Ultraconserved elements data for Amarsipus and Pelagiaria

Amarsipus carlsbergi is a rare mesopelagic fish distributed in the Indian and Pacific Oceans, and is the only species classified in the family Amarsipidae. Since its description in 1969, phylogenetic hypotheses have varied regarding its relationship with other percomorph lineages, but most have indicated a close relationship with the traditional suborder Stromateoidei. Molecular phylogenies place families previously classified in Stromateoidei within a diverse clade– Pelagiaria– that includes fishes such as tunas, cutlassfishes, and pomfrets. A recent analysis of a small number of loci resolved a clade containing Amarsipus and the stromateoid lineage Tetragonurus. A subsequent high-throughput sequence phylogeny based on ultraconserved elements (UCEs) of Pelagiaria lacked Amarsipus, but revealed both strong support for stromateoid paraphyly and high levels of gene tree incongruence. We gathered UCE sequence data for 610 UCE loci from Amarsipus and integrate these with samples from all remaining pelagiarian families. This provides a taxonomically comprehensive phylogenomic framework to test the evolutionary relationships of Amarsipus, and evaluate the support for stromateoid monophyly. As in previous studies, our analyses find high levels of gene tree topological discordance with regard to some deeper pelagiarian inter-relationships. However, we resolve Amarsipus as the sister lineage of a clade containing Tetragonurus and a family not considered a stromateoid lineage, Chiasmodontidae. This relationship is supported by both high gene tree concordance and node support. Our analyses also provide strong support for the paraphyly of Stromateoidei, casting uncertainty on previous hypotheses of the evolution of morphological traits across members of Pelagiaria.卡尔贝格阿玛西普鱼（Amarsipus carlsbergi）是一种珍稀的中层深海鱼类，分布于印度洋与太平洋海域，为阿玛西普鱼科（Amarsipidae）下的唯一物种。自1969年该物种被正式描述以来，学界关于其与其他鲈形总目（percomorph）支系的系统发育关系存在诸多假说，但绝大多数假说均支持其与传统鲳亚目（Stromateoidei）存在较近亲缘关系。 分子系统发育研究将此前归类于鲳亚目的各科置于一个多样性演化支——大洋鱼群（Pelagiaria）——之中，该演化支包含金枪鱼、带鱼、鲳鱼等大洋性鱼类。早期针对少量基因座的分析曾构建出包含阿玛西普鱼与鲳亚目支系方尾鲳属（Tetragonurus）的演化支。后续一项基于超保守元件（ultraconserved elements, UCEs）的大洋鱼群高通量测序系统发育研究未纳入阿玛西普鱼，但同时为鲳亚目的并系群属性提供了强支持，并揭示了极高的基因树不一致性水平。 本研究采集了阿玛西普鱼的610个UCE基因座的测序数据，并将其与其余所有大洋鱼群各科的样本进行整合分析。本研究所构建的分类学全覆盖系统发育组学框架，可用于检验阿玛西普鱼的演化关系，并评估鲳亚目单系性的支持证据。 与既往研究结果一致，本研究的分析同样发现，针对大洋鱼群部分深层类群的系统发育关系，基因树拓扑结构存在较高水平的不一致性。但本研究明确了阿玛西普鱼为一支演化支的姊妹支系，该演化支包含方尾鲳属以及此前未被归入鲳亚目的叉齿鱼科（Chiasmodontidae），这一关系得到了高基因树一致性与节点支持度的双重验证。本研究同时为鲳亚目的并系性提供了强有力的支持，这一结果对此前针对大洋鱼群类群形态性状演化的相关假说带来了不确定性。