Rebooting the human mitochondrial phylogeny: An automated and scalable methodology with expert knowledge

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Blanco, Roberto ^a   Mayordomo, Elvira ^a   Montoya, Julio ^a,b   Ruiz Pesini, Eduardo ^a,b,c  

^a UNIVERSITY OF ZARAGOZA   (Spain)

^b CENTRO DE INVESTIGACIÓN BIOMÉDICA EN RED DE ENFERMEDADES RARAS CIBERER   (Spain)

^c Agencia Aragonesa para la Investigación y el Desarrollo   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL COSTS; COMPUTATIONAL PROBLEM; COMPUTATIONAL SCALABILITY; MITOCHONDRIAL DNA; OUTLIER DETECTION; PHYLOGENETIC STUDIES; PHYLOGENETIC TREES; SEQUENCE DATABASE;

ALGORITHMS; BIOLOGY; GENES; SCALABILITY;

AUTOMATION;

MITOCHONDRIAL DNA;

ALGORITHM; ARTICLE; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; HUMAN; METHODOLOGY; MITOCHONDRION; PHYLOGENY; SEQUENCE ALIGNMENT;

ALGORITHMS; DNA, MITOCHONDRIAL; GENETIC VARIATION; HUMANS; MITOCHONDRIA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 79956021026     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-174     Document Type: Article

References (51)

1. Torroni A, Achilli A, Macaulay V, Richards M, Bandelt HJ. Harvesting the fruit of the human mtDNA tree. Trends Genet 2006, 22:339-345. 10.1016/j.tig.2006.04.001, 16678300.
2. Cann RL, Stoneking M, Wilson AC. Mitochondrial DNA and human evolution. Nature 1987, 325:31-36. 10.1038/325031a0, 3025745.
3. Ruiz-Pesini E, Mishmar D, Brandon M, Procaccio V, Wallace DC. Effects of purifying and adaptive selection on regional variation in human mtDNA. Science 2004, 303:223-226. 10.1126/science.1088434, 14716012.
4. Wallace DC. A mitochondrial paradigm of metabolic and degenerative diseases, aging, and cancer: a dawn for evolutionary medicine. Annu Rev Genet 2005, 39:359-407. 10.1146/annurev.genet.39.110304.095751, 2821041, 16285865.
5. Cavalli-Sforza LL. The Human Genome Diversity Project: past, present and future. Nat Rev Genet 2005, 6:333-340.
6. Ruiz-Pesini E, Lott MT, Procaccio V, Poole JC, Brandon MC, Mishmar D, Yi C, Kreuziger J, Baldi P, Wallace DC. An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res 2007, 35:D823-D828. 10.1093/nar/gkl927, 1781213, 17178747.
7. Blanco R, Mayordomo E. ZARAMIT: a system for the evolutionary study of human mitochondrial DNA. Lect Notes Comput Sci 2009, 5518:1139-1142.
8. van Oven M, Kayser M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 2008, 29:E386-E394.
9. Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, Salas A, Oppenheimer S, Macaulay V, Richards MB. Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet 2009, 84:740-759. 10.1016/j.ajhg.2009.05.001, 2694979, 19500773.
10. Gasparre G, Porcelli AM, Bonora E, Pennisi LF, Toller M, Iommarini L, Ghelli A, Moretti M, Betts CM, Martinelli GN, Ceroni AR, Curcio F, Carelli V, Rugolo M, Tallini G, Romeo G. Disruptive mitochondrial DNA mutations in complex I subunits are markers of oncocytic phenotype in thyroid tumors. Proc Natl Acad Sci USA 2007, 104:9001-9006. 10.1073/pnas.0703056104, 1885617, 17517629.
11. Bi R, Zhang AM, Zhang W, Kong QP, Wu BL, Yang XH, Wang D, Zou Y, Zhang YP, Yao YG. The acquisition of an inheritable 50-bp deletion in the human mtDNA control region does not affect the mtDNA copy number in peripheral blood cells. Hum Mutat 2010, 31:538-543.
12. Behar DM, Blue-Smith J, Soria-Hernanz DF, Tzur S, Hadid Y, Bormans C, Moen A, Tyler-Smith C, Quintana-Murci L, Wells RS, . Genographic Consortium A novel 154-bp deletion in the human mitochondrial DNA control region in healthy individuals. Hum Mutat 2008, 29:1387-1391. 10.1002/humu.20835, 2697596, 18629826, Genographic Consortium.
13. Rajkumar R, Banerjee J, Gunturi HB, Trivedi R, Kashyap VK. Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages. BMC Evol Biol 2005, 5:26. 10.1186/1471-2148-5-26, 1079809, 15804362.
14. Arnason U, Gullberg A, Janke A, Kullberg M. Mitogenomic analyses of caniform relationships. Mol Phylogenet Evol 2007, 45:863-874. 10.1016/j.ympev.2007.06.019, 17919938.
15. Family Tree DNA. , http://www.familytreedna.com/
16. Abu-Amero KK, Larruga JM, Cabrera VM, González AM. Mitochondrial DNA structure in the Arabian Peninsula. BMC Evol Biol 2008, 8:45. 10.1186/1471-2148-8-45, 2268671, 18269758.
17. Yao YG, Kong QP, Salas A, Bandelt HJ. Pseudomitochondrial genome haunts disease studies. J Med Genet 2008, 45:769-772. 10.1136/jmg.2008.059782, 18611982.
18. Fornarino S, Pala M, Battaglia V, Maranta R, Achilli A, Modiano G, Torroni A, Semino O, Santachiara-Benerecetti SA. Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation. BMC Evol Biol 2009, 9:154. 10.1186/1471-2148-9-154, 2720951, 19573232.
19. Malhi RS, Cybulski JS, Tito RY, Johnson J, Harry H, Dan C. Brief communication: mitochondrial haplotype C4c confirmed as a founding genome in the Americas. Am J Phys Anthropol 2010, 141:494-497.
20. Gunnarsdóttir ED, Li M, Bauchet M, Finstermeier K, Stoneking M. High-throughput sequencing of complete human mtDNA genomes from the Philippines. Genome Res 2011, 21:1-11. 10.1101/gr.107615.110, 21147912.
21. Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PLF, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano HA, Ronan M, Rothberg JM, Egholm M, Rudan P, Brajković D, Kućan T, Gušić I, Wikström M, Laakkonen L, Kelso J, Slatkin M, Pääbo S. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 2008, 134:416-426. 10.1016/j.cell.2008.06.021, 2602844, 18692465.
22. Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajković D, Kućan T, Gušić I, Schmitz R, Doronichev VB, Golovanova LV, de la Rasilla M, Fortea J, Rosas A, Pääbo S. Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 2009, 325:318-321. 10.1126/science.1174462, 19608918.
23. Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, Pääbo S. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 2010, 464:894-897. 10.1038/nature08976, 20336068.
24. Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PLF, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, Pääbo S. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 2010, 468:1053-1060. 10.1038/nature09710, 21179161.
25. Simplified mtDNA lineages. , http://www.mitomap.org/pub/MITOMAP/MitomapFigures/simple-tree-mitomap2009.pdf
26. Blanco R, Mayordomo E, Montes E, Mayo R, Alberto A. Scalable phylogenetics through input preprocessing. Adv Soft Comp 2010, 74:123-130.
27. Gusfield D. Efficient algorithms for inferring evolutionary trees. Networks 1991, 21:19-28.
28. Blanco R. Structural parsimony: reductions in sequence space. Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine 2010, 57-61.
29. Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48:443-453. 10.1016/0022-2836(70)90057-4, 5420325.
30. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol 1981, 147:195-197. 10.1016/0022-2836(81)90087-5, 7265238.
31. Blanco R, de Miguel Casado G, Requeno JI, Colom JM. Temporal logics for phylogenetic analysis via model checking. Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops 2010, 152-157.
32. Han MV, Zmasek CM. phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 2009, 10:356. 10.1186/1471-2105-10-356, 2774328, 19860910.
33. Posada D, Crandall KA. Selecting the best-fit model of nucleotide substitution. Syst Biol 2001, 50:580-601.
34. Attimonelli M, Accetturo M, Santamaria M, Lascaro D, Scioscia G, Pappadà G, Russo L, Zanchetta L, Tommaseo-Ponzetta M. HmtDB, a human mitochondrial genomic resource based on variability studies supporting population genetics and biomedical research. BMC Bioinformatics 2005, 6(Suppl 4):S4. 10.1186/1471-2105-6-S4-S4, 1866381, 16351753.
35. ZARAMIT project website. , http://www.zaramit.org/
36. Zmasek CM, Eddy SR. ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics 2001, 17:383-384. 10.1093/bioinformatics/17.4.383, 11301314.
37. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Research 2011, 39:D32-D37. 10.1093/nar/gkq1079, 3013681, 21071399.
38. Pereira L, Freitas F, Fernandes V, Pereira JB, Costa MD, Costa S, Máximo V, Macaulay V, Rocha R, Samuels DC. The diversity present in 5140 human mitochondrial genomes. Am J Hum Genet 2009, 84:628-640. 10.1016/j.ajhg.2009.04.013, 2681004, 19426953.
39. Wang L, Jiang T. On the complexity of multiple sequence alignment. J Comput Biol 1994, 1:337-348. 10.1089/cmb.1994.1.337, 8790475.
40. Bonizzoni P, Della Vedova G. The complexity of multiple sequence alignment with SP-score that is a metric. Theor Comput Sci 2001, 259:63-79.
41. Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG. Sequence and organization of the human mitochondrial genome. Nature 1981, 290:457-465. 10.1038/290457a0, 7219534.
42. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 1999, 23:147. 10.1038/13779, 10508508.
43. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
44. Foulds LR, Graham RL. The Steiner problem in phylogeny is NP-complete. Adv Appl Math 1982, 3:43-49.
45. Day WHE. Computational complexity of inferring phylogenies from dissimilarity matrices. Bull Math Biol 1987, 49:461-467.
46. Posada D. jModelTest: phylogenetic model averaging. Mol Biol Evol 2008, 25:1253-1256. 10.1093/molbev/msn083, 18397919.
47. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
48. Hillis DM, Bull JJ. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol 1993, 42:182-192.
49. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690. 10.1093/bioinformatics/btl446, 16928733.
50. Stamatakis A. Phylogenetic models of rate heterogeneity: a high performance computing perspective. Proceedings of the 20th IEEE International Parallel & Distributed Processing Symposium 2006, 278.
51. Maddison WP. Reconstructing character evolution on polytomous cladograms. Cladistics 1989, 5:365-377.