Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics.
Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics.
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DOI：
10.1093/sysbio/syx058
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发表时间：
2017-11-01
影响因子：
6.5
通讯作者：
Baker AJ
中科院分区：
文献类型：
--
作者：
Edwards SV;Cloutier A;Baker AJ
非编码标记作为基因组分析的工具具有特别的吸引力，因为至少在脊椎动物中，它们似乎不太受谱系之间GC含量的强烈变化的影响。迄今为止，超保守元件（UCEs）和内含子已被最广泛使用的非编码标记。在这里，我们分析和研究的一种新型的非编码标记，保守的非外显子元件（CNEEs），其中包括非编码元件，估计在一组物种的进化速度慢于中性速率的进化特性。虽然它们通常包括UCE，但CNEE与UCE不同，因为它们不是超保守的，最重要的是，仅分析核心区域，而不是核心及其侧翼区域。使用一个数据集的16只鸟加上一个短吻鳄外群，和3600-3800个位点的标记类型，我们发现，虽然CNEE的变化比生物信息学衍生的UCE或内含子，并在某些情况下表现出较慢的方法来分支分辨率所确定的基因组二次抽样，CNEE比对的质量是上级的其他标记，更少的差距和丢失的物种。系统发育分辨率使用合并的方法是可比的三种标记类型，与大多数节点被完全和一致地解决。比较三种标记类型的系统发育结果表明，一个分支，雀形目猎鹰分支的姐妹群，解决不同的CNEE和UCE或内含子之间的中度（70%）自举支持。总的来说，CNEE似乎是有前途的，作为一个基因组标记，产生系统发育分辨率高达UCE和内含子，但更少的差距，更少的模糊性，在比对和核苷酸取代的模式更符合假设的常用方法的系统发育分析。
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 nonexonic 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.
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影响因子：
3.3
作者：
Burbrink, Frank T.;Pyron, R. Alexander
通讯作者：
Pyron, R. Alexander
影响因子：
2.7
作者：
Borowiec ML
通讯作者：
Borowiec ML
DOI：
10.1126/science.1254449
发表时间：
2014-12-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Green RE;Braun EL;Armstrong J;Earl D;Nguyen N;Hickey G;Vandewege MW;St John JA;Capella-Gutiérrez S;Castoe TA;Kern C;Fujita MK;Opazo JC;Jurka J;Kojima KK;Caballero J;Hubley RM;Smit AF;Platt RN;Lavoie CA;Ramakodi MP;Finger JW Jr;Suh A;Isberg SR;Miles L;Chong AY;Jaratlerdsiri W;Gongora J;Moran C;Iriarte A;McCormack J;Burgess SC;Edwards SV;Lyons E;Williams C;Breen M;Howard JT;Gresham CR;Peterson DG;Schmitz J;Pollock DD;Haussler D;Triplett EW;Zhang G;Irie N;Jarvis ED;Brochu CA;Schmidt CJ;McCarthy FM;Faircloth BC;Hoffmann FG;Glenn TC;Gabaldón T;Paten B;Ray DA
通讯作者：
Ray DA
影响因子：
10.7
作者：
Groussin, Mathieu;Hobbs, Joanne K.;Gouy, Manolo
通讯作者：
Gouy, Manolo
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T