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探究棕榈科（Arecaceae）的系统发育关系，但该科内部分类群的演化关联仍存在歧义，尤以包含椰子与油棕的物种多样性最高的亚科——槟榔亚科（Arecoideae）内的类群关系最为突出。本研究通过对比两种下一代靶向质体富集（targeted plastid-enrichment）方法，以解析槟榔亚科的系统发育关系。
方法：本研究采用下一代测序（next-generation sequencing）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（hybrid gene capture）技术富集叶绿体（chloroplast）靶序列；选取10个类群分别采用两种方法富集以进行对照。本研究共获取14个槟榔亚科族级类群的31个代表物种，以及5个外类群的叶绿体序列数据。采用最大似然法（maximum likelihood）、最大简约法（maximum parsimony）与贝叶斯分析法（Bayesian analyses）重建系统发育树。
关键结果：长距离PCR与杂交基因捕获均可有效富集质体基因组，且二者的测序覆盖度相近。槟榔亚科被证实为单系类群，其中颊萼藤族（Chamaedoreeae）为最早分化的支系，这表明三数花的发育特征是不含颊萼藤族的槟榔亚科演化支的共衍征。本研究在该类群中恢复出3个主要演化支：皇家椰族/莱茵茨椰族/椰子族（Roystoneeae/Reinhardtieae/Cocoseae，简称RRC）、槟榔族/Euterpeae/Geonomateae/Leopoldinieae/Manicarieae/Pelagodoxeae（核心槟榔亚支，core arecoids）以及Podococceae/Oranieae/Sclerospermeae（简称POS）。在核心槟榔亚支中，槟榔族+Euterpeae演化支被明确分辨。POS演化支为RRC+核心槟榔亚支演化支的姊妹群，这暗示这三个演化支的共同祖先分布区位于南美洲。
结论：本研究构建的质体基因组系统发育树，为此前研究中模糊不清的分类关系提供了可靠的解析结果，并为棕榈科演化研究带来了新的认知。