Phylogenetic Relationships and Evolution in the Strelitziaceae (Zingiberales)

Cron, G.V.; Pirone, Cary; Bartlett, Madelaine; Kress, W. John; Specht, Chelsea D.

doi:10.1600/036364412x648562

Cited by 20 publications

(19 citation statements)

References 71 publications

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“…The coalescent analysis using ASTRAL-II did not show support for some relationships, but the validity of applying these approaches remains unclear ( Gatesy & Springer, 2013 ; Gatesy & Springer, 2014 ; Mirarab et al, 2014 ). Importantly, the relationships found here are not in conflict with existing well supported hypotheses for generic-level relationships ( Kress, Prince & Williams, 2002 ; Johansen, 2005 ; Prince & Kress, 2006 ; Specht, 2006 ; Kress et al, 2007 ; Prince, 2010 ; Li et al, 2010 ; Cron et al, 2012 ), indicating that our method is identifying orthologs and that the data produced should be useful at finer phylogenetic scales as well a deep ones.…”

Section: Discussionsupporting

confidence: 56%

Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage

Sass

Iles

Barrett

et al. 2016

PeerJ

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The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated to be monophyletic, phylogenetic relationships among these families remain unresolved. Neither combined morphological and molecular studies nor recent attempts to resolve family relationships using sequence data from whole plastomes has resulted in a well-supported, family-level phylogenetic hypothesis of relationships. Here we approach this challenge by leveraging the complete genome of one member of the order, Musa acuminata, together with transcriptome information from each of the other seven families to design a set of nuclear loci that can be enriched from highly divergent taxa with a single array-based capture of indexed genomic DNA. A total of 494 exons from 418 nuclear genes were captured for 53 ingroup taxa. The entire plastid genome was also captured for the same 53 taxa. Of the total genes captured, 308 nuclear and 68 plastid genes were used for phylogenetic estimation. The concatenated plastid and nuclear dataset supports the position of Musaceae as sister to the remaining seven families. Moreover, the combined dataset recovers known intra- and inter-family phylogenetic relationships with generally high bootstrap support. This is a flexible and cost effective method that gives the broader plant biology community a tool for generating phylogenomic scale sequence data in non-model systems at varying evolutionary depths.

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Section: Discussionsupporting

confidence: 56%

Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage

Sass

Iles

Barrett

et al. 2016

PeerJ

View full text Add to dashboard Cite

show abstract

“…The coalescent analysis using ASTRAL-II did not show support for some relationships, but the validity of applying these approaches remains unclear (Gatesy & Springer, 2013, 2014Mirarab et al, 2014). Importantly, the relationships found here are not in conflict with existing well supported hypotheses for generic-level relationships (Kress, Prince & Williams, 2002;Johansen, 2005;Prince & Kress, 2006;Specht, 2006;Kress et al, 2007;Prince, 2010;Li et al, 2010;Cron et al, 2012), indicating that our method is identifying orthologs and that the data produced should be useful at finer phylogenetic scales as well a deep ones.…”

Section: Discussionmentioning

confidence: 56%

Peer Review #1 of "Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage (v0.1)"

Bi¹

2016

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The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated to be monophyletic, phylogenetic relationships among these families remain unresolved. Neither combined morphological and molecular studies nor recent attempts to resolve family relationships using sequence data from whole plastomes has resulted in a wellsupported, ordinal-level phylogenetic hypothesis of relationships. Here we approach this challenge by leveraging the complete genome of one member of the order, Musa acuminata, together with transcriptome information from each of the other seven families to design a set of nuclear loci that can be enriched from highly divergent taxa with a single array-based capture of indexed genomic DNA. A total of 494 exons from 418 nuclear genes were captured for 53 ingroup taxa. The entire plastid genome was also captured for the same 53 taxa. Of the total genes captured, 308 nuclear and 68 plastid genes were used for phylogenetic estimation. The concatenated plastid and nuclear dataset supports the position of Musaceae as sister to the remaining seven families. Moreover, the combined dataset recovers known intra-and inter-family phylogenetic relationships with generally high bootstrap support. This is a flexible and cost effective method that gives the broader plant biology community a tool for generating phylogenomic scale sequence data in nonmodel systems at varying evolutionary depths.

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“…To extrapolate consistency, homoplasy and retention indices, intrafamiliar relationships were established based on the following studies: Cannaceae (Prince, 2010), Costaceae (Specht, 2006), Marantaceae (Prince and Kress, 2006), Musaceae (Liu et al , 2010), Strelitziaceae (Cron et al , 2012), Zingiberaceae (Wood et al , 2000; Kress et al , 2002, 2007; Leong-Škorničková et al, 2011). …”

Section: Methodsmentioning

confidence: 99%

Species diversity driven by morphological and ecological disparity: a case study of comparative seed morphology and anatomy across a large monocot order

Benedict¹,

Smith²,

Specht³

et al. 2015

AoB PLANTS

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The banana and ginger group, order Zingiberales, comprises of exceptionally diverse, primarily tropical, plants. Within Zingiberales, the ginger family (Zingiberaceae) is unique in being not only the most species-rich but also the most disparate in terms of their morphology and anatomy, and the only group with a substantial number of species in temperate environments. Multiple radiations into temperate habitats were found to not be driven by morphological change, but instead may point to a genetic plasticity in the family that provided opportunities for speciation events not found anywhere else in the order.

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Phylogenetic Relationships and Evolution in the Strelitziaceae (Zingiberales)

Cited by 20 publications

References 71 publications

Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage

Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage

Peer Review #1 of "Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage (v0.1)"

Species diversity driven by morphological and ecological disparity: a case study of comparative seed morphology and anatomy across a large monocot order

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