Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study.
Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study.
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DOI：
10.1371/journal.pone.0082615
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Mitter CW
中科院分区：
文献类型：
--
作者：
Bazinet AL;Cummings MP;Mitter KT;Mitter CW
最近的分子系统发育研究的昆虫命令鳞翅目已经强大的解决家庭水平的分歧，在大多数超家庭，和大多数分歧之间的相对物种贫困的早期出现的超家庭。与此形成鲜明对比的是，更高级的蛾和蝴蝶的超家族之间的关系，包括巨大的多样性分支Apoditrysia（约。145，000种）大多数情况下，支持不足。这种不确定性，反过来，限制了我们辨别起源，年龄和假设促进Apoditrysia壮观的多样化特征的进化后果的能力。沿着apoditrysian“骨干”的低支持率可能反映了快速的多样化。如果是这样的话，通过大幅增加基因样本来加强分辨率可能是可行的，但案例研究很少。我们探索了下一代测序的潜力，以最终解决apoditrysian关系。我们使用转录组RNA-Seq在40个apoditrysians加上4个外类群的广泛样本中生成1579个pupirusorthostransferase基因序列，我们从以前发表的数据中添加了两个分类群。与之前和同时进行的19个基因分析的结果相比，对46个分类单元、741个基因矩阵进行的系统发育分析（通过严格过滤消除了包含任何明显旁系同源物的直系同源群）使Apoditrysia内更深节点的自助支持总体显着增加。高支持度主要局限于广义的巨大分支Obtectomera，其中12个节点中有11个节点对着多个超家族的bootstrap支持度为100%。强有力的支持节点与以前的研究中的分组几乎没有冲突，并且几乎不受分类群采样变化的影响，这表明它们反映了真实的信号，而不是大规模基因采样的伪影。相比之下，强有力的支持，看到只有2的11个更深的节点之间的“较低”，非obtectomerapoditrysians。这些代表了一个更难的系统发育问题，其中一个解决途径可能包括进一步增加基因采样，以及改进的同源性分配。
Recent molecular phylogenetic studies of the insect order Lepidoptera have robustly resolved family-level divergences within most superfamilies, and most divergences among the relatively species-poor early-arising superfamilies. In sharp contrast, relationships among the superfamilies of more advanced moths and butterflies that comprise the mega-diverse clade Apoditrysia (ca. 145,000 spp.) remain mostly poorly supported. This uncertainty, in turn, limits our ability to discern the origins, ages and evolutionary consequences of traits hypothesized to promote the spectacular diversification of Apoditrysia. Low support along the apoditrysian “backbone” probably reflects rapid diversification. If so, it may be feasible to strengthen resolution by radically increasing the gene sample, but case studies have been few. We explored the potential of next-generation sequencing to conclusively resolve apoditrysian relationships. We used transcriptome RNA-Seq to generate 1579 putatively orthologous gene sequences across a broad sample of 40 apoditrysians plus four outgroups, to which we added two taxa from previously published data. Phylogenetic analysis of a 46-taxon, 741-gene matrix, resulting from a strict filter that eliminated ortholog groups containing any apparent paralogs, yielded dramatic overall increase in bootstrap support for deeper nodes within Apoditrysia as compared to results from previous and concurrent 19-gene analyses. High support was restricted mainly to the huge subclade Obtectomera broadly defined, in which 11 of 12 nodes subtending multiple superfamilies had bootstrap support of 100%. The strongly supported nodes showed little conflict with groupings from previous studies, and were little affected by changes in taxon sampling, suggesting that they reflect true signal rather than artifacts of massive gene sampling. In contrast, strong support was seen at only 2 of 11 deeper nodes among the “lower”, non-obtectomeran apoditrysians. These represent a much harder phylogenetic problem, for which one path to resolution might include further increase in gene sampling, together with improved orthology assignments.
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影响因子：
64.8
作者：
Dasmahapatra, Kanchon K.;Walters, James R.;Briscoe, Adriana D.;Davey, John W.;Whibley, Annabel;Nadeau, Nicola J.;Zimin, Aleksey V.;Hughes, Daniel S. T.;Ferguson, Laura C.;Martin, Simon H.;Salazar, Camilo;Lewis, James J.;Adler, Sebastian;Ahn, Seung-Joon;Baker, Dean A.;Baxter, Simon W.;Chamberlain, Nicola L.;Chauhan, Ritika;Counterman, Brian A.;Dalmay, Tamas;Gilbert, Lawrence E.;Gordon, Karl;Heckel, David G.;Hines, Heather M.;Hoff, Katharina J.;Holland, Peter W. H.;Jacquin-Joly, Emmanuelle;Jiggins, Francis M.;Jones, Robert T.;Kapan, Durrell D.;Kersey, Paul;Lamas, Gerardo;Lawson, Daniel;Mapleson, Daniel;Maroja, Luana S.;Martin, Arnaud;Moxon, Simon;Palmer, William J.;Papa, Riccardo;Papanicolaou, Alexie;Pauchet, Yannick;Ray, David A.;Rosser, Neil;Salzberg, Steven L.;Supple, Megan A.;Surridge, Alison;Tenger-Trolander, Ayse;Vogel, Heiko;Wilkinson, Paul A.;Wilson, Derek;Yorke, James A.;Yuan, Furong;Balmuth, Alexi L.;Eland, Cathlene;Gharbi, Karim;Thomson, Marian;Gibbs, Richard A.;Han, Yi;Jayaseelan, Joy C.;Kovar, Christie;Mathew, Tittu;Muzny, Donna M.;Ongeri, Fiona;Pu, Ling-Ling;Qu, Jiaxin;Thornton, Rebecca L.;Worley, Kim C.;Wu, Yuan-Qing;Linares, Mauricio;Blaxter, Mark L.;Ffrench-Constant, Richard H.;Joron, Mathieu;Kronforst, Marcus R.;Mullen, Sean P.;Reed, Robert D.;Scherer, Steven E.;Richards, Stephen;Mallet, James;McMillan, W. Owen;Jiggins, Chris D.
通讯作者：
Jiggins, Chris D.
影响因子：
6.5
作者：
Cho, Soowon;Zwick, Andreas;Parr, Cynthia
通讯作者：
Parr, Cynthia
DOI：
10.1016/j.future.2006.07.009
发表时间：
2007-03-01
影响因子：
7.5
作者：
Bazinet, Adam L.;Myers, Daniel S.;Cummings, Michael P.
通讯作者：
Cummings, Michael P.
影响因子：
14.9
作者：
Duan J;Li R;Cheng D;Fan W;Zha X;Cheng T;Wu Y;Wang J;Mita K;Xiang Z;Xia Q
通讯作者：
Xia Q
影响因子：
3.3
作者：
EHRLICH, PR;RAVEN, PH
通讯作者：
RAVEN, PH