The intellectual content of taxonomy: a comment on DNA taxonomy
The intellectual content of taxonomy: a comment on DNA taxonomy
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DOI：
10.1016/s0169-5347(02)00060-5
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发表时间：
2003-02-01
影响因子：
16.8
通讯作者：
Wheeler, Q
中科院分区：
文献类型：
--
作者：
Lipscomb, D;Platnick, N;Wheeler, Q
Tautz等人[1]提议用这样一种系统来“解决”缺乏适当的分类和有效的鉴定工具(所谓的“分类学障碍”)，即用一种系统取代现有的分类，在这种系统中，生物基因组的极小一部分被测序，并被用来对所讨论的生物进行分类和识别。然而，这一提议的改变的理由是似是而非的，不太可能产生一个进步的研究计划。这样的系统已经用于不可培养的原核生物，目前我们所能做的最好的事情是从环境中收集序列数据，编译结果的数据库，并构建只反映这些序列所显示的相似程度的“分类”。这充其量是对真实分类学的讽刺，在这种情况下，5%的差异被认为是同种的(别管人类和黑猩猩的差异可能要小得多)。微生物学家将是第一个同意这一观点的人，当生物体能够被培养并研究它们的其他属性时，我们可以做得比这更好。那么，为什么要把所有其他生物的分类降低到这个贫穷的状态呢？DNA分类学所谓的优势经不起严格的审查。例如，声称一个序列不受主观评估的影响，忽视了比对不同长度的序列、区分同源序列和同源序列，甚至为任何特定的分类学研究选择合适的基因的困难。同样，认为DNA鉴定将减少有时因分类学名称改变而导致的混乱的假设是不合理的。DNA序列识别标签可以改善混淆的唯一方法是，所使用的基因序列在物种的所有成员中是恒定的，但在所有其他物种中是不同的。没有证据表明大多数基因都符合这些标准，任何符合这些标准的诊断特征都会起作用--它不一定是分子的。通过其他方法更有效地解决“分类障碍”。Tautz等人[1]实质上是在暗示，如果我们都像那些致力于目前无法培养的分类群的微生物学家一样对我们的有机体一无所知，那么当一个群体中有知识的专家在没有将他们所有的知识传授给其他人的情况下去世时，世界将不再受到影响。诸如美国-国家科学基金会的PEET[加强分类学专业知识的伙伴关系》(2003年)：http://www.国家科学基金会。Gov/pubsys/ods/getpub。CFM？提供资金培训新一代系统主义者的[nsf00140]，代表了比简单地抛弃我们迄今所了解的关于有机体多样性的一切要有效得多的解决方案。分类学可能确实受到威胁，但最大的威胁可能来自那些篡夺其成长和繁荣所需资源的人。
Tautz et al.[1] propose to ‘solve’the lack of adequate classifications and effective identification tools (the socalled ‘taxonomic impediment’) by replacing existing classifications with a system in which an infinitesimally tiny fraction of an organism’s genome is sequenced and used both to classify and identify the organism in question. The rationale for this suggested change, however, is specious and unlikely to produce a progressive research program. Such a system is already in use for unculturable prokaryotes, where the best we can do at present is collect sequence data from the environment, compile data bases of the results, and construct ‘classifications’ that reflect only the degree of similarity displayed by those sequences. This produces what is at best a caricature of real taxonomy, in which sequences that diverge by, 5% are considered ‘conspecific’(never mind that humans and chimpanzees might be far less divergent than that). Microbiologists would be the first to agree that, when the organisms can be cultured and their other attributes studied, we can do far better than this. Why, then, reduce the taxonomy of all other organisms to this impoverished state? The supposed advantages of DNA taxonomy do not stand up to rigorous scrutiny. For example, the claim that a sequence ‘is not influenced by subjective assessments’ ignores the difficulty of aligning sequences of different length, distinguishing paralogs from orthologs, or even selecting appropriate genes for any particular taxonomic study. Similarly, the supposition that DNA identification will lessen the confusion that sometimes results when taxonomic names change is unjustified. The only way that a DNA sequence identification tag could ameliorate confusion would be if the gene sequence used were constant among all members of the species but different in all other species. There is no evidence that most genes meet these criteria, and any diagnostic character that meets these criteria would work–it need not be molecular.The ‘taxonomic impediment’is more effectively addressed by other means. Tautz et al.[1] are, in essence, suggesting that if we all become as ignorant of our organisms as are, perforce, those microbiologists working on currently unculturable taxa, the world would no longer suffer when knowledgeable specialists in a group die without having communicated all their knowledge to others. Programs such as the US–NSF’s PEET [Partnerships for Enhancing Expertise in Taxonomy (2003): http://www. nsf. gov/pubsys/ods/getpub. cfm? nsf00140], which provides funding to train a new generation of systematists, represent solutions far more effective than simply discarding everything we have learned to date about organismic diversity. Taxonomy might indeed be threatened, but the greatest threats might be from those who would usurp the resources that it needs to grow and thrive.