Krauss Veiko, Thümmler Christian, Georgi Franziska, Lehmann Jörg, Stadler Peter F, Eisenhardt Carina
Department of Genetics, Institute of Biology II, University of Leipzig, Leipzig, Germany.
Mol Biol Evol. 2008 May;25(5):821-30. doi: 10.1093/molbev/msn013. Epub 2008 Feb 21.
Today, the reconstruction of the organismal evolutionary tree is based mainly on molecular sequence data. However, sequence data are sometimes insufficient to reliably resolve in particular deep branches. Thus, it is highly desirable to find novel, more reliable types of phylogenetic markers that can be derived from the wealth of genomic data. Here, we consider the gain of introns close to older preexisting ones. Because correct splicing is impeded by very small exons, nearby pairs of introns very rarely coexist, that is, the gain of the new intron is nearly always associated with the loss of the old intron. Both events may even be directly connected as in cases of intron migration. Therefore, it should be possible to identify one of the introns as ancient (plesiomorphic) and the other as novel (derived or apomorphic). To test the suitability of such near intron pairs (NIPs) as a marker class for phylogenetic analysis, we undertook an analysis of the evolutionary positions of bees and wasps (Hymenoptera) and beetles (Coleoptera) in relation to moths (Lepidoptera) and dipterans (Diptera) using recently completed genome project data. By scanning 758 putatively orthologous gene structures of Apis mellifera (Hymenoptera) and Tribolium castaneum (Coleoptera), we identified 189 pairs of introns, one from each species, which are located less than 50 nt from each other. A comparison with genes from 5 other holometabolan and 9 metazoan outgroup genomes resulted in 22 shared derived intron positions found in beetle as well as in butterflies and/or dipterans. This strongly supports a basal position of hymenopterans in the holometabolous insect tree. In addition, we found 31 and 12 intron positions apomorphic for A. mellifera and T. castaneum, respectively, which seem to represent changes inside these branches. Another 12 intron pairs indicate parallel intron gains or extraordinarily small exons. In conclusion, we show here that the analysis of phylogenetically nested, nearby intron pairs is suitable to identify evolutionarily younger intron positions and to determine their relative age, which should be of equal importance for the understanding of intron evolution and the reconstruction of the eukaryotic tree.
如今，生物进化树的重建主要基于分子序列数据。然而，序列数据有时不足以可靠地解析某些特定的深层分支。因此，非常有必要找到可以从丰富的基因组数据中获得的新型、更可靠的系统发育标记类型。在这里，我们考虑靠近较老的已存在内含子的内含子获得情况。由于非常小的外显子会阻碍正确的剪接，相邻的内含子对很少共存，也就是说，新内含子的获得几乎总是与旧内含子的丢失相关联。这两个事件甚至可能像内含子迁移的情况那样直接相关。因此，应该能够将其中一个内含子鉴定为古老的（祖征的），另一个鉴定为新的（衍生的或衍征的）。为了测试这种近内含子对（NIPs）作为系统发育分析标记类别的适用性，我们利用最近完成的基因组计划数据，对蜜蜂和黄蜂（膜翅目）以及甲虫（鞘翅目）相对于蛾（鳞翅目）和双翅目昆虫的进化位置进行了分析。通过扫描意大利蜜蜂（膜翅目）和赤拟谷盗（鞘翅目）的758个假定直系同源基因结构，我们鉴定出189对内含子，每个物种各一个，它们彼此之间的距离小于50个核苷酸。与来自其他5种全变态昆虫和9种后生动物外群基因组的基因进行比较，结果在甲虫以及蝴蝶和/或双翅目中发现了22个共享的衍生内含子位置。这有力地支持了膜翅目昆虫在全变态昆虫进化树中的基部位置。此外，我们分别发现了31个和12个意大利蜜蜂和赤拟谷盗特有的内含子位置，这似乎代表了这些分支内部的变化。另外12对内含子对表明存在平行的内含子获得或异常小的外显子。总之，我们在此表明，对系统发育上嵌套的相邻内含子对进行分析，适合于鉴定进化上较年轻的内含子位置并确定它们的相对年龄，这对于理解内含子进化和重建真核生物进化树应该具有同等重要性。
