Plastome phylogenomics of Poaceae: alternate topologies depend on alignment gaps
Plastome phylogenomics of Poaceae: alternate topologies depend on alignment gaps
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DOI：
10.1093/botlinnean/boz060
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发表时间：
2020-01-01
影响因子：
2.4
通讯作者：
Clark, Dylan C.
中科院分区：
文献类型：
--
作者：
Duvall, Melvin R.;Burke, Sean, V;Clark, Dylan C.
在禾本科中，c. 5000种被称为“PACMAD”的草。两种假说解释了深刻的PACMAD关系：“anastrotidoid姐妹”和“panicoid姐妹”假说。在每种情况下，命名的亚科是姐妹所有其他分类群。这些假设进行了调查与数据分区从质体基因组（质体）的169草，包括5个新测序的plastidoids。对塑性体进行40次分析，连续添加通过序列比对引入的更多缺口位置，直到包括所有这些位置。比对缺口包括低复杂性、AT丰富的区域。没有间隙，panicoid姐妹假说（P（ACMAD））适度支持，但随着间隙逐渐添加到输入矩阵中，拓扑结构和支持值波动通过一个过渡区，剥离阈值从2-11%，直到弱支持anastictidoid姐妹拓扑结构检索。支持值的artititidoid姐妹拓扑结构，然后上升和平稳的剩余分析，直到所有的差距是允许的。事实上，在很大程度上检索到的acrotitidoid姐妹假说时，包括缺口的位置表明，这一结果可能是人为的。深刻的PACMAD拓扑结构的知识，明确影响我们的理解PACMAD草辐射到开放的栖息地。
In Poaceae there is an evolutionary radiation of c. 5000 species called the 'PACMAD' grasses. Two hypotheses explain deep PACMAD relationships: the 'aristidoid sister' and the 'panicoid sister' hypotheses. In each case, the named subfamily is sister to all other taxa. These hypotheses were investigated with data partitions from plastid genomes (plastomes) of 169 grasses including five newly sequenced aristidoids. Plastomes were analysed 40 times with successive addition of more gapped positions introduced by sequence alignment, until all such positions were included. Alignment gaps include low complexity, AT-rich regions. Without gaps, the panicoid sister hypothesis (P(ACMAD)) was moderately supported, but as gaps were gradually added into the input matrix, the topology and support values fluctuated through a transition zone with stripping thresholds from 2-11% until a weakly supported aristidoid sister topology was retrieved. Support values for the aristidoid sister topology then rose and plateaued for remaining analyses until all gaps were allowed. The fact that the aristidoid sister hypothesis was retrieved largely when gapped positions were included suggests that this result might be artefactual. Knowledge of the deep PACMAD topology explicitly impacts our understanding of the radiation of PACMAD grasses into open habitats.