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Analyses of mitochondrial amino acid sequence datasets support the proposal that specimens of Hypodontus macropi from three species of macropodid hosts represent distinct species.

Jabbar A, Beveridge I, Mohandas N, Chilton NB, Littlewood DT, Jex AR, Gasser RB - BMC Evol. Biol. (2013)

Bottom Line: Pairwise comparisons of the amino acid sequences predicted from these three mt genomes revealed differences of 5.8% to 18%.In addition, sliding window analysis of the mt genomes defined variable regions for future population genetic studies of H. macropi in different macropodid hosts and geographical regions around Australia.The present analyses of inferred mt protein sequence datasets clearly supported the hypothesis that H. macropi from M. robustus robustus, M. bicolor and T. billardierii represent distinct species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Faculty of Veterinary Science, The University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia. jabbara@unimelb.edu.au.

ABSTRACT

Background: Hypodontus macropi is a common intestinal nematode of a range of kangaroos and wallabies (macropodid marsupials). Based on previous multilocus enzyme electrophoresis (MEE) and nuclear ribosomal DNA sequence data sets, H. macropi has been proposed to be complex of species. To test this proposal using independent molecular data, we sequenced the whole mitochondrial (mt) genomes of individuals of H. macropi from three different species of hosts (Macropus robustus robustus, Thylogale billardierii and Macropus [Wallabia] bicolor) as well as that of Macropicola ocydromi (a related nematode), and undertook a comparative analysis of the amino acid sequence datasets derived from these genomes.

Results: The mt genomes sequenced by next-generation (454) technology from H. macropi from the three host species varied from 13,634 bp to 13,699 bp in size. Pairwise comparisons of the amino acid sequences predicted from these three mt genomes revealed differences of 5.8% to 18%. Phylogenetic analysis of the amino acid sequence data sets using Bayesian Inference (BI) showed that H. macropi from the three different host species formed distinct, well-supported clades. In addition, sliding window analysis of the mt genomes defined variable regions for future population genetic studies of H. macropi in different macropodid hosts and geographical regions around Australia.

Conclusions: The present analyses of inferred mt protein sequence datasets clearly supported the hypothesis that H. macropi from M. robustus robustus, M. bicolor and T. billardierii represent distinct species.

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Phylogenetic analysis of the concatenated amino acid sequences for protein coding genes ofHypodontus macropi. Concatenated amino acid sequence data for all protein coding mitochondrial genes for three operational taxonomic units of H. macropi, from Macropus robustus robustus, Macropus bicolor, Thylogale billardierii, and from Macropicola ocydromi sequenced here as well as other concatenated sequence data representing complete mitochondrial genomes of Chabertia ovina, Oesophagostomum dentatum and Strongylus vulgaris (Strongyloidea) were analyzed using Bayesian Inference. The numbers above each tree branch represent the statistical support for each node (based on posterior probability score).
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Figure 2: Phylogenetic analysis of the concatenated amino acid sequences for protein coding genes ofHypodontus macropi. Concatenated amino acid sequence data for all protein coding mitochondrial genes for three operational taxonomic units of H. macropi, from Macropus robustus robustus, Macropus bicolor, Thylogale billardierii, and from Macropicola ocydromi sequenced here as well as other concatenated sequence data representing complete mitochondrial genomes of Chabertia ovina, Oesophagostomum dentatum and Strongylus vulgaris (Strongyloidea) were analyzed using Bayesian Inference. The numbers above each tree branch represent the statistical support for each node (based on posterior probability score).

Mentions: Pairwise comparisons of the amino acid (aa) sequences predicted for each of the 12 protein coding mt genes from OTU-C, OTU-G and OTU-J of H. macropi from the hosts M. robustus, M. bicolor and T. billardierii, respectively, are shown in Table 4. Most variation was detected in NAD6 between OTU-C and OTU-J (29%) and between OTU-G and OTU-J (26.9%), and in NAD4L between OTU-C and OTU-G (15.4%); moderate variation was detected in NAD1, NAD2, NAD3, NAD4 and NAD5 (mean: 9.8%) among the OTUs; least variation was detected in COX1, COX2 and COX3 (1.7-4.3%). Pairwise comparisons of concatenated amino acid sequences revealed sequence differences of 5.8% (OTU-C versus OTU-G), 18% (OTU-C versus OTU-J) and 10.0% (OTU-G versus OTU-J) (Table 4). These percentages are substantially higher than those detected within species of strongyloid nematodes [17,18,23]. Pairwise comparisons of the concatenated amino acid sequence of Ma. ocydromi with those of OTU-C, OTU-G and OTU-J revealed sequence differences of 30.4%, 15.9% and 31.0%, respectively (Table 5). The phylogenetic analysis of the aa sequence data showed that all three OTUs of H. macropi and Ma. ocydromi formed a distinct group, with maximum statistical support (posterior probability [pp] = 1.00), to the exclusion of the other strongyloid nematodes included here (i.e., Oesophagostomum dentatum, Chabertia ovina and Strongylus vulgaris) (Figure 2). In this analysis, OTU-C from M. r. robustus grouped together with Ma. ocydromi (pp = 1.00) to the exclusion of OTU-G (M. bicolor) and OTU-J (T. billardierii). While the three OTUs of H. macropi did form a group with C. ovina, statistical support for this grouping was moderate (pp = 0.74) (Figure 2).


Analyses of mitochondrial amino acid sequence datasets support the proposal that specimens of Hypodontus macropi from three species of macropodid hosts represent distinct species.

Jabbar A, Beveridge I, Mohandas N, Chilton NB, Littlewood DT, Jex AR, Gasser RB - BMC Evol. Biol. (2013)

Phylogenetic analysis of the concatenated amino acid sequences for protein coding genes ofHypodontus macropi. Concatenated amino acid sequence data for all protein coding mitochondrial genes for three operational taxonomic units of H. macropi, from Macropus robustus robustus, Macropus bicolor, Thylogale billardierii, and from Macropicola ocydromi sequenced here as well as other concatenated sequence data representing complete mitochondrial genomes of Chabertia ovina, Oesophagostomum dentatum and Strongylus vulgaris (Strongyloidea) were analyzed using Bayesian Inference. The numbers above each tree branch represent the statistical support for each node (based on posterior probability score).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4222732&req=5

Figure 2: Phylogenetic analysis of the concatenated amino acid sequences for protein coding genes ofHypodontus macropi. Concatenated amino acid sequence data for all protein coding mitochondrial genes for three operational taxonomic units of H. macropi, from Macropus robustus robustus, Macropus bicolor, Thylogale billardierii, and from Macropicola ocydromi sequenced here as well as other concatenated sequence data representing complete mitochondrial genomes of Chabertia ovina, Oesophagostomum dentatum and Strongylus vulgaris (Strongyloidea) were analyzed using Bayesian Inference. The numbers above each tree branch represent the statistical support for each node (based on posterior probability score).
Mentions: Pairwise comparisons of the amino acid (aa) sequences predicted for each of the 12 protein coding mt genes from OTU-C, OTU-G and OTU-J of H. macropi from the hosts M. robustus, M. bicolor and T. billardierii, respectively, are shown in Table 4. Most variation was detected in NAD6 between OTU-C and OTU-J (29%) and between OTU-G and OTU-J (26.9%), and in NAD4L between OTU-C and OTU-G (15.4%); moderate variation was detected in NAD1, NAD2, NAD3, NAD4 and NAD5 (mean: 9.8%) among the OTUs; least variation was detected in COX1, COX2 and COX3 (1.7-4.3%). Pairwise comparisons of concatenated amino acid sequences revealed sequence differences of 5.8% (OTU-C versus OTU-G), 18% (OTU-C versus OTU-J) and 10.0% (OTU-G versus OTU-J) (Table 4). These percentages are substantially higher than those detected within species of strongyloid nematodes [17,18,23]. Pairwise comparisons of the concatenated amino acid sequence of Ma. ocydromi with those of OTU-C, OTU-G and OTU-J revealed sequence differences of 30.4%, 15.9% and 31.0%, respectively (Table 5). The phylogenetic analysis of the aa sequence data showed that all three OTUs of H. macropi and Ma. ocydromi formed a distinct group, with maximum statistical support (posterior probability [pp] = 1.00), to the exclusion of the other strongyloid nematodes included here (i.e., Oesophagostomum dentatum, Chabertia ovina and Strongylus vulgaris) (Figure 2). In this analysis, OTU-C from M. r. robustus grouped together with Ma. ocydromi (pp = 1.00) to the exclusion of OTU-G (M. bicolor) and OTU-J (T. billardierii). While the three OTUs of H. macropi did form a group with C. ovina, statistical support for this grouping was moderate (pp = 0.74) (Figure 2).

Bottom Line: Pairwise comparisons of the amino acid sequences predicted from these three mt genomes revealed differences of 5.8% to 18%.In addition, sliding window analysis of the mt genomes defined variable regions for future population genetic studies of H. macropi in different macropodid hosts and geographical regions around Australia.The present analyses of inferred mt protein sequence datasets clearly supported the hypothesis that H. macropi from M. robustus robustus, M. bicolor and T. billardierii represent distinct species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Faculty of Veterinary Science, The University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia. jabbara@unimelb.edu.au.

ABSTRACT

Background: Hypodontus macropi is a common intestinal nematode of a range of kangaroos and wallabies (macropodid marsupials). Based on previous multilocus enzyme electrophoresis (MEE) and nuclear ribosomal DNA sequence data sets, H. macropi has been proposed to be complex of species. To test this proposal using independent molecular data, we sequenced the whole mitochondrial (mt) genomes of individuals of H. macropi from three different species of hosts (Macropus robustus robustus, Thylogale billardierii and Macropus [Wallabia] bicolor) as well as that of Macropicola ocydromi (a related nematode), and undertook a comparative analysis of the amino acid sequence datasets derived from these genomes.

Results: The mt genomes sequenced by next-generation (454) technology from H. macropi from the three host species varied from 13,634 bp to 13,699 bp in size. Pairwise comparisons of the amino acid sequences predicted from these three mt genomes revealed differences of 5.8% to 18%. Phylogenetic analysis of the amino acid sequence data sets using Bayesian Inference (BI) showed that H. macropi from the three different host species formed distinct, well-supported clades. In addition, sliding window analysis of the mt genomes defined variable regions for future population genetic studies of H. macropi in different macropodid hosts and geographical regions around Australia.

Conclusions: The present analyses of inferred mt protein sequence datasets clearly supported the hypothesis that H. macropi from M. robustus robustus, M. bicolor and T. billardierii represent distinct species.

Show MeSH