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New Phytol. 2016 Jan;209(2):855-70. doi: 10.1111/nph.13617. Epub 2015 Sep 9.

Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots.

Author information

1
Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA.
2
Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA.
3
Royal Botanic Gardens, Kew, Richmond, TW9 3AB, UK.
4
Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
5
Department of Genetics and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, 5005, Australia.
6
Herbarium, The Huntington Library, Art Collection, and Botanical Gardens, San Marino, CA, 91108, USA.
7
Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA, 92521, USA.
8
L. H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA.
9
Donald Danforth Plant Science Center, St Louis, MO, 63132, USA.
10
Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
11
Pfizer Laboratory of Molecular Systematics, New York Botanical Garden, Bronx, NY, 10458, USA.

Abstract

Despite progress based on multilocus, phylogenetic studies of the palms (order Arecales, family Arecaceae), uncertainty remains in resolution/support among major clades and for the placement of the palms among the commelinid monocots. Palms and related commelinids represent a classic case of substitution rate heterogeneity that has not been investigated in the genomic era. To address questions of relationships, support and rate variation among palms and commelinid relatives, 39 plastomes representing the palms and related family Dasypogonaceae were generated via genome skimming and integrated within a monocot-wide matrix for phylogenetic and molecular evolutionary analyses. Support was strong for 'deep' relationships among the commelinid orders, among the five palm subfamilies, and among tribes of the subfamily Coryphoideae. Additionally, there was extreme heterogeneity in the plastid substitution rates across the commelinid orders indicated by model based analyses, with c. 22 rate shifts, and significant departure from a global clock. To date, this study represents the most comprehensively sampled matrix of plastomes assembled for monocot angiosperms, providing genome-scale support for phylogenetic relationships of monocot angiosperms, and lays the phylogenetic groundwork for comparative analyses of the drivers and correlates of such drastic differences in substitution rates across a diverse and significant clade.

KEYWORDS:

Arecaceae; Palmae; Poaceae; chloroplast; phylogenomics; plastome; rate heterogeneity

PMID:
26350789
DOI:
10.1111/nph.13617
[Indexed for MEDLINE]
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