Background: The Charadriiformes provide a good source for researching evolution owing to their diverse distribution, behavior, morphology, and ecology. However, in the Charadrii, family-level relationships remain understudied, and the monophyly of Charadriidae is also a subject of controversy. Method: In the present study, we generated complete mitogenomes for two species, Charadrius leschenaultii and Charadrius mongolus, which were found to be 16,905 bp and 16,844 bp in length, respectively. Among the 13 protein codon genes, we observed variation in the rate of nonsynonymous substitution rates, with the slowest rate found in COI and the fastest rate observed in ATP8. The Ka/Ks ratio for all Charadriidae species was significantly lower than one, which inferred that the protein-coding genes underwent purifying selection. Result: Phylogenetic analysis based on the genes of Cyt b, 12S and ND2 revealed that the genus Pluvialis is the sister group of three families (Haematopodidae, Ibidorhynchidae, Recurvirostridae). However, the phylogenetic analysis based on complete mitogenomes indicated that the genus Pluvialis is within the Charadriidae family. Conclusion: This study highlights the importance of carefully selecting the number of genes used to obtain accurate estimates of the species tree. It also suggests that relying on partial mtDNA genes with fast-evolving rates may lead to misleading results when resolving the Pluvialis sister group. Future research should focus on sequencing more mitogenomes at different taxonomic levels to gain a better understanding of the features and phylogenetic relationships within the Charadriiformes order.

中文翻译：

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基于完整线粒体基因组的鳖科分类地位和系统发育关系

背景：Charadriiformes因其多样化的分布、行为、形态和生态而为研究进化提供了良好的来源。然而，在Charadrii中，科级关系仍未得到充分研究，并且Charadriidae的单系性也是一个争议的话题。方法：在本研究中，我们生成了两个物种 Charadrius leschenaultii 和 Charadrius monglus 的完整线粒体基因组，发现它们的长度分别为 16,905 bp 和 16,844 bp。在 13 个蛋白质密码子基因中，我们观察到非同义替换率的变化，COI 中的速率最慢，ATP8 中的速率最快。所有Charadriidae物种的Ka/Ks比均显着低于1，这推断蛋白质编码基因经历了纯化选择。结果：基于Cyt b、12S和ND2基因的系统发育分析表明，雨生鱼属是三个科(Haematopodidae、Ibidorhynchidae、Recurvirostridae)的姐妹群。然而，基于完整线粒体基因组的系统发育分析表明，雨生鱼属属于鳖科。结论：这项研究强调了仔细选择用于获得物种树准确估计的基因数量的重要性。它还表明，在解析雨生菌姐妹群时，依赖快速进化的部分线粒体DNA基因可能会导致误导性结果。未来的研究应侧重于在不同分类水平上对更多有丝分裂基因组进行测序，以更好地了解 Charadriiformes 目内的特征和系统发育关系。