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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.

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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 genetic distance on bootstrap support for the three hypotheses from analysis of 100 nuclear proteins with four taxa. (A, B) show bootstrap support for Coelomata; (C, D) for Ecdysozoa; (E, F) for Hypothesis III. Proteins were ordered from slowest evolving to fastest evolving based on two criteria: vertebrate-arthropod pairwise distance (diamonds) and nematode branch length (squares). Proteins were concatenated into ten groups often (A, C, E) and five groups of twenty (B, D, F). Graphs show rate from slowest to fastest evolving (left to right). Trend lines are indicated (solid for vertebrate-arthropod distance, dashed for nematode branch length).
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Figure 3: Effect of genetic distance on bootstrap support for the three hypotheses from analysis of 100 nuclear proteins with four taxa. (A, B) show bootstrap support for Coelomata; (C, D) for Ecdysozoa; (E, F) for Hypothesis III. Proteins were ordered from slowest evolving to fastest evolving based on two criteria: vertebrate-arthropod pairwise distance (diamonds) and nematode branch length (squares). Proteins were concatenated into ten groups often (A, C, E) and five groups of twenty (B, D, F). Graphs show rate from slowest to fastest evolving (left to right). Trend lines are indicated (solid for vertebrate-arthropod distance, dashed for nematode branch length).

Mentions: If nematodes cluster basally because of long-branch attraction, then the strongest support for Ecdysozoa should be obtained with the slowest evolving proteins. This was tested in an analysis of 36 nuclear proteins [8], but the results were equivocal. Therefore, we tested this suggestion with our four-taxon data set of 100 proteins, ordered by rate of evolution. Rate orders were determined in two ways: (i) nematode branch length and (ii) vertebrate-arthropod pairwise distance. The 100 proteins were grouped into concatenations of 10 proteins and 20 proteins to increase statistical resolution. The results show support for Coelomata at all rate orders, but the support is significant with the slowest evolving proteins, regardless of rate measure or number of proteins combined (Fig. 3). Concatenations of slow evolving proteins also show compositional homogeneity (pairwise disparity index test, P < 0.05) [21], suggesting the basal position of the nematode results from true phylogenetic signal and not compositional bias. Support for Coelomata was weakest with the fastest evolving proteins (which also showed compositional heterogeneity), indicating that Ecdysozoa, not Coelomata, may be the result of a rate bias, compositional bias, or other artifact.


The evolutionary position of nematodes.

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

Effect of genetic distance on bootstrap support for the three hypotheses from analysis of 100 nuclear proteins with four taxa. (A, B) show bootstrap support for Coelomata; (C, D) for Ecdysozoa; (E, F) for Hypothesis III. Proteins were ordered from slowest evolving to fastest evolving based on two criteria: vertebrate-arthropod pairwise distance (diamonds) and nematode branch length (squares). Proteins were concatenated into ten groups often (A, C, E) and five groups of twenty (B, D, F). Graphs show rate from slowest to fastest evolving (left to right). Trend lines are indicated (solid for vertebrate-arthropod distance, dashed for nematode branch length).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC102755&req=5

Figure 3: Effect of genetic distance on bootstrap support for the three hypotheses from analysis of 100 nuclear proteins with four taxa. (A, B) show bootstrap support for Coelomata; (C, D) for Ecdysozoa; (E, F) for Hypothesis III. Proteins were ordered from slowest evolving to fastest evolving based on two criteria: vertebrate-arthropod pairwise distance (diamonds) and nematode branch length (squares). Proteins were concatenated into ten groups often (A, C, E) and five groups of twenty (B, D, F). Graphs show rate from slowest to fastest evolving (left to right). Trend lines are indicated (solid for vertebrate-arthropod distance, dashed for nematode branch length).
Mentions: If nematodes cluster basally because of long-branch attraction, then the strongest support for Ecdysozoa should be obtained with the slowest evolving proteins. This was tested in an analysis of 36 nuclear proteins [8], but the results were equivocal. Therefore, we tested this suggestion with our four-taxon data set of 100 proteins, ordered by rate of evolution. Rate orders were determined in two ways: (i) nematode branch length and (ii) vertebrate-arthropod pairwise distance. The 100 proteins were grouped into concatenations of 10 proteins and 20 proteins to increase statistical resolution. The results show support for Coelomata at all rate orders, but the support is significant with the slowest evolving proteins, regardless of rate measure or number of proteins combined (Fig. 3). Concatenations of slow evolving proteins also show compositional homogeneity (pairwise disparity index test, P < 0.05) [21], suggesting the basal position of the nematode results from true phylogenetic signal and not compositional bias. Support for Coelomata was weakest with the fastest evolving proteins (which also showed compositional heterogeneity), indicating that Ecdysozoa, not Coelomata, may be the result of a rate bias, compositional bias, or other artifact.

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