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A multi gene sequence-based phylogeny of the Musaceae (banana) family.

Christelová P, Valárik M, Hřibová E, De Langhe E, Doležel J - BMC Evol. Biol. (2011)

Bottom Line: Nucleotide variation within the sample confirmed the close relationship of Australimusa and Callimusa sections and showed that Eumusa and Rhodochlamys sections are not reciprocally monophyletic, which supports the previous claims for the merger between the two latter sections.The gene sequence-based phylogeny presented here provides a substantial insight into the course of speciation within the Musaceae.An understanding of the main phylogenetic relationships between banana species will help to fine-tune the taxonomy of Musaceae.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, 772 00 Olomouc, Czech Republic.

ABSTRACT

Background: The classification of the Musaceae (banana) family species and their phylogenetic inter-relationships remain controversial, in part due to limited nucleotide information to complement the morphological and physiological characters. In this work the evolutionary relationships within the Musaceae family were studied using 13 species and DNA sequences obtained from a set of 19 unlinked nuclear genes.

Results: The 19 gene sequences represented a sample of ~16 kb of genome sequence (~73% intronic). The sequence data were also used to obtain estimates for the divergence times of the Musaceae genera and Musa sections. Nucleotide variation within the sample confirmed the close relationship of Australimusa and Callimusa sections and showed that Eumusa and Rhodochlamys sections are not reciprocally monophyletic, which supports the previous claims for the merger between the two latter sections. Divergence time analysis supported the previous dating of the Musaceae crown age to the Cretaceous/Tertiary boundary (~ 69 Mya), and the evolution of Musa to ~50 Mya. The first estimates for the divergence times of the four Musa sections were also obtained.

Conclusions: The gene sequence-based phylogeny presented here provides a substantial insight into the course of speciation within the Musaceae. An understanding of the main phylogenetic relationships between banana species will help to fine-tune the taxonomy of Musaceae.

Show MeSH
Transitions and transversions versus divergence plots. The estimated number of transitions and transversions for each pairwise comparison was plotted against the genetic distance calculated with the TN93 model [80] for (1) dataset A, (2) dataset B, (3) exonic sequence, (4) intronic sequence. Transitions outnumber transversions along with the linear increase in the genetic distance. This pattern can be interpreted as indicating that substitution saturation has not been reached, so that the data can be expected to provide sufficient phylogenetic signal.
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Figure 1: Transitions and transversions versus divergence plots. The estimated number of transitions and transversions for each pairwise comparison was plotted against the genetic distance calculated with the TN93 model [80] for (1) dataset A, (2) dataset B, (3) exonic sequence, (4) intronic sequence. Transitions outnumber transversions along with the linear increase in the genetic distance. This pattern can be interpreted as indicating that substitution saturation has not been reached, so that the data can be expected to provide sufficient phylogenetic signal.

Mentions: Nucleotide sequences are considered to be phylogenetically informative until they reach the substitution saturation. At this point, it is no longer possible to deduce whether an observed similarity between a pair of sequences results from their common ancestry or whether this has occurred by chance [61]. To avoid the inclusion of non-informative sequence, the level of substitution saturation was evaluated by plotting transitions and transversions against the genetic distance for both datasets A and B, as well as for the exonic and intronic sequence separately. This procedure showed that the frequency of both transitions and transversions increased linearly along with divergence (Figure 1) with transitions outnumbering transversions. This indicates that the saturation plateau was not reached, and the data still retained sufficient phylogenetic signal.


A multi gene sequence-based phylogeny of the Musaceae (banana) family.

Christelová P, Valárik M, Hřibová E, De Langhe E, Doležel J - BMC Evol. Biol. (2011)

Transitions and transversions versus divergence plots. The estimated number of transitions and transversions for each pairwise comparison was plotted against the genetic distance calculated with the TN93 model [80] for (1) dataset A, (2) dataset B, (3) exonic sequence, (4) intronic sequence. Transitions outnumber transversions along with the linear increase in the genetic distance. This pattern can be interpreted as indicating that substitution saturation has not been reached, so that the data can be expected to provide sufficient phylogenetic signal.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3102628&req=5

Figure 1: Transitions and transversions versus divergence plots. The estimated number of transitions and transversions for each pairwise comparison was plotted against the genetic distance calculated with the TN93 model [80] for (1) dataset A, (2) dataset B, (3) exonic sequence, (4) intronic sequence. Transitions outnumber transversions along with the linear increase in the genetic distance. This pattern can be interpreted as indicating that substitution saturation has not been reached, so that the data can be expected to provide sufficient phylogenetic signal.
Mentions: Nucleotide sequences are considered to be phylogenetically informative until they reach the substitution saturation. At this point, it is no longer possible to deduce whether an observed similarity between a pair of sequences results from their common ancestry or whether this has occurred by chance [61]. To avoid the inclusion of non-informative sequence, the level of substitution saturation was evaluated by plotting transitions and transversions against the genetic distance for both datasets A and B, as well as for the exonic and intronic sequence separately. This procedure showed that the frequency of both transitions and transversions increased linearly along with divergence (Figure 1) with transitions outnumbering transversions. This indicates that the saturation plateau was not reached, and the data still retained sufficient phylogenetic signal.

Bottom Line: Nucleotide variation within the sample confirmed the close relationship of Australimusa and Callimusa sections and showed that Eumusa and Rhodochlamys sections are not reciprocally monophyletic, which supports the previous claims for the merger between the two latter sections.The gene sequence-based phylogeny presented here provides a substantial insight into the course of speciation within the Musaceae.An understanding of the main phylogenetic relationships between banana species will help to fine-tune the taxonomy of Musaceae.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, 772 00 Olomouc, Czech Republic.

ABSTRACT

Background: The classification of the Musaceae (banana) family species and their phylogenetic inter-relationships remain controversial, in part due to limited nucleotide information to complement the morphological and physiological characters. In this work the evolutionary relationships within the Musaceae family were studied using 13 species and DNA sequences obtained from a set of 19 unlinked nuclear genes.

Results: The 19 gene sequences represented a sample of ~16 kb of genome sequence (~73% intronic). The sequence data were also used to obtain estimates for the divergence times of the Musaceae genera and Musa sections. Nucleotide variation within the sample confirmed the close relationship of Australimusa and Callimusa sections and showed that Eumusa and Rhodochlamys sections are not reciprocally monophyletic, which supports the previous claims for the merger between the two latter sections. Divergence time analysis supported the previous dating of the Musaceae crown age to the Cretaceous/Tertiary boundary (~ 69 Mya), and the evolution of Musa to ~50 Mya. The first estimates for the divergence times of the four Musa sections were also obtained.

Conclusions: The gene sequence-based phylogeny presented here provides a substantial insight into the course of speciation within the Musaceae. An understanding of the main phylogenetic relationships between banana species will help to fine-tune the taxonomy of Musaceae.

Show MeSH