Phylogenetic Signal of Indels and the Neoavian Radiation
Phylogenetic Signal of Indels and the Neoavian Radiation
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DOI：
10.3390/d11070108
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发表时间：
2019-07-01
期刊：
影响因子：
2.4
通讯作者：
Mirarab, Siavash
中科院分区：
文献类型：
--
作者：
Houde, Peter;Braun, Edward L.;Mirarab, Siavash
Neoaves的早期放疗被假设为一种难治性的“硬多切除术”。我们探索插入/缺失等位基因（indels）的基本特性，这是一种未充分利用的基因组数据形式，有可能帮助解决这个问题。我们在所有新鸟类目的48个代表中从> 7000个泛基因组内含子和超保守元件（UCE）基因座中获得> 500万个插入缺失。我们发现，内含子和UCE indel表现出较少的同源性比核苷酸（nt）的数据。使用indel数据估计的基因树比使用nt数据估计的基因树分辨率低。然而，准确的物种树算法（ASTRAL）的物种树估计使用indels一般类似于基于nt的ASTRAL树，虽然支持度较低。然而，当我们将indel基因树与nt基因树结合起来时，indel基因树的力量变得清晰起来，包括UCE的惊人结果。单独的UCE indel和nt ASTRAL树彼此不一致，并且与内含子ASTRAL树不一致;然而，组合的indel+nt ASTRAL树与内含子树一致得多。最后，结合插入缺失和nt数据的内含子和UCE提供了足够的权力，以减少的范围，以前提出了几个超序谱系的Neoaves的polytomy。
The early radiation of Neoaves has been hypothesized to be an intractable "hard polytomy". We explore the fundamental properties of insertion/deletion alleles (indels), an under-utilized form of genomic data with the potential to help solve this. We scored > 5 million indels from > 7000 pan-genomic intronic and ultraconserved element (UCE) loci in 48 representatives of all neoavian orders. We found that intronic and UCE indels exhibited less homoplasy than nucleotide (nt) data. Gene trees estimated using indel data were less resolved than those estimated using nt data. Nevertheless, Accurate Species TRee Algorithm (ASTRAL) species trees estimated using indels were generally similar to nt-based ASTRAL trees, albeit with lower support. However, the power of indel gene trees became clear when we combined them with nt gene trees, including a striking result for UCEs. The individual UCE indel and nt ASTRAL trees were incongruent with each other and with the intron ASTRAL trees; however, the combined indel+nt ASTRAL tree was much more congruent with the intronic trees. Finally, combining indel and nt data for both introns and UCEs provided sufficient power to reduce the scope of the polytomy that was previously proposed for several supraordinal lineages of Neoaves.