Analyses of mitochondrial amino acid sequence datasets support the proposal that specimens of Hypodontus macropi from three species of macropodid hosts represent distinct species

BMC Evolutionary Biology

Volumn 13, Issue 1, 2013, Pages

  Jabbar, Abdul ^a   Beveridge, Ian ^a   Mohandas, Namitha ^a   Chilton, Neil B ^b   Littlewood, D Timothy J ^c   Jex, Aaron R ^a   Gasser, Robin B ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b UNIVERSITY OF SASKATCHEWAN   (Canada)

^c DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

Genetics; Hypodontus macropi; Kangaroo; Mitochondrial genome; Next generation sequencing; Sliding window analysis; Systematics; Wallaby

Indexed keywords

AMINO ACID; CLADISTICS; DATA SET; ELECTROKINESIS; GENETIC ANALYSIS; GENOME; GEOGRAPHICAL REGION; MARSUPIAL; MITOCHONDRION; MOLECULAR ANALYSIS; TAXONOMY;

AUSTRALIA;

HYPODONTUS MACROPI; MACROPODIDAE; MACROPUS; MACROPUS ROBUSTUS ROBUSTUS; METATHERIA; THYLOGALE BILLARDIERII; WALLABIA BICOLOR;

HELMINTH PROTEIN; MITOCHONDRIAL PROTEIN; RIBOSOME DNA;

ANIMAL; AUSTRALIA; BAYES THEOREM; CHEMISTRY; CLASSIFICATION; ENZYMOLOGY; GENETICS; KANGAROO; MITOCHONDRIAL GENOME; PARASITOLOGY; PHYLOGENY; STRONGYLOIDEA; ARTICLE;

ANIMALS; AUSTRALIA; BAYES THEOREM; DNA, RIBOSOMAL; GENOME, MITOCHONDRIAL; HELMINTH PROTEINS; MACROPODIDAE; MITOCHONDRIAL PROTEINS; PHYLOGENY; STRONGYLOIDEA;

EID: 84887910836     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-13-259     Document Type: Article

References (55)

1. Mönnig HO, Hypodontus macropi, n. gen., n. sp., a hookworm of the kangaroo Pretoria: Union of South Africa 15th Annual Report of the Director of Veterinary Services. 1929 303 306
2. Hypodontus macropi Mönnig, 1929, a hook-worm like parasite of macropodid marsupials. Beveridge I, J Helminthol 1979 53 229 244 10.1017/S0022149X00006015 575542
3. Hypodontus macropi Mönnig, 1929 from a Bennett's wallaby Macropus rufogrisea. Setasuban P, Arundel JH, Southeast Asian J Trop Med Public Health 1996 7 102 105
4. Helminth parasites of grey kangaroos, Macropus giganteus Shaw and M. fuliginosus (Desmarest), in eastern Australia. Beveridge I, Arundel JH, Aust Wildlife Res 1979 6 69 77 10.1071/WR9790069
5. Helminth parasites of rock wallabies, Petrogale spp. (Marsupialia) from Queensland. Beveridge I, Spratt DM, Close RL, Barker SC, Sharman GB, Aust Wildlife Res 1989 39 691 702
6. Parasites of the Proserpine Rock Wallaby, Petrogale persephone (Marsupialia: Macropodidae). Begg M, Beveridge I, Chilton NB, Johnson PM, O'Callaghan MG, Aust Mammal 1996 18 45 53
7. Helminth parasites of the purple-necked rock wallaby, Petrogale lateralis purpureicollis, from Queensland. Bradley C, Beveridge I, Chilton NB, Johnson PM, Trans Roy Soc South Aust 2000 124 37 40
8. Detection by allozyme electrophoresis of cryptic species of Hypodontus macropi (Nematoda: Strongyloidea) from macropodid marsupials. Chilton NB, Beveridge I, Andrews RH, Int J Parasitol 1992 22 271 279 10.1016/S0020-7519(05) 80004-9 1639562
9. Differences in a ribosomal DNA sequence of morphologically indistinguishable species within the Hypodontus macropi complex (Nematoda: Strongyloidea). Chilton NB, Gasser RB, Beveridge I, Int J Parasitol 1995 25 647 651 10.1016/0020-7519(94)00171-J 7635644
10. Mutation scanning analysis of sequence heterogeneity in the second internal transcribed spacer (rDNA) within some members of the Hypodontus macropi (Nematoda: Strongyloidea) complex. Gasser RB, Zhu X, Beveridge I, Chilton N, Electrophoresis 2001 22 1076 1085 10.1002/1522-2683()22:6<1076::AID- ELPS1076>3.0.CO;2-8 11358128
11. Genetic variation within the Hypodontus macropi (Nematoda: Strongyloidea) complex from macropodid marsupial hosts in Australia. Chilton NB, Jabbar A, Huby-Chilton F, Jex A, Gasser RB, Beveridge I, Electrophoresis 2012 33 3544 3554 10.1002/elps.201200364 23161349
12. Molecular ecology of parasites: elucidating ecological and microevolutionary processes. Criscione CD, Poulin R, Blouin MS, Mol Ecol 2005 14 2247 2257 10.1111/j.1365-294X.2005.02587.x 15969711
13. The use of nuclear ribosomal DNA markers for the identification of bursate nematodes (order Strongylida) and for the diagnosis of infections. Chilton NB, Anim Health Res Rev 2004 5 171 87
14. Molecular tools-advances, opportunities and prospects. Gasser RB, Vet Parasitol 2006 136 69 89 10.1016/j.vetpar.2005.12.002 16457951
15. Towards practical, DNA-based diagnostic methods for parasitic nematodes of livestock-bionomic and biotechnological implications. Gasser RB, Bott NJ, Chilton NB, Hunt P, Beveridge I, Biotechnol Adv 2008 26 325 34 10.1016/j.biotechadv.2008.03.003 18502076
16. Mitochondrial genomes of parasitic flatworms. Le TH, Blair D, McManus DP, Trends Parasitol 2002 18 206 213 10.1016/S1471-4922(02)02252-3 11983601
17. The mitochondrial genomics of parasitic nematodes of socio-economic importance: recent progress, and implications for population genetics and systematics. Hu M, Chilton NB, Gasser RB, Adv Parasitol 2004 56 133 212 14710997
18. Mitochondrial genomes of parasitic nematodes-progress and perspectives. Hu M, Gasser RB, Trends Parasitol 2006 22 78 84 10.1016/j.pt.2005.12.003 16377245
19. Making the most of mitochondrial genomes-markers for phylogeny, molecular ecology and barcodes in Schistosoma (Platyhelminths: Digenea). Zarowiecki MZ, Huyse T, Littlewood DT, Int J Parasitol 2007 37 1401 1418 10.1016/j.ijpara.2007. 04.014 17570370
20. Toward next-generation sequencing of mitochondrial genomes-focus on parasitic worms of animals and biotechnological implications. Jex AR, Littlewood DT, Gasser RB, Biotechnol Adv 2010 28 151 159 10.1016/j.biotechadv.2009.11.002 19913084
21. An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes. Jex AR, Hall RS, Littlewood DT, Gasser RB, Nucleic Acids Res 2010 38 522 533 10.1093/nar/gkp883 19892826
22. The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Okimoto R, Macfarlane L, Clary D, Wolstenholme DR, Genetics 1992 130 471 498 1551572
23. Comparative analysis of mitochondrial genome data for Necator americanus from two endemic regions reveals substantial genetic variation. Hu M, Chilton NB, Abs El-Osta YG, Gasser RB, Int J Parasitol 2003 33 955 963 10.1016/S0020-7519(03)00129-2 12906879
24. Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative atp8 and normally structured tRNAs and has a gene arrangement relatable to those of coelomate metazoans. Lavrov DV, Brown WM, Genetics 2001 157 621 637 11156984
25. The mitochondrial genomes of the human hookworms, Ancylostoma duodenale and Necator americanus (Nematoda: Secernentea). Hu M, Chilton NB, Gasser RB, Int J Parasitol 2002 32 145 158 10.1016/S0020-7519(01)00316-2 11812491
26. Onchocerca volvulus: limited heterogeneity in the nuclear and mitochondrial genomes. Keddie EM, Higazi T, Boakye D, Merriweather A, Wooten MC, Unnasch TR, Exp Parasitol 1999 93 198 206 10.1006/expr.1999.4450 10600445
27. The mitochondrial genome of Strongyloides stercoralis (Nematoda)-idiosyncratic gene order and evolutionary implications. Hu M, Chilton NB, Gasser RB, Int J Parasitol 2003 33 1393 1408 10.1016/S0020-7519(03)00130-9 14527522
28. The mitochondrial genome of Xiphinema americanum sensu stricto (Nematoda: Enoplea): considerable economization in the length and structural features of encoded genes. He Y, Jones J, Armstrong M, Lamberti F, Moens M, J Mol Evol 2005 61 819 833 10.1007/s00239-005-0102-7 16315110
29. A single nucleotide polymorphism map of the mitochondrial genome of the parasitic nematode Cooperia oncophora. Van der Veer M, de Vries E, Parasitology 2004 128 421 431 10.1017/S0031182003004633 15151148
30. Evidence for the frequent use of TTG as the translation initiation codon of mitochondrial protein genes in the nematodes, Ascaris suum and Caenorhabditis elegans. Okimoto R, Macfarlane JL, Wolstenholme DR, Nucleic Acids Res 1999 18 6113 6118
31. The mitochondrial genome of Onchocerca volvulus: sequence, structure and phylogenetic analysis. Keddie EM, Higazi T, Unnasch TR, Mol Biochem Parasitol 1998 95 111 127 10.1016/S0166-6851(98)00102-9 9763293
32. Structure and organization of the mitochondrial genome of the canine heartworm, Dirofilaria immitis. Hu M, Gasser RB, Abs El-Osta YG, Chilton NB, Parasitology 2003 127 37 51 10.1017/S0031182003003275 12885187
33. Integrating molecular and morphological approaches for characterizing parasite cryptic species: implications for parasitology. Nadler SA, Pérez-Ponce de León G, Parasitology 2011 138 1688 1709 10.1017/S003118201000168X 21281559
34. Sibling species within Macropostrongyloides baylisi (Nematoda: Strongyloidea) from macropodid marsupials. Beveridge I, Chilton NB, Andrews RH, Int J Parasitol 1993 23 21 33 10.1016/0020-7519(93)90094-F 8468133
35. The helminth fauna of Australasian marsupials: origins and evolutionary biology. Beveridge I, Spratt DM, Adv Parasitol 1996 37 136 254
36. Genetic evidence for a complex of species within Rugopharynx australis (Mönnig, 1926) (Nematoda: Strongyloidea) from macropodid marsupials. Chilton NB, Andrews RH, Beveridge I, Syst Parasitol 1996 34 125 133 10.1007/BF00009686
37. Revision of the Rugopharynx australis (Moennig, 1926) complex (Nematoda: Strongyloidea) from macropodid marsupials. Beveridge I, Chilton NB, Invert Taxon 1999 13 805 843 10.1071/IT98017
38. Genetic variation within species of the nematode genus Cloacina (Strongyloidea: Cloacininae) parasitic in the stomachs of rock wallabies, Petrogale spp. (Marsupialia: Macropodidae) in Queensland. Chilton NB, Huby-Chilton F, Johnson PM, Beveridge I, Gasser RB, Aust J Zool 2009 57 1 10 10.1071/ZO08068
39. Avise JC, Molecular markers, natural history and evolution New York: Chapman and Hall 1994
40. Species delimitation and nematode biodiversity: phylogenies rule. Nadler SA, Nematol 2002 4 615 625 10.1163/15685410260438908
41. Populations biology of parasitic nematodes: applications of genetic markers. Anderson TJC, Blouin MS, Beech RN, Adv Parasitol 1998 41 219 283 9734295
42. Single-strand conformation polymorphism (SSCP) for the analysis of genetic variation. Gasser RB, Hu M, Chilton NB, Campbell BE, Jex AR, Otranto D, Cafarchia C, Beveridge I, Zhu XQ, Nat Protoc 2006 1 3121 3128 17406575
43. Next-generation DNA sequencing methods. Mardis E, Ann Rev Genomics Human Genet 2008 9 387 402 10.1146/annurev.genom.9.081307.164359
44. Long PCR amplification of the entire mitochondrial genome from individual helminths for direct sequencing. Hu M, Jex AR, Campbell BE, Gasser RB, Nat Protoc 2007 2 2339 2344 10.1038/nprot.2007.358 17947975
45. Genome sequencing in microfabricated high-density picolitre reactors. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage K, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, et al. Nature 2005 437 376 380 16056220
46. CAP3: A DNA sequence assembly program. Huang X, Madan A, Genome Res 1999 9 868 877 10.1101/gr.9.9.868 10508846
47. OGRe: a relational database for comparative analysis of mitochondrial genomes. Jameson D, Gibson AP, Hudelot C, Higgs PG, Nucleic Acids Res 2003 31 202 206 10.1093/nar/gkg077 12519982
48. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Edgar RC, Nucleic Acids Res 2004 32 1792 1797 10.1093/nar/gkh340 15034147
49. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Hall TA, Nucleic Acids Symp Ser 1999 41 95 98
50. MRBAYES: Bayesian inference of phylogeny. Huelsenbeck JP, Ronquist F, Bioinformatics 2001 17 754 755 10.1093/bioinformatics/17.8.754 11524383
51. MrBayes 3: Bayesian phylogenetic inference under mixed models. Ronquist F, Huelsenbeck JP, Bioinformatics 2003 19 1572 1574 [45] 10.1093/bioinformatics/ btg180 12912839
52. ProtTest: Selection of best-fit models of protein evolution. Abascal F, Zardoya R, Posada D, Bioinformatics 2005 21 2104 2105 10.1093/bioinformatics/ bti263 15647292
53. Evolutionary trees from nucleic acid and protein sequences. Bishop MJ, Friday AE, Proc R Soc Lond B Biol Sci 1985 226 271 302 10.1098/rspb.1985.0096
54. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R, Bioinformatics 2003 19 2496 2497 10.1093/bioinformatics/btg359 14668244
55. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Gouy M, Guindon S, Gascuel O, Mol Biol Evol 2010 27 221 224 10.1093/molbev/msp259 19854763