Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer

BMC Evolutionary Biology

Volumn 11, Issue 1, 2011, Pages

  Stiller, John W ^a  

^a EAST CAROLINA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRYPSIS; DATA SET; ENDOSYMBIONT; EUKARYOTE; EVOLUTIONARY BIOLOGY; EXPERIMENTAL DESIGN; GENETIC ANALYSIS; GENOMICS; HYPOTHESIS TESTING; PHYLOGENETICS; PHYLOGENY; STATISTICAL ANALYSIS;

EUKARYOTA;

ARTICLE; BIOLOGICAL MODEL; BIOLOGY; GENETICS; GENOME; GENOMICS; HORIZONTAL GENE TRANSFER; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; SYMBIOSIS;

COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENOME; GENOMICS; MODELS, GENETIC; PHYLOGENY; SYMBIOSIS;

EID: 80052858002     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-259     Document Type: Article

References (63)

1. Chromalveolates and the Evolution of Plastids by Secondary Endosymbiosis. Keeling PJ, J Euk Microbiol 2009 56 1 1 8 10.1111/j.1550-7408.2008.00371.x 19335769
2. The origin of plastids. Howe CJ, Barbrook AC, Nisbet RER, Lockhart PJ, Larkum AWD, Phil Trans Royal So B-Biol Sci 2008 363 1504 2675 2685 10.1098/rstb.2008.0050 (Pubitemid 351989765)
3. Plastid endosymbiosis, genome evolution and the origin of green plants. Stiller JW, Trends Plant Sci 2007 12 9 391 396 10.1016/j.tplants.2007.08.002 17698402 (Pubitemid 47362793)
4. Chromalveolate plastids: direct descent or multiple endosymbioses? Bodyl A, Stiller JW, Mackiewicz P, Trends Ecol Evol 2009 24 3 119 121 10.1016/j.tree.2008.11.003 19200617
5. Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes. Nozaki H, Maruyama S, Matsuzaki M, Nakada T, Kato S, Misawa K, Mol Phyl Evol 2009 53 3 872 880 10.1016/j.ympev.2009.08.015
6. The Puzzle of Plastid Evolution. Archibald JM, Curr Biol 2009 19 2 81 R88 10.1016/j.cub.2008.11.067 19174147
7. A hypothesis for plastid evolution in chromalveolates. Sanchez-Puerta MV, Delwiche CF, J Phycol 2008 44 5 1097 1107 10.1111/j.1529-8817.2008.00559.x
8. Shopping for plastids. Larkum AWD, Lockhart PJ, Howe CJ, Trends Plant Sci 2007 12 5 189 195 10.1016/j.tplants.2007.03.011 17416546 (Pubitemid 46710472)
9. A plastid in the making: Evidence for a second primary endosymbiosis. Marin B, Nowack ECM, Melkonian M, Protist 2005 156 4 425 432 10.1016/j.protis.2005.09.001 16310747 (Pubitemid 41682020)
10. Chromatophore genome sequence of Paulinella sheds light on acquisition of photosynthesis by eukaryotes. Nowack ECM, Melkonian M, Glockner G, Curr Biol 2008 18 6 410 418 10.1016/j.cub.2008.02.051 18356055
11. The origin of plastids and their spread via secondary symbiosis. Delwiche CF, Palmer JD, Plant Syst Evol 1997 53 86
12. Plastid evolution. Gould SB, Waller RR, McFadden GI, Ann Review Plant Biol 2008 59 491 517 10.1146/annurev.arplant.59.032607.092915 (Pubitemid 351813040)
13. The symbiotic birth and spread of plastids: How many times and whodunit? Palmer JD, J Phycol 2003 39 1 4 11 10.1046/j.1529-8817.2003.02185.x (Pubitemid 36229963)
14. Principles of protein and lipid targeting in secondary symbiogenesis: Euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. Cavalier-Smith T, J Euk Microbiol 1999 46 4 347 366 10.1111/j.1550-7408.1999.tb04614.x 18092388 (Pubitemid 29395704)
15. A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. Janouskovec J, Horak A, Obornik M, Lukes J, Keeling PJ, Proc Natl Acad Sci USA 2010 107 24 10949 10954 10.1073/pnas.1003335107 20534454
16. Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms. Moustafa A, Beszteri B, Maier UG, Bowler C, Valentin K, Bhattacharya D, Science 2009 324 5935 1724 1726 10.1126/science.1172983 19556510
17. Serial replacement of a diatom endosymbiont in the marine dinoflagellate Peridinium quinquecorne (Peridiniales, Dinophyceae). Horiguchi T, Takano Y, Phycol Res 2006 54 3 193 200 10.1111/j.1440-1835.2006.00426.x (Pubitemid 44400914)
18. Serial replacement of diatom endosymbionts in two freshwater dinoflagenates, Peridiniopsis spp. (Peridiniales, Dinophyceae). Takano Y, Hansen G, Fujita D, Horiguchi T, Phycologia 2008 47 1 41 53 10.2216/07-36.1 (Pubitemid 351160079)
19. Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids. Maruyama S, Suzaki T, Weber APM, Archibald JM, Nozaki H, BMC Evol Biol 2011 11 11 10.1186/1471-2148-11-11 21226948
20. Dinoflagellate nuclear SSU rRNA phylogeny suggests multiple plastid losses and replacements. Saldarriaga JF, Taylor FJR, Keeling PJ, Cavalier-Smith T, J Mol Evol 2001 53 3 204 213 10.1007/s002390010210 11523007 (Pubitemid 32783795)
21. Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Huang J, Gogarten JP, Genome Biol 2007 8 6 99 10.1186/gb-2007-8-6-r99 17547748 (Pubitemid 351903180)
22. The eukaryotic tree of life: endosymbiosis takes its TOL. Lane CE, Archibald JM, Trends Ecol Evol 2008 23 5 268 275 10.1016/j.tree.2008.02.004 18378040 (Pubitemid 351626208)
23. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D, Proc Natl Acad Sci USA 2002 99 19 12246 12251 10.1073/pnas.182432999 12218172
24. Cyanobacterial contribution to algal nuclear genomes a primarily limited to plastid functions. Reyes-Prieto A, Hackett JD, Soares MB, Bonaldo MF, Bhattacharya D, Curr Biol 2006 16 23 2320 2325 10.1016/j.cub.2006.09.063 17141613 (Pubitemid 44821835)
25. Sizing up the genomic footprint of endosymbiosis. Elias M, Archibald JM, Bioessays 2009 31 12 1273 1279 10.1002/bies.200900117 19921698
26. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Tyler BM, Tripathy S, Zhang XM, Dehal P, Jiang RHY, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, et al. Science 2006 313 5791 1261 1266 10.1126/science.1128796 16946064 (Pubitemid 44330944)
27. Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic. Reyes-Prieto A, Moustafa A, Bhattacharya D, Curr Biol 2008 18 13 956 962 10.1016/j.cub.2008.05.042 18595706
28. PhyloGena-a user-friendly system for automated phylogenetic annotation of unknown sequences. Hanekamp K, Bohnebeck U, Beszteri B, Valentin K, Bioinformatics 2007 23 7 793 801 10.1093/bioinformatics/btm016 17332025 (Pubitemid 47049912)
29. PhyloGenie: automated phylome generation and analysis. Frickey T, Lupas AN, Nucl Acids Res 2004 32 17 5231 5238 10.1093/nar/gkh867 15459293 (Pubitemid 39445511)
30. Phylogenomics. Philippe H, Delsuc F, Brinkmann H, Lartillot N, Ann Rev Ecol Evol Syst 2005 36 541 562 10.1146/annurev.ecolsys.35.112202.130205 (Pubitemid 43068870)
31. A review of long-branch attraction. Bergsten J, Cladistics 2005 21 2 163 193 10.1111/j.1096-0031.2005.00059.x (Pubitemid 40817232)
32. Phylogenetic inference using whole Genomes. Ranala B, Yang ZH, Ann Rev Genom Human Genet 2008 9 217 231 10.1146/annurev.genom.9.081307.164407
33. Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Rodriguez-Ezpeleta N, Brinkmann H, Burey SC, Roure B, Burger G, Loffelhardt W, Bohnert HJ, Philippe H, Lang BF, Curr Biol 2005 15 14 1325 1330 10.1016/j.cub.2005.06.040 16051178 (Pubitemid 41026601)
34. Red and Green Algal Monophyly and Extensive Gene Sharing Found in a Rich Repertoire of Red Algal Genes. Chan CX, Yang EC, Banerjee T, Yoon HS, Martone PT, Estevez JM, Bhattacharya D, Curr Biol 2011 21 4 328 333 10.1016/j.cub.2011. 01.037 21315598
35. Broadly sampled multigene trees of eukaryotes. Yoon HS, Grant J, Tekle YI, Wu M, Chaon BC, Cole JC, Logsdon JM, Patterson DJ, Bhattacharya D, Katz LA, BMC Evol Biol 2008 8 14 10.1186/1471-2148-8-14 18205932 (Pubitemid 351294825)
36. The origin of red algae: Implications for plastid evolution. Stiller JW, Hall BD, Proc Natl Acad Sci USA 1997 94 9 4520 4525 10.1073/pnas.94.9.4520 9114022 (Pubitemid 27194274)
37. Plastid Origin and Evolution: New Models Provide Insights into Old Problems. Chan CX, Gross J, Yoon HS, Bhattacharya D, Plant Physiol 2011 155 4 1552 1560 10.1104/pp.111.173500 21343425
38. Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes. Burki F, Shalchian-Tabrizi K, Pawlowski J, Biol Lett 2008 4 4 366 369 10.1098/rsbl.2008.0224 18522922 (Pubitemid 351961461)
39. Do plastid-related characters support the chromalveolate hypothesis? Bodyl A, J Phycol 2005 41 3 712 719 10.1111/j.1529-8817.2005.00091.x (Pubitemid 40832026)
40. Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates. Burki F, Inagaki Y, Brate J, Archibald JM, Keeling PJ, Cavalier-Smith T, Sakaguchi M, Hashimoto T, Horak A, Kumar S, et al. Genome Biol Evol 2009 231 238
41. Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Patron NJ, Inagaki Y, Keeling PJ, Curr Biol 2007 17 10 887 891 10.1016/j.cub.2007.03.069 17462896 (Pubitemid 46702668)
42. Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes and stramenopiles. Baurain D, Brinkmann H, Petersen J, Rodriguez-Ezpeleta N, Stechmann A, Demoulin V, Roger AJ, Burger G, Lang BF, Philippe H, Mol Biol Evol 2010 27 7 1698 1709 10.1093/molbev/msq059 20194427
43. Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses? Stiller JW, Huang JL, Ding Q, Tian J, Goodwillie C, BMC Genomics 2009 10 484 10.1186/1471-2164-10-484 19843329
44. Phylogeny of Primary Photosynthetic Eukaryotes as Deduced from Slowly Evolving Nuclear Genes. Nozaki H, Iseki M, Hasegawa M, Misawa K, Nakada T, Sasaki N, Watanabe M, Mol Biol Evol 2007 24 8 1592 1595 10.1093/molbev/msm091 17488739 (Pubitemid 47236691)
45. Heterotachy and tree building: A case study with plastids and eubacteria. Lockhart P, Novis P, Milligan BG, Riden J, Rambaut A, Larkum T, Mol Biol Evol 2006 23 1 40 45 16151191 (Pubitemid 41785951)
46. Algal Genes in the Closest Relatives of Animals. Sun GL, Yang ZF, Ishwar A, Huang JL, Mol Biol Evol 2010 27 12 2879 2889 10.1093/molbev/msq175 20627874
47. Testing congruence in phylogenomic analysis. Leigh JW, Susko E, Baumgartner M, Roger AJ, Syst Biol 2008 57 1 104 115 10.1080/10635150801910436 18288620
48. Cases in which parsimony or compatibility methods will be positively misleading. Felsenstein J, Syst Zool 1978 25 401 410
49. Signatures of Ecological Resource Availability in the Animal and Plant Proteomes. Elser JJ, Fagan WF, Subramanian S, Kumar S, Mol Biol Evol 2006 23 10 1946 1951 10.1093/molbev/msl068 16870683 (Pubitemid 44412881)
50. Causes and evolutionary significance of genetic convergence. Christin PA, Weinreich DM, Besnard G, Trends Genet 2010 26 9 400 405 10.1016/j.tig.2010.06. 005 20685006
51. The prokaryotic tree of life: past, present. and future? McInerney JO, Cotton JA, Pisani D, Trends Ecol Evol 2008 23 5 276 281 10.1016/j.tree.2008.01. 008 18367290 (Pubitemid 351626203)
52. Long-branch attraction and the rDNA model of early eukaryotic evolution. Stiller JW, Hall BD, Mol Biol Evol 1999 16 9 1270 1279 10939894 (Pubitemid 29409871)
53. Microsporidia are related to Fungi: Evidence from the largest subunit of RNA polymerase II and other proteins. Hirt RP, Logsdon JM, Healy B, Dorey MW, Doolittle WF, Embley TM, Proc Natl Acad Sci USA 1999 96 2 580 585 10.1073/pnas.96.2.580 9892676 (Pubitemid 29061251)
54. Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions. Philippe H, Lopez P, Brinkmann H, Budin K, Germot A, Laurent J, Moreira D, Muller M, Le Guyader H, Proc Biol Sci 2000 267 1449 1213 1221 10.1098/rspb.2000.1130 10902687 (Pubitemid 30438420)
55. Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites. Gruenheit N, Lockhart PJ, Steel M, Martin W, Mol Biol Evol 2008 25 7 1512 1520 10.1093/molbev/msn098 18424773 (Pubitemid 351882028)
56. Heterotachy processes in rhodophyte-derived secondhand plastid genes: Implications for addressing the origin and evolution of dinoflagellate plastids. Shalchian-Tabrizi K, Skanseng M, Ronquist F, Klaveness D, Bachvaroff TR, Delwiche CF, Botnen A, Tengs T, Jakobsen KS, Mol Biol Evol 2006 23 8 1504 1515 10.1093/molbev/msl011 16699169 (Pubitemid 44297409)
57. Mathematical elegance with biochemical realism: The covarion model of molecular evolution. Penny D, McComish BJ, Charleston MA, Hendy MD, J Mol Evol 2001 53 6 711 723 10.1007/s002390010258 11677631 (Pubitemid 32989425)
58. Bayesian estimation of concordance among gene trees. Ane C, Larget B, Baum DA, Smith SD, Rokas A, Mol Biol Evol 2007 24 2 412 426 17095535 (Pubitemid 46204374)
59. The Gene Evolution Model and Computing Its Associated Probabilities. Arvestad L, Lagergren J, Sennblad B, J Acm 2009 56 2 44
60. A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer. Csuros M, Miklos I, Res Comp Mol Biol Proc 2006 3909 206 220 10.1007/11732990-18 (Pubitemid 44019157)
61. A Survey of Combinatorial Methods for Phylogenetic Networks. Huson DH, Scornavacca C, Genome Biol Evol 2011 3 23 35 10.1093/gbe/evq077 21081312
62. Biases in phylogenetic estimation can be caused by random sequence segments. Susko E, Spencer M, Roger AJ, J Mol Evol 2005 61 3 351 359 10.1007/s00239-004-0352-9 16044245 (Pubitemid 41355860)
63. Horizontal gene transfer in eukaryotic evolution. Keeling PJ, Palmer JD, Nat Rev Genet 2008 9 8 605 618 10.1038/nrg2386 18591983