成都生物所在PLOS ONE报道系统发育基因组学研究新方法

系统发育基因组学研究，主要是利用基因组/转录组数据和基因组学方法解决重要类群的进化关系，从而揭示物种起源与分化以及多样性形成机制等重要问题。与传统的系统发育研究相比，系统发育基因组学具有信息量大、结果可靠的优点。

但是在这个新兴的领域，研究方法的发展严重滞后于数据量的爆炸式增长。传统的方法在处理成千上万个基因数据时运算较慢，存在难以克服的系统误差(如速率异质性)。为此，科研人员新提出了“一个基因一个性状”的系统发育基因组学研究方法，以更好地适应系统发育基因组学发展的要求。

龟在四足动物中的系统发育位置长期以来备受争议。在龟是和鸟类还是蜥蜴的亲缘关系更近的问题上，不同的研究会存在相互矛盾的结论。

中国科学院成都生物研究所系统进化与保育学科组吕彬博士和傅金钟研究员通过测定乌龟的转录组，得到了4584个同源基因，同时使用了传统方法和“一个基因一个性状”的方法进行推断。传统的系统学方法强烈地支持龟与鸟和鳄鱼的亲缘关系最近，但是对于每个基因的研究却发现龟的系统发育位置存在大量的不一致性。

“一个基因一个性状”的方法不仅能够更加高效地使用基因组海量数据进行计算，而且能够真实地反映出这种不确定性。新方法与传统方法相辅相成，能够更好地推动系统发育基因组学的普及和发展。

该研究受中国博士后基金、国家自然科学基金和中国科学院知识创新工程项目等资助，结果于近期发表在PLoS ONE上。

原文摘要：

Using Genes as Characters and a Parsimony Analysis to Explore the Phylogenetic Position of Turtles

Bin Lu, Weizhao Yang, Qiang Dai, Jinzhong Fu

The phylogenetic position of turtles within the vertebrate tree of life remains controversial. Conflicting conclusions from different studies are likely a consequence of systematic error in the tree construction process, rather than random error from small amounts of data. Using genomic data, we evaluate the phylogenetic position of turtles with both conventional concatenated data analysis and a “genes as characters” approach. Two datasets were constructed, one with seven species (human, opossum, zebra finch, chicken, green anole, Chinese pond turtle, and western clawed frog) and 4584 orthologous genes, and the second with four additional species (soft-shelled turtle, Nile crocodile, royal python, and tuatara) but only 1638 genes. Our concatenated data analysis strongly supported turtle as the sister-group to archosaurs (the archosaur hypothesis), similar to several recent genomic data based studies using similar methods. When using genes as characters and gene trees as character-state trees with equal weighting for each gene, however, our parsimony analysis suggested that turtles are possibly sister-group to diapsids, archosaurs, or lepidosaurs. None of these resolutions were strongly supported by bootstraps. Furthermore, our incongruence analysis clearly demonstrated that there is a large amount of inconsistency among genes and most of the conflict relates to the placement of turtles. We conclude that the uncertain placement of turtles is a reflection of the true state of nature. Concatenated data analysis of large and heterogeneous datasets likely suffers from systematic error and over-estimates of confidence as a consequence of a large number of characters. Using genes as characters offers an alternative for phylogenomic analysis. It has potential to reduce systematic error, such as data heterogeneity and long-branch attraction, and it can also avoid problems associated with computation time and model selection. Finally, treating genes as characters provides a convenient method for examining gene and genome evolution.

标签: 乌龟 成都生物所 同源基因 发育基因组学

作者：中科院