Losing the plot: DNA “barcodes” and taxonomy
Losing the plot: DNA “barcodes” and taxonomy
复制标题
失去情节：DNA“条形码”和分类学
作者：
Q. Wheeler
经过几十年的忽视，分类学即将复兴(英国上议院，2002年；惠勒，2004年)。到目前为止，分类学的“大问题”似乎是难以克服的大问题(Cracraft，2002；Page等人，2005)。分类学的理论进步已经使分类具有预测性，种和特征的假说可测试，以及名称具有高度信息性(Hennig，1966；Nelson和Platnick，1981；Wiley，1981；Schoch，1986；Scheh，2000；Wheeler和Meier，2000)。阻碍分类学知识发展的障碍正在迅速消失。由美国国家科学基金会资助的四个“行星生物多样性调查”(PBI)项目在短短五年内描述或重新描述了5000多个物种，并建立了一个合作的范例。这只是个开端而已。新的网络基础设施有望以数量级的速度进一步增长(Page等人，2005年；Atkins等人，2003年)。其他NSF项目正在培养新一代分类学家(Rodman和Cody，2003)，挑战专著作者应用创新工具(RevSys)，并利用丰富的分子数据完成包容性系统发育(ATOL)。由于生物多样性危机(威尔逊，1985,1992)，我们只有短暂的机会来探索和记录物种多样性。可悲的是，对物种鉴定有用的分子数据正被劫持(如“DNA条形码”)。这威胁了几十年来的理论和实践进展(Ebach和Holdrege，2005)，并忽视了分类学的科学目标(Nelson和Platnick，1981；Cracraft，2002；Lipscomb等人，2003；Wheeler，2004)。从失败的“表现学”范式中吸取的代价高昂的教训被遗忘了，DNA“条形码”将重复其错误(Prendini，2005)。没有分类学来回答“这是什么物种？”这个问题。我们可以回答这个问题，因为分类学研究探索地球的物种、它们的分布、关系、复杂特征和分类(Hennig，1966；Nelson和Platnick，1981；Cracraft，2002)，产生可转移到识别系统的知识。条形码和任何鉴定工具一样，只是在从同源性到同构性、物种和单系性等多个层面上应用从测试假说中获得的知识。在没有测试的情况下，随着新的特征和标本的出现，“物种”对世界的信息变得更少。这就是传统修编和专著出版的原因。物种概念的数量令人印象深刻，它们的相对优劣也存在争论(Mayden，1997；Claridge等人，1997；Wheeler和Meier，2000)。为什么物种概念会受到如此长久的关注？因为物种是系统发育、生态系统和分类的要素，对比较生物学至关重要，并且在微观和宏观进化之间占据着独特的边界(Nixon和Wheeler，1992；Wheeler，1999)。Hebert等人。(2005)得出结论，他们发现了新物种，但没有提到任何标准，也没有引用任何关于物种概念的文献。它们展示了遗传瓶颈和变异，但这在进化上意味着什么？当物种被缩小到任意的遗传距离时，什么都不是。Barrett和Hebert(2005)批评蜘蛛分类学家“过度依赖生殖器来确定物种边界”，然后转而以压倒性多数依赖COI。形态指标的物候学不能反映进化模式，基于DNA的物候学也不能(Farris，1979；Ridley，1986；De Queiroz and Good，1997)。从表现学中学到的好经验，比如使用许多字符，也被条码编码者遗忘了。Schindel和Miller(2005)说，条形码并不打算取代形态学，但可以考虑Tautz等人。(2003)和以下内容：“基于COI的身份识别系统无疑将提供超过*通信作者所能实现的分类解析。电子邮件地址：q.hueler@nhm.ac.uk
After decades of neglect, taxonomy is on the threshold of a renaissance (House of Lords, 2002; Wheeler, 2004). The ‘‘big questions’’ of taxonomy seemed insurmountably large, until now (Cracraft, 2002; Page et al., 2005). Theoretical advances in taxonomy have made classifications predictive, hypotheses of species and characters testable, and names highly informative (Hennig, 1966; Nelson and Platnick, 1981; Wiley, 1981; Schoch, 1986; Schuh, 2000; Wheeler and Meier, 2000). Impediments to the growth of taxonomic knowledge are rapidly disappearing. Four ‘‘Planetary Biodiversity Inventory’’ (PBI) projects funded by the NSF are describing or re-describing more than 5000 species in just five years and forging a collaborative paradigm. This is just the beginning. New cyber-infrastructures promise further increases by orders of magnitude (Page et al., 2005; Atkins et al., 2003). Other NSF programs are educating a new generation of taxonomists (Rodman and Cody, 2003), challenging monographers to apply innovative tools (RevSys), and capitalizing on abundant molecular data to complete an inclusive phylogeny (AToL). Because of the biodiversity crisis (Wilson, 1985, 1992), we have but a fleeting chance to explore and document species diversity. Tragically, molecular data useful for species identification is being hijacked (as ‘‘DNA barcoding’’). This threatens theoretical and practical advances of decades (Ebach and Holdrege, 2005) and loses sight of the science goals of taxonomy (Nelson and Platnick, 1981; Cracraft, 2002; Lipscomb et al., 2003; Wheeler, 2004). Costly lessons learned from the failed ‘‘phenetics’’ paradigm are forgotten and DNA ‘‘barcoding’’ would repeat its mistakes (Prendini, 2005). Taxonomy does not exist to answer the question ‘‘What species is this?’’ We can answer it because taxonomic research explores Earth’s species, their distributions, relationships, complex characters and classification (Hennig, 1966; Nelson and Platnick, 1981; Cracraft, 2002) producing knowledge transferable to identification systems. Barcoding, like any identification tool, merely applies knowledge derived from tested hypotheses on many levels from homology to synapomorphy, species and monophyly. In the absence of testing, ‘‘species’’ become less informative about the world as new characters and specimens become known. This is the reason for traditional revisions and monographs. An impressive number of species concepts exist, their relative merits debated (Mayden, 1997; Claridge et al., 1997; Wheeler and Meier, 2000). Why are species concepts of such perennial interest? Because species are the elements of phylogeny, ecosystems, and classifications, essential for comparative biology, and occupy the unique boundary between microand macro-evolution (Nixon and Wheeler, 1992; Wheeler, 1999). Hebert et al. (2005) conclude they have found new species yet mention no criteria for nor cite any literature on species concepts. They demonstrate genetic bottlenecks and variation, but what does that mean evolutionarily? Nothing when species are reduced to arbitrary genetic distances. Barrett and Hebert (2005) criticize spider taxonomists for ‘‘overwhelming reliance on genitalia for the determination of species boundaries’’ then proceed to overwhelmingly rely on COI instead. Phenetics of morphology metrics did not reflect evolutionary patterns and neither can DNA-based phenetics (Farris, 1979; Ridley, 1986; De Queiroz and Good, 1997). Good lessons from phenetics, such as using many characters, have been forgotten by barcoders too. Schindel and Miller (2005) say that barcoders do not intend to replace morphology, but consider Tautz et al. (2003) and the following: ‘‘A COI-based identification system will undoubtedly provide taxonomic resolution that exceeds that which can be achieved through *Corresponding author. E-mail address: q.wheeler@nhm.ac.uk