Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies
Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies
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DOI：
10.1016/j.ympev.2008.03.024
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发表时间：
2008-07-01
影响因子：
4.1
通讯作者：
Thollesson, M.
中科院分区：
文献类型：
--
作者：
Pleijel, F.;Jondelius, U.;Thollesson, M.
分子数据已经彻底改变了系统分类学和系统发育研究，现在在系统实验室中经常使用。大多数发表分子系统发育的期刊都要求将序列存储在可访问的存储库中，例如GenBank。然而，随着更多分子数据的出现，人们越来越关注这些数据的分类来源（Funk等人，2005；Goldblatt等人，1992；Nilsson等人，2006；Ruedas等人，2000；Schander和Willassen, 2005； Peterson等人，2007）。虽然有些分类群似乎被很好地描绘出来，而且很容易识别，但其他分类群仍然只能由少数专家来识别。如今，基因库中存在大量标记错误的序列，除非加以纠正，否则这些序列将继续与错误的分类群相关联。凭单构成了数据与分类群之间的重要联系，并提供了一种验证已测序标本分类特性的手段。然而，只有少数期刊要求将与遗传信息相关的凭证存放在博物馆或其他机构。此外，在GenBank目前没有专门的领域来规范凭证。没有凭证，一项研究就不能被证实或不被证实，用户必须依靠进行鉴定的人的权威。这在科学上是不可接受的，我们在此恳请拥有公共数据存储库的期刊和组织始终要求凭证存放在公众可访问的集合中。我们还提出了不同种类凭证的术语，以反映其在研究标本分类鉴定中的价值。作为当前形势的一个例子，我们浏览了2006年出版的这期杂志。不包括任何新序列的研究，例如，理论贡献，被排除在外，然后我们对凭证进行评分，如果它们已存放在机构或博物馆，并附有个人识别号码，则视为研究中存在。在那一年发表的205篇相关论文中，46%的论文包含了指定凭证，因为这些研究要么是基于已经存放的标本，要么是因为新存放的标本是为了这个目的。因此，54%的研究没有指定的凭证，这意味着超过一半的研究没有任何其他系统学家评估数据来源的可能性。
Molecular data have revolutionized systematics and phylogenetic research, and are now routinely used in systematic laboratories. Most journals publishing molecular phylogenies require that the sequences be deposited in accessible repositories, such as GenBank. However, as more molecular data become available, there is a growing concern about the taxonomic origin of these data (Funk et al., 2005; Goldblatt et al., 1992; Nilsson et al., 2006; Ruedas et al., 2000; Schander and Willassen, 2005; Peterson et al., 2007). Although some taxa appear to be well delineated and easy enough to recognize, others still can only be identified by a handful of specialists. Today there is a large number of sequences deposited at GenBank that are incorrectly labeled and, unless remedied, these will continuously be associated with the wrong taxa. Vouchers constitute an essential link between data and taxa, and provide a means to verify the taxonomic identity of the specimens sequenced. However, only a minority of journals require that vouchers connected to the genetic information be deposited in museums or other institutions. Furthermore, at GenBank there is currently no dedicated field for specification of vouchers. Without vouchers, a study cannot be confirmed or disconfirmed, and users have to rely on the authority of the person making the identification. This is a scientifically unacceptable procedure, and we here plead for journals and organizations hosting public data repositories to consistently require vouchers deposited in publicly accessible collections. We also suggest a terminology for different kinds of vouchers, reflecting their value in taxonomic identification of the study specimen.As an example of the current situation we browsed the issues of this journal published in 2006. Studies not including any new sequences, eg, theoretical contributions, were excluded, and we then scored vouchers as present in a study if they had been deposited at an institution or museum and were accompanied by individual identification numbers. Of 205 relevant papers published that year, 46% included designated vouchers, either since the studies were based on already deposited specimens, or because specimens were newly deposited for the purpose. Consequently, for 54% of the studies there were no specified vouchers, meaning that more than half of the studies were published without any possibility for other systematists to asses the origin of the data.