Semenchenko Alexander A, Krasheninnikov Andrei B, Seliverstov Nikita A, Khamenkova Elena V, Vinnikov Kirill A
Laboratory of Freshwater Hydrobiology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia.
Laboratory of Hydrobiology, Institute of Biological Problems of the North, Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia.
J Insect Sci. 2025 Jul 15;25(4). doi: 10.1093/jisesa/ieaf064.
We examine mitochondrial DNA as a source of data to estimate phylogenetic relationships within the Chironomidae (Diptera). Previous studies have shown that mitogenomes often produce ambiguous phylogenetic topologies that are inconsistent with both morphological and multi-locus molecular data. In this study, we sequenced 18 new mitogenomes representing 5 subfamilies, including the first available sequence for Protanypodinae. These were combined with 65 previously annotated chironomids mitogenomes, 8 additional individuals assembled from SRA data, and 8 outgroup taxa. Phylogenetic reconstructions were performed using complete protein-coding genes (PCGs), the first and second codon positions of PCGs (PCG 12), with and without ribosomal genes (12S rDNA and 16S rDNA), and amino acid sequences (AA). Both Bayesian Inference and Maximum Likelihood approaches were implemented. Three alternative outgroup compositions were tested: (i) chironomids only, with restricted rooting on Podonominae; (ii) Ceratopogonidae and Culicidae; and (iii) a diverse selection of Culicomorpha. We found that the AA, PCG12, and PCG 12 + rDNA datasets, when coupled with the third outgroup combination, provide the strongest phylogenetic signal, with the highest effective sample size and log-likelihood scores. In most cases, the resulting tree topologieswere congruent between mitochondrial and multi-locus data. However, some consistent differences in topologies were observed, leading to differences in divergence time estimates. Our phylogenetic study indicates paraphyly of Orthocladiinae due to the positions of Brillia Kieffer and Abiskomyia Edwards, suggesting that a comprehensive integrative revision of this subfamily is required. We conclude that the reliability of the mitochondrial phylogenetic signal improves with the increased taxon sampling.
我们研究线粒体DNA作为一种数据来源，以估计摇蚊科（双翅目）内部的系统发育关系。先前的研究表明，线粒体基因组通常会产生模糊的系统发育拓扑结构，这与形态学和多基因座分子数据均不一致。在本研究中，我们对代表5个亚科的18个新的线粒体基因组进行了测序，包括原摇蚊亚科的首个可用序列。这些序列与65个先前注释的摇蚊线粒体基因组、从SRA数据组装的另外8个个体以及8个外类群分类单元相结合。使用完整的蛋白质编码基因（PCG）、PCG的第一和第二密码子位置（PCG 12），有或没有核糖体基因（12S rDNA和16S rDNA）以及氨基酸序列（AA）进行系统发育重建。同时实施了贝叶斯推断和最大似然法。测试了三种替代的外类群组成：（i）仅摇蚊科，在长足摇蚊亚科上进行受限生根；（ii）蠓科和蚊科；以及（iii）库蚊亚目多种分类单元的选择。我们发现，AA、PCG12和PCG 12 + rDNA数据集，与第三种外类群组合相结合时，提供了最强的系统发育信号，具有最高的有效样本量和对数似然分数。在大多数情况下，线粒体数据和多基因座数据所得的树形拓扑结构是一致的。然而，观察到拓扑结构存在一些一致的差异，导致分歧时间估计存在差异。我们的系统发育研究表明，由于布里摇蚊属的基弗摇蚊和阿比斯库摇蚊属的爱德华兹摇蚊的位置，直突摇蚊亚科是并系的，这表明需要对该亚科进行全面的综合修订。我们得出结论，随着分类单元采样的增加，线粒体系统发育信号的可靠性会提高。
