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The evolutionary position of nematodes.

Blair JE, Ikeo K, Gojobori T, Hedges SB - BMC Evol. Biol. (2002)

Bottom Line: Instead, we found significant support for the traditional hypothesis, Coelomata.Our result is robust to different rates of sequence change among genes and lineages, different numbers of taxa, and different species of nematodes.We conclude that insects (arthropods) are genetically and evolutionarily closer to humans than to nematode worms.

View Article: PubMed Central - HTML - PubMed

Affiliation: Astrobiology Research Center and Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA. jeb322@psu.edu

ABSTRACT

Background: The complete genomes of three animals have been sequenced by global research efforts: a nematode worm (Caenorhabditis elegans), an insect (Drosophila melanogaster), and a vertebrate (Homo sapiens). Remarkably, their relationships have yet to be clarified. The confusion concerns the enigmatic position of nematodes. Traditionally, nematodes have occupied a basal position, in part because they lack a true body cavity. However, the leading hypothesis now joins nematodes with arthropods in a molting clade, Ecdysozoa, based on data from several genes.

Results: We tested the Ecdysozoa hypothesis with analyses of more than 100 nuclear protein alignments, under conditions that would expose biases, and found that it was not supported. Instead, we found significant support for the traditional hypothesis, Coelomata. Our result is robust to different rates of sequence change among genes and lineages, different numbers of taxa, and different species of nematodes.

Conclusion: We conclude that insects (arthropods) are genetically and evolutionarily closer to humans than to nematode worms.

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Effect of rate constancy on bootstrap support for Coelomata in four-taxon analysis. Graphs show results before application of tests (left, 0-level) followed by increasing stringency (5, 10, 40% significance) of the chi-square test [22] (circles) and Z-test [23] (triangles); the 5% level is normally used. (A) number of proteins passing rate constancy at each cutoff level. (B) relative nematode branch length upon concatenation of all rate constant proteins at each level. (C) bootstrap support for Coelomata for each rate-constant concatenation.
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Figure 5: Effect of rate constancy on bootstrap support for Coelomata in four-taxon analysis. Graphs show results before application of tests (left, 0-level) followed by increasing stringency (5, 10, 40% significance) of the chi-square test [22] (circles) and Z-test [23] (triangles); the 5% level is normally used. (A) number of proteins passing rate constancy at each cutoff level. (B) relative nematode branch length upon concatenation of all rate constant proteins at each level. (C) bootstrap support for Coelomata for each rate-constant concatenation.

Mentions: Finally, the affect of lineage-specific rate variation on support for Coelomata was tested with the use of relative rate tests. Presumably, the selective elimination of genes with long branches will increase statistical support for the correct topology. Individual proteins from the four-taxon data set were each subjected to two different relative rate tests [22,23]. Proteins determined to be rate-constant at the typically applied stringency level (5% significance), and at two greater stringency levels (10% and 40% significance) were concatenated and bootstrap support was determined using neighbor joining. The results of the two tests were similar. As stringency increased, 40–83% of proteins were rejected, and the relative nematode branch length (to the arthropod and vertebrate branches) dropped from 16% to 0%. However, in all cases, Coelomata remained highly significant (Fig. 5). Thus, the suggestion that a basal position of nematodes is the result of long-branch attraction [3] can be rejected.


The evolutionary position of nematodes.

Blair JE, Ikeo K, Gojobori T, Hedges SB - BMC Evol. Biol. (2002)

Effect of rate constancy on bootstrap support for Coelomata in four-taxon analysis. Graphs show results before application of tests (left, 0-level) followed by increasing stringency (5, 10, 40% significance) of the chi-square test [22] (circles) and Z-test [23] (triangles); the 5% level is normally used. (A) number of proteins passing rate constancy at each cutoff level. (B) relative nematode branch length upon concatenation of all rate constant proteins at each level. (C) bootstrap support for Coelomata for each rate-constant concatenation.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC102755&req=5

Figure 5: Effect of rate constancy on bootstrap support for Coelomata in four-taxon analysis. Graphs show results before application of tests (left, 0-level) followed by increasing stringency (5, 10, 40% significance) of the chi-square test [22] (circles) and Z-test [23] (triangles); the 5% level is normally used. (A) number of proteins passing rate constancy at each cutoff level. (B) relative nematode branch length upon concatenation of all rate constant proteins at each level. (C) bootstrap support for Coelomata for each rate-constant concatenation.
Mentions: Finally, the affect of lineage-specific rate variation on support for Coelomata was tested with the use of relative rate tests. Presumably, the selective elimination of genes with long branches will increase statistical support for the correct topology. Individual proteins from the four-taxon data set were each subjected to two different relative rate tests [22,23]. Proteins determined to be rate-constant at the typically applied stringency level (5% significance), and at two greater stringency levels (10% and 40% significance) were concatenated and bootstrap support was determined using neighbor joining. The results of the two tests were similar. As stringency increased, 40–83% of proteins were rejected, and the relative nematode branch length (to the arthropod and vertebrate branches) dropped from 16% to 0%. However, in all cases, Coelomata remained highly significant (Fig. 5). Thus, the suggestion that a basal position of nematodes is the result of long-branch attraction [3] can be rejected.

Bottom Line: Instead, we found significant support for the traditional hypothesis, Coelomata.Our result is robust to different rates of sequence change among genes and lineages, different numbers of taxa, and different species of nematodes.We conclude that insects (arthropods) are genetically and evolutionarily closer to humans than to nematode worms.

View Article: PubMed Central - HTML - PubMed

Affiliation: Astrobiology Research Center and Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA. jeb322@psu.edu

ABSTRACT

Background: The complete genomes of three animals have been sequenced by global research efforts: a nematode worm (Caenorhabditis elegans), an insect (Drosophila melanogaster), and a vertebrate (Homo sapiens). Remarkably, their relationships have yet to be clarified. The confusion concerns the enigmatic position of nematodes. Traditionally, nematodes have occupied a basal position, in part because they lack a true body cavity. However, the leading hypothesis now joins nematodes with arthropods in a molting clade, Ecdysozoa, based on data from several genes.

Results: We tested the Ecdysozoa hypothesis with analyses of more than 100 nuclear protein alignments, under conditions that would expose biases, and found that it was not supported. Instead, we found significant support for the traditional hypothesis, Coelomata. Our result is robust to different rates of sequence change among genes and lineages, different numbers of taxa, and different species of nematodes.

Conclusion: We conclude that insects (arthropods) are genetically and evolutionarily closer to humans than to nematode worms.

Show MeSH
Related in: MedlinePlus