Phylogenetic Analysis of the Plastid Inverted Repeat for 244 Species: Insights into Deeper-Level Angiosperm Relationships from a Long, Slowly Evolving Sequence Region

Phylogenetic Analysis of the Plastid Inverted Repeat for 244 Species: Insights into Deeper-Level Angiosperm Relationships from a Long, Slowly Evolving Sequence Region

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 plast...

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Bibliographic Details
Published in:International journal of plant sciences Vol. 172; no. 4; pp. 541 - 558
Main 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, Roolse, Piedrahita, Ana, Xi, Zhenxiang, Davis, Charles C, Soltis, Pamela S
Format: Journal Article
Language:English
Published: Chicago University of Chicago Press 01-05-2011
University of Chicago, acting through its Press
Subjects:
Angiosperms
Berberidopsidales
Biological taxonomies
Caryophyllales
data collection
Datasets
Dilleniaceae
Evolution
Flowers & plants
Gene expression
Genomes
Genomics
Hardwood trees
Maximum likelihood method
Phylogenetics
phylogeny
Plant sciences
Plastids
Santalales
Saxifragales
Taxa
Topology
Vitaceae
phylogenetics
plastid inverted repeat
large data sets
Angiosperm Tree of Life
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Summary: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.
ISSN:1058-5893
1537-5315
DOI:10.1086/658923