Conflicting phylogenetic signals in the SlX1/Y1 gene in Silene

BMC Evolutionary Biology

Volumn 8, Issue 1, 2008, Pages

  Rautenberg, Anja ^a   Filatov, Dmitry ^b   Svennblad, Bodil ^a   Heidari, Nahid ^a   Oxelman, Bengt ^a,c  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

VEGETABLE PROTEIN;

ARTICLE; CLASSIFICATION; GENE DUPLICATION; GENETIC RECOMBINATION; GENETICS; MOLECULAR GENETICS; PHYLOGENY; PLANT CHROMOSOME; SILENE;

CHROMOSOMES, PLANT; GENE DUPLICATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT PROTEINS; RECOMBINATION, GENETIC; SILENE;

EID: 60549117866     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-8-299     Document Type: Article

References (63)

1. Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy. JJ Doyle, Syst Bot 1992 17 1 144 163 10.2307/2419070
2. Species Trees from Gene Trees: Reconstructing Bayesian Posterior Distributions of a Species Phylogeny Using Estimated Gene Tree Distributions. L Liu DK Pearl, Syst Biol 2007 56 3 504 514 10.1080/10635150701429982 17562474
3. Discordance between Nuclear and Chloroplast Phylogenies in the Heuchera Group (Saxifragaceae). DE Soltis RK Kuzoff, Evolution 1995 49 4 727 742 10.2307/2410326
4. Nonuniform Concerted Evolution and Chloroplast Capture: Heterogeneity of Observed Introgression Patterns in Three Molecular Data Partition Phylogenies of Asian Mitella (Saxifragaceae). Y Okuyama N Fujii M Wakabayashi A Kawakita M Ito M Watanabe N Murakami M Kato, Mol Biol Evol 2005 22 2 285 296 10.1093/molbev/msi016 15483320
5. Origin and Evolution of a Circumpolar Polyploid Species Complex in Silene (Caryophyllaceae) Inferred from Low Copy Nuclear RNA Polymerase Introns, rDNA, and Chloroplast DNA. M Popp P Erixon F Eggens B Oxelman, Syst Bot 2005 30 2 302 313 10.1600/0363644054223648
6. Reticulate phylogenetics and phytogeographical structure of Heliosperma (Sileneae, Caryophyllaceae) inferred from chloroplast and nuclear DNA sequences. B Frajman B Oxelman, Mol Phylogenet Evol 2007 43 1 140 155 10.1016/j.ympev. 2006.11.003 17188521
7. Phylogenetic Incongruence: Window into Genome History and Molecular Evolution. JF Wendel JJ Doyle, Molecular systematics of plants II: DNA sequencing New York: Chapman & Hall, Soltis DE, Soltis PS, Doyle JJ, 1998 265 296
8. Relationships between Gene Trees and Species Trees. P Pamilo M Nei, Mol Biol Evol 1988 5 5 568 583 3193878
9. Gene tree distributions under the coalescent process. JH Degnan LA Salter, Evolution 2005 59 1 24 37 15792224
10. Discordance of Species Trees with Their Most Likely Gene Trees. JH Degnan NA Rosenberg, PLoS Genetics 2006 2 5 0762 0768 10.1371/journal.pgen.0020068
11. Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence. LS Kubatko JH Degnan, Syst Biol 2007 56 1 17 24 10.1080/10635150601146041 17366134
12. Reconstructing patterns of reticulate evolution in plants. CR Linder LH Rieseberg, Am J Bot 2004 91 10 1700 1708 18677414 10.3732/ajb.91.10.1700
13. Evolution of a RNA Polymerase Gene Family in Silene Caryophyllaceae) - Incomplete Concerted Evolution and Topological Congruence Among Paralogues. M Popp B Oxelman, Syst Biol 2004 53 6 914 932 10.1080/10635150490888840 15764560
14. Utility of Low-Copy Nuclear Gene Sequences in Plant Phylogenetics. T Sang, Crit Rev Biochem Mol Biol 2002 37 3 121 147 10.1080/10409230290771474 12139440
15. L.A.S. Johnson Review No. 2: Use of nuclear genes for phylogeny reconstruction in plants. RL Small RC Cronn JF Wendel, Austral Syst Bot 2004 17 145 170 10.1071/SB03015
16. The phylogenetic placement of Chondrichthyes: inferences from analysis of multiple genes and implications for comparative studies. A Martin, Genetica 2001 111 349 357 10.1023/A:1013747532647 11841179
17. Concerted Evolution of Repetitive DNA Sequences in Eukaryotes. JF Elder Jr BJ Turner, Q Rev Biol 1995 70 3 297 320 10.1086/419073 7568673
18. Rapid duplication and loss of genes coding for the chains of hemoglobin. EA Zimmer SL Martin SM Beverley YW Kant AC Wilson, Proc Natl Acad Sci USA 1980 77 4 2158 2162 6929543 10.1073/pnas.77.4.2158
19. Orthology, paralogy and proposed classification for paralog subtypes. ELL Sonnhammer EV Koonin, Trends Genet 2002 18 12 619 620 10.1016/S0168-9525(02) 02793-2 12446146
20. Detection of specific sequences among DNA fragments separated by gel electrophoresis. EM Southern, J Mol Biol 1975 98 3 503 517 10.1016/S0022- 2836(75)80083-0 1195397
21. OrthologID: automation of genome-scale ortholog identification within a parsimony framework. JC Chiu EK Lee MG Egan IN Sarkar GM Coruzzi R DeSalle, Bioinformatics (Oxford, England) 2006 22 6 699 707 10.1093/bioinformatics/btk040 16410324
22. Surveys of Gene Families Using Polymerase Chain Reaction: PCR Selection and PCR Drift. A Wagner N Blackstone P Cartwright M Dick B Misof P Snow GP Wagner J Bartels M Murtha J Pendleton, Syst Biol 1994 43 2 250 261 10.2307/2413465
23. Hybrid origins and homoploid reticulate evolution within Heliosperma (Sileneae, Caryophyllaceae) - a multigene phylogenetic approach with relative dating. B Frajman F Eggens B Oxelman, Taxonomy and Reticulate Phylogeny of Heliosperma and Related Genera (Sileneae, Caryophyllaceae). PhD Thesis Uppsala University, Frajman B, 2007
24. SlY1, the first active gene cloned from a plant Y chromosome, encodes a WD-repeat protein. C Delichère J Veuskens M Hernould N Barbacar A Mouras I Negrutiu F Monéger, EMBO J 1999 18 15 4169 4179 10428956 10.1093/emboj/18.15.4169
25. Low variability in a Y-linked plant gene and its implications for Y-chromosome evolution. DA Filatov F Monéger I Negrutiu D Charlesworth, Nature 2000 404 388 390 10.1038/35006057 10746725
26. DNA Diversity in Sex-Linked and Autosomal Genes of the Plant Species Silene latifolia and Silene dioica. DA Filatov V Laporte C Vitte D Charlesworth, Mol Biol Evol 2001 18 1442 1454 11470835
27. A gradual process of recombination restriction in the evolutionary history of the sex chromosomes in dioecious plants. M Nicolas G Marais V Hykelova B Janousek V Laporte B Vyskot D Mouchiroud I Negrutiu D Charlesworth F Monéger, PLoS Biol 2005 3 1 e4 15630476 10.1371/journal.pbio.0030004
28. Substitution Rates in the X- and Y-Linked Genes of the Plants, Silene latifolia and S. dioica. DA Filatov D Charlesworth, Mol Biol Evol 2002 19 6 898 907 12032246
29. Analysis and Evolution of Two Functional Y-Linked Loci in a Plant Sex Chromosome System. I Atanassov C Delichère DA Filatov D Charlesworth I Negrutiu F Monéger, Mol Biol Evol 2001 18 12 2162 2168 11719565
30. Systematics of Euromediterranean Silene (Caryophyllaceae): evidence from a phylogenetic analysis using ITS sequences. C Desfeux B Lejeune, C R Acad Sci III 1996 319 351 358 18383631
31. Generic boundaries in the tribe Sileneae (Caryophyllaceae) as inferred from nuclear rDNA sequences. B Oxelman M Lidén, Taxon 1995 44 525 542 10.2307/1223498
32. A revised generic classification of the tribe Sileneae (Caryophyllaceae). B Oxelman M Lidén RK Rabeler M Popp, Nordic J Bot 2001 20 743 748 10.1111/j.1756-1051.2000.tb00760.x
33. Chloroplast rps16 intron phylogeny of the tribe Sileneae (Caryophyllaceae). B Oxelman M Lidén D Berglund, Pl Syst Evol 1997 206 393 410 10.1007/BF00987959
34. Reticulate or treelike chloroplast DNA evolution in Sileneae (Caryophyllaceae)? P Erixon B Oxelman, Mol Phylogenet Evol 2008 48 313 325 10.1016/j.ympev.2008.04.015 18490181
35. Silene (Caryophyllaceae) in Greece: a subgeneric and sectional classification. W Greuter, Taxon 1995 44 543 581 10.2307/1223499
36. Chloroplast DNA variation in Silene section Elisanthe Demonstrates Silene noctiflora L. is not Properly Classified. JM Sandbrink LJNM Geurts TWJ Gadella J van Brederode, Biochem Syst Ecol 1989 17 7/8 539 549 10.1016/0305-1978(89) 90097-5
37. Recombinant DNA Sequences Generated by PCR Amplification. RD Bradley DA Hillis, Mol Biol Evol 1997 14 5 592 593 9159937
38. Stimulation and suppression of PCR-mediated recombination. MSB Judo AB Wedel C Wilson, Nucleic Acids Res 1998 26 7 1819 1825 9512558 10.1093/nar/26.7.1819
39. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. RK Saiki DH Gelfand S Stoffel SJ Scharf R Higuchi GT Horn KB Mullis HA Erlich, Science 1988 239 4839 487 491 10.1126/science.2448875 2448875
40. Z Yang, Computational Molecular Evolution Oxford: Oxford University Press 2006
41. Horizontal gene transfer in plants. AO Richardson JD Palmer, J Exp Bot 2007 58 1 1 9 17030541 10.1093/jxb/erl148
42. Horizontal Transfer of a Plant Transposon. X Diao M Freeling D Lisch, PLoS Biol 2006 4 1 e5 16336045 10.1371/journal.pbio.0040005
43. The introgression of a functional nuclear gene from Poa to Festuca ovina. L Ghatnekar M Jaarola BO Bengtsson, Proc Roy Soc B 2006 273 395 399 10.1098/rspb.2005.3355
44. Polyploid and Hybrid Evolution in Roses East of the Rocky Mountains. S Joly JR Starr WH Lewis A Bruneau, Am J Bot 2006 93 3 412 425 10.3732/ajb.93.3.412
45. Silene. AO Chater SM Walters JR Akeroyd, Flora Europaea Cambridge: Cambridge University Press, Tutin TG, Burges NA, Chater AO, Edmondson JR, Heywood VH, Moore DM, Valentine DH, Walters SM, Webb, DA, 2 1993 1 191 218
46. Etude de diverses particularités caryotypiques des genres Silene, Lychnis et Melandrium. N Degraeve, Bol Soc Brot Ser 2 1980 53 595 643
47. The Staden Sequence Analysis Package. R Staden, Mol Biotechnol 1996 5 233 241 10.1007/BF02900361 8837029
48. Phred, Phrap, Consed. http://www.phrap.org
49. QuickAlign: a new alignment editor. J Müller K Müller, Plant Molecular Biology Reporter 2003 21 5 10.1007/BF02773390
50. Gaps as characters in sequence-based phylogenetic analyses. MP Simmons H Ochoterena, Syst Biol 2000 49 2 369 381 10.1080/10635159950173889 12118412
51. SeqState - primer design and sequence statistics for phylogenetic DNA data sets. K Müller, Appl Bioinformatics 2005 4 65 69 10.2165/00822942- 200504010-00008 16000015
52. Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm. SL Kosakovsky Pond D Posada MB Gravenor CH Woelk SDW Frost, Mol Biol Evol 2006 23 10 1891 1901 10.1093/molbev/msl051 16818476
53. Datamonkey.org resource for recombination analysis. http://www. datamonkey.org/GARD/
54. BEAST: Bayesian evolutionary analysis by sampling trees. AJ Drummond A Rambaut, BMC Evol Biol 2007 7 214 17996036 10.1186/1471-2148-7-214
55. Relaxed Phylogenetics and Dating with Confidence. AJ Drummond SYW Ho MJ Phillips A Rambaut, PLoS Biol 2006 4 5 e88 16683862 10.1371/journal.pbio.0040088
56. MrModeltest v2. JAA Nylander, http://www.abc.se/∼nylander/
57. Tracer v1.4. A Rambaut AJ Drummond, http://beast.bio.ed.ac.uk/Tracer
58. FigTree. A Rambaut, http://tree.bio.ed.ac.uk/software/figtree/
59. DL Swofford, PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4 Sunderland, Massachusetts: Sinauer Associates 2002
60. 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
61. Index Herbariorum: A global directory of public herbaria and associated staff. PK Holmgren NH Holmgren, New York Botanical Garden's Virtual Herbarium http://sweetgum.nybg.org/ih/
62. Sileneae Database. http://www.sileneae.info
63. Beta mathematics handbook: concepts, theorems, methods, algorithms, formulas, graphs, tables. L Rde B Westergren, Lund: Studentlitteratur; Bromley: Chartwell-Bratt 1990