Phylogenetic Analysis Of The Plastid Inverted Repeat For 244 Species: Insights Into Deeper-level Angiosperm Relationships From A Long, Slowly Evolving Sequence Region

Title:
Phylogenetic Analysis Of The Plastid Inverted Repeat For 244 Species: Insights Into Deeper-level Angiosperm Relationships From A Long, Slowly Evolving Sequence Region
Authors:
Moore, Michael J.; Hassan, Nasr; Gitzendanner, Matthew A.; Bruenn, Riva A.; Croley, Matthew; Vandeventer, Alexia; Horn, James W.; Dhingra, Amit; Brockington, Samuel F.; Latvis, Maribeth; Ramdial, Jeremy; Alexandre, Roosle; Piedrahita, Ana; Xi, Zhenxiang; Davis, Charles C.; Soltis, Pamela S.; Soltis, Douglas E.
Abstract:
Recent plastid phylogenomic studies have helped clarify the backbone phylogeny of angiosperms. However, the relatively limited taxon sampling in these studies has precluded strongly supported resolution of some regions of angiosperm phylogeny. Other recent work has suggested that the 25,000-bp plastid inverted repeat (IR) region may be a valuable source of characters for resolving these remaining problematic nodes. Consequently, we aligned all available angiosperm IR sequences to produce a matrix of 24,702 aligned bases for 246 accessions, including 36 new accessions. Maximum likelihood analyses of the complete data set yielded a generally well-supported topology that is highly congruent with those of recent plastid phylogenomic analyses. However, reducing taxon sampling to match a recent 83-gene plastid analysis resulted in significant changes in bootstrap support at some nodes. Notably, IR analyses resolved Pentapetalae into three well-supported clades: (1) superasterids (comprising Santalales, Caryophyllales, Berberidopsidales, and Asteridae), (2) superrosids (comprising Vitaceae, Saxifragales, and Rosidae), and (3) Dilleniaceae. These results provide important new evidence for a stable, well-supported phylogenetic framework for angiosperms and demonstrate the utility of IR data for resolving the deeper levels of angiosperm phylogeny. They also reiterate the importance of carefully considering taxon sampling in phylogenomic studies.
Citation:
Moore, Michael J., Nasr Hassan, Matthew A. Gitzendanner, Riva A. Bruenn, et al. 2011. "Phylogenetic Analysis Of The Plastid Inverted Repeat For 244 Species: Insights Into Deeper-level Angiosperm Relationships From A Long, Slowly Evolving Sequence Region." International Journal Of Plant Sciences 172(4): 541-558.
Publisher:
University of Chicago Press
DATE ISSUED:
2011-05
Department:
Biology
Type:
article
PUBLISHED VERSION:
10.1086/658923
PERMANENT LINK:
http://hdl.handle.net/11282/310108

Full metadata record

DC FieldValue Language
dc.contributor.authorMoore, Michael J.en_US
dc.contributor.authorHassan, Nasren_US
dc.contributor.authorGitzendanner, Matthew A.en_US
dc.contributor.authorBruenn, Riva A.en_US
dc.contributor.authorCroley, Matthewen_US
dc.contributor.authorVandeventer, Alexiaen_US
dc.contributor.authorHorn, James W.en_US
dc.contributor.authorDhingra, Amiten_US
dc.contributor.authorBrockington, Samuel F.en_US
dc.contributor.authorLatvis, Maribethen_US
dc.contributor.authorRamdial, Jeremyen_US
dc.contributor.authorAlexandre, Roosleen_US
dc.contributor.authorPiedrahita, Anaen_US
dc.contributor.authorXi, Zhenxiangen_US
dc.contributor.authorDavis, Charles C.en_US
dc.contributor.authorSoltis, Pamela S.en_US
dc.contributor.authorSoltis, Douglas E.en_US
dc.date.accessioned2013-12-23T16:25:33Zen
dc.date.available2013-12-23T16:25:33Zen
dc.date.issued2011-05en
dc.identifier.citationMoore, Michael J., Nasr Hassan, Matthew A. Gitzendanner, Riva A. Bruenn, et al. 2011. "Phylogenetic Analysis Of The Plastid Inverted Repeat For 244 Species: Insights Into Deeper-level Angiosperm Relationships From A Long, Slowly Evolving Sequence Region." International Journal Of Plant Sciences 172(4): 541-558.en_US
dc.identifier.issn1058-5893en_US
dc.identifier.urihttp://hdl.handle.net/11282/310108en
dc.description.abstractRecent plastid phylogenomic studies have helped clarify the backbone phylogeny of angiosperms. However, the relatively limited taxon sampling in these studies has precluded strongly supported resolution of some regions of angiosperm phylogeny. Other recent work has suggested that the 25,000-bp plastid inverted repeat (IR) region may be a valuable source of characters for resolving these remaining problematic nodes. Consequently, we aligned all available angiosperm IR sequences to produce a matrix of 24,702 aligned bases for 246 accessions, including 36 new accessions. Maximum likelihood analyses of the complete data set yielded a generally well-supported topology that is highly congruent with those of recent plastid phylogenomic analyses. However, reducing taxon sampling to match a recent 83-gene plastid analysis resulted in significant changes in bootstrap support at some nodes. Notably, IR analyses resolved Pentapetalae into three well-supported clades: (1) superasterids (comprising Santalales, Caryophyllales, Berberidopsidales, and Asteridae), (2) superrosids (comprising Vitaceae, Saxifragales, and Rosidae), and (3) Dilleniaceae. These results provide important new evidence for a stable, well-supported phylogenetic framework for angiosperms and demonstrate the utility of IR data for resolving the deeper levels of angiosperm phylogeny. They also reiterate the importance of carefully considering taxon sampling in phylogenomic studies.en_US
dc.publisherUniversity of Chicago Pressen_US
dc.identifier.doi10.1086/658923en
dc.subject.departmentBiologyen_US
dc.titlePhylogenetic Analysis Of The Plastid Inverted Repeat For 244 Species: Insights Into Deeper-level Angiosperm Relationships From A Long, Slowly Evolving Sequence Regionen_US
dc.typearticleen_US
dc.identifier.journalInternational Journal Of Plant Sciencesen_US
dc.identifier.volume172en_US
dc.identifier.issue4en_US
dc.identifier.startpage541en_US
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