Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using plastid sequences derived from next-generation sequencing

• Published in: American journal of botany Vol. 102; no. 6; pp. 888 - 899
• Main Authors: Comer, Jason R., Zomlefer, Wendy B., Barrett, Craig F., Davis, Jerrold I., Stevenson, Dennis Wm, Heyduk, Karolina, Leebens-Mack, James H.
• Format: Journal Article
• Language: English
• Published: United States Botanical Society of America, Inc 01.06.2015; Botanical Society of America
• Subjects: Arecaceae; Arecaceae - genetics; Arecoideae; Base Sequence; Chloroplasts; gene capture; Genomes; High-Throughput Nucleotide Sequencing - methods; Likelihood Functions; Morphology; next‐generation sequencing; oil palm; Phylogenetics; Phylogeny; Plastids; Plastids - genetics; Polymerase Chain Reaction; Species Specificity; Trees; Arecaceae; Arecoideae; phylogenetics; oil palm; gene capture; next-generation sequencing
• ISSN: 0002-9122; 1537-2197
• DOI: 10.3732/ajb.1500057

• Premise of the study: Several studies have incorporated molecular and morphological data to study the phylogeny of the palms (Arecaceae), but some relationships within the family remain ambiguous—particularly those within Arecoideae, the most diverse subfamily including coconut and oil palm. Here, two next-generation, targeted plastid-enrichment methods were compared and used to elucidate Arecoideae phylogeny. • Methods: Next-generation sequencing techniques were used to generate a plastid genome data set. Long range PCR and hybrid gene capture were used to enrich for chloroplast targets. Ten taxa were enriched using both methods for comparison. Chloroplast sequence data were generated for 31 representatives of the 14 Arecoideae tribes and five outgroup taxa. The phylogeny was reconstructed using maximum likelihood, maximum parsimony, and Bayesian analyses. • Key results: Long range PCR and hybrid gene capture both enriched the plastid genome and provided similar sequencing coverage. Subfamily Arecoideae was resolved as monophyletic with tribe Chamaedoreeae as the earliest-diverging lineage, implying that the development of flowers in triads defines a synapomorphy for the Arecoideae clade excluding Chamaedoreeae. Three major clades within this group were recovered: Roystoneeae/Reinhardtieae/Cocoseae (RRC), Areceae/Euterpeae/Geonomateae/Leopoldinieae/Manicarieae/Pelagodoxeae (core arecoids), and Podococceae/Oranieae/Sclerospermeae (POS). An Areceae + Euterpeae clade was resolved within the core arecoids. The POS clade was sister to a RRC + core arecoids clade, implying a shared ancestral area in South America for these three clades. • Conclusions: The plastome phylogeny recovered here provides robust resolution of previously ambiguous studies and new insights into palm evolution.