How to describe a cryptic species? Practical challenges of molecular taxonomy.
How to describe a cryptic species? Practical challenges of molecular taxonomy.
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DOI：
10.1186/1742-9994-10-59
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发表时间：
2013-09-27
影响因子：
2.8
通讯作者：
Schrödl M
中科院分区：
文献类型：
--
作者：
Jörger KM;Schrödl M
物种划分的分子方法正在迅速发展，被广泛认为是在生物多样性危机时期发现物种和面对分类障碍的快速有效的手段。然而，到目前为止，这种形式的DNA分类经常是不完整的，缺乏正式物种描述的最后一步，从而增强了而不是减少了分类上的障碍。DNA序列信息提供了有价值的诊断特征--至少对神秘物种来说--甚至可以作为分类描述的支柱。为此，必须找到一些实际问题的解决方案，包括提供分子数据以满足每个描述必须满足的形式要求的方法。最近，多基因条形码和分子物种描述相结合的方法揭示了海洋小型动物鼻涕虫属Pontohedyle(Acochlidia，Heterobranchia)至少12个或多或少神秘的物种的辐射。所有已确定的候选物种都由基于线粒体和核标记的不同方法的共识很好地划定了界限。本文提供的Pontohedyle Vrucosa的详细显微解剖重新描述，甚至没有揭示出可靠的特征来诊断该属内的两个主要支系。因此，我们基于四个遗传标记(线粒体细胞色素C氧化酶亚基I、16S rRNA、核28S和18S rRNA)对3个先前有效的Pontohedyle物种进行了表征，并正式描述了9个神秘的新物种(P.kepii sp.)。Nov.，P.joni sp.Nov.、小蜂科P.neridae sp.Nov.、百合草P.liliae sp.Nov.、Wiggi P.wiggi sp.Nov.、文氏拟青霉P.wenzli sp.Nov.，P.peteryalli sp.Nov.、马氏链霉菌P.martynovi sp.Nov.，Yurihookeri sp.11月)应用分子分类学，根据四个标记的DNA序列中的诊断核苷酸。由于动物的微小尺寸，整个标本都被用来提取，因此正模是提取的DNA(‘DNA类型’)的凭证。我们使用字符属性组织系统(CAOS)来确定诊断核苷酸，探索对输入数据和数据处理的依赖，并旨在为未来的研究在诊断中实现最大的可追溯性。对应用DNA分类学的挑战、陷阱和必要的考虑进行了严格的评估。为了描述神秘的物种，分类学中的传统证据线需要修改。例如，DNA序列信息甚至可以作为分类描述的支柱。目前的贡献表明，几乎不需要修改就可以整合到基于分子数据的传统分类学新诊断中。鼓励分类学团体加入讨论，制定分子分类学的质量标准，理想的形式是分子物种划定程序的自动最后一步。
Molecular methods of species delineation are rapidly developing and widely considered as fast and efficient means to discover species and face the 'taxonomic impediment’ in times of biodiversity crisis. So far, however, this form of DNA taxonomy frequently remains incomplete, lacking the final step of formal species description, thus enhancing rather than reducing impediments in taxonomy. DNA sequence information contributes valuable diagnostic characters and –at least for cryptic species – could even serve as the backbone of a taxonomic description. To this end solutions for a number of practical problems must be found, including a way in which molecular data can be presented to fulfill the formal requirements every description must meet. Multi-gene barcoding and a combined molecular species delineation approach recently revealed a radiation of at least 12 more or less cryptic species in the marine meiofaunal slug genus Pontohedyle (Acochlidia, Heterobranchia). All identified candidate species are well delimited by a consensus across different methods based on mitochondrial and nuclear markers. The detailed microanatomical redescription of Pontohedyle verrucosa provided in the present paper does not reveal reliable characters for diagnosing even the two major clades identified within the genus on molecular data. We thus characterize three previously valid Pontohedyle species based on four genetic markers (mitochondrial cytochrome c oxidase subunit I, 16S rRNA, nuclear 28S and 18S rRNA) and formally describe nine cryptic new species (P. kepii sp. nov., P. joni sp. nov., P. neridae sp. nov., P. liliae sp. nov., P. wiggi sp. nov., P. wenzli sp. nov., P. peteryalli sp. nov., P. martynovi sp. nov., P. yurihookeri sp. nov.) applying molecular taxonomy, based on diagnostic nucleotides in DNA sequences of the four markers. Due to the minute size of the animals, entire specimens were used for extraction, consequently the holotype is a voucher of extracted DNA ('DNA-type’). We used the Character Attribute Organization System (CAOS) to determine diagnostic nucleotides, explore the dependence on input data and data processing, and aim for maximum traceability in our diagnoses for future research. Challenges, pitfalls and necessary considerations for applied DNA taxonomy are critically evaluated. To describe cryptic species traditional lines of evidence in taxonomy need to be modified. DNA sequence information, for example, could even serve as the backbone of a taxonomic description. The present contribution demonstrates that few adaptations are needed to integrate into traditional taxonomy novel diagnoses based on molecular data. The taxonomic community is encouraged to join the discussion and develop a quality standard for molecular taxonomy, ideally in the form of an automated final step in molecular species delineation procedures.
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