Arthropod Phylogenetics in Light of Three Novel Millipede (Myriapoda: Diplopoda) Mitochondrial Genomes with Comments on the Appropriateness of Mitochondrial Genome Sequence Data for Inferring Deep Level Relationships

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Brewer, Michael S ^a,b   Swafford, Lynn ^a   Spruill, Chad L ^a   Bond, Jason E ^c  

^a EAST CAROLINA UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c AUBURN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ANIMAL TISSUE; APPALACHIORIA FALCIFERA; ARTHROPOD; ARTICLE; CONTROLLED STUDY; GENE CONSTRUCT; GENE LOCUS; GENE SEQUENCE; GENE TRANSLOCATION; GENETIC CODE; MILLIPEDE; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; MYRIAPODA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; POLYPHYLY; SPECIES DIFFERENTIATION; SYNTENY;

ANIMALS; ARTHROPODS; BASE SEQUENCE; CLASSIFICATION; DNA, MITOCHONDRIAL; GENOME, INSECT; GENOME, MITOCHONDRIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SYNTENY;

EID: 84880295812     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0068005     Document Type: Article

References (72)

1. Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, et al. (2010) Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463: 1079-U1098 doi:10.1038/nature08742.
2. Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B, (2011) How Many Species Are There on Earth and in the Ocean? PLoS Biol 9: e1001127 doi:10.1371/journal.pbio.1001127.t002.
3. Hamilton AJ, Basset Y, Benke KK, Grimbacher PS, Miller SE, et al. (2010) Quantifying Uncertainty in Estimation of Tropical Arthropod Species Richness. The American Naturalist 176: 90-95 doi:10.1086/652998.
4. Brewer MS, Sierwald P, Bond JE, (2012) Millipede Taxonomy after 250 Years: Classification and Taxonomic Practices in a Mega-Diverse yet Understudied Arthropod Group. PLoS ONE 7: e37240 doi:10.1371/journal.pone.0037240.t004.
5. Hoffman R, Golovatch S, Adis J, de Morais J (2002) Diplopoda. Pages 505-533 in Amazonian Arachnida and Myriapoda (J Adis, ed) Pensoft, Sofia-Moscow: 505-533.
6. Sierwald P, Bond JE, (2007) Current status of the myriapod class diplopoda (Millipedes): Taxonomic diversity and phylogeny. Annu Rev Entomol 52: 401-420 doi:10.1146/annurev.ento.52.111805.090210.
7. Bond J, Sierwald P, (2002) Cryptic speciation in the Anadenobolus excisus millipede species complex on the Island of Jamaica. Evolution 56: 1123-1135.
8. Bond J, Sierwald P, (2003) Molecular taxonomy of the Anadenobolus excisus (Diplopoda: Spirobolida: Rhinocricidae) species-group on the Caribbean island of Jamaica. Invertebr Syst 17: 515-528 doi:10.1072/IS03004.
9. Marek PE, Bond JE, (2006) Phylogenetic systematics of the colorful, cyanide-producing millipedes of Appalachia (Polydesmida, Xystodesmidae, Apheloriini) using a total evidence Bayesian approach. Molecular Phylogenetics and Evolution 41: 704-729 doi:10.1016/j.ympev.2006.05.043.
10. Marek PE, Bond JE (2007) A reassessment of apheloriine millipede phylogeny: additional taxa, Bayesian inference, and direct optimization (Polydesmida: Xystodesmidae). Zootaxa: 27-39.
11. Marek PE, Bond JE, (2009) A Mullerian mimicry ring in Appalachian millipedes. P Natl Acad Sci Usa 106: 9755-9760 doi:10.1073/pnas.0810408106.
12. Walker MJ, Stockman AK, Marek PE, Bond JE, (2009) Pleistocene glacial refugia across the Appalachian Mountains and coastal plain in the millipede genus Narceus: Evidence from population genetic, phylogeographic, and paleoclimatic data. BMC Evolutionary Biology 9: 25 doi:---10.1186/1471-2148-9-25.
13. Pitz KM, Sierwald P, (2010) Phylogeny of the millipede order Spirobolida (Arthropoda: Diplopoda: Helminthomorpha). Cladistics 26: 497-525.
14. Marek P, Papaj D, Yeager J, Molina S, Moore W, (2011) Bioluminescent aposematism in millipedes. CURBIO 21: R680-R681 doi:10.1016/j.cub.2011.08.012.
15. Spelda J, Reip H, Oliveira Biener U, Melzer R, (2011) Barcoding Fauna Bavarica: Myriapoda - a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda). ZOOKEYS 156: 123 doi:10.3897/zookeys.156.2176.
16. Wesener T, Raupach MJ, Decker P, (2011) Mountain Refugia Play a Role in Soil Arthropod Speciation on Madagascar: A Case Study of the Endemic Giant Fire-Millipede Genus Aphistogoniulus. PLoS ONE 6: e28035 doi:10.1371/journal.pone.0028035.t003.
17. Regier J, Shultz J, (2001) A phylogenetic analysis of Myriapoda (Arthropoda) using two nuclear protein-encoding genes. Zool J Linn Soc-Lond 132: 469-486.
18. Regier J, Wilson H, Shultz J, (2005) Phylogenetic analysis of Myriapoda using three nuclear protein-coding genes. Molecular Phylogenetics and Evolution 34: 147-158 doi:10.1016/j.ympev.2004.09.005.
19. Sierwald P, Shear W, Shelley R, Bond J, (2003) Millipede phylogeny revisited in the light of the enigmatic order Siphoniulida. J Zool Syst Evol Res 41: 87-99.
20. Boore J, Brown W, (1998) Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr Opin Genet Dev 8: 668-674.
21. Zhang P, Wake DB, (2009) Higher-level salamander relationships and divergence dates inferred from complete mitochondrial genomes. Molecular Phylogenetics and Evolution 53: 492-508 doi:10.1016/j.ympev.2009.07.010.
22. Zhang P, Papenfuss T, Wake M, Qu L, Wake D, (2008) Phylogeny and biogeography of the family Salamandridae (Amphibia: Caudata) inferred from complete mitochondrial genomes. Molecular Phylogenetics and Evolution 49: 586-597.
23. White TR, Conrad MM, Tseng R, Balayan S, Golding R, et al. (2011) Ten new complete mitochondrial genomes of pulmonates (Mollusca: Gastropoda) and their impact on phylogenetic relationships. BMC Evolutionary Biology 11: 295 doi:---10.1186/1471-2148-11-295.
24. Perseke M, Bernhard D, Fritzsch G, Bruemmer F, Stadler PF, et al. (2010) Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: Insights in phylogenetic relationships of Echinodermata. Molecular Phylogenetics and Evolution 56: 201-211 doi:10.1016/j.ympev.2010.01.035.
25. Hwang U, Friedrich M, Tautz D, Park C, Kim W, (2001) Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature 413: 154-157.
26. Gai Y, Song D, Sun H, Yang Q, Zhou K, (2008) The complete mitochondrial genome of Symphylella sp. (Myriapoda: Symphyla): Extensive gene order rearrangement and evidence in favor of Progoneata. Molecular Phylogenetics and Evolution 49: 574-585 doi:10.1016/j.ympev.2008.08.010.
27. Negrisolo E, Minelli A, Valle G, (2004) The mitochondrial genome of the house centipede Scutigera and the monophyly versus paraphyly of myriapods. Mol Biol Evol 21: 770-780 doi:10.1093/molbev/msh078.
28. Curole JP, Kocher TD, (1999) Mitogenomics: digging deeper with complete mitochondrial genomes. Trends Ecol Evol 14: 394-398.
29. Delsuc F, Phillips MJ, Penny D, (2003) Comment on" Hexapod origins: monophyletic or paraphyletic?.". Science 301: 1482-1482.
30. Cameron SL, Miller KB, D'Haese CA, Whiting MF, Barker SC, (2004) Mitochondrial genome data alone are not enough to unambiguously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Arthropoda). Cladistics 20: 534-557.
31. Rota-Stabelli O, Kayal E, Gleeson D, Daub J, Boore JL, et al. (2010) Ecdysozoan Mitogenomics: Evidence for a Common Origin of the Legged Invertebrates, the Panarthropoda. Genome Biology and Evolution 2: 425-440 doi:10.1093/gbe/evq030.
32. Foster P, Jermiin L, Hickey D, (1997) Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J Mol Evol 44: 282-288.
33. Gibson A, Gowri-Shankar V, Higgs P, Rattray M, (2005) A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods. Mol Biol Evol 22: 251-264 doi:10.1093/molbev/msi012.
34. Saccone C, Gissi C, Reyes A, Larizza A, Sbisa E, et al. (2002) Mitochondrial DNA in metazoa: degree of freedom in a frozen event Vol. 286: 3-12.
35. Perna N, Kocher T, (1995) Patterns of Nucleotide Composition at Fourfold Degenerate Sites of Animal Mitochondrial Genomes. J Mol Evol 41: 353-358.
36. Helfenbein K, Brown W, Boore J, (2001) The complete mitochondrial genome of the articulate brachiopod Terebratalia transversa. Mol Biol Evol 18: 1734-1744.
37. Jones M, Gantenbein B, Fet V, Blaxter M, (2007) The effect of model choice on phylogenetic inference using mitochondrial sequence data: Lessons from the scorpions. Molecular Phylogenetics and Evolution 43: 583-595 doi:10.1016/j.ympev.2006.11.017.
38. Masta SE, Longhorn SJ, Boore JL, (2009) Arachnid relationships based on mitochondrial genomes: Asymmetric nucleotide and amino acid bias affects phylogenetic analyses. Molecular Phylogenetics and Evolution 50: 117-128 doi:10.1016/j.ympev.2008.10.010.
39. Felsenstein J, (1978) Cases in Which Parsimony or Compatibility Methods Will Be Positively Misleading. Syst Zool 27: 401-410.
40. Brinkmann H, van der Giezen M, Zhou Y, de Raucourt GP, Philippe H, (2005) An Empirical Assessment of Long-Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics. Syst Biol 54: 743-757 doi:10.1080/10635150500234609.
41. Rota-Stabelli O, Telford MJ, (2008) A multi criterion approach for the selection of optimal outgroups in phylogeny: Recovering some support for Mandibulata over Myriochelata using mitogenomics. Molecular Phylogenetics and Evolution 48: 103-111 doi:10.1016/j.ympev.2008.03.033.
42. Lartillot N, Philippe H, (2004) A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 21: 1095-1109 doi:10.1093/molbev/msh112.
43. Talavera G, Castresana J, (2007) Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments. Syst Biol 56: 564-577 doi:10.1080/10635150701472164.
44. Lavrov D, Brown W, Boore J, (2000) A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. P Natl Acad Sci Usa 97: 13738-13742.
45. Podsiadlowski L, Kohlhagen H, Koch M, (2007) The complete mitochondrial genome of Scutigerella causeyae (Myriapoda: Symphyla) and the phylogenetic position of Symphyla. Molecular Phylogenetics and Evolution 45: 251-260 doi:10.1016/j.ympev.2007.07.017.
46. Lavrov D, Boore J, Brown W, (2002) Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss. Mol Biol Evol 19: 163.
47. Woo H-J, Lee Y-S, Park S-J, Lim J-T, Jang K-H, et al. (2007) Complete mitochondrial genome of a troglobite millipede Antrokoreana gracilipes (Diplopoda, Juliformia, Julida), and juliformian phylogeny. Mol Cells 23: 182-191.
48. Chen W-J, Bu Y, Carapelli A, Dallai R, Li S, et al. (2011) The mitochondrial genome of Sinentomon erythranum (Arthropoda: Hexapoda: Protura): an example of highly divergent evolution. BMC Evolutionary Biology 11: 246 doi:---10.1186/1471-2148-11-246.
49. Braband A, Cameron SL, Podsiadlowski L, Daniels SR, Mayer G, (2010) The mitochondrial genome of the onychophoran Opisthopatus cinctipes (Peripatopsidae) reflects the ancestral mitochondrial gene arrangement of Panarthropoda and Ecdysozoa. Molecular Phylogenetics and Evolution 57: 285-292 doi:10.1016/j.ympev.2010.05.011.
50. Silvestre D, Dowton M, Arias MC, (2008) The mitochondrial genome of the stingless bee Melipona bicolor (Hymenoptera, Apidae, Meliponini): Sequence, gene organization and a unique tRNA translocation event conserved across the tribe Meliponini. Genet Mol Biol 31: 451-460.
51. Rehm P, Borner J, Meusemann K, Reumont von BM, Simon S, et al. (2011) Dating the arthropod tree based on large-scale transcriptome data. Molecular Phylogenetics and Evolution 61: 880-887 doi:10.1016/j.ympev.2011.09.003.
52. Shear WA (2011) Class Diplopoda de Blainville in Gervais, 1844. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa: 159-164.
53. Meusemann K, Reumont von BM, Simon S, Roeding F, Strauss S, et al. (2010) A Phylogenomic Approach to Resolve the Arthropod Tree of Life. Mol Biol Evol 27: 2451-2464 doi:10.1093/molbev/msq130.
54. Rota-Stabelli O, Campbell L, Brinkmann H, Edgecombe GD, Longhorn SJ, et al. (2010) A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata. P Roy Soc B-Biol Sci 278: 298-306 doi:10.1098/rspb.2010.0590.
55. Regier JC, Shultz JW, Ganley ARD, Hussey A, Shi D, et al. (2008) Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein-Coding Nuclear Gene Sequence. Syst Biol 57: 920-938 doi:10.1080/10635150802570791.
56. Ballard J, Whitlock M, (2004) The incomplete natural history of mitochondria. Mol Ecol 13: 729-744 doi:10.1046/j.1365-294X.2003.02063.x.
57. Shelley R, (1984) A Synopsis of the Milliped Genus Abacion Rafinesque (Callipodida, Caspiopetalidae). Can J Zool 62: 980-988.
58. Shelley R, McAllister C, Tanabe T, (2005) A synopsis of the milliped genus Brachycybe Wood, 1864 (Platydesmida: Andrognathidae). Fragmenta Faunistica 48: 137-166.
59. Simon C, Frati F, Beckenbach A, Crespi B, LIU H, et al. (1994) Evolution, Weighting, and Phylogenetic Utility of Mitochondrial Gene-Sequences and a Compilation of Conserved Polymerase Chain-Reaction Primers. Ann Entomol Soc Am 87: 651-701.
60. Hwang U, Park C, Yong T, Kim W, (2001) One-step PCR amplification of complete arthropod mitochondrial genomes. Molecular Phylogenetics and Evolution 19: 345-352.
61. Swafford L, Bond JE, (2009) The symbiotic mites of some Appalachian Xystodesmidae (Diplopoda: Polydesmida) and the complete mitochondrial genome sequence of the mite Stylochyrus rarior (Berlese) (Acari: Mesostigmata: Ologamasidae). Invertebr Syst 23: 445-451 doi:10.1071/IS09036.
62. Lowe T, Eddy S, (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
63. Klimov PB, O'Connor BM, (2009) Improved tRNA prediction in the American house dust mite reveals widespread occurrence of extremely short minimal tRNAs in acariform mites. Bmc Genomics 10: 598 doi:---10.1186/1471-2164-10-598.
64. Katoh K, Misawa K, Kuma K, Miyata T, (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30: 3059-3066.
65. Katoh K, Toh H, (2008) Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9: 286-298 doi:10.1093/bib/bbn013.
66. Grant BJ, Rodrigues APC, ElSawy KM, McCammon JA, Caves LSD, (2006) Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics 22: 2695-2696 doi:10.1093/bioinformatics/btl461.
67. Team RCD (2009) R: A Language and Environment for Statistical Computing. Available: http://www.r-project.org.
68. Stamatakis A, (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690 doi:10.1093/bioinformatics/btl446.
69. Lartillot N, Lepage T, Blanquart S, (2009) PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25: 2286-2288 doi:10.1093/bioinformatics/btp368.
70. Blanquart S, Lartillot N, (2008) A Site- and Time-Heterogeneous Model of Amino Acid Replacement. Mol Biol Evol 25: 842-858 doi:10.1093/molbev/msn018.
71. López-Giráldez F, Townsend JP, (2011) PhyDesign: an online application for profiling phylogenetic informativeness. BMC Evolutionary Biology 11: 152 doi:---10.1186/1471-2148-11-152.
72. Paradis E, Claude J, Strimmer K, (2004) APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20: 289-290 doi:10.1093/bioinformatics/btg412.