Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots

Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots

Premise of the Study We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot‐wide divergence times and rates of species diversification. Methods We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification...

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Bibliographic Details
Published in:American journal of botany Vol. 105; no. 11; pp. 1888 - 1910
Main Authors: Givnish, Thomas J., Zuluaga, Alejandro, Spalink, Daniel, Gomez, Marybel Soto, Lam, Vivienne K. Y., Saarela, Jeffrey M., Sass, Chodon, Iles, William J. D., de Sousa, Danilo José Lima, Leebens-Mack, James, Pires, J. Chris, Zomlefer, Wendy B., Gandolfo, Maria A., Davis, Jerrold I., Stevenson, Dennis W., dePamphilis, Claude, Specht, Chelsea D., Graham, Sean W., Barrett, Craig F., Ané, Cécile
Format: Journal Article
Language:English
Published: United States John Wiley and Sons, Inc 01-11-2018
Botanical Society of America, Inc
Subjects:
aquatic origin
Biodiversity
chloroplast
Cretaceous
Diagnostic systems
Divergence
divergence times
diversification
Evolution
Floating plants
fossil calibration
Genes
Genomics
molecular phylogeny
monocot syndrome
monocotyledons
mycoheterotrophy
Phylogenetics
Phylogeny
Plant biology
Plastids
Plastomes
RESEARCH ARTICLE
Species
Zingiberales
Zingiberales
chloroplast
divergence times
molecular phylogeny
aquatic origin
monocotyledons
diversification
mycoheterotrophy
monocot syndrome
fossil calibration
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Summary:Premise of the Study We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot‐wide divergence times and rates of species diversification. Methods We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth. Key Results Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. Net species diversification underwent four large‐scale accelerations in PACMAD‐BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae‐Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non‐coding regions in identifying and supporting short, deep branches. Conclusions We provide the first resolved, well‐supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome‐scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).
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content type line 23
ISSN:0002-9122
1537-2197
DOI:10.1002/ajb2.1178