Phylogenetic analysis of seven WRKY genes across the palm subtribe Attaleinae (Arecaceae) [corrected] identifies Syagrus as sister group of the coconut.

Alan W Meerow,Larry Noblick,James W Borrone,Thomas L P Couvreur,William J Hahn,Raymond J Schnell,Nora H Oleas,Kyoko Nakamura,Margarita Mauro-Herrera,David N Kuhn,Simon Joly

doi:10.1371/journal.pone.0007353

Abstract

BackgroundThe Cocoseae is one of 13 tribes of Arecaceae subfam. Arecoideae, and contains a number of palms with significant economic importance, including the monotypic and pantropical Cocos nucifera L., the coconut, the origins of which have been one of the “abominable mysteries” of palm systematics for decades. Previous studies with predominantly plastid genes weakly supported American ancestry for the coconut but ambiguous sister relationships. In this paper, we use multiple single copy nuclear loci to address the phylogeny of the Cocoseae subtribe Attaleinae, and resolve the closest extant relative of the coconut.Methodology/Principal FindingsWe present the results of combined analysis of DNA sequences of seven WRKY transcription factor loci across 72 samples of Arecaceae tribe Cocoseae subtribe Attaleinae, representing all genera classified within the subtribe, and three outgroup taxa with maximum parsimony, maximum likelihood, and Bayesian approaches, producing highly congruent and well-resolved trees that robustly identify the genus Syagrus as sister to Cocos and resolve novel and well-supported relationships among the other genera of the Attaleinae. We also address incongruence among the gene trees with gene tree reconciliation analysis, and assign estimated ages to the nodes of our tree.Conclusions/SignificanceThis study represents the as yet most extensive phylogenetic analyses of Cocoseae subtribe Attaleinae. We present a well-resolved and supported phylogeny of the subtribe that robustly indicates a sister relationship between Cocos and Syagrus. This is not only of biogeographic interest, but will also open fruitful avenues of inquiry regarding evolution of functional genes useful for crop improvement. Establishment of two major clades of American Attaleinae occurred in the Oligocene (ca. 37 MYBP) in Eastern Brazil. The divergence of Cocos from Syagrus is estimated at 35 MYBP. The biogeographic and morphological congruence that we see for clades resolved in the Attaleinae suggests that WRKY loci are informative markers for investigating the phylogenetic relationships of the palm family.

Highlights

Cocos nucifera L., the coconut, is a charismatic monotypic genus forming a dominant part of littoral vegetation across the tropics
Maximum parsimony (MP) strict and maximum likelihood (ML) bootstrap consensus trees are available as supplemental Figures S1–4
WRKY genes, members of the WRKY-GCM1 superfamily [41,42], contain a highly conserved DNA binding domain about 60 amino acids in length composed of the conserved WRKYGQK sequence followed by a C2H2- or C2HC-type zinc finger motif

Summary

Introduction

Cocos nucifera L., the coconut, is a charismatic monotypic genus forming a dominant part of littoral vegetation across the tropics. Cocos nucifera is pantropically distributed, a present day range significantly influenced both by a seed well-adapted to oceanic dispersal and the species’ importance to humans [2,3,4]. Because of this wide geographic range, the biogeographic origins of the coconut have been one of the ‘‘abominable mysteries’’ of palm systematics for decades [5]. Arecoideae, and contains a number of palms with significant economic importance, including the monotypic and pantropical Cocos nucifera L., the coconut, the origins of which have been one of the ‘‘abominable mysteries’’ of palm systematics for decades.

Methods

Results

Conclusion