A randomisation test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree

Rodrigo, Allen G.; Kelly‐Borges, Michelle; Bergquist, Patricia R.; Bergquist, Peter L.

doi:10.1080/0028825x.1993.10419503

Cited by 118 publications

(107 citation statements)

References 18 publications

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“…However, as other authors have argued (31,34), evolutionary trees estimated from a single gene should be treated with caution. The degree to which lateral transfer of genetic material has occurred and the effects of ancestral polymorphism and selection cannot be readily estimated.…”

Section: Resultsmentioning

confidence: 99%

Phylogeny of Twenty Thermus Isolates Constructed from 16S rRNA Gene Sequence Data

Saul

Rodrigo

Reeves

et al. 1993

International Journal of Systematic Bacteriology

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The sequences of the 16s rRNA genes of 20 lltermus isolates were determined to a high fidelity by using automated DNA sequencing and fluorescent-dye-labelled primers. The strains tested included members of the three validly named Thennus species and representatives of major taxonomic clusters defined previously for this genus. The parsimony method was used to reconstruct the phylogeny of the strains from the aligned sequences, and a bootstrap analysis revealed a number of well-supported clades. Our results are not consistent with groupings inferred from numerical taxonomy data but support the conjecture that the genus Thennus contains more species than the three currently recognized species.Since the original description of the genus Thermus by Brock and Freeze (4), the ubiquitous nature of members of this taxon has been demonstrated by the ready isolation of strains from neutral-pH thermal areas around the world (reviewed in reference 48). The genus Thermus represents a deep eubacterial branch (16) and contains three validly named species: Thermus aquaticus (4), Thermus ruber (26), and Thermus filiformis (20). Many other Thermus isolates have been described in some detail but have not yet been validly named; the taxonomy of the genus is still incomplete. While there is general agreement that T. ruber and T. aquaticus are taxonomically and phylogenetically distinct (17), it is still unclear whether the yellow-pigmented isolates that grow at 70°C constitute a single species or more than one species. In a numerical taxonomic study Hudson et al. (21) discerned eight species groups which were separated at a simple matching coefficient value of 65%, while Williams (47) suggested that there are at least four genospecies on the basis of DNA-DNA hybridization data and other properties. In both cases there were strong indications that strains isolated from the same thermal region shared common properties and grouped together. A comparison of results is difficult because different strains have been used in different studies.In this study the sequences of the 16s rRNA genes of 20 Thermus strains were determined by using a procedure developed specifically to provide high-fidelity data with an automated DNA sequencer, and the aligned sequences were subjected to phylogenetic analysis. The complete 16s rRNA gene sequence of "Thermus thermophilus" HB8 (29) and a partial sequence of T. aquaticus (45) were available from other sources, but the results described below were derived from our own sequence versions. The 20 strains included representatives of the major clusters defined in the study of Hudson et al. (21) and the three validly named species, as well as two "T. thermophilus" strains (HB8 and HB27) and '' Thermus flavus . "Phylogenetic systematics is a two-stage process. The first stage is the estimation of a phylogenetic tree, and for this we used aligned sequence data and reconstructed the phylogeny by using the criterion of maximum parsimony (44). The * Corresponding author. second stage is the translation of the phyl...

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Section: Resultsmentioning

confidence: 99%

Phylogeny of Twenty Thermus Isolates Constructed from 16S rRNA Gene Sequence Data

Saul

Rodrigo

Reeves

et al. 1993

International Journal of Systematic Bacteriology

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“…This use of consensus analysis is inappropriate for two reasons (Mirkin et al, 1995): first, consensus methods cannot accommodate differing sets of terminal entities (Page, 1996), such as arises from gene trees exhibiting polymorphism or simply from gene trees with sequences sampled from different species; and second, consensus trees do not represent real biological events. Rodrigo et al (1993) have advocated a sequenceexcision procedure, wherein problem sequences are excised, the data sets tested for homogeneity, and the procedure repeated until the null hypothesis that two data sets represent character samples from the same phylogeny cannot be rejected. Excising sequences, however, may not be the best way to accommodate gene tree conflict (see below).…”

Section: Inferring Species Trees From Gene Treesmentioning

confidence: 99%

Inferring Species Trees from Gene Trees: A Phylogenetic Analysis of the Elapidae (Serpentes) Based on the Amino Acid Sequences of Venom Proteins

Slowinski

Knight

Rooney

1997

Molecular Phylogenetics and Evolution

124

103

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Toward the goal of recovering the phylogenetic relationships among elapid snakes, we separately found the shortest trees from the amino acid sequences for the venom proteins phospholipase A 2 and the short neurotoxin, collectively representing 32 species in 16 genera. We then applied a method we term gene tree parsimony for inferring species trees from gene trees that works by finding the species tree which minimizes the number of deep coalescences or gene duplications plus unsampled sequences necessary to fit each gene tree to the species tree. This procedure, which is both logical and generally applicable, avoids many of the problems of previous approaches for inferring species trees from gene trees. The results support a division of the elapids examined into sister groups of the Australian and marine (laticaudines and hydrophiines) species, and the African and Asian species. Within the former clade, the sea snakes are shown to be diphyletic, with the laticaudines and hydrophiines having separate origins. This finding is corroborated by previous studies, which provide support for the usefulness of gene tree parsimony.

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“…This is a procedure where the sequence data for a single taxon are removed from both data sets to remove possible misinformative data (Rodrigo et al, 1993). This procedure was performed by first generating a 50 % majority rule consensus tree, from the equally parsimonious trees generated in the above topology analysis, for each of the ITS sequence data sets.…”

Section: Congruence Studies Of Its1 and Its2 Sequence Datamentioning

confidence: 99%

“…Following this, a test based on that of Rodrigo et al (1993) was performed to identify if differences observed in the topologies of the phylogenetic trees generated from the ITS1 and ITS2 data sets were significantly different or the result of sampling error. MP trees were generated from both the ITS1 and ITS2 sequence data sets using the seven taxa common to both data sets (MTM, M1057, GJS90-90, TR112, US1, HEND and TR90), as well as the four outgroups mentioned previously.…”

Section: Congruence Studies Of Its1 and Its2 Sequence Datamentioning

confidence: 99%

Examination of Trichoderma phylogenies derived from ribosomal DNA sequence data

Dodd

Crowhurst

Rodrigo

et al. 2000

Mycological Research

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Ribosomal DNA sequences were assessed for their usefulness in distinguishing among Trichoderma isolates and for their robustness in resolving their phylogenetic relationships. DNA sequences from the D2 region of the 28S rRNA gene were determined for 50 Trichoderma isolates representing seven species. Eight distinct sequence types existed, and were mostly consistent with groupings based on morphology. Sequence variability within the D2 region alone was not sufficient to provide a reliable phylogeny. Sequences from the ITS1, 5.8S and ITS2 regions were subsequently determined for 18 of the isolates. Eight distinct ITS sequence types were detected among these 18 isolates. The ITS sequence types were generally consistent with morphology, ITS1 sequence data supported the identification of the Th3 T. harzianum group of Muthumeenakshi et al. (1994) as T. atroviride. The data also confirmed that the biocontrol strains of this study were different from those causing disease problems in the mushroom industry in Europe and North America. Results from the phylogenetic analysis stress the importance of testing the robustness of data used to predict phylogenies. Two ITS sequence data sets for the same group of isolates produced significantly different phylogenies. Congruence analysis detected that T. inhamatum (GJS90-90) was corrupting tree topologies and ' first order pruning ' was performed by removing its sequence from the two ITS data sets. Subsequent differences in the topologies of pruned ITS1 and ITS2 trees were attributed to a lack of phylogenetic information in the ITS2 sequence region. Although ITS sequences successfully differentiated among morphologically distinct isolates within Trichoderma, it did not provide a sufficient phylogenetic signal to resolve all of their relationships.

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A randomisation test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree

Cited by 118 publications

References 18 publications

Phylogeny of Twenty Thermus Isolates Constructed from 16S rRNA Gene Sequence Data

Phylogeny of Twenty Thermus Isolates Constructed from 16S rRNA Gene Sequence Data

Inferring Species Trees from Gene Trees: A Phylogenetic Analysis of the Elapidae (Serpentes) Based on the Amino Acid Sequences of Venom Proteins

Examination of Trichoderma phylogenies derived from ribosomal DNA sequence data

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