSALIS PARVA; HYALOMMA; METASTRIATA; MITOCHONDRIAL GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROMOTER REGION; RHIPICENTOR; RHIPICEPHALINAE; SPECIES DIVERSITY;

ANIMALS; GENOME, MITOCHONDRIAL; IXODIDAE; PHYLOGENY; RNA, RIBOSOMAL; SPECIES SPECIFICITY;

ACARI; AMBLYOMMA; AMBLYOMMA CAJENNENSE; BOTHRIOCROTON; DERMACENTOR; HAEMAPHYSALIS; HAEMAPHYSALIS HUMEROSA; HAEMAPHYSALIS INERMIS; HAEMAPHYSALIS PARVA; HYALOMMA; IXODIDA; RHIPICENTOR; RHIPICEPHALUS;

EID: 84877823778     PISSN: 1877959X     EISSN: 18779603     Source Type: Journal    
DOI: 10.1016/j.ttbdis.2013.02.002     Document Type: Article

References (51)

1. Barker S.C., Murrell A. Systematics and evolution of ticks with a list of valid genus and species names. Parasitology 2004, 129:S15-S36.
2. Bazinet A.L., Cummings M.P. The Lattice Project: a grid research and production environment combining multiple grid computing models. Distributed & Grid Computing - Science Made Transparent for Everyone. Principles, Applications and Supporting Communities 2008, 2-13. Rechenkraft.net, Marburg. M.H.W. Weber (Ed.).
3. Bazinet A.L., Cummings M.P. Computing the tree of life - leveraging the power of desktop and service grids. Proceedings of the Fifth Workshop on Desktop Grids and Volunteer Computing Systems (PCGrid 2011) 2011.
4. Bazinet A.L., Myers D.S., Fuetsch J., Cummings M.P. Grid services base library: a high-level, procedural application program interface for writing Globus-based Grid services. Future Gener. Comput. Syst. 2007, 23:517-522.
5. Black W., Roehrdanz R. Mitochondrial gene order is not conserved in arthropods: prostriate and metastriate tick mitochondrial genomes. Mol. Biol. Evol. 1998, 15:1772-1785.
6. Black W.C., Klompen J.S.H., Keirans J.E. Phylogenetic relationships among tick subfamilies (Ixodida: Ixodidae: Argasidae) based on the 18S nuclear rDNA gene. Mol. Phylogenet. Evol. 1997, 7:129-144.
7. Beati L., Keirans J.E. Analysis of the systematic relationships among ticks of the genera Rhipicephalus and Boophilus (Acari: Ixodidae) based on mitochondrial 12S ribosomal DNA gene sequences and morphological characters. J. Parasitol. 2001, 87:32-48.
8. Burger T.D., Shao R., Beati L., Miller H., Barker S.C. Phylogenetic analysis of ticks (Acari: Ixodida) using mitochondrial genomes and nuclear rRNA genes indicates that the genus Amblyomma is polyphyletic. Mol. Phylogenet. Evol. 2012, 64:45-55.
9. Campbell N.J.H., Barker S.C. An unprecedented major rearrangement in an arthropod mitochondrial genome. Mol. Biol. Evol. 1998, 15:1786-1787.
10. Campbell N.J.H., Barker S.C. The novel mitochondrial gene arrangement of the cattle tick. Boophilus microplus: fivefold tandem repetition of a coding region. Mol. Biol. Evol. 1999, 16:732-740.
11. Campbell N.J.H., Sturm R.A., Barker S.C. Large mitochondrial repeats multiplied during the polymerase chain reaction. Mol. Ecol. Notes 2001, 1:336-340.
12. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 2000, 17:540-552.
13. Conant G.C., Wolfe K.H. GenomeVx: simple web-based creation of editable circular chromosome maps. Bioinformatics 2008, 24:861-862.
14. Cummings M.P., Handley S.A., Myers D.S., Reed D.L., Rokas A., Winka K. Comparing bootstrap and posterior probability values in the four-taxon case. Syst. Biol. 2003, 52:477-487.
15. Cummings M.P., Huskamp J.C. Grid computing. Educause Rev. 2005, 40:116-117.
16. Darriba D., Taboada G.L., Doallo R., Posada D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 2011, 27:1164-1165.
17. Dobson S.J., Barker S.C. Phylogeny of the hard ticks (Ixodidae) inferred from 18S rRNA indicates that the genus Aponomma is paraphyletic. Mol. Phylogenet. Evol. 1999, 11:288-295.
18. Drummond A., Ashton B., Buxton S., Cheung M., Cooper A., Heled J., Kearse M., Moir R., Stones-Havas S., Sturrock S., Thierer T., Wilson A. Geneious v5.1 2010, Available from. http://www.geneious.com/.
19. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
20. Gillespie J.J., McKenna C.H., Yoder M.J., Gutell R.R., Johnston J.S., Kathirithamby J., Cognato A.I. Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted-wing parasites (Insecta: Strepsiptera). Insect Mol. Biol. 2005, 14:625-643.
21. Guglielmone A.A., Robbins R.G., Apanaskevich D.A., Petney T.N., Estrada-Peña A., Horak I.G., Shao R., Barker S.C. The Argasidae, Ixodidae and Nuttalliellidae (Acari: Ixodida) of the world: a list of valid species names. Zootaxa 2010, 2528:1-28.
22. Hillis D.M., Dixon M.T. Ribosomal DNA: molecular evolution and phylogenetic inference. Q. Rev. Biol. 1991, 66:411-453.
23. Hoogstraal H., Aeschlimann A. Tick-host specificity. Bull. Soc. Entomol. Suisse 1982, 55:5-32.
24. Hoogstraal H., Kim K.C. Tick and mammal coevolution, with emphasis on Haemaphysalis. Coevolution of Parasitic Arthropods and Mammals 1985, 505-568. John Wiley & Sons, New York. K.C. Kim (Ed.).
25. Kambhampati S., Smith P.T. PCR primers for the amplification of four insect mitochondrial gene fragments. Insect Mol. Biol. 1995, 4:233-236.
26. Katoh K., Misawa K., Kuma K., Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002, 30:3059-3066.
27. Kaufman, T.S., 1972. A revision of the genus Aponomma Neumann, 1899 (Acarina: Ixodidae). Unpublished Ph.D. Dissertation Thesis. University of Maryland, p. 389.
28. Klompen H., Dobson S.J., Barker S.C. A new subfamily, Bothriocrotoninae n. subfA., for the genus Bothriocroton Keirans, King & Sharrad, 1994 status amend. (Ixodida: Ixodidae), and the synonymy of Aponomma Neumann, 1899 with Amblyomma Koch, 1844. Syst. Parasitol. 2002, 53:101-107.
29. Klompen J.S.H., Black W.C., Keirans J.E., Norris D.E. Systematics and biogeography of hard ticks, a total evidence approach. Cladistics: Int. J. Willi Hennig Soc. 2000, 16:79-102.
30. Klompen J.S.H., Black W.C., Keirans J.E., Oliver J.H. Evolution of ticks. Annu. Rev. Entomol. 1996, 41:141-161.
31. Klompen J.S.H., Oliver J.H., Keirans J.E., Homsher P.J. A re-evaluation of relationships in the Metastriata (Acari: Parasitiformes: Ixodidae). Syst. Parasitol. 1997, 38:1-24.
32. Kolonin, G.V., 2009. Fauna of the Ixodid Ticks of the World (Acari, Ixodidae), Moscow. http://www.kolonin.org/.
33. Laslett D., Canback B. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 2008, 24:172-175.
34. Lowe T.M., Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25:955-964.
35. Mangold A.J., Bargues M.D., Mas-Coma S. Mitochondrial 16S rDNA sequences and phylogenetic relationships of species of Rhipicephalus and other tick genera among Metastriata (Acari: Ixodidae). Parasitol. Res. 1998, 84:478-484.
36. Miller H.C., Conrad A.M., Barker S.C., Daugherty C.H. Distribution and phylogenetic analyses of an endangered tick, Amblyomma sphenodonti. N.Z. J. Zool. 2007, 34:97-105.
37. Murrell A., Campell N.J.H., Barker S.C. A total-evidence phylogeny of ticks provides insights into the evolution of life cycles and biogeography. Mol. Phylogenet. Evol. 2001, 21:244-258.
38. Myers D.S., Bazinet A.L., Cummings M.P. Expanding the reach of Grid computing: combining Globus- and BOINC-based systems. Grids for Bioinformatics and Computational Biology, Wiley Book Series on Parallel and Distributed Computing 2008, 71-85. John Wiley & Sons, New York. E.-G. Talbi, A. Zomaya (Eds.).
39. Myers D.S., Cummings M.P. Necessity is the mother of invention: a simple grid computing system using commodity tools. J. Parallel Distrib. Comput. 2003, 53:578-589.
40. Norris D.E., Klompen J.S.H., Black W.C. Comparison of the mitochondrial 12S and 16S ribosomal DNA genes in resolving phylogenetic relationships among hard ticks (Acari: Ixodidae). Ann. Entomol. Soc. Am. 1999, 92:117-129.
41. Nuttall G.H.F., Warburton C. Ticks. A monograph of the Ixodida. Part III. The Genus Haemaphysalis 1915, 349-550. Cambridge University Press, London.
42. Posada D. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
43. Shao R., Aoki Y., Mitani H., Tabuchi N., Barker S.C., Fukunaga M. The mitochondrial genomes of soft ticks have an arrangement of genes that has remained unchanged for over 400 million years. Insect Mol. Biol. 2004, 13:219-224.
44. Shao R., Fukunaga M., Barker S.C. The mitochondrial genomes of ticks and their kin: a review plus the description of the mitochondrial genomes of Amblyomma triguttatum and Ornithodoros porcinus. Proceedings of the Fifth International Conference on Ticks and Tick-Borne Pathogens 2005.
45. Shao R.F., Barker S.C., Mitani H., Aoki Y., Fukunaga M. Evolution of duplicate control regions in the mitochondrial genomes of metazoa: a case study with Australasian Ixodes ticks. Mol. Biol. Evol. 2005, 22:620-629.
46. Shimodaira H., Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 2001, 17:1246-1247.
47. Simon C., Frati F., Beckenbach A., Crespi B., Liu H., Flook P. Evolution, weighting, and phylogenetic utility of mitochondrial gene-sequences and a compilation of conserved polymeraes chain reaction primers. Ann. Entomol. Soc. Am. 1994, 87:651-701.
48. Sukumaran J., Holder M.T. DendroPy: a Python library for phylogenetic computing. Bioinformatics 2010, 26:1569-1571.
49. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
50. Whiting M.F., Carpenter J.C., Wheeler Q.D., Wheeler W.C. The Strepsiptera problem: phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology. Syst. Biol. 1997, 46:1-68.
51. Zwickl, D.J., 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. Dissertation. The University of Texas at Austin.