Exploring contradictory phylogenetic relationships in yeasts

FEMS Yeast Research

Volumn 8, Issue 4, 2008, Pages 641-650

  Wu, Qiong ^a   James, Steve A ^b   Roberts, Ian N ^b   Moulton, Vincent ^a   Huber, Katharina T ^a  

^a UNIVERSITY OF EAST ANGLIA   (United Kingdom)

^b INSTITUTE OF FOOD RESEARCH   (United Kingdom)

Author keywords

Consensus network; Multigene analysis; Neighbor Net; Phylogenetic network; Yeast taxonomy

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA HYBRIDIZATION; GENE SEQUENCE; MITOCHONDRIAL GENE; MULTIGENE FAMILY; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; SACCHAROMYCES; TAXONOMY; YEAST;

DNA, FUNGAL; DNA, MITOCHONDRIAL; GENES, FUNGAL; PHYLOGENY; SACCHAROMYCETALES;

SACCHAROMYCETACEAE;

EID: 43549124170     PISSN: 15671356     EISSN: 15671364     Source Type: Journal    
DOI: 10.1111/j.1567-1364.2008.00362.x     Document Type: Article

References (48)

1. Bandelt HJ Dress (1992) A canonical decomposition theory for metrics on a finite set. Adv Math 92 : 47 105.
2. Barnett JA, Payne RW Yarrow D (2000) Yeasts: Characteristics and Identification, 3rd edn, pp. 1 5. Cambridge University Press, Cambridge, UK.
3. Boekhout T, Theelen B, Diaz M, Fell JW, Hop WCJ, Abeln ECA, Dromer F Meyer W (2001) Hybrid genotypes in the pathogenic yeast Cryptococcus neoformans. Microbiology 147 : 891 907.
4. Børsting C, Hummel R, Schultz ER, Rose TM, Pedersen MB, Knudsen J Kristiansen K (1997) Saccharomyces carlsbergensis contains two functional genes encoding the acyl-CoA-binding protein, one similar to the ACB1 gene from S. cerevisiae and one identical to the ACB1 gene from S. monacensis. Yeast 13 : 1409 1421.
5. Bovers M, Hagen F, Kuramae EE, Diaz MR, Spanjaard L, Dromer F, Hoogveld HL Boekhout T (2006) Unique hybrids between the fungal pathogens Cryptococcus neoformans and Cryptococcus gattii. FEMS Yeast Res 6 : 599 607.
6. Bryant D Moulton V (2004) Neighbor-Net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 21 : 255 265.
7. Buneman P (1971) The recovery of trees from measures of dissimilarity. Mathematics in the Archaeological and Historical Sciences (Hodson FR, Kendall DG Tautu PT, eds), pp. 387 395. Edinburgh University Press, Edinburgh, UK.
8. Cai J, Roberts IN Collins MD (1996) Phylogenetic relationships among members of the ascomycetous yeast genera Brettanomyces, Debaryomyces, Dekkera, and Kluyveromyces deduced by small-subunit rRNA gene sequences. Int J Syst Bacteriol 46 : 542 549.
9. Casaregola S, Nguyen HV, Lapathitis G, Kotyk A Gaillardin C (2001) Analysis of the constitution of the beer yeast genome by PCR, sequencing and subtelomeric sequence hybridization. Int J Syst Evol Microbiol 51 : 1607 1618.
10. de Barros Lopes M, Bellon JR, Shirley NJ Ganter PF (2002) Evidence for multiple interspecific hybridization in Saccharomyces sensu stricto species. FEMS Yeast Res 1 : 323 331.
11. Demain AL, Phaff HJ Kurtzman CP (1998) The industrial and agricultural significance of yeasts. The Yeasts, A Taxonomic Study, 4th edn (Kurtzman CP Fell JW, eds), pp. 13 19. Elsevier, Amsterdam, the Netherlands.
12. Dohm JC, Vingron M Staub E (2006) Horizontal gene transfer in aminoactyl-tRNA synthase including leucine-specific subtypes. J Mol Evol 63 : 437 447.
13. Dujon B (2006) Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution. Trends Genet 22 : 375 387.
14. Dutilh BE, van Noort V, van der Heijden RTJM, Boekhout T, Snel B Huynen MA (2007) Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinformatics 23 : 815 824.
15. Fell JW, Boekhout T, Fonseca A, Scorzetti G Statzell-Tallman A (2000) Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis. Int J Syst Evol Microbiol 50 : 1351 1371.
16. Fitzpatrick DA, Creevey CJ McInerney JO (2006a) Genome phylogenies indicate a meaningful α-proteobacterial phylogeny and support a grouping of the mitochondria with the rickettsiales. Mol Biol Evol 23 : 74 85.
17. Fitzpatrick DA, Logue ME, Stajich EJ Butler G (2006b) A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol 6 : 99.
18. Fleet GH (1990) Food spoilage yeasts. Yeast Technology (Spencer JFT Spencer DM, eds), pp. 124 166. Springer, Berlin, Germany.
19. Fundyga RE, Kuykendall RJ, Lee-Yang W Lott TJ (2004) Evidence for aneuploidy and recombination in the human commensal yeast Candida parapsilosis. Infect Genet Evol 4 : 37 43.
20. Goffeau A (1997) The yeast genome directory. Nature 387 : 5 6.
21. González SS, Barrio E, Gafner J Querol A (2006) Natural hybrids from Saccharomyces cerevisiae, Saccharomyces bayanus and Saccharomyces kudriavzevii in wine fermentations. FEMS Yeast Res 6 : 1221 1234.
22. Groth C, Hansen J Piskur J (1999) A natural chimeric yeast containing genetic material from three species. Int J Syst Bacteriol 49 : 1933 1938.
23. Holland BR Moulton V (2003) Consensus network: a method for visualising incompatibilities in collections of trees. WABI 2003 Lecture notes Bioinform 2812 : 165 176.
24. Holland BR, Huber KT, Moulton V Lockhart PJ (2004) Using consensus networks to visualize contradictory evidence for species phylogeny. Mol Biol Evol 21 : 1459 1461.
25. Holland BR, Jermiin LS Moulton V (2006) Improved consensus network techniques for genome-scale phylogeny. Mol Biol Evol 23 : 848 855.
26. Huber KT Moulton V (2005) Phylogenetic networks. Mathematics of Evolution and Phylogeny (Gascuel O, ed), pp. 178 200. Oxford University Press, Oxford, UK.
27. Huson DH Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23 : 254 267.
28. James SA, Collins MD Roberts IN (1994) Genetic interrelationships among species of the genus Zygosaccharomyces as revealed by small-subunit rRNA gene sequences. Yeast 10 : 871 881.
29. James SA, Cai J, Roberts IN Collins MD (1997) A phylogenetic analysis of the genus Saccharomyces based on 18S rRNA gene sequences: description of Saccharomyces kunashirensis sp. nov. and Saccharomyces martiniae sp. nov. Int J Syst Bacteriol 47 : 453 460.
30. James SA, Bond CJ, Stratford M Roberts IN (2005) Molecular evidence for the existence of natural hybrids in the genus Zygosaccharomyces. FEMS Yeast Res 5 : 747 755.
31. Kellis M, Patterson N, Endrizzi M, Birren B Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423 : 241 254.
32. Kuramae EE, Robert V, Snel B Boekhout T (2006) Conflicting phylogenetic position of Schizosaccharomyces pombe. Genomics 88 : 387 393.
33. Kurtzman CP (2003) Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora. FEMS Yeast Res 4 : 233 245.
34. Kurtzman CP Robnett CJ (1994) Synonymy of the yeast genera Wingea and Debaryomyces. Antonie van Leeuwenhoek 66 : 337 342.
35. Kurtzman CP Robnett CJ (1998) Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large-subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek 73 : 331 371.
36. Kurtzman CP Robnett CJ (2003) Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses. FEMS Yeast Res 3 : 417 432.
37. Kurtzman CP, Albertyn J Basehoar-Powers E (2007) Multigene phylogenetic analysis of the Lipomycetaceae and the proposed transfer of Zygozyma species to Lipomyces and Babjevia anomala to Dipodascopsis. FEMS Yeast Res 7 : 1027 1034.
38. Le Jeune C, Lollier M, Demuyter C, Erny C, Legras J-L, Aigle M Masneuf-Pomarède I (2007) Characterization of natural hybrids of Saccharomyces cerevisiae and Saccharomyces bayanus var. uvarum. FEMS Yeast Res 7 : 540 549.
39. Liti G, Peruffo A, James SA, Roberts IN Louis EJ (2005) Inferences of evolutionary relationships from a population survey of LTR-retrotransposons and telomeric-associated sequences in the Saccharomyces sensu stricto complex. Yeast 22 : 177 192.
40. Margush T McMorris FR (1981) Consensus n-trees. B Math Biol 43 : 239 244.
41. Marinoni G Lachance M-A (2004) Speciation in the large-spored Metschnikowia clade and establishment of a new species, Metschnikowia borealis comb. nov. FEMS Yeast Res 4 : 587 596.
42. Martin W, Deusch O, Stawski N, Grünheit N Goremykin V (2005) Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution. Trends Plant Sci 10 : 203 209.
43. Masneuf I, Hansen J, Groth C, Piskur J Dubourdieu D (1998) New hybrids between Saccharomyces sensu stricto yeast species found among wine and cider production strains. Appl Environ Microbiol 64 : 3887 3892.
44. Morrison DA (2005) Networks in phylogenetic analysis: new tools for population biology. Int J Parasitol 35 : 567 582.
45. Nguyen H.-V, Lepingle A Gaillardin C (2000) Molecular typing demonstrates homogeneity of Saccharomyces uvarum strains and reveals the existence of hybrids between S. uvarum and S. cerevisiae, including the S. bayanus type strain CBS 380. Syst Appl Microbiol 23 : 71 85.
46. Rokas A, Williams BL, King N Carroll SB (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425 : 798 804.
47. Saitou N Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 : 406 425.
48. Woolfit M, Rozpdowska E, Piskur J Wolfe KH (2007) Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis. Eukaryotic Cell 6 : 721 733.