The ITS region of groundwater amphipods: Length, secondary structure and phylogenetic information content in Crangonyctoids and Niphargids

Journal of Zoological Systematics and Evolutionary Research

Volumn 51, Issue 1, 2013, Pages 19-28

  Kornobis, Etienne ^a   Pálsson, Snæbjörn ^a  

^a UNIVERSITY OF ICELAND   (Iceland)

Author keywords

Amphipoda; Crangonyctoidea; Internal transcribed spacer; Niphargus; Phylogeny; Secondary structure

Indexed keywords

AMPHIPOD; DIVERGENCE; ENDEMIC SPECIES; FRESHWATER ECOSYSTEM; GENETIC MARKER; MOLECULAR ANALYSIS; PHYLOGENETICS; PHYLOGENY; RECONSTRUCTION; TAXONOMY;

ICELAND;

AMPHIPODA; ANIMALIA; CRANGONYCTOIDEA; CRANGONYX; CRYMOSTYGIUS THINGVALLENSIS; METAZOA; NIPHARGIDAE; NIPHARGUS;

EID: 84872668059     PISSN: 09475745     EISSN: 14390469     Source Type: Journal    
DOI: 10.1111/jzs.12006     Document Type: Article

References (74)

1. Akaike H (1974) A new look at the statistical model identification. IEEE Trans Automat Contr 19:716-723.
2. Álvarez I, Wendel J (2003) Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol 29:417-434.
3. Bate CS (1859) On the genus Niphargus (Schiödte). Proc Dublin Univ Zool Bot Assoc 1:237-244.
4. Ben-David T, Melamed S, Gerson U, Morin S (2007) ITS2 sequences as barcodes for identifying and analyzing spider mites (Acari: Tetranychidae). Exp Appl Acarol 41:169-181.
5. Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF (2008) RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics 9:474.
6. Borutzky EW (1928) Materialien über die Fauna der unterirdischen Gewässer: Crangonyx chlebnikovi n. sp. (Amphipoda) aus den Höhlen des mittleren Urals. Zool Anz 77:253-259.
7. Bousfield EL (1973) Shallow-Water Gammaridean Amphipoda of New England. Cornell University Press, Ithaca and London, 312 pp.
8. Bousfield EL (1977) A new look at the systematics of gammaroidean Amphipoda of the world. Crustaceana 4:282-316.
9. Bousfield EL (1989) Revised morphological relationships within the amphipod genera Pontoporeia and Gammaracanthus and the "glacial relict" significance of their postglacial distributions. Can J Fish Aquat Sci 46:1714-1725.
10. Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L (2009) Fast statistical alignment. PLoS Comput Biol 5:e1000392.
11. Buchheim MA, Keller A, Koetschan C, Förster F, Merget B, Wolf M (2011) Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life. PLoS ONE 6:e16931.
12. Chen CA, Chang CC, Wei NV, Chen CH, Lein YT, Lin HE, Dai CF, Wallace CC (2004) Secondary structure and phylogenetic utility of the ribosomal internal transcribed spacer 2 (ITS2) in scleractinian corals. Zool Stud 43:759-771.
13. Chevreux E (1901) Amphipodes des eaux souterraines de France et d'Algérie. Bull Soc Zool Fr 26:168-239.
14. Chow S, Ueno Y, Toyokawa M, Oohara I, Takeyama H (2009) Preliminary analysis of length and GC content variation in the ribosomal first internal transcribed spacer (ITS1) of marine animals. Mar Biotechnol 11:301-306.
15. Chu KH, Li CP, Ho HY (2001) The First Internal Transcribed Spacer (ITS-1) of ribosomal DNA as a molecular marker for phylogenetic and population analyses in crustacea. Mar Biotechnol 3:355-361.
16. Coleman AW (2007) Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Res 35:3322-3329.
17. Cope ED (1872) On the Wyandotte Cave and its fauna. Am Nat 6:406-422.
18. Côté CA, Peculis BA (2001) Role of the ITS2-proximal stem and evidence for indirect recognition of processing sites in pre-rRNA processing in yeast. Nucleic Acids Res 29:2106-2116.
19. Dana JD (1853) Crustacea. In: United States Exploring Expedition, During the Years 1838, 1839, 1840, 1841, 1842, Under the Command of Charles Wilkes. U.S.N. C., Philadelphia.
20. Deng W, Maust BS, Nickle DC, Learn GH, Liu Y, Heath L, Kosakovsky Pond SL, Mullins JI (2010) DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites. Biotechniques 48:405-408.
21. Dray S, Dufour AB (2007) The ade4 package: implementing the duality diagram for ecologists. J Stat Softw 22:1-20.
22. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797.
23. Englisch U (2001) Analyse der phylogenie der Amphipoda mit hilfe von sequenzen des gens der RNA der kleinen ribosomalen untereinheit, PhD thesis, 311 pp.
24. Fišer C, Sket B, Trontelj P (2008) A phylogenetic perspective on 160 years of troubled taxonomy of Niphargus (Crustacea: Amphipoda). Zool Scr 37:665-680.
25. Flot J-F (2010) Vers une taxonomie moléculaire des amphipodes du genre Niphargus: exemples d'utilisation de séquences d'ADN pour l'identification des espèces. Bull Soc Sci Nat Ouest Fr 32:62-68.
26. Flot J-F, Wörheide G, Dattagupta S (2010) Unsuspected diversity of Niphargus amphipods in the chemoautotrophic cave ecosystem of Frasassi, central Italy. BMC Evol Biol 10:171.
27. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704.
28. Hadjiolova KV, Normann A, Cavaillé J, Soupène E, Mazan S, Hadjiolov AA, Bachellerie JP (1994) Processing of truncated mouse or human rRNA transcribed from ribosomal minigenes transfected into mouse cells. Mol Cell Biol 14:4044-4056.
29. Hall T (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98.
30. Harpke D, Peterson A (2008) Extensive 5.8S nrDNA polymorphism in Mammillaria (Cactaceae) with special reference to the identification of pseudogenic internal transcribed spacer regions. J Plant Res 121:261-270.
31. Harris DJ, Crandall KA (2000) Intragenomic variation within ITS1 and ITS2 of freshwater crayfishes (Decapoda: Cambaridae): implications for phylogenetic and microsatellite studies. Mol Biol Evol 17:284-291.
32. Hay WP (1902) Observations on the crustacean fauna of Nickajack Cave, Tennessee and vicinity. Proc US Nat Mus 25:417-439.
33. Hlinka O, Murrell A, Barker S (2002) Evolution of the secondary structure of the rRNA internal transcribed spacer 2 (ITS2) in hard ticks (Ixodidae, Arthropoda). Heredity 2:275-279.
34. Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31:3429-3431.
35. Holsinger JR (1967) Systematics, speciation, and distribution of the subterranean amphipod genus Stygonectes (Gammaridae). Bull US Nat Mus 259:1-176.
36. Holsinger JR (1978) Systematics of the Subterranean Amphipod genus Stygobromus (Crangonyctidae): part II. Species of the Eastern United States. Smithson Contrib Zool 266:1-144.
37. Hou Z, Fu J, Li S (2007) A molecular phylogeny of the genus Gammarus (Crustacea: Amphipoda) based on mitochondrial and nuclear genes. Mol Phylogenet Evol 45:596-611.
38. Hřibová E, Čížková J, Christelová P, Taudien S, de Langhe E, Doležel J (2011) The ITS1-5.8S-ITS2 sequence region in the Musaceae: structure, diversity and use in molecular phylogeny. PLoS ONE 6:e17863.
39. Insua A, Lopez-Piñón M, Freire R (2003) Sequence analysis of the ribosomal DNA internal transcribed spacer region in some scallop species (Mollusca: Bivalvia: Pectinidae). Genome 604:595-604.
40. Karaman GS (1932) Beitrag zur Kenntnis der Süsswasser-Amphipoden. Prirodoslovne Razprave 2:179-232.
41. Karaman GS (1985) New data on the genus Niphargus Schiödte (Fam. Niphargidae) in Italy and the adjacent regions. Contribution to the knowledge of amphipods 138. Boll Mus Civ St Nat Verona 12:209-228.
42. Karaman GS, Borowsky B, Dattagupta S (2010) Two new species of the genus Niphargus Schiödte, 1849 (Amphipoda, Fam. Niphargidae) from the Frasassi cave system in Central Italy. Zootaxa 2439:35-52.
43. Keller A, Schleicher T, Schultz J, Müller T, Dandekar T, Wolf M (2009) 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene 430:50-57.
44. Keller A, Förster F, Müller T, Dandekar T, Schultz J, Wolf M (2010) Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. Biol Direct 5:4.
45. Ki J-S, Dahms H-U, Kim I-C, Park H, Hop H, Lee J-S (2011) Molecular relationships of gammaridean amphipods from Arctic sea ice. Polar Biol 34:1559-1569.
46. Koetschan C, Forster F, Keller A, Schleicher T, Ruderisch B, Schwarz R, Muller T, Wolf M, Schultz J (2010) The ITS2 Database III-sequences and structures for phylogeny. Nucleic Acids Res 38:275-279.
47. Kornobis E, Pálsson S (2011) Discordance in variation of the ITS region and the mitochondrial COI gene in the subterranean amphipod Crangonyx islandicus. J Mol Evol 73:34-44.
48. Kornobis E, Pálsson S, Kristjánsson BK, Svavarsson J (2010) Molecular evidence of the survival of subterranean amphipods (Arthropoda) during Ice Age underneath glaciers in Iceland. Mol Ecol 19:2516-2530.
49. Kornobis E, Pálsson S, Sidorov DA, Holsinger JR, Kristjánsson BK (2011) Molecular taxonomy and phylogenetic affinities of two groundwater amphipods, Crangonyx islandicus and Crymostygius thingvallensis, endemic to Iceland. Mol Phylogenet Evol 58:527-539.
50. Kornobis E, Pálsson S, Svavarsson J (2012) Classification of Crangonyx islandicus (Amphipoda, Crangonyctidae) based on morphological characters and comparison with molecular phylogenies. Zootaxa 3233:52-66.
51. Kristjansson BK, Svavarsson J (2004) Crymostygidae, a new family of subterranean freshwater gammaridean amphipods (Crustacea) recorded from subarctic Europe. J Nat Hist 38:1881-1894.
52. Lefébure T, Douady CJ, Gouy M, Trontelj P, Briolay J, Gibert J. (2006) Phylogeography of a subterranean amphipod reveals cryptic diversity and dynamic evolution in extreme environments. Mol Ecol 15:1797-1806.
53. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209-220.
54. Musters W, Boon K, van der Sande CA, van Heerikhuizen H, Planta RJ (1990) Functional analysis of transcribed ribosomal DNA spacers of yeast. EMBO J 9:3989-3996.
55. van Nues RW, Rientjes JM, Morré SA, Mollee E, Planta RJ, Venema J, Raué HA (1995) Evolutionarily conserved structural elements are critical for processing of Internal Transcribed Spacer 2 from Saccharomyces cerevisiae precursor ribosomal RNA. J Mol Biol 250:24-36.
56. Paradis E, Claude J, Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289-290.
57. Peay KG, Kennedy PG, Bruns TD (2008) Fungal community ecology: a hybrid beast with a molecular master. Bioscience 58:799-810.
58. Pilgrim EM, Scharold JV, Darling JA, Kelly JR (2009) Genetic structure of the benthic amphipod Diporeia (Amphipoda: Pontoporeiidae) and its relationship to abundance in Lake Superior. Can J Fish Aquat Sci 66:1318-1327.
59. Posada D, Buckley TR (2004) Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and bayesian approaches over likelihood ratio tests. Syst Biol 53:793-808.
60. R Development Core Team (2010) R: A Language and Environment for Statistical Computing. Foundation for Statistical Computing, Vienna.
61. Schiødte JC (1849). Bidrag til den underjordiske Fauna. Bianco Luno, Kjöbenhavn, 39 p.
62. Schultz J, Wolf M (2009) ITS2 sequence-structure analysis in phylogenetics: a how-to manual for molecular systematics. Mol Phylogenet Evol 52:520-523.
63. Seibel PN, Müller T, Dandekar T, Wolf M (2008) Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. BMC Res Notes 1:91.
64. Smith SI (1873) Crustacea, ex. Isopoda. In A.E. Verrill's "Report upon the invertebrate animals of Vineyard Sound" U.S. Commission of Fish and Fisheries. Pt. 1. Report on the Condition of the Sea Fisheries of the South Coast of New England in 1871 and 1872, pp 295-778.
65. Song ZK, Wang XZ, Liang GQ (2008) Molecular evolution and phylogenetic utility of the internal transcribed spacer 2 (ITS2) in Calyptratae (Diptera: Brachycera). J Mol Evol 67:448-464.
66. Sotka EE, Wares JP, Hay ME (2003) Geographic and genetic variation in feeding preference for chemically defended seaweeds. Evolution 57:2262-2276.
67. Stocsits RR, Letsch H, Hertel J, Misof B, Stadler PF (2009) Accurate and efficient reconstruction of deep phylogenies from structured RNAs. Nucleic Acids Res 37:6184-6193.
68. Svavarsson J, Kristjánsson BK (2006) Crangonyx islandicus sp. nov., a subterranean freshwater amphipod (Crustacea, Amphipoda, Crangonyctidae) from springs in lava fields in Iceland. Zootaxa 1365:1-17.
69. Tippery NP, Les DH (2008) Phylogenetic analysis of the internal transcribed spacer (ITS) region in Menyanthaceae using predicted secondary structure. Mol Phylogenet Evol 49:526-537.
70. Väinölä R, Witt JDS, Grabowski M, Bradbury JH, Jazdzewski K, Sket B (2008) Global diversity of amphipods (Amphipoda; Crustacea) in freshwater. Hydrobiologia 5:241-255.
71. Wang S, Bao Z, Li N, Zhang L, Hu J (2007) Analysis of the secondary structure of ITS1 in Pectinidae: implications for phylogenetic reconstruction and structural evolution. Mar Biotechnol 9:231-242.
72. Wolf M, Ruderisch B, Dandekar T, Schultz J, Müller T (2008) ProfDistS: (profile-) distance based phylogeny on sequence-structure alignments. Bioinformatics 24:2401-2402.
73. Wrzesniowski A (1877) Über die anatomie der Amphipoden. Z Wiss Zool 28:403-406.
74. Yao H, Song J, Liu C, Luo K, Han J, Li Y, Pang X, Xu H, Zhu Y, Xiao P, Chen S (2010) Use of ITS2 region as the universal DNA barcode for plants and animals. PLoS ONE 5:e13102.