Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria
Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria
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古代快速辐射解释了念珠藻蓝藻基因树和良好支持的系统发育树之间的大多数冲突
DOI：
10.1093/sysbio/syad008
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发表时间：
2023
影响因子：
6.5
通讯作者：
Lutzoni, François
中科院分区：
文献类型：
--
作者：
Pardo-De la Hoz, Carlos J.;Magain, Nicolas;Piatkowski, Bryan;Cornet, Luc;Dal Forno, Manuela;Carbone, Ignazio;Miadlikowska, Jolanta;Lutzoni, François
由于广泛的水平基因转移（HGT），前体基因组通常被认为是不一定共享相同进化历史的基因的马赛克。因此，将原核生物的进化关系表示为分叉树长期以来一直存在争议。然而，研究报告的冲突之间的基因树来自非同源基因组数据集表明，这些冲突可能是人工制品或进化过程的结果，而不是HGT，如不完整的谱系排序，低系统发育信号，和系统错误，由于替代模型错误指定。在这里，我们提出了一个广泛的探索结果的系统发育冲突的蓝藻念珠藻目，以前的研究推断强烈支持冲突的关系时，使用不同的级联Nostocales基因组数据集。我们发现，大多数这些冲突集中在深集群的念珠藻属植物的短节间，其中绝大多数的个体基因具有较低的分辨率。然后，我们推断系统发育网络检测HGT事件，同时也占不完整的谱系排序。我们的研究结果表明，基因树之间的大多数冲突可能是由于不完整的谱系排序与古老的快速辐射，而不是HGT。此外，这种辐射的短节间符合异常区的预期，即，树参数空间的一个区域，其中物种树与其最可能的基因树不一致。我们表明，串联不同的基因座可以恢复到17个不同的和良好的支持的关系内的假定异常区的念珠藻目，对应于观察到的冲突之间的支持良好的树木的基础上串联的数据集从以前的研究。我们的研究结果强调了快速辐射的重要作用，作为一个潜在的原因，强烈冲突的系统发育关系时，使用的细菌的基因组数据集。我们建议，polytomies可能是最合适的系统发育表示这些快速辐射的异常区的一部分，特别是当所有可能的基因组标记已被认为是推断这些hepatogenies。【异常带;细菌;水平基因转移;不完全谱系分类;念珠藻目;染色体组冲突;快速辐射;根丝藻。】
Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation;Rhizonema.]