2016年7月18日，《Nature Genetics》期刊在线发表了题为“Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism”的研究论文。研究作者来自奥地利、德国、瑞士等国。

目前已知拟南芥属共有27个物种，其中完成了全基因组测序的包括拟南芥（Arabidopsis thaliana）和琴叶拟南芥（Arabidopsis lyrata）两个物种。这篇论文的主要内容是对拟南芥属的94个个体做了基因组重测序——覆盖拟南芥属所有的物种及它们涉及的地理范围。

（图片来源：http://dx.doi.org/10.1038/ng.3617）

作为模式植物的拟南芥（Arabidopsis thaliana），是最早完成全基因组测序的植物物种——2000年将论文发表于 Nature。关于拟南芥基因组的测序和重测序的研究已经被科学家们翻来覆去从各个角度去做，比如最近有两篇分别发表在 PNAS 和 Cell 上，“植物基因组”公众号都做过介绍：《1135个拟南芥基因组测序的论文发表于Cell》和《二代+三代测序获得N50为12.8 Mb的拟南芥Ler基因组组装》。值得注意的是，之前的研究大多集中于 Arabidopsis thaliana 这个物种的不同品系、生态型，最多扩展到琴叶 Arabidopsis lyrata。所以现在，这些欧洲的科学家又想出了一个新点子——把拟南芥整个属都测一遍（二代测序）。照这个趋势下去，说不定将来还会有人用三代测序将拟南芥属所有物种再测一遍呢^_^。

虽说对拟南芥属全部物种做基因组重测序很酷炫，但是把研究范围扩展到整个属，各个物种间的基因组差异必然较大，会导致 reads mapping 的比率很低——只有43%，而且只覆盖了作为模版的 Arabidopsis thaliana 基因组的66%。令人头疼的不止有这一点，这篇论文分析了 9119 个基因的进化树，发现除了拟南芥不同品系的基因总是聚在一起（100%的基因树支持）——染色体数目和别的不同，存在生殖隔离；多数 A. cebennensis 和 A. pedemontana 也能聚在一起（63%的基因树支持）；但是其它物种的基因树上就比较混乱了，毕竟有些物种之间在实验上是可以杂交的。

看到结果中基因树上的混乱，我在想做作者们当时的内心会不会是崩溃的——理论上，基因树和物种树应该是一致的啊——于是乎，作者们提出了一个论断：用物种分叉树来表示物种分化这种理论是不对的！论文的结束语是：Evidence for genome-wide contradictions between gene trees and species trees is rapidly accumulating in a wide range of species, raising the question of whether this should lead to a reevaluation of the utility of the tree as model for speciation45,46. We think it should, but time will tell。［旁白：时间会证明我们是对的^_^］

标题：Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism（http://dx.doi.org/10.1038/ng.3617）

摘要：The notion of species as reproductively isolated units related through a bifurcating tree implies that gene trees should generally agree with the species tree and that sister taxa should not share polymorphisms unless they diverged recently and should be equally closely related to outgroups. It is now possible to evaluate this model systematically. We sequenced multiple individuals from 27 described taxa representing the entire Arabidopsis genus. Cluster analysis identified seven groups, corresponding to described species that capture the structure of the genus. However, at the level of gene trees, only the separation of Arabidopsis thaliana from the remaining species was universally supported, and, overall, the amount of shared polymorphism demonstrated that reproductive isolation was considerably more recent than the estimated divergence times. We uncovered multiple cases of past gene flow that contradict a bifurcating species tree. Finally, we showed that the pattern of divergence differs between gene ontologies, suggesting a role for selection.

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