Data from: Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using next-gen derived plastid sequences

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.研究背景：已有多项研究结合分子与形态学数据对棕榈科（Arecaceae）的系统发育展开探究，但该科内部分类群间的亲缘关系仍存在歧义，尤以槟榔亚科（Arecoideae）为甚——该亚科是包含椰子与油棕在内的物种多样性最高的棕榈亚科。本研究对比并采用两种新一代靶向质体富集（targeted plastid-enrichment）方法，以解析槟榔亚科的系统发育关系。 研究方法：依托新一代测序技术构建质体基因组（plastid genome）数据集，通过长距离PCR与杂交基因捕获技术富集叶绿体（chloroplast）靶序列。选取10个分类群同时采用两种方法进行富集以作对照。针对槟榔亚科14个族的31个代表物种以及5个外类群（outgroup），获取其叶绿体序列数据。分别采用最大似然法（maximum likelihood）、最大简约法（maximum parsimony）与贝叶斯分析（Bayesian analyses）重建系统发育树。 主要结果：长距离PCR与杂交基因捕获均可实现质体基因组富集，且二者提供的测序覆盖度相近。槟榔亚科被鉴定为单系群（monophyletic），其最早分化的演化支为榔色木族（Chamaedoreeae），这表明三数花的发育特征可作为排除榔色木族后的槟榔亚科分支的共衍征（synapomorphy）。本研究解析得到该类群内的三个主要演化支：Roystoneeae/Reinhardtieae/Cocoseae（简称RRC）、Areceae/Euterpeae/Geonomateae/Leopoldinieae/Manicarieae/Pelagodoxeae（核心槟榔类群）以及Podococceae/Oranieae/Sclerospermeae（简称POS）。在核心槟榔类群中，棕榈族（Areceae）与Euterpeae聚为一支。POS演化支为RRC与核心槟榔类群组成的演化支的姊妹群，这暗示这三个演化支拥有共同的南美祖先分布区。 研究结论：本研究获得的质体基因组系统发育树，解决了既往研究中存在歧义的分类关系，为棕榈科演化研究提供了全新的认知。