Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics

Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved non-exonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and ~3600 - ~3800 loci per marker type, we found that although CNEEs were less variable than bioinformatically-derived UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by phylogenomic subsampling, the quality of CNEE alignments was superior to those of the other markers, with fewer gaps and missing species. Phylogenetic resolution using coalescent approaches was comparable among the three marker types, with most nodes being fully and congruently resolved. Comparison of phylogenetic results across the three marker types indicated that one branch, the sister group to the passerine+falcon clade, was resolved differently and with moderate (> 70%) bootstrap support between CNEEs and UCEs or introns. Overall, CNEEs appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis.非编码标记作为系统发育基因组学分析工具具有独特应用价值，至少在脊椎动物类群中，它们受不同谱系间GC含量剧烈变异的影响相对更小。迄今为止，超保守元件（ultraconserved elements, UCEs）与内含子（introns）是应用最为广泛的两类非编码标记。本研究聚焦一类新型非编码标记：保守非外显子元件（conserved non-exonic elements, CNEEs），这类标记指在多物种类群中进化速率估算值低于中性进化速率（neutral rate）的非编码序列元件。尽管保守非外显子元件常包含超保守元件，但二者存在显著区别：前者并非严格意义上的超保守序列，且最为关键的是，分析时仅选取其核心区域，而非核心区域与侧翼序列的组合。本研究以包含16种鸟类及1个鳄类外类群的数据集为基础，针对每种标记类型获取约3600至3800个基因座，分析结果显示：尽管保守非外显子元件的变异程度低于生物信息学方法获取的超保守元件或内含子，且在部分场景下，通过系统发育基因组学亚采样分析得到的分支解析速度相对较慢，但其序列比对质量显著优于其余两类标记，表现为比对中存在的空位与缺失物种更少。采用溯祖分析方法（coalescent approaches）进行系统发育解析时，三类标记的解析效果相当，绝大多数节点均得到了完全且一致的解析。对三类标记的系统发育分析结果进行比较后发现，存在一个分支的解析结果存在差异：即雀形目+隼形目支系（passerine+falcon clade）的姊妹群分支，在保守非外显子元件与超保守元件或内含子的分析结果中，当自举支持值（bootstrap support）达到中等强度（>70%）时，二者的拓扑结构不一致。总体而言，保守非外显子元件作为系统发育基因组学标记颇具应用前景：其系统发育解析效能与超保守元件及内含子不相上下，但比对序列中空位更少、比对歧义性更低，且核苷酸替换模式更贴合当前主流系统发育分析方法所采用的假设前提。