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备独特应用价值，至少在脊椎动物类群中，其受不同谱系间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）与内含子是应用最为广泛的两类非编码标记。本研究针对一类新型非编码标记——保守非外显子元件（conserved non-exonic elements, CNEEs）的进化特性展开系统分析与研究；该类标记指的是在多个物种类群中进化速率慢于中性进化速率的非编码序列元件。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：其一，保守非外显子元件并非超保守序列；其二，最为关键的是，分析仅针对其核心区域开展，而非同时覆盖核心区域及其侧翼序列。本研究以包含16种鸟类及作为外类群的短吻鳄在内的数据集为研究材料，针对每类标记分别获取约3600~3800个位点。分析结果显示：尽管保守非外显子元件的变异程度低于基于生物信息学方法获得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子采样得到的分支解析进度相对迟缓，但其比对序列质量显著优于其余两类标记，表现为存在更少的序列缺口与缺失物种序列。采用溯祖分析法开展的系统发育解析结果在三类标记间表现相当，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+隼形目支系的姊妹群，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，该分支的自展支持率中等（>70%）且分类关系不同。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，其获得的系统发育解析度与超保守元件及内含子相当，但具备更少的序列缺口、更低的比对歧义性，且核苷酸替换模式更符合常用系统发育分析方法的假设前提。