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The complete mitochondrial genome of the sea spider Achelia bituberculata (Pycnogonida, Ammotheidae): arthropod ground pattern of gene arrangement.

Park SJ, Lee YS, Hwang UW - BMC Genomics (2007)

Bottom Line: This controversy has recently been rekindled by differences in the conclusions based on neuroanatomical data concerning the chelifore and the patterns of Hox expression.Phylogenetic analyses based on mitochondrial protein-coding genes showed that Pycnogonida may be authentic arachnids (= aquatic arachnids) within Chelicerata sensu lato, as indicated by the name 'sea spider,' and suggest that the Cormogonida theory - that the pycnogonids are a sister group of all other arthropods - should be rejected.However, in view of the relatively weak node confidence, strand-biased nucleotide composition and long-branch attraction artifact, further more intensive studies seem necessary to resolve the exact position of the pycnogonids.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Teachers College, Kyungpook National University, Daegu 702-701, Korea. shinju@knu.ac.kr

ABSTRACT

Background: The phylogenetic position of pycnogonids is a long-standing and controversial issue in arthropod phylogeny. This controversy has recently been rekindled by differences in the conclusions based on neuroanatomical data concerning the chelifore and the patterns of Hox expression. The mitochondrial genome of a sea spider, Nymphon gracile (Pycnogonida, Nymphonidae), was recently reported in an attempt to address this issue. However, N. gracile appears to be a long-branch taxon on the phylogenetic tree and exhibits a number of peculiar features, such as 10 tRNA translocations and even an inversion of several protein-coding genes. Sequences of other pycnogonid mitochondrial genomes are needed if the position of pycnogonids is to be elucidated on this basis.

Results: The complete mitochondrial genome (15,474 bp) of a sea spider (Achelia bituberculata) belonging to the family Ammotheidae, which combines a number of anatomical features considered plesiomorphic with respect to other pycnogonids, was sequenced and characterized. The genome organization shows the features typical of most metazoan animal genomes (37 tightly-packed genes). The overall gene arrangement is completely identical to the arthropod ground pattern, with one exception: the position of the trnQ gene between the rrnS gene and the control region. Maximum likelihood and Bayesian inference trees inferred from the amino acid sequences of mitochondrial protein-coding genes consistently indicate that the pycnogonids (A. bituberculata and N. gracile) may be closely related to the clade of Acari and Araneae.

Conclusion: The complete mitochondrial genome sequence of A. bituberculata (Family Ammotheidae) and the previously-reported partial sequence of Endeis spinosa show the gene arrangement patterns typical of arthropods (Limulus-like), but they differ markedly from that of N. gracile. Phylogenetic analyses based on mitochondrial protein-coding genes showed that Pycnogonida may be authentic arachnids (= aquatic arachnids) within Chelicerata sensu lato, as indicated by the name 'sea spider,' and suggest that the Cormogonida theory - that the pycnogonids are a sister group of all other arthropods - should be rejected. However, in view of the relatively weak node confidence, strand-biased nucleotide composition and long-branch attraction artifact, further more intensive studies seem necessary to resolve the exact position of the pycnogonids.

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Maximum likelihood tree inferred from amino acid residues deduced from 12 mitochondrial protein-coding genes of 30 arthropods and 4 non-arthropods. The pycnogonids Achelia bituberculata and Nymphon gracile appear within the monophyletic Chelicerata with high node confidence values. Scorpiones are placed as the basal arachnid group. The inclusion of Pycnogonida within Arachnida is shown in this tree. The monophylies of Pancrustacea (Crustacea plus Hexapoda) and Myriochelata or Paradoxopoda (Myriapoda and Chelicerata) are strongly supported. The numbers above/below the branches indicate the node confidence values: BPML (bootstrap proportion in the maximum likelihood analysis), BPBI (bootstrap proportion in Bayesian inference) and BPP (Bayesian posterior probability) in order. The tree was obtained from a final alignment 2232 aa sites in length (refer to Materials and Methods for more detailed information). The log likelihood value of the best tree is -72575.641555. For more detail information about the taxon, refer to Table 1.
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Figure 6: Maximum likelihood tree inferred from amino acid residues deduced from 12 mitochondrial protein-coding genes of 30 arthropods and 4 non-arthropods. The pycnogonids Achelia bituberculata and Nymphon gracile appear within the monophyletic Chelicerata with high node confidence values. Scorpiones are placed as the basal arachnid group. The inclusion of Pycnogonida within Arachnida is shown in this tree. The monophylies of Pancrustacea (Crustacea plus Hexapoda) and Myriochelata or Paradoxopoda (Myriapoda and Chelicerata) are strongly supported. The numbers above/below the branches indicate the node confidence values: BPML (bootstrap proportion in the maximum likelihood analysis), BPBI (bootstrap proportion in Bayesian inference) and BPP (Bayesian posterior probability) in order. The tree was obtained from a final alignment 2232 aa sites in length (refer to Materials and Methods for more detailed information). The log likelihood value of the best tree is -72575.641555. For more detail information about the taxon, refer to Table 1.

Mentions: As shown in Fig. 6, phylogenetic analyses based on the amino acid sequences of 12 protein-coding genes for 30 arthropods and 4 outgroups (1 onychophoran, 2 annelids and 1 mollusk) as shown in Table 1 indicate that Pycnogonida, including A. bituberculata and N. gracile, are clustered together (BPML = 100, BPBI = 100, BPP = 1.0), and located within the monophyletic Chelicerata (BPML = 85, BPBI = 92, BPP = 1.0). L. polyphemus appears to be a sister of all the other chelicerates (= Arachnida). Although a monophyletic Arachnida (Scorpiones, Araneae and Acari) including Pycnogonida is supported by node confidence values that are very low (BPML = 55, BPBI = 48), Scorpiones are placed as the most basal arachnids and Pycnogonida, Araneae and Acari form a monophyletic group (BPML = 80, BPBI = 73, BPP = 0.99); Pycnogonida is identified as a sister group of the clade of Araneae and Acari within Arachnida.


The complete mitochondrial genome of the sea spider Achelia bituberculata (Pycnogonida, Ammotheidae): arthropod ground pattern of gene arrangement.

Park SJ, Lee YS, Hwang UW - BMC Genomics (2007)

Maximum likelihood tree inferred from amino acid residues deduced from 12 mitochondrial protein-coding genes of 30 arthropods and 4 non-arthropods. The pycnogonids Achelia bituberculata and Nymphon gracile appear within the monophyletic Chelicerata with high node confidence values. Scorpiones are placed as the basal arachnid group. The inclusion of Pycnogonida within Arachnida is shown in this tree. The monophylies of Pancrustacea (Crustacea plus Hexapoda) and Myriochelata or Paradoxopoda (Myriapoda and Chelicerata) are strongly supported. The numbers above/below the branches indicate the node confidence values: BPML (bootstrap proportion in the maximum likelihood analysis), BPBI (bootstrap proportion in Bayesian inference) and BPP (Bayesian posterior probability) in order. The tree was obtained from a final alignment 2232 aa sites in length (refer to Materials and Methods for more detailed information). The log likelihood value of the best tree is -72575.641555. For more detail information about the taxon, refer to Table 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2194727&req=5

Figure 6: Maximum likelihood tree inferred from amino acid residues deduced from 12 mitochondrial protein-coding genes of 30 arthropods and 4 non-arthropods. The pycnogonids Achelia bituberculata and Nymphon gracile appear within the monophyletic Chelicerata with high node confidence values. Scorpiones are placed as the basal arachnid group. The inclusion of Pycnogonida within Arachnida is shown in this tree. The monophylies of Pancrustacea (Crustacea plus Hexapoda) and Myriochelata or Paradoxopoda (Myriapoda and Chelicerata) are strongly supported. The numbers above/below the branches indicate the node confidence values: BPML (bootstrap proportion in the maximum likelihood analysis), BPBI (bootstrap proportion in Bayesian inference) and BPP (Bayesian posterior probability) in order. The tree was obtained from a final alignment 2232 aa sites in length (refer to Materials and Methods for more detailed information). The log likelihood value of the best tree is -72575.641555. For more detail information about the taxon, refer to Table 1.
Mentions: As shown in Fig. 6, phylogenetic analyses based on the amino acid sequences of 12 protein-coding genes for 30 arthropods and 4 outgroups (1 onychophoran, 2 annelids and 1 mollusk) as shown in Table 1 indicate that Pycnogonida, including A. bituberculata and N. gracile, are clustered together (BPML = 100, BPBI = 100, BPP = 1.0), and located within the monophyletic Chelicerata (BPML = 85, BPBI = 92, BPP = 1.0). L. polyphemus appears to be a sister of all the other chelicerates (= Arachnida). Although a monophyletic Arachnida (Scorpiones, Araneae and Acari) including Pycnogonida is supported by node confidence values that are very low (BPML = 55, BPBI = 48), Scorpiones are placed as the most basal arachnids and Pycnogonida, Araneae and Acari form a monophyletic group (BPML = 80, BPBI = 73, BPP = 0.99); Pycnogonida is identified as a sister group of the clade of Araneae and Acari within Arachnida.

Bottom Line: This controversy has recently been rekindled by differences in the conclusions based on neuroanatomical data concerning the chelifore and the patterns of Hox expression.Phylogenetic analyses based on mitochondrial protein-coding genes showed that Pycnogonida may be authentic arachnids (= aquatic arachnids) within Chelicerata sensu lato, as indicated by the name 'sea spider,' and suggest that the Cormogonida theory - that the pycnogonids are a sister group of all other arthropods - should be rejected.However, in view of the relatively weak node confidence, strand-biased nucleotide composition and long-branch attraction artifact, further more intensive studies seem necessary to resolve the exact position of the pycnogonids.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Teachers College, Kyungpook National University, Daegu 702-701, Korea. shinju@knu.ac.kr

ABSTRACT

Background: The phylogenetic position of pycnogonids is a long-standing and controversial issue in arthropod phylogeny. This controversy has recently been rekindled by differences in the conclusions based on neuroanatomical data concerning the chelifore and the patterns of Hox expression. The mitochondrial genome of a sea spider, Nymphon gracile (Pycnogonida, Nymphonidae), was recently reported in an attempt to address this issue. However, N. gracile appears to be a long-branch taxon on the phylogenetic tree and exhibits a number of peculiar features, such as 10 tRNA translocations and even an inversion of several protein-coding genes. Sequences of other pycnogonid mitochondrial genomes are needed if the position of pycnogonids is to be elucidated on this basis.

Results: The complete mitochondrial genome (15,474 bp) of a sea spider (Achelia bituberculata) belonging to the family Ammotheidae, which combines a number of anatomical features considered plesiomorphic with respect to other pycnogonids, was sequenced and characterized. The genome organization shows the features typical of most metazoan animal genomes (37 tightly-packed genes). The overall gene arrangement is completely identical to the arthropod ground pattern, with one exception: the position of the trnQ gene between the rrnS gene and the control region. Maximum likelihood and Bayesian inference trees inferred from the amino acid sequences of mitochondrial protein-coding genes consistently indicate that the pycnogonids (A. bituberculata and N. gracile) may be closely related to the clade of Acari and Araneae.

Conclusion: The complete mitochondrial genome sequence of A. bituberculata (Family Ammotheidae) and the previously-reported partial sequence of Endeis spinosa show the gene arrangement patterns typical of arthropods (Limulus-like), but they differ markedly from that of N. gracile. Phylogenetic analyses based on mitochondrial protein-coding genes showed that Pycnogonida may be authentic arachnids (= aquatic arachnids) within Chelicerata sensu lato, as indicated by the name 'sea spider,' and suggest that the Cormogonida theory - that the pycnogonids are a sister group of all other arthropods - should be rejected. However, in view of the relatively weak node confidence, strand-biased nucleotide composition and long-branch attraction artifact, further more intensive studies seem necessary to resolve the exact position of the pycnogonids.

Show MeSH
Related in: MedlinePlus