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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.

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A phylogenetic tree based on dataset A sequence, with E. ventricosum as outgroup. Values above the branches indicate bootstrap support for MP and ML, respectively. Clades I and II indicate known taxonomic divisions within the Musaceae. Clade I: Eumusa (M. acuminata [A genome] and M. balbisiana [B genome]) plus Rhodochlamys (M. mannii and M. ornata) entries. Clade II: Australimusa (M. textilis, M. maclayi and Fe'i) and Callimusa (M. coccinea and M. beccarii) entries.
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Figure 2: A phylogenetic tree based on dataset A sequence, with E. ventricosum as outgroup. Values above the branches indicate bootstrap support for MP and ML, respectively. Clades I and II indicate known taxonomic divisions within the Musaceae. Clade I: Eumusa (M. acuminata [A genome] and M. balbisiana [B genome]) plus Rhodochlamys (M. mannii and M. ornata) entries. Clade II: Australimusa (M. textilis, M. maclayi and Fe'i) and Callimusa (M. coccinea and M. beccarii) entries.

Mentions: The reconstruction of phylogenetic relationships between the selected taxa representing the Musaceae family was performed by two different criterion-based methods (maximum parsimony; MP and maximum likelihood; ML) and by a third complementary approach based on the Bayesian inference method (BI). Data were first executed in MrModeltest v.2.3 [44] in order to select the most appropriate model of evolution to be used for phylogenetic analyses. The Akaike Information Criterion was chosen [63] to be implemented in maximum likelihood and Bayesian analysis, as it was reported to have preferable performance in model selection compared to likelihood ratio tests [64]. The evolutionary models selected for the phylogenetic reconstruction are detailed in Table 3. The MP analysis based on the individual gene fragment sequences produced more than one most parsimonious tree for eight of the 19 sequences (Additional File 2). In 15 of the 19 phylogenies there were unresolved polytomies. Clades I (Eumusa + Rhodochlamys) and II (Australimusa + Callimusa) were fully recovered (Figure 2), except for gene fragment g-4, the sequence of which comprised one of the shortest intron sequences and the lowest proportion of phylogenetically informative positions. A similar result was obtained by ML analysis, in which partially resolved phylogenies applied to 15 of the 19 sequences, with an altered topology appearing within either clade I or II for gene fragments g-5, g-12, g-17 and g-19 (Additional File 2).


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)

A phylogenetic tree based on dataset A sequence, with E. ventricosum as outgroup. Values above the branches indicate bootstrap support for MP and ML, respectively. Clades I and II indicate known taxonomic divisions within the Musaceae. Clade I: Eumusa (M. acuminata [A genome] and M. balbisiana [B genome]) plus Rhodochlamys (M. mannii and M. ornata) entries. Clade II: Australimusa (M. textilis, M. maclayi and Fe'i) and Callimusa (M. coccinea and M. beccarii) entries.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: A phylogenetic tree based on dataset A sequence, with E. ventricosum as outgroup. Values above the branches indicate bootstrap support for MP and ML, respectively. Clades I and II indicate known taxonomic divisions within the Musaceae. Clade I: Eumusa (M. acuminata [A genome] and M. balbisiana [B genome]) plus Rhodochlamys (M. mannii and M. ornata) entries. Clade II: Australimusa (M. textilis, M. maclayi and Fe'i) and Callimusa (M. coccinea and M. beccarii) entries.
Mentions: The reconstruction of phylogenetic relationships between the selected taxa representing the Musaceae family was performed by two different criterion-based methods (maximum parsimony; MP and maximum likelihood; ML) and by a third complementary approach based on the Bayesian inference method (BI). Data were first executed in MrModeltest v.2.3 [44] in order to select the most appropriate model of evolution to be used for phylogenetic analyses. The Akaike Information Criterion was chosen [63] to be implemented in maximum likelihood and Bayesian analysis, as it was reported to have preferable performance in model selection compared to likelihood ratio tests [64]. The evolutionary models selected for the phylogenetic reconstruction are detailed in Table 3. The MP analysis based on the individual gene fragment sequences produced more than one most parsimonious tree for eight of the 19 sequences (Additional File 2). In 15 of the 19 phylogenies there were unresolved polytomies. Clades I (Eumusa + Rhodochlamys) and II (Australimusa + Callimusa) were fully recovered (Figure 2), except for gene fragment g-4, the sequence of which comprised one of the shortest intron sequences and the lowest proportion of phylogenetically informative positions. A similar result was obtained by ML analysis, in which partially resolved phylogenies applied to 15 of the 19 sequences, with an altered topology appearing within either clade I or II for gene fragments g-5, g-12, g-17 and g-19 (Additional File 2).

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