Lindgren Annie R, Anderson Frank E
The Center for Life in Extreme Environments, Department of Biology, Portland State University, 1719 SW 10th Ave, SRTC Rm 246, Portland, OR 97201, USA.
Department of Zoology, Southern Illinois University, Carbondale, IL, USA.
Mol Phylogenet Evol. 2018 Jan;118:330-342. doi: 10.1016/j.ympev.2017.10.004. Epub 2017 Oct 6.
Historically, deep-level relationships within the molluscan class Cephalopoda (squids, cuttlefishes, octopods and their relatives) have remained elusive due in part to the considerable morphological diversity of extant taxa, a limited fossil record for species that lack a calcareous shell and difficulties in sampling open ocean taxa. Many conflicts identified by morphologists in the early 1900s remain unresolved today in spite of advances in morphological, molecular and analytical methods. In this study we assess the utility of transcriptome data for resolving cephalopod phylogeny, with special focus on the orders of Decapodiformes (open-eye squids, bobtail squids, cuttlefishes and relatives). To do so, we took new and previously published transcriptome data and used a unique cephalopod core ortholog set to generate a dataset that was subjected to an array of filtering and analytical methods to assess the impacts of: taxon sampling, ortholog number, compositional and rate heterogeneity and incongruence across loci. Analyses indicated that datasets that maximized taxonomic coverage but included fewer orthologs were less stable than datasets that sacrificed taxon sampling to increase the number of orthologs. Clades recovered irrespective of dataset, filtering or analytical method included Octopodiformes (Vampyroteuthis infernalis + octopods), Decapodiformes (squids, cuttlefishes and their relatives), and orders Oegopsida (open-eyed squids) and Myopsida (e.g., loliginid squids). Ordinal-level relationships within Decapodiformes were the most susceptible to dataset perturbation, further emphasizing the challenges associated with uncovering relationships at deep nodes in the cephalopod tree of life.
从历史上看，软体动物门头足纲（鱿鱼、乌贼、章鱼及其近亲）内部的深层次关系一直难以捉摸，部分原因在于现存分类群具有相当大的形态多样性，缺乏钙质外壳的物种化石记录有限，以及对远洋分类群进行采样存在困难。尽管形态学、分子学和分析方法有所进步，但20世纪初形态学家发现的许多冲突至今仍未得到解决。在本研究中，我们评估了转录组数据在解析头足类系统发育方面的效用，特别关注十腕总目（睁眼鱿鱼、短尾鱿鱼、乌贼及其近亲）的各个目。为此，我们采用了新的和先前发表的转录组数据，并使用一组独特的头足类核心直系同源基因来生成一个数据集，该数据集经过一系列过滤和分析方法，以评估以下因素的影响：分类群采样、直系同源基因数量、组成和速率异质性以及不同基因座之间的不一致性。分析表明，最大化分类学覆盖范围但包含较少直系同源基因的数据集，比为增加直系同源基因数量而牺牲分类群采样的数据集更不稳定。无论数据集、过滤或分析方法如何，所恢复的类群包括八腕总目（幽灵蛸 + 章鱼）、十腕总目（鱿鱼、乌贼及其近亲），以及开眼亚目（睁眼鱿鱼）和闭眼亚目（例如枪乌贼科鱿鱼）。十腕总目内部的目级关系最容易受到数据集扰动的影响，这进一步凸显了在头足类生命树的深层节点揭示关系所面临的挑战。
