Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study
Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study
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DOI：
10.1016/j.ympev.2020.106769
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发表时间：
2020-11-01
影响因子：
4.1
通讯作者：
Muchhala, Nathan
中科院分区：
文献类型：
--
作者：
Bagley, Justin C.;Uribe-Convers, Simon;Muchhala, Nathan
靶向序列捕获技术是一种很有前途的大规模基因组学研究方法。然而，快速进化的辐射提出了显着的挑战，系统发育推断（如不完整的谱系排序（ILS），系统发育噪声），和有针对性的核基因座，以解决物种树的能力，尽管这些问题仍然研究甚少。我们测试的效用，有针对性的序列捕获推断系统发育关系，在快速，最近的被子植物辐射，重点Burmeistera风铃草（桔梗科），其中多样化到130种在不到3百万年。我们比较了超重叠群（外显子加侧翼序列），外显子，侧翼只有506-546个位点（类似于470万个碱基）的数据集估计46 Burmeistera物种/谱系和10个外群类群的同源性。核基因座解决骨干节点和许多一致的内部关系，高度支持串联和聚结为基础的物种树分析，和推论在很大程度上是强大的缺失类群和基地组成的偏见的影响。然而，物种树在数据集之间是不一致的，基因树表现出非常高的冲突水平（类似于4-60%的一致性，类似于40-99%的冲突），而不仅仅是由基因树分辨率差驱动的。较高的基因树异质性在较短的分支表明ILS的重要作用，如预期的快速辐射。系统发育信息分析还表明，这种不一致性是由于在短的内部分支的低分辨率，与ILS一致，以及在更深的节点的同源性，外显子表现出更大的风险不正确的拓扑结构，由于同源性比其他数据集。我们的研究结果表明，有针对性的序列捕获是可行的，解决快速，最近的被子植物辐射，并基于超重叠群比对包含核外显子和侧翼序列的结果有更高的系统发育效用和准确性比单独。我们使用我们的研究结果，为未来的目标捕获为基础的研究Burmeistera和其他快速被子植物辐射，包括这样的研究应该分析超重叠群，以最大限度地提高基因座的系统发育信息内容提出切实可行的建议。
Targeted sequence capture is a promising approach for large-scale phylogenomics. However, rapid evolutionary radiations pose significant challenges for phylogenetic inference (e.g. incomplete lineages sorting (ILS), phylogenetic noise), and the ability of targeted nuclear loci to resolve species trees despite such issues remains poorly studied. We test the utility of targeted sequence capture for inferring phylogenetic relationships in rapid, recent angiosperm radiations, focusing on Burmeistera bellflowers (Campanulaceae), which diversified into -130 species over less than 3 million years. We compared phylogenies estimated from supercontig (exons plus flanking sequences), exon-only, and flanking-only datasets with 506-546 loci (similar to 4.7 million bases) for 46 Burmeistera species/lineages and 10 outgroup taxa. Nuclear loci resolved backbone nodes and many congruent internal relationships with high support in concatenation and coalescent-based species tree analyses, and inferences were largely robust to effects of missing taxa and base composition biases. Nevertheless, species trees were incongruent between datasets, and gene trees exhibited remarkably high levels of conflict (similar to 4-60% congruence, similar to 40-99% conflict) not simply driven by poor gene tree resolution. Higher gene tree heterogeneity at shorter branches suggests an important role of ILS, as expected for rapid radiations. Phylogenetic informativeness analyses also suggest this incongruence has resulted from low resolving power at short internal branches, consistent with ILS, and homoplasy at deeper nodes, with exons exhibiting much greater risk of incorrect topologies due to homoplasy than other datasets. Our findings suggest that targeted sequence capture is feasible for resolving rapid, recent angiosperm radiations, and that results based on supercontig alignments containing nuclear exons and flanking sequences have higher phylogenetic utility and accuracy than either alone. We use our results to make practical recommendations for future target capture-based studies of Burmeistera and other rapid angiosperm radiations, including that such studies should analyze supercontigs to maximize the phylogenetic information content of loci.