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Revealing pancrustacean relationships: phylogenetic analysis of ribosomal protein genes places Collembola (springtails) in a monophyletic Hexapoda and reinforces the discrepancy between mitochondrial and nuclear DNA markers.

Timmermans MJ, Roelofs D, Mariën J, van Straalen NM - BMC Evol. Biol. (2008)

Bottom Line: Phylogenetic tree reconstructions, using Maximum Likelihood, Maximum Parsimony, and Bayesian methods, resulted in a topology that supports monophyly of Hexapoda.This underpins the inconsistency between nuclear and mitochondrial datasets when analyzing pancrustacean relationships.Caution is needed when applying mitochondrial markers in deep phylogeny.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Animal Ecology, VU University Amsterdam, Amsterdam, The Netherlands. martijn.timmermans@falw.vu.nl

ABSTRACT

Background: In recent years, several new hypotheses on phylogenetic relations among arthropods have been proposed on the basis of DNA sequences. One of the challenged hypotheses is the monophyly of hexapods. This discussion originated from analyses based on mitochondrial DNA datasets that, due to an unusual positioning of Collembola, suggested that the hexapod body plan evolved at least twice. Here, we re-evaluate the position of Collembola using ribosomal protein gene sequences.

Results: In total 48 ribosomal proteins were obtained for the collembolan Folsomia candida. These 48 sequences were aligned with sequence data on 35 other ecdysozoans. Each ribosomal protein gene was available for 25% to 86% of the taxa. However, the total sequence information was unequally distributed over the taxa and ranged between 4% and 100%. A concatenated dataset was constructed (5034 inferred amino acids in length), of which ~66% of the positions were filled. Phylogenetic tree reconstructions, using Maximum Likelihood, Maximum Parsimony, and Bayesian methods, resulted in a topology that supports monophyly of Hexapoda.

Conclusion: Although ribosomal proteins in general may not evolve independently, they once more appear highly valuable for phylogenetic reconstruction. Our analyses clearly suggest that Hexapoda is monophyletic. This underpins the inconsistency between nuclear and mitochondrial datasets when analyzing pancrustacean relationships. Caution is needed when applying mitochondrial markers in deep phylogeny.

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Ternplot showing "similarity' between Folsomia candida and Apis mellifera, Daphnia magna and Caenorhabditis elegans, respectively. Each dot represents one ribosomal protein. The four dots that are visible on the three edges represent five genes that were unavailable for one of the three species. Two dots/genes overlap. RpS30 was not mapped on this graph, as analysis of our RpS30 alignment resulted in a Kimura protein distance that was larger than one: Kimura protein distance C. elegans and F. candida = 1.14.
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Figure 1: Ternplot showing "similarity' between Folsomia candida and Apis mellifera, Daphnia magna and Caenorhabditis elegans, respectively. Each dot represents one ribosomal protein. The four dots that are visible on the three edges represent five genes that were unavailable for one of the three species. Two dots/genes overlap. RpS30 was not mapped on this graph, as analysis of our RpS30 alignment resulted in a Kimura protein distance that was larger than one: Kimura protein distance C. elegans and F. candida = 1.14.

Mentions: We calculated "similarity" values between the amino acid sequences of F. candida and three well-represented species (C. elegans (most-distant outgroup), Daphnia magna and A. mellifera). These values were mapped onto a ternary graph (Figure 1). Almost all points cluster in the lower region of the ternary graph, showing that for almost all genes the distance between F. candida and C. elegans is greater than the distance between F. candida and A. mellifera. The graph also shows that most genes of F. candida are more "similar" to A. mellifera, while some have more in common with D. magna.


Revealing pancrustacean relationships: phylogenetic analysis of ribosomal protein genes places Collembola (springtails) in a monophyletic Hexapoda and reinforces the discrepancy between mitochondrial and nuclear DNA markers.

Timmermans MJ, Roelofs D, Mariën J, van Straalen NM - BMC Evol. Biol. (2008)

Ternplot showing "similarity' between Folsomia candida and Apis mellifera, Daphnia magna and Caenorhabditis elegans, respectively. Each dot represents one ribosomal protein. The four dots that are visible on the three edges represent five genes that were unavailable for one of the three species. Two dots/genes overlap. RpS30 was not mapped on this graph, as analysis of our RpS30 alignment resulted in a Kimura protein distance that was larger than one: Kimura protein distance C. elegans and F. candida = 1.14.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2315649&req=5

Figure 1: Ternplot showing "similarity' between Folsomia candida and Apis mellifera, Daphnia magna and Caenorhabditis elegans, respectively. Each dot represents one ribosomal protein. The four dots that are visible on the three edges represent five genes that were unavailable for one of the three species. Two dots/genes overlap. RpS30 was not mapped on this graph, as analysis of our RpS30 alignment resulted in a Kimura protein distance that was larger than one: Kimura protein distance C. elegans and F. candida = 1.14.
Mentions: We calculated "similarity" values between the amino acid sequences of F. candida and three well-represented species (C. elegans (most-distant outgroup), Daphnia magna and A. mellifera). These values were mapped onto a ternary graph (Figure 1). Almost all points cluster in the lower region of the ternary graph, showing that for almost all genes the distance between F. candida and C. elegans is greater than the distance between F. candida and A. mellifera. The graph also shows that most genes of F. candida are more "similar" to A. mellifera, while some have more in common with D. magna.

Bottom Line: Phylogenetic tree reconstructions, using Maximum Likelihood, Maximum Parsimony, and Bayesian methods, resulted in a topology that supports monophyly of Hexapoda.This underpins the inconsistency between nuclear and mitochondrial datasets when analyzing pancrustacean relationships.Caution is needed when applying mitochondrial markers in deep phylogeny.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Animal Ecology, VU University Amsterdam, Amsterdam, The Netherlands. martijn.timmermans@falw.vu.nl

ABSTRACT

Background: In recent years, several new hypotheses on phylogenetic relations among arthropods have been proposed on the basis of DNA sequences. One of the challenged hypotheses is the monophyly of hexapods. This discussion originated from analyses based on mitochondrial DNA datasets that, due to an unusual positioning of Collembola, suggested that the hexapod body plan evolved at least twice. Here, we re-evaluate the position of Collembola using ribosomal protein gene sequences.

Results: In total 48 ribosomal proteins were obtained for the collembolan Folsomia candida. These 48 sequences were aligned with sequence data on 35 other ecdysozoans. Each ribosomal protein gene was available for 25% to 86% of the taxa. However, the total sequence information was unequally distributed over the taxa and ranged between 4% and 100%. A concatenated dataset was constructed (5034 inferred amino acids in length), of which ~66% of the positions were filled. Phylogenetic tree reconstructions, using Maximum Likelihood, Maximum Parsimony, and Bayesian methods, resulted in a topology that supports monophyly of Hexapoda.

Conclusion: Although ribosomal proteins in general may not evolve independently, they once more appear highly valuable for phylogenetic reconstruction. Our analyses clearly suggest that Hexapoda is monophyletic. This underpins the inconsistency between nuclear and mitochondrial datasets when analyzing pancrustacean relationships. Caution is needed when applying mitochondrial markers in deep phylogeny.

Show MeSH