Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements.
Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements.
复制标题
DOI：
10.1016/j.ympev.2018.03.033
复制
发表时间：
2018-09
影响因子：
4.1
通讯作者：
Alfaro ME
中科院分区：
文献类型：
--
作者：
Gilbert PS;Wu J;Simon MW;Sinsheimer JS;Alfaro ME
尽管进行了基因组规模的分析，但新冠鸟类之间的高层关系仍然存在争议。众所周知，Neoaves超目的位置很难解决，因为它们涉及到深分裂，然后是短的节间。使用我们的方法，我们调查了根据其系统发育信噪比过滤UCE基因座是否有助于解析Neoaves生命树中的关键节点。我们发现，我们对高信噪比过滤后的数据集的分析结果与未过滤的结果不一致，但与全基因组分析一致。这些关系包括Columbea+Passerea姐妹关系和Phaethontimorphae+Aequornithia姐妹关系。我们还发现，对最近节点的统计支持增加了(即Pelecanidae+Ardeidae姐妹关系，Eucavitaves分支，以及Otidiformes+Musphagiformes姐妹关系)。我们还发现，对建立良好的分支的支持减少了，这可能是由于移除了信噪比适中的站点。我们的结果表明，基于信噪比的过滤是解决系统发育数据集中有问题的分裂的有用工具。
Despite genome scale analyses, high-level relationships among Neoaves birds remain contentious. The placements of the Neoaves superorders are notoriously difficult to resolve because they involve deep splits followed by short internodes. Using our approach, we investigate whether filtering UCE loci on their phylogenetic signal to noise ratio helps to resolve key nodes in the Neoaves tree of life. We find that our analysis of data sets filtered for high signal to noise ratio results in topologies that are inconsistent with unfiltered results but that are congruent with whole-genome analyses. These relationships include the Columbea + Passerea sister relationship and the Phaethontimorphae + Aequornithia sister relationship. We also find increased statistical support for more recent nodes (i.e. the Pelecanidae + Ardeidae sister relationship, the Eucavitaves clade, and the Otidiformes + Musophagiformes sister relationship). We also find instances where support is reduced for well-established clades, possibly due to the removal of sites with moderate signal-to-noise ratio. Our results suggest that filtering on the basis of signal to noise ratio is a useful tool for resolving problematic splits in phylogenomic data sets.
登录
查看更多内容
DOI：
10.1126/science.1253451
发表时间：
2014-12-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jarvis ED;Mirarab S;Aberer AJ;Li B;Houde P;Li C;Ho SY;Faircloth BC;Nabholz B;Howard JT;Suh A;Weber CC;da Fonseca RR;Li J;Zhang F;Li H;Zhou L;Narula N;Liu L;Ganapathy G;Boussau B;Bayzid MS;Zavidovych V;Subramanian S;Gabaldón T;Capella-Gutiérrez S;Huerta-Cepas J;Rekepalli B;Munch K;Schierup M;Lindow B;Warren WC;Ray D;Green RE;Bruford MW;Zhan X;Dixon A;Li S;Li N;Huang Y;Derryberry EP;Bertelsen MF;Sheldon FH;Brumfield RT;Mello CV;Lovell PV;Wirthlin M;Schneider MP;Prosdocimi F;Samaniego JA;Vargas Velazquez AM;Alfaro-Núñez A;Campos PF;Petersen B;Sicheritz-Ponten T;Pas A;Bailey T;Scofield P;Bunce M;Lambert DM;Zhou Q;Perelman P;Driskell AC;Shapiro B;Xiong Z;Zeng Y;Liu S;Li Z;Liu B;Wu K;Xiao J;Yinqi X;Zheng Q;Zhang Y;Yang H;Wang J;Smeds L;Rheindt FE;Braun M;Fjeldsa J;Orlando L;Barker FK;Jønsson KA;Johnson W;Koepfli KP;O'Brien S;Haussler D;Ryder OA;Rahbek C;Willerslev E;Graves GR;Glenn TC;McCormack J;Burt D;Ellegren H;Alström P;Edwards SV;Stamatakis A;Mindell DP;Cracraft J;Braun EL;Warnow T;Jun W;Gilbert MT;Zhang G
通讯作者：
Zhang G
影响因子：
3.4
作者：
Fiorini N;Lefort V;Chevenet F;Berry V;Chifolleau AM
通讯作者：
Chifolleau AM
影响因子：
3.4
作者：
Dornburg A;Fisk JN;Tamagnan J;Townsend JP
通讯作者：
Townsend JP
影响因子：
3.7
作者：
Faircloth BC;Sorenson L;Santini F;Alfaro ME
通讯作者：
Alfaro ME
影响因子：
3.7
作者：
McCormack JE;Harvey MG;Faircloth BC;Crawford NG;Glenn TC;Brumfield RT
通讯作者：
Brumfield RT