Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America.
PLoS One. 2013 Dec 4;8(12):e82615. doi: 10.1371/journal.pone.0082615. eCollection 2013.
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.
最近对鳞翅目昆虫目进行的分子系统发育研究，在大多数超科中稳健地解决了科级别的分歧，并且在相对物种较少的早期出现的超科中，大多数分歧也得到了解决。相比之下，在构成巨型多样化的无翅亚纲（约 145,000 种）的更高级的蛾和蝴蝶的超级科之间的关系仍然大多支持不足。这种不确定性反过来又限制了我们辨别被假设为促进无翅亚纲多样化的特征的起源、年龄和进化后果的能力。无翅亚纲“骨干”中的低支持率可能反映了快速多样化。如果是这样，通过大幅度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在解决无翅亚纲关系方面的潜力。我们使用转录组 RNA-Seq 在广泛的 40 种无翅亚纲样本加上四个外群中生成了 1579 个假定的直系同源基因序列，我们还将两个来自先前发表的数据的分类单元添加到其中。对一个包含 46 个分类单元和 741 个基因的矩阵进行的系统发育分析，该矩阵是通过严格筛选消除包含任何明显的旁系同源物的直系同源物组而得出的，与以前和同时进行的 19 个基因分析相比，无翅亚纲中较深节点的自举支持率显著增加。高支持率主要局限于广义的Obtectomera 巨大亚类，其中支撑 12 个超级科的 11 个节点的自举支持率为 100%。强烈支持的节点与以前的研究结果的分组几乎没有冲突，并且受分类单元采样变化的影响很小，这表明它们反映了真实的信号，而不是大量基因采样的假象。相比之下，在较低的非 Obtectomera 无翅亚纲中，只有 11 个较深节点中的 2 个得到了强烈支持。这些代表了一个更加困难的系统发育问题，解决该问题的一种途径可能包括进一步增加基因采样，同时改进直系同源物的分配。
