Future trypanosomatid phylogenies: refined homologies, supertrees and networks

Stothard, J. Russell

doi:10.1590/s0074-02762000000400014

Mem. Inst. Oswaldo Cruz

2000

DOI: 10.1590/s0074-02762000000400014

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Future trypanosomatid phylogenies: refined homologies, supertrees and networks

J. Russell Stothard

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Cited by 3 publications

(2 citation statements)

References 21 publications

(25 reference statements)

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“…Large-scale supertrees already exist for all extant species of the mammalian orders Primates (Purvis, 1995a;Purvis and Webster, 1999) and Carnivora (BinindaEmonds et al, 1999), for the major clades within the legume subfamily Papilionoideae (Wojciechowski et al, 2000), and for the family-level relationships of all extant mammals (Liu et al, 2001). Furthermore, supertree construction has been identi ed as the key to producing comprehensive phylogenies for problematic clades (e.g., the kinetoplastid protozoa Trypanosomatidae; Stothard, 2000).…”

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confidence: 99%

Assessment of the Accuracy of Matrix Representation with Parsimony Analysis Supertree Construction

2001

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Despite the growing popularity of supertree construction for combining phylogenetic information to produce more inclusive phylogenies, large-scale performance testing of this method has not been done. Through simulation, we tested the accuracy of the most widely used supertree method, matrix representation with parsimony analysis (MRP), with respect to a (maximum parsimony) total evidence solution and a known model tree. When source trees overlap completely, MRP provided a reasonable approximation of the total evidence tree; agreement was usually > 85%. Performance improved slightly when using smaller, more numerous, or more congruent source trees, and especially when elements were weighted in proportion to the bootstrap frequencies of the nodes they represented on each source tree ("weighted MRP"). Although total evidence always estimated the model tree slightly better than nonweighted MRP methods, weighted MRP in turn usually out-performed total evidence slightly. When source studies were even moderately nonoverlapping (i.e., sharing only three-quarters of the taxa), the high proportion of missing data caused a loss in resolution that severely degraded the performance for all methods, including total evidence. In such cases, even combining more trees, which had positive effects elsewhere, did not improve accuracy. Instead, "seeding" the supertree or total evidence analyses with a single largely complete study improved performance substantially. This finding could be an important strategy for any studies that seek to combine phylogenetic information. Overall, our results suggest that MRP supertree construction provides a reasonable approximation of a total evidence solution and that weighted MRP should be used whenever possible.

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confidence: 99%

Assessment of the Accuracy of Matrix Representation with Parsimony Analysis Supertree Construction

2001

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“…Large-scale supertrees already exist for all extant species of the mammalian orders Primates (Purvis, 1995a;Purvis and Webster, 1999) and Carnivora (Bininda-Emonds et al, 1999), for the major clades within the legume subfamily Papilionoideae (Wojciechowski et al, 2000), and for the family-level relationships of all extant mammals (Liu et al, 2001). Furthermore, supertree construction has been identi ed as the key to producing comprehensive phylogenies for problematic clades (e.g., the kinetoplastid protozoa Trypanosomatidae; Stothard, 2000).…”

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confidence: 99%

Assessment of the Accuracy of Matrix Representation with Parsimony Analysis Supertree Construction

Bininda‐Emonds¹,

Sanderson²

2001

Systematic Biology

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PHYLOGENETIC POSITION OF THE GIANT ANURAN TRYPANOSOMES TRYPANOSOMA CHATTONI, TRYPANOSOMA FALLISI, TRYPANOSOMA MEGA, TRYPANOSOMA NEVEULEMAIREI, AND TRYPANOSOMA RANARUM INFERREDFROM 18S rRNA GENE SEQUENCES

Martin

Wright

Barta

et al. 2002

Journal of Parasitology

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Phylogenetic relationships within the kinetoplastid flagellates were inferred from comparisons of small-subunit ribosomal RNA gene sequences. These included 5 new gene sequences, Trypanosoma fallisi (2,239 bp), Trypanosoma chattoni (2,180 bp), Trypanosoma mega (2,211 bp), Trypanosoma neveulemairei (2,197 bp), and Trypanosoma ranarum (2,203 bp). Trees produced using maximum-parsimony and distance-matrix methods (least-squares, neighbor-joining, and maximum-likelihood), supported by strong bootstrap and quartet-puzzle analyses, indicated that the trypanosomes are a monophyletic group that divides into 2 major lineages, the salivarian trypanosomes and the nonsalivarian trypanosomes. The nonsalivarian trypanosomes further divide into 2 lineages, 1 containing trypanosomes of birds, mammals, and reptiles and the other containing trypanosomes of fish, reptiles, and anurans. Among the giant trypanosomes, T. chattoni is clearly shown to be distantly related to all the other anuran trypanosome species. Trypanosoma mega is closely associated with T. fallisi and T. ranarum, whereas T. neveulemairei and Trypanosoma rotatorium are sister taxa. The branching order of the anuran trypanosomes suggests that some toad trypanosomes may have evolved by host switching from frogs to toads.

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Future trypanosomatid phylogenies: refined homologies, supertrees and networks

Cited by 3 publications

References 21 publications

Assessment of the Accuracy of Matrix Representation with Parsimony Analysis Supertree Construction

Assessment of the Accuracy of Matrix Representation with Parsimony Analysis Supertree Construction

Assessment of the Accuracy of Matrix Representation with Parsimony Analysis Supertree Construction

PHYLOGENETIC POSITION OF THE GIANT ANURAN TRYPANOSOMES TRYPANOSOMA CHATTONI, TRYPANOSOMA FALLISI, TRYPANOSOMA MEGA, TRYPANOSOMA NEVEULEMAIREI, AND TRYPANOSOMA RANARUM INFERREDFROM 18S rRNA GENE SEQUENCES

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