Base composition, selection, and phylogenetic significance of indels in the recombination activating gene-1 in vertebrates

Frontiers in Zoology

Volumn 6, Issue 1, 2009, Pages

  Chiari, Ylenia ^a,b   Van Der Meijden, Arie ^c   Madsen, Ole ^d   Vences, Miguel ^e   Meyer, Axel ^a  

^a UNIVERSITY OF KONSTANZ   (Germany)

^b INSTITUT DES SCIENCES DE L EVOLUTION   (France)

^c CENTRO DE INVESTIGAÇÃO EM BIODIVERSIDADE E RECURSOS GENÉTICOS   (Portugal)

^d WAGENINGEN UNIVERSITY   (Netherlands)

^e TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACTINOPTERYGII; AMPHIBIA; AVES; CHONDRICHTHYES; CROCODYLIDAE (ALL CROCODILES); LEPIDOSAURIA; MAMMALIA; TESTUDINES; VERTEBRATA;

EID: 74549187044     PISSN: None     EISSN: 17429994     Source Type: Journal    
DOI: 10.1186/1742-9994-6-32     Document Type: Article

References (47)

1. Animal phylogeny and large-scale sequencing: progress and pitfall. H Brinkmann H Philippe, J Syst Evol 2008 46 274 286
2. Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction. MS Springer RW DeBry C Douady HM Amrine O Madsen WW de Jong MJ Stanhope, Mol Biol Evol 2001 18 132 143 11158372
3. Additional support for Afrotheria and Paenungulata, the performance of mitochondrial versus nuclear genes, and the impact of data partitions with heterogeneous base composition. MS Springer HM Amrine A Burk MJ Stanhope, Syst Biol 1999 48 65 75 10.1080/106351599260445 12078646
4. On the best evolutionary rate for phylogenetic analysis. Z Yang, Syst Biol 1998 47 125 133 10.1080/106351598261067 12064232
5. Is homoplasy or lineage sorting the source of incongruent mtDNA and nuclear gene trees in the stiff-tailed ducks (Nomonyx-Oyxyura)? KG McCracker MD Sorenson, Syst Biol 2005 54 35 55 10.1080/10635150590910249 15805009
6. Recovering evolutionary trees under a more realistic model of sequence evolution. PJ Lockhart MA Steel MD Hendy D Penny, Mol Biol Evol 1994 11 605 612 19391266
7. Genome-scale phylogeny and the detection of systematic biases. MJ Phillips F Delsuc D Penny, Mol Biol Evol 2004 21 1455 1458 10.1093/molbev/msh137 15084674
8. Basal divergences in birds and the phylogenetic utility of the nuclear RAG1 gene. JG Groth GF Barrowclough, Mol Phylogenet Evol 1999 12 115 123 10.1006/mpev.1998.0603 10381315
9. New evidence for parallel evolution of color patterns in Malagasy poison frogs (Mantella). Y Chiari M Vences DR Vieites F Rabemananjara P Bora OR Ravoahangimalala A Meyer, Mol Ecol 2004 13 3763 3774 10.1111/j.1365-294X.2004. 02367.x 15548289
10. Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG1. AF Hugall R Foster MSY Lee, Syst Biol 2007 56 543 563 10.1080/10635150701477825 17654361
11. A phylogenetic review of the African leaf chameleons: genus Rhampholeon (Chamaeleonidae): the role of vicariance and climate change in speciation. CA Matthee CR Tilbury T Townsend, Proc R Soc Lond B 2004 271 1967 1975 10.1098/rspb.2004.2806
12. Molecular phylogenetics and evolution of turtles. JG Krenz GJP Naylor HB Shaffer FJ Janzen, Mol Phylogenet Evol 2005 37 178 191 10.1016/j.ympev.2005.04. 027 15964217
13. Substitution rates of organelle and nuclear genes in sharks: implicating metabolic rate (again). AP Martin, Mol Biol Evol 1999 16 996 1002 10406116
14. Novel phylogenetic relationships of the enigmatic brevicipitine and scaphiophrynine toads as revealed by sequences from the nuclear RAG1 gene. A van der Meijden M Vences A Meyer, Proc R Soc Lond B (Suppl) 2004 271 378 S381 10.1098/rsbl.2004.0196
15. Evolution of RAG1 in polyploid clawed frogs. BJ Evans DB Kelley DJ Melnick DC Cannatella, Mol Biol Evol 2005 22 1193 1207 10.1093/molbev/msi104 15703243
16. Late changes in spliceosomal introns define clades in vertebrate evolution. B Venkatesh Y Ning S Brenner, Proc Natl Acad Sci USA 1999 96 10267 10271 10.1073/pnas.96.18.10267 10468597
17. Putting the pieces together: identification and characterization of structural domains in the V(D)J recombination protein Rag1. P De KK Rodgers, Immunol Rev 2004 200 70 82 10.1111/j.0105-2896.2004.00154.x 15242397
18. Immunobiology 5: the immune system in health and disease. CA Janeway P Travers M Walport M Schlomchick, Garland Publishing, New York 2001
19. The recombination-activating gene 1 of Pleurodeles waltl (urodele amphibian) is transcribed in lymphoid tissues and in the central nervous system. C Frippiat P Kremarik A Ropars C Dournon J-P Frippiat, Immunogenetics 2001 52 264 275 10.1007/s002510000275 11220629
20. V(D)J recombination and the evolution of the adaptive immune system. E Market FN Papavasiliou, PLoS Biol 2003 1 24 27 10.1371/journal.pbio.0000016 (Pubitemid 39112187)
21. Mutational analysis of Rag1 and Rag2 identifies three catalytic amino acids in Rag1 critical for both cleavage steps of V(D)J recombination. MA Landree JA Wibbenmeyer DB Roth, Genes Dev 2008 13 3059 3069 10.1101/gad.13.23. 3059
22. Length variation in the N-terminal domain of the recombination-activating gene 1 (Rag1) across squamates. J Melville JM Hale, Mol Phylogenet Evol 2009 52 898 903 10.1016/j.ympev.2008.12.027 19603552
23. Base-compositional heterogeneity in the RAG1 locus among didelphid marsupials: implications for phylogenetic inference and the evolution of GC content. KF Gruber RS Voss SA Jansa, Syst Biol 2007 56 83 96 10.1080/10635150601182939 17366139
24. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol 2007 24 1596 1599 10.1093/molbev/msm092 17488738
25. DNAcollapser. http://www.birc.au.dk/∼biopv/php/fabox/dnacollapser.php
26. UniProt. http://www.uniprot.org/
27. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. K Tamura M Nei, Mol Biol Evol 1993 10 512 526 8336541
28. Disparity Index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. S Kumar SR Gadagkar, Genetics 2001 158 1321 1327 11454778
29. R: A Language and Environment for Statistical Computing. Version 2.7.2. The R Development Core Team, 2008
30. PAML 4: a program package for phylogenetic analysis by maximum likelihood. Z Yang, Mol Biol Evol 2007 24 1586 1591 10.1093/molbev/msm088 17483113
31. Pervasive adaptive evolution in mammalian fertilization proteins. WJ Swanson R Nielsen Q Yang, Mol Biol Evol 2003 20 18 20 12519901
32. PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods), version 4b8. DL Swofford, Sinauer, Sunderland, MA 2002
33. A molecular analysis of the interrelationships of tetraodontiform fishes (Acanthomorpha: Tetraodontiformes). NI Holcroft, Mol Phylogenet Evol 2005 34 525 544 10.1016/j.ympev.2004.11.003 15683927
34. Global patterns of diversification in the history of modern amphibians. K Roelants DJ Gower M Wilkinson SP Loader SD Biju K Guillaume L Moriau F Bossuyt, P Natl Acad Sci USA 2007 104 887 892 10.1073/pnas.0608378104 (Pubitemid 46154706)
35. Molecular phylogenetic evidence for paraphyly of the genus Sooglossus, with the description of a new genus of Seychellean frogs. A Van der Meijden R Boistel J Gerlach A Ohler M Vences A Meyer, Biol J Linn Soc 2007 91 347 359 10.1111/j.1095-8312.2007.00800.x (Pubitemid 47037832)
36. Initial diversification of living amphibians predated the breakup of Pangea. D San Mauro M Vences M Alcobendas R Zardoya A Meyer, Am Nat 2005 165 590 599 10.1086/429523 15795855
37. Combined nuclear and mitochondrial DNA sequences resolve generic relationships within the Cracidae (Galliformes, Aves). SL Pereira AJ Baker A Wajntal, Syst Biol 2002 51 946 958 10.1080/10635150290102519 12554460
38. A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data. FK Barker GF Barrowclough JG Groth, Proc R Soc Lond B 2002 269 295 308 10.1098/rspb.2001.1883 (Pubitemid 34162556)
39. Phylogeny and diversification of the largest avian radiation. FK Barker A Cibios P Schikler J Feinstein J Cracraft, Proc Natl Acad Sci 2004 101 11040 11045 10.1073/pnas.0401892101 15263073
40. Troubleshooting molecular phylogenetic analyses. MJ Sanderson HB Shaffer, Annu Rev Ecol Syst 2002 33 49 72 10.1146/annurev.ecolsys.33.010802.150509 (Pubitemid 36048805)
41. Molecular phylogeny: pitfall and progress. D Moreira H Philippe, Int Microbiol 2000 3 9 16 10963328
42. The RAG1 exon in the avian order Caprimulgiformes: phylogeny, heterozygosity, and base composition. GF Barrowclough JG Groth LA Mertz, Mol Phylogenet Evol 2006 41 238 248 10.1016/j.ympev.2006.05.013 16814574
43. Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates. B Venkatesh MV Erdmann S Brenner, Proc Natl Acad Sci USA 2001 98 11382 11387 10.1073/pnas.201415598 11553795
44. Nuclear DNA phylogeny of the squirrels (Mammalia: Rodentia) and the evolution of arboreality from c-myc and Rag1. SJ Steppan BL Storz RS Hoffman, Mol Phylogenet Evol 2004 30 703 719 10.1016/S1055-7903(03)00204-5 15012949
45. Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree. WW de Jong MAM van Dijk C Poux G Kappé T van Rheede O Madsen, Mol Phylogenet Evol 2003 28 328 340 10.1016/S1055-7903(03) 00116-7 12878469
46. Molecules consolidate the placental mammal tree. MS Springer MJ Stanhope O Madsen WW de Jong, Trends Ecol Evol 2004 19 430 438 10.1016/j.tree.2004.05.006 16701301
47. Bayes empirical bayes inference of amino acid sites under positive selection. Z Yang WSW Wong R Nielsen, Mol Biol Evol 2005 22 1107 1118 10.1093/molbev/msi097 15689528