Phylogenetic relationships among arecoid palms (Arecaceae: Arecoideae)

Abstract

Background and aims: The Arecoideae is the largest and most diverse of the five subfamilies of palms (Arecaceae/Palmae), containing >50 % of the species in the family. Despite its importance, phylogenetic relationships among Arecoideae are poorly understood. Here the most densely sampled phylogenetic analysis of Arecoideae available to date is presented. The results are used to test the current classification of the subfamily and to identify priority areas for future research.

Methods: DNA sequence data for the low-copy nuclear genes PRK and RPB2 were collected from 190 palm species, covering 103 (96 %) genera of Arecoideae. The data were analysed using the parsimony ratchet, maximum likelihood, and both likelihood and parsimony bootstrapping.

Key results and conclusions: Despite the recovery of paralogues and pseudogenes in a small number of taxa, PRK and RPB2 were both highly informative, producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Simultaneous analyses of the combined data sets provided additional resolution and support. Two areas of incongruence between PRK and RPB2 were strongly supported by the bootstrap relating to the placement of tribes Chamaedoreeae, Iriarteeae and Reinhardtieae; the causes of this incongruence remain uncertain. The current classification within Arecoideae was strongly supported by the present data. Of the 14 tribes and 14 sub-tribes in the classification, only five sub-tribes from tribe Areceae (Basseliniinae, Linospadicinae, Oncospermatinae, Rhopalostylidinae and Verschaffeltiinae) failed to receive support. Three major higher level clades were strongly supported: (1) the RRC clade (Roystoneeae, Reinhardtieae and Cocoseae), (2) the POS clade (Podococceae, Oranieae and Sclerospermeae) and (3) the core arecoid clade (Areceae, Euterpeae, Geonomateae, Leopoldinieae, Manicarieae and Pelagodoxeae). However, new data sources are required to elucidate ambiguities that remain in phylogenetic relationships among and within the major groups of Arecoideae, as well as within the Areceae, the largest tribe in the palm family.

Fig. 1.

Strict consensus trees from parsimony ratchet analyses of the PRK (number of MP trees, 3856; MP tree length, 1460; CI, 0·45; RI, 0·78; RC, 0·35) and RPB2 (number of MP trees, 3742; MP tree length, 1562; CI, 0·52; RI, 0·79; RC, 0·41) data sets. Values above the branches are MP/ML bootstrap percentages. Groups recognized in the classification of Dransfield et al. (2005, 2008) and major clades mentioned in the text are indicated. The asterisk indicates that the core arecoid clade in this tree also includes tribe Iriarteeae. Labels with a dotted line indicate that the group is only resolved in part. Key to abbreviations, Ar, Areceae; Arc, Archontophoenicinae; Are, Arecinae; At, Attaleinae; Ba, Basseliniinae; Bc, Bactridinae; Ca, Carpoxylinae; Ch, Chamaedoreeae; Cl, Clinospermatinae; Co, Cocoseae; Dy, Dypsidinae; El, Elaeidinae; Eu, Euterpeae; Ge, Geonomateae; Ir, Iriarteeae; Le, Leopoldinieae; Li, Linospadicinae; Ma, Manicarieae; On, Oncospermatinae; Or, Oranieae; Pe, Pelagodoxeae; Po, Podococceae; Pt, Ptychospermatinae; Re, Reinhardtieae; Ro, Roystoneeae; Sc, Sclerospermeae; Ve, Verschaffeltiinae.

Fig. 2.

Strict consensus trees from parsimony ratchet analyses of the PRK and RPB2 data sets, tribe Areceae only, continued from Fig. 1. See legend to Fig. 1 for further details and key to abbreviations. The taxon labelled Masoala madagascariensis L&D represents the PRK sequence published by Lewis and Doyle (2002).

Fig. 3.

Strict consensus trees from parsimony ratchet analyses of the combined analysis of PRK and RPB2 (number of MP trees, 3662; MP tree length, 2855; CI, 0·48; RI, 0·74; RC, 0·36). See legend to Fig. 1 for further details and key to abbreviations.

Fig. 4.

Strict consensus trees from parsimony ratchet analyses of the combined analysis of PRK and RPB2, tribe Areceae only, continued from Fig. 3. See legend to Fig. 1 for further details and key to abbreviations.

Fig. 5.

Summary trees depicting inter-tribal relationships resolved in this study compared with the three most relevant previous studies (Hahn, 2002a; Asmussen et al., 2006; Baker et al., 2009). Note that tribe Pelagodoxeae was not sampled by Hahn (2002a). Plastid DNA regions sampled by Hahn (2002a) were atpB, rbcL, ndhF, trnQ–rps16 and trnD–trnT, and those sampled by Asmussen et al. (2006) were matK, rbcL, rps16 intron, trnL intron and trnL–F spacer. Baker et al. (2009) combined 16 published data sets including those of Hahn and Asmussen et al. and existing data for PRK and RPB2 (e.g. Norup et al., 2006; Savolainen et al., 2006). Bold branches indicate relationships supported by bootstrap percentages ≥85 % (for both MP and ML, where available). For the supertree of Baker et al. (2009), bold branches indicate relationships supported by five or more input trees (s ≥5). Remaining branches are supported by <85 BP (or for the supertree s <5) except for dotted branches that are not supported by >50 BP (or for the supertree s = 1). * indicates tribes that are not resolved as monophyletic. Sub-tribes of Areceae are not shown here. Key to clade annotations: 1, core arecoid clade (Areceae, Euterpeae, Geonomateae, Leopoldinieae, Manicarieae and Pelagodoxeae); 2, POS clade (Podococceae, Oranieae and Sclerospermeae); 3, Oranieae–Sclerospermeae clade; 4, RRC clade (Roystoneeae, Reinhardtieae and Cocoseae); and 5, Reinhardtieae–Cocoseae clade.