Phylogeny of the nematode genus Pristionchus and implications for biodiversity, biogeography and the evolution of hermaphroditism

BMC Evolutionary Biology

Volumn 7, Issue , 2007, Pages

  Mayer, Werner E ^a   Herrmann, Matthias ^a   Sommer, Ralf J ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIODIVERSITY; BIOGEOGRAPHY; EVOLUTION; HERMAPHRODITISM; NEMATODE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRISTIONCHUS PACIFICUS; ANIMAL; CLASSIFICATION; ECOSYSTEM; EUROPE; EXPRESSED SEQUENCE TAG; FEMALE; FERTILITY; GENE; GENETICS; GENOME; JAPAN; MALE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYSIOLOGY; SEX CHROMOSOME; SOUTH AFRICA; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION; WESTERN HEMISPHERE;

CAENORHABDITIS; CAENORHABDITIS ELEGANS; COLEOPTERA; LEPTINOTARSA DECEMLINEATA; NEMATODA; PRISTIONCHUS; PRISTIONCHUS PACIFICUS; SCARABAEIDAE;

COMPLEMENTARY DNA; HELMINTH DNA; HELMINTH PROTEIN; RIBOSOME PROTEIN;

AMERICAS; ANIMALS; BIODIVERSITY; DNA, COMPLEMENTARY; DNA, HELMINTH; ECOSYSTEM; EUROPE; EVOLUTION; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; FEMALE; FERTILITY; GENES, HELMINTH; GENETIC SPECIATION; GENOME; HELMINTH PROTEINS; HERMAPHRODITISM; JAPAN; MALE; MOLECULAR SEQUENCE DATA; NEMATODA; PHYLOGENY; RIBOSOMAL PROTEINS; SEX CHROMOSOMES; SOUTH AFRICA; SPECIES SPECIFICITY;

EID: 34447625059     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-7-104     Document Type: Article

References (54)

1. Pristionchus pacificus: a well-rounded nematode. RL Hong RJ Sommer, Bioessays 2006 28 651 659 10.1002/bies.20404 16700067
2. Nematodes of the genus Pristionchus are closely associated with scarab beetles and the Colorado potato beetle in Western Europe. M Herrmann WE Mayer RJ Sommer, Zoology 2006 109 96 108 10.1016/j.zool.2006.03.001 16616467
3. Sex, bugs and Haldane's rule: the nematode genus Pristionchus in the United States. M Herrmann WE Mayer RJ Sommer, Frontiers in Zoology 2006 http://www.frontiersinzoology.com/content/3/1/14 16968539
4. The nematode Pristionchus pacificus (Nematoda: Diplogastridae) is associated with the Oriental beetle Exomala orientalis (Coleoptera: Scarabaeidae) in Japan. M Herrmann WE Mayer RL Hong S Kienle R Minasaki RJ Sommer, Zool Sciences 2007
5. Chemoattraction in Pristionchus nematodes and implications for insect recognition. RL Hong RJ Sommer, Curr Biol 2007 16 2359 2365 10.1016/j.cub.2006. 10.031
6. Comparative and functional morphology of the buccal cavity of Diplogastrina (Nematoda) and a first outline of the phylogeny of this taxon. A Fürst von Lieven W Sudhaus, J Zool Syst Evol Research 2000 38 37 63 10.1046/j.1439-0469.2000.381125.x
7. A phylogenetic classification and catalogue of the Diplogastridae (Secernentea, Nematoda). W Sudhaus A Fürst von Lieven, J Nem Morph Syst 2003 6 43 90
8. A molecular evolutionary framework for the phylum Nematoda. ML Blaxter P de Ley JR Garey LX Liu P Scheldeman A Vierstraete JR Vanfleteren LY Mackey M Dorris LM Frisse JT Vida K Thomas, Nature 1998 392 71 75 10.1038/32160 9510248
9. Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward crown clades. M Holterman A van der Wurff S van den Elsen H van Megen T Bongers O Holovachov J Bakker J Helder, Mol Biol Evol 2006 23 1792 1800 10.1093/molbev/msl044 16790472
10. Mutations causing transformation of sexual phenotype in the nematode Caenorhabditis elegans. JA Hodgkin S Brenner, Genetics 1977 86 275 287 560330
11. Conservation of the global sex determination gene tra-1 in distantly related nematodes. A Pires-daSilva RJ Sommer, Genes Dev 2004 18 1198 1208 15155582 10.1101/gad.293504
12. The evolution of developmental mechanisms. D Rudel RJ Sommer, Dev Biol 2003 264 15 37 10.1016/S0012-1606(03)00353-1 14623229
13. Conservation and diversification of Wnt signalling function during the evolution of nematode vulva development. M Zheng Messerschmidt B Jungblut RJ Sommer, Nat Genet 2005 37 300 304 10.1038/ng1512 15696167
14. HAIRY-like transcription factors and the evolution of the nematode vulva equivalence group. B Schlager W Röseler M Zheng A Gutierrez RJ Sommer, Curr Biol 2006 16 1386 1394 10.1016/j.cub.2006.06.058 16860737
15. A bacterial artificial chromosome-based genetic linkage map of the nematode Pristionchus pacificus. J Srinivasan W Sinz C Lanz A Brand R Nandakumar G Raddatz H Witte H Keller I Kipping A Pires-daSilva T Jesse J Millare M de Both SC Schuster RJ Sommer, Genetics 2002 162 129 134 12242228
16. An integrated physical and genetic map of the nematode Pristionchus pacificus. J Srinivasan W Sinz T Jesse L Wiggers-Perebolte K Jansen J Buntjer M van der Meulen RJ Sommer, Mol Genet Genom 2003 269 715 722 10.1007/s00438-003- 0881-8
17. NHGRI Adds 18 Organisms to Sequencing Pipeline. Genome.gov, 2004 http://www.nhgri.nih.gov/12511858
18. Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus. C Dieterich W Röseler P Sobetzko RJ Sommer, Nucleic Acids Res 2007 35 498 502 10.1093/nar/gkl804
19. Distinct patterns of genetic diversity in Pristionchus pacificus and Caenorhabditis elegans, two partially selfing nematodes with cosmopolitan distribution. H Zauner WE Mayer M Herrmann A Weller M Erwig RJ Sommer, Mol Ecol 2007 16 1267 1280 10.1111/j.1365-294X.2006.03222.x 17391412
20. Molecular barcodes for soil nematode identification. R Floyd E Abebe A Papert M Blaxter, Mol Ecol 2002 11 839 850 10.1046/j.1365-294X.2002.01485.x 11972769
21. The Phylogenetic relationships of Caenorhabditis and other rhabditids (August 11, 2005). K Kiontke DHA Fitch, WormBook, ed The C. elegans Research Community, WormBook http://www.wormbook.org doi/10.1895/wormbook.1.11.1
22. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. M Nei T Gojobori, Mol Biol Evol 1986 3 418 426 3444411
23. Pattern of synonymous and nonsynonymous substitutions: An indicator of mechanisms of molecular evolution. Y Ina, J Genet 1996 75 91 115
24. MEGA3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment. S Kumar K Tamura M Nei, Brief Bioinform 2004 5 150 163 10.1093/bib/5.2.150 15260895
25. Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. SR Gadagkar MS Rosenberg S Kumar, J Exp Zoo (Mol Dev Evol) 2005 304B 64 74 10.1002/jez.b.21026
26. Some probabilistic and statistical problems in the analysis of DNA sequences. S Tavaré Some mathematical questions in biology: DNA sequence analysis Providence, RI: Amer Math Soc, Miura RM, 1986 57 86
27. Modeltest: testing the model of DNA substitution. D Posada KA Crandall, Bioinformatics 1998 14 817 818 10.1093/bioinformatics/14.9.817 9918953
28. DL Swofford, PAUP: Phylogenetic Analysis Using Parsimony (and other methods). Version 4.0b10 Sunderland, Massachusetts: Sinauer Associates 2002
29. BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. O Gascuel, Mol Biol Evol 1997 14 685 695 9254330
30. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. M Hasegawa K Kishino T Yano, J Mol Evol 1985 22 160 174 10.1007/BF02101694 3934395
31. MRBAYES: Bayesian inference of phylogenetic trees. JP Huelsenbeck F Ronquist, Bioinformatics 2001 17 754 755 10.1093/bioinformatics/17.8.754 11524383
32. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. HA Schmidt K Strimmer M Vingron A von Haeseler, Bioinformatics 2002 18 502 504 10.1093/bioinformatics/18.3.502 11934758
33. A simple method to visualize phylogenetic content of a sequence alignment. K Strimmer A von Haeseler, Proc Natl Acad Sci USA 2002 94 6815 6819 10.1073/pnas.94.13.6815
34. Redescription of Diplogasteroides nasuensis Takaki, 1941 and D. magnus Völk, 1950 (Nematoda: Diplogastrina) associated with Scarabaeidae (Coleoptera). K Kiontke A Manegold W Sudhaus, Nematology 2001 3 817 832 10.1163/156854101753625317
35. Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. K Kiontke NP Gavin Y Raynes C Roehrig F Piano DHA Fitch, Proc Natl Acad Sci USA 2004 101 9003 9008 15184656 10.1073/pnas.0403094101
36. Haldane's rule. HA Orr, Annu Rev Ecol Syst 1997 28 195 218 10.1146/annurev.ecolsys.28.1.195
37. The voyage of an invasive species across continents: genetic diversity of North American and European Colorado potato beetle populations. A Grapputo S Boman L Lindstrom A Lyytinen J Mappes, Mol Ecol 2005 14 4207 4219 16313587
38. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. M Hajibabaei GAC Singer DN Paul PDN Hebert DA Hickey, Trends Genet 2007 23 doi:10.1016/j.tig.2007.02.001 17316886
39. JN Thompson, The Geographic Mosaic of Coevolution Chicago and London: The University of Chicago Press 2006
40. Basal relationships of Coleoptera inferred from 18S rDNA sequences. MS Caterino VL Shull PM Hammond AP Vogler, Zoologica Scripta 2002 31 41 49 10.1046/j.0300-3256.2001.00092.x
41. www.pristionchus.org. http://www.pristionchus.org
42. WormBase. http://www.wormbase.org
43. GenBank. http://www.ncbi.nlm.nih.gov
44. "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs". SF Altschul TL Madden AA Schäffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997 25 3389 3402 9254694 10.1093/nar/25.17.3389
45. SeqPup version 0.6f: a biosequence editor and analysis application. DG Gilbert, 1996 http://iubio.bio.indiana.edu/soft/molbio
46. A new look at the statistical model identification. H Akaike, IEEE Trans Automatic Control 1974 19 716 723 10.1109/TAC.1974.1100705
47. The neighbor-joining method: a new method for reconstructing phylogenetic trees. N Saitou M Nei, Mol Bio Evol 1987 4 4 406 425
48. Confidence limits on phylogenies: An approach using the bootstrap. J Felsenstein, Evolution 1985 39 783 791 10.2307/2408678
49. Morphological, genetic and molecular description of Pristionchus pacificus sp.n. (Nematoda: Neodiplogastridae). RJ Sommer L Carta S-Y Kim PW Sternberg, Fundam Appl Nematol 1996 19 511 521
50. Notes on the free-living nematodes. FA Potts, Quarterly Journal of microscopical Science 1910 55 433 485
51. Estimating the nema population of soil, with special reference to the sugar beet and root gall nemas, Heterodera schachtii Schmidt and H. radicicola (Greef) Muller, and with a description of Tylencholaimus aequalis n.sp. NA Cobb, Agricultural Technology Circular. Bureau of Plant Industry U.S. Department of Agriculture, Washington, DC, USA 1918
52. Essais d'hybridation chez les nématodes. E Maupas, Bulletin Biologique France et Belgique 1919 52 466 498
53. Pristionchus uniformis sp. n. (Nematoda, Rhabditida, Diplogasteridae) a facultative parasite of Leptinotarsa decemlineata Say and Melolontha melolontha L. in Poland. Morphology and biology. A Fedorko S Stanuszek, Acta Parasitologica Polonica 1971 19 95 112
54. Diplogaster entomophaga. n. sp., a new Diplogaster (Diplogasteridae, Nematodes) found on a Pamphilius stellatus (Christ) (Tenthredinidae, Hymenoptera). G Steiner, Zoologischer Anzeiger 1929 80 143 145