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（noncoding markers）作为系统发育基因组学分析（phylogenomic analysis）工具具备独特的应用优势，至少在脊椎动物（vertebrates）中，它们受不同谱系间GC含量（GC content）剧烈变异的影响较小。迄今为止，超保守元件（ultraconserved elements, UCEs）和内含子（introns）是应用最为广泛的非编码标记。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）的进化特性展开分析与研究：这类元件指在多个物种类群中进化速率慢于中性进化速率（neutral rate）的非编码序列。尽管保守非外显子元件常包含超保守元件，但二者存在显著差异：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，分析时仅选取其核心区域，而非核心区域及其侧翼序列。
本研究使用包含16种鸟类以及作为外类群（outgroup）的短吻鳄的数据集，每个标记类型对应约3600至3800个位点（loci）。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，且在部分情况下，通过系统发育基因组学亚采样（phylogenomic subsampling）分析可知，其达到分支解析度的速度更为缓慢，但保守非外显子元件的比对序列（alignments）质量优于另外两类标记，具体表现为空位（gaps）更少、缺失物种更少。
采用溯祖分析方法（coalescent approaches）进行系统发育解析的结果表明，三类标记的解析能力相当，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分歧：即雀形目+隼形目分支（passerine+falcon clade）的姊妹群，保守非外显子元件与超保守元件或内含子得到的解析结果不同，且前者的自展支持率（bootstrap support）达中等水平（>70%）。
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：其可获得的系统发育解析度与超保守元件、内含子相当，但空位更少、比对序列的歧义性更低，且核苷酸替换（nucleotide substitution）模式更符合常用系统发育分析方法的假设前提。