Exploring Tree-Like and Non-Tree-Like Patterns Using Genome Sequences: An Example Using the Inbreeding Plant Species Arabidopsis thaliana (L.) Heynh.
Exploring Tree-Like and Non-Tree-Like Patterns Using Genome Sequences: An Example Using the Inbreeding Plant Species Arabidopsis thaliana (L.) Heynh.
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DOI：
10.1093/sysbio/syv039
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发表时间：
2015-09
影响因子：
6.5
通讯作者：
Noah W M Stenz;B. Larget;D. Baum;C. Ané
中科院分区：
文献类型：
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作者：
Noah W M Stenz;B. Larget;D. Baum;C. Ané
基因组序列数据包含丰富的家系历史信息，但提取和解释这些信息的方法还没有完全开发出来。我们分析了多个自交植物拟南芥的基因组序列，目的是为了更好地了解其系谱历史。正如从同一物种的材料中所预期的那样，我们发现核基因树之间有很大的不一致性。尽管如此，我们在假设所有不一致都是由于不完全谱系排序的假设下，推导出了最优种群树。为了应对数据的规模(许多基因和许多分类群)，我们的流水线基于并行计算，并将问题划分为四个分类单元树。然而，仅仅因为一棵种群树可以被估计并不意味着多物种合并模型的假设成立。因此，我们实施了一种新的非参数检验来评估种群树是否充分解释了观察到的四重组频率(每个四分类单元集合的每个分辨率的基因树的频率)。这个测试还考虑了其他模型：泛混和部分分解的种群树，即一些节点折叠成局部泛混的树。我们发现，部分分解的种群树提供了与数据最匹配的结果，为拟南芥中的树状结构提供了证据，定性上类似于不同密切相关物种之间的预期结构。此外，我们表明，偏离预期的模式可以用来识别渗透的实例，并在英国接触到的生态型中检测到一个明显的网状结构。我们的研究说明了我们如何使用基因组序列数据来评估系统发育关系是严格意义上的树状关系还是网状关系。
Genome sequence data contain abundant information about genealogical history, but methods for extracting and interpreting this information are not yet fully developed. We analyzed genome sequences for multiple accessions of the selfing plant, Arabidopsis thaliana, with the goal of better understanding its genealogical history. As expected from accessions of the same species, we found much discordance between nuclear gene trees. Nonetheless, we inferred the optimal population tree under the assumption that all discordance is due to incomplete lineage sorting. To cope with the size of the data (many genes and many taxa), our pipeline is based on parallel computing and divides the problem into four-taxon trees. However, just because a population tree can be estimated does not mean that the assumptions of the multispecies coalescent model hold. Therefore, we implemented a new, nonparametric test to evaluate whether a population tree adequately explains the observed quartet frequencies (the frequencies of gene trees with each resolution of each four-taxon set). This test also considers other models: panmixia and a partially resolved population tree, that is, a tree in which some nodes are collapsed into local panmixia. We found that a partially resolved population tree provides the best fit to the data, providing evidence for tree-like structure within A. thaliana, qualitatively similar to what might be expected between different, closely related species. Further, we show that the pattern of deviation from expectations can be used to identify instances of introgression and detect one clear case of reticulation among ecotypes that have come into contact in the United Kingdom. Our study illustrates how we can use genome sequence data to evaluate whether phylogenetic relationships are strictly tree-like or reticulating.