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The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes.

Bourlat SJ, Rota-Stabelli O, Lanfear R, Telford MJ - BMC Evol. Biol. (2009)

Bottom Line: Xenoturbella bocki is a morphologically simple benthic marine worm recently found to belong among the deuterostomes.Phylogenetic analyses of the mitochondrial sequence indicate a weakly supported placement as a basal deuterostome, a result that may be the effect of compositional bias.Finally, while phylogenetic analyses of the mitochondrial sequences support a basal deuterostome placement, support for this decreases with the use of more sophisticated models of sequence evolution.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Invertebrate Zoology, Swedish Museum of Natural History, Stockholm, Sweden. sarah.bourlat@nrm.se

ABSTRACT

Background: Mitochondrial genome comparisons contribute in multiple ways when inferring animal relationships. As well as primary sequence data, rare genomic changes such as gene order, shared gene boundaries and genetic code changes, which are unlikely to have arisen through convergent evolution, are useful tools in resolving deep phylogenies. Xenoturbella bocki is a morphologically simple benthic marine worm recently found to belong among the deuterostomes. Here we present analyses comparing the Xenoturbella bocki mitochondrial gene order, genetic code and control region to those of other metazoan groups.

Results: The complete mitochondrial genome sequence of Xenoturbella bocki was determined. The gene order is most similar to that of the chordates and the hemichordates, indicating that this conserved mitochondrial gene order might be ancestral to the deuterostome clade. Using data from all phyla of deuterostomes, we infer the ancestral mitochondrial gene order for this clade. Using inversion and breakpoint analyses of metazoan mitochondrial genomes, we test conflicting hypotheses for the phylogenetic placement of Xenoturbella and find a closer affinity to the hemichordates than to other metazoan groups. Comparative analyses of the control region reveal similarities in the transcription initiation and termination sites and origin of replication of Xenoturbella with those of the vertebrates. Phylogenetic analyses of the mitochondrial sequence indicate a weakly supported placement as a basal deuterostome, a result that may be the effect of compositional bias.

Conclusion: The mitochondrial genome of Xenoturbella bocki has a very conserved gene arrangement in the deuterostome group, strikingly similar to that of the hemichordates and the chordates, and thus to the ancestral deuterostome gene order. Similarity to the hemichordates in particular is suggested by inversion and breakpoint analysis. Finally, while phylogenetic analyses of the mitochondrial sequences support a basal deuterostome placement, support for this decreases with the use of more sophisticated models of sequence evolution.

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Consensus tree from bayesian analysis using the CAT-BP model. The model is able to recover the monophyly of Chordata, but does not resolve the position of Xenoturbella within monophyletic Deuterostomia. Branch length for the Urochordata has been halved.
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Figure 4: Consensus tree from bayesian analysis using the CAT-BP model. The model is able to recover the monophyly of Chordata, but does not resolve the position of Xenoturbella within monophyletic Deuterostomia. Branch length for the Urochordata has been halved.

Mentions: Using PhyloBayes and modelling protein evolution with the CAT model [32], Xenoturbella is still recovered as a basal deuterostome, but with low support (61 pp) and the urochordates are recovered as deuterostomes with high support (95 pp), even if within paraphyletic echinoderms, rather than with the chordates. Using CAT-BP [33], which accounts for compositional heterogeneity within lineages, the urochordates are finally recovered as basal chordates, even if with tepid support (pp 57) (see figure 4). Interestingly, using CAT-BP the position of Xenoturbella is unresolved, implying that signal supporting a basal deuterostome position for Xenoturbella finally decreases to below 50%.


The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes.

Bourlat SJ, Rota-Stabelli O, Lanfear R, Telford MJ - BMC Evol. Biol. (2009)

Consensus tree from bayesian analysis using the CAT-BP model. The model is able to recover the monophyly of Chordata, but does not resolve the position of Xenoturbella within monophyletic Deuterostomia. Branch length for the Urochordata has been halved.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2697986&req=5

Figure 4: Consensus tree from bayesian analysis using the CAT-BP model. The model is able to recover the monophyly of Chordata, but does not resolve the position of Xenoturbella within monophyletic Deuterostomia. Branch length for the Urochordata has been halved.
Mentions: Using PhyloBayes and modelling protein evolution with the CAT model [32], Xenoturbella is still recovered as a basal deuterostome, but with low support (61 pp) and the urochordates are recovered as deuterostomes with high support (95 pp), even if within paraphyletic echinoderms, rather than with the chordates. Using CAT-BP [33], which accounts for compositional heterogeneity within lineages, the urochordates are finally recovered as basal chordates, even if with tepid support (pp 57) (see figure 4). Interestingly, using CAT-BP the position of Xenoturbella is unresolved, implying that signal supporting a basal deuterostome position for Xenoturbella finally decreases to below 50%.

Bottom Line: Xenoturbella bocki is a morphologically simple benthic marine worm recently found to belong among the deuterostomes.Phylogenetic analyses of the mitochondrial sequence indicate a weakly supported placement as a basal deuterostome, a result that may be the effect of compositional bias.Finally, while phylogenetic analyses of the mitochondrial sequences support a basal deuterostome placement, support for this decreases with the use of more sophisticated models of sequence evolution.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Invertebrate Zoology, Swedish Museum of Natural History, Stockholm, Sweden. sarah.bourlat@nrm.se

ABSTRACT

Background: Mitochondrial genome comparisons contribute in multiple ways when inferring animal relationships. As well as primary sequence data, rare genomic changes such as gene order, shared gene boundaries and genetic code changes, which are unlikely to have arisen through convergent evolution, are useful tools in resolving deep phylogenies. Xenoturbella bocki is a morphologically simple benthic marine worm recently found to belong among the deuterostomes. Here we present analyses comparing the Xenoturbella bocki mitochondrial gene order, genetic code and control region to those of other metazoan groups.

Results: The complete mitochondrial genome sequence of Xenoturbella bocki was determined. The gene order is most similar to that of the chordates and the hemichordates, indicating that this conserved mitochondrial gene order might be ancestral to the deuterostome clade. Using data from all phyla of deuterostomes, we infer the ancestral mitochondrial gene order for this clade. Using inversion and breakpoint analyses of metazoan mitochondrial genomes, we test conflicting hypotheses for the phylogenetic placement of Xenoturbella and find a closer affinity to the hemichordates than to other metazoan groups. Comparative analyses of the control region reveal similarities in the transcription initiation and termination sites and origin of replication of Xenoturbella with those of the vertebrates. Phylogenetic analyses of the mitochondrial sequence indicate a weakly supported placement as a basal deuterostome, a result that may be the effect of compositional bias.

Conclusion: The mitochondrial genome of Xenoturbella bocki has a very conserved gene arrangement in the deuterostome group, strikingly similar to that of the hemichordates and the chordates, and thus to the ancestral deuterostome gene order. Similarity to the hemichordates in particular is suggested by inversion and breakpoint analysis. Finally, while phylogenetic analyses of the mitochondrial sequences support a basal deuterostome placement, support for this decreases with the use of more sophisticated models of sequence evolution.

Show MeSH
Related in: MedlinePlus