College of Life Science, Foshan University, Foshan, 528231, Guangdong, China.
CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.
BMC Genomics. 2018 May 25;19(1):400. doi: 10.1186/s12864-018-4788-5.
The monophyly of flatfishes has not been supported in many molecular phylogenetic studies. The monophyly of Pleuronectoidei, which comprises all but one family of flatfishes, is broadly supported. However, the Psettodoidei, comprising the single family Psettodidae, is often found to be most closely related to other carangimorphs based on substantial sequencing efforts and diversely analytical methods. In this study, we examined why this particular result is often obtained.
The mitogenomes of five flatfishes were determined. Select mitogenomes of representative carangimorph species were further employed for phylogenetic and molecular clock analyses. Our phylogenetic results do not fully support Psettodes as a sister group to pleuronectoids or other carangimorphs. And results also supported the evidence of long-branch attraction between Psettodes and the adjacent clades. Two chronograms, derived from Bayesian relaxed-clock methods, suggest that over a short period in the early Paleocene, a series of important evolutionary events occurred in carangimorphs.
Based on insights provided by the molecular clock, we propose the following evolutionary explanation for the difficulty in determining the phylogenetic position of Psettodes: The initial diversification of Psettodes was very close in time to the initial diversification of carangimorphs, and the primary diversification time of pleuronectoids, the other suborder of flatfishes, occurred later than that of some percomorph taxa. Additionally, the clade of Psettodes is long and naked branch, which supports the uncertainty of its phylogenetic placement. Finally, we confirmed the monophyly of flatfishes, which was accepted by most ichthyologists.
许多分子系统发育研究都没有支持比目鱼类的单系性。除了比目鱼科外，还包含了所有的鲽形目鱼类，其单系性得到了广泛的支持。然而，鲷科，仅包含一个鲷科，通常基于大量的测序工作和不同的分析方法，被发现与其他鲹形目鱼类关系最密切。在本研究中，我们研究了为什么经常得到这个特定的结果。
测定了五种比目鱼的线粒体基因组。进一步选择了代表鲹形目物种的线粒体基因组进行系统发育和分子钟分析。我们的系统发育结果不完全支持 Psettodes 是鲽形目或其他鲹形目鱼类的姐妹群。结果还支持了 Psettodes 与相邻分支之间存在长枝吸引的证据。两个基于贝叶斯松弛时钟方法的系统发育树表明，在古新世早期的一个短时间内，鲹形目鱼类发生了一系列重要的进化事件。
基于分子钟提供的见解，我们提出了以下进化解释，以说明确定 Psettodes 系统发育位置的困难：Psettodes 的初始多样化时间非常接近鲹形目鱼类的初始多样化时间，而比目鱼科的其他亚目鱼类的主要多样化时间晚于一些鲈形目鱼类的多样化时间。此外，Psettodes 分支是长而裸露的分支，这支持了其系统发育位置的不确定性。最后，我们确认了比目鱼的单系性，这被大多数鱼类学家所接受。
