Phylotranscriptomic Analysis Based on Coalescence was Less Influenced by the Evolving Rates and the Number of Genes: A Case Study in Ericales.
Phylotranscriptomic Analysis Based on Coalescence was Less Influenced by the Evolving Rates and the Number of Genes: A Case Study in Ericales.
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DOI：
10.4137/ebo.s22448
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发表时间：
2015
期刊：
影响因子：
--
通讯作者：
Ge XJ
中科院分区：
文献类型：
--
作者：
Zhang L;Wu W;Yan HF;Ge XJ
高通量测序技术的进步产生了大量的转录组学数据，这些数据越来越多地用于系统发育重建。然而，处理大量基因的庞大数据集，甚至确定最佳分析方法都是具有挑战性的。通过从头测序和检索公共数据库数据，我们确定了221个同源蛋白编码基因，重建了以快速古代辐射为特征的鸡脚目的系统发育。用代表不同科的7种作为内群。连接和聚结方法都得到了与先前研究相同的良好支持的拓扑结构，只有两个节点与先前报道的关系相冲突。结果表明，分区策略可以改进传统的连接方法。快速进化的基因对串联分析有负面影响，而缓慢进化的基因对聚并分析有轻微影响。与真实数据和模拟数据的连接方法相比，合并方法通常能更好地适应速率异质性，并且需要较少的基因来产生良好支持的拓扑结构。
Advances in high-throughput sequencing have generated a vast amount of transcriptomic data that are being increasingly used in phylogenetic reconstruction. However, processing the vast datasets for a huge number of genes and even identifying optimal analytical methodology are challenging. Through de novo sequenced and retrieved data from public databases, we identified 221 orthologous protein-coding genes to reconstruct the phylogeny of Ericales, an order characterized by rapid ancient radiation. Seven species representing different families in Ericales were used as in-groups. Both concatenation and coalescence methods yielded the same well-supported topology as previous studies, with only two nodes conflicting with previously reported relationships. The results revealed that a partitioning strategy could improve the traditional concatenation methodology. Rapidly evolving genes negatively affected the concatenation analysis, while slowly evolving genes slightly affected the coalescence analysis. The coalescence methods usually accommodated rate heterogeneity better and required fewer genes to yield well-supported topologies than the concatenation methods with both real and simulated data.