How many novel eukaryotic 'kingdoms'? Pitfalls and limitations of environmental DNA surveys.
How many novel eukaryotic 'kingdoms'? Pitfalls and limitations of environmental DNA surveys.
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DOI：
10.1186/1741-7007-2-13
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发表时间：
2004-06-04
期刊：
影响因子：
5.4
通讯作者：
Pawlowski J
中科院分区：
文献类型：
--
作者：
Berney C;Fahrni J;Pawlowski J
在过去的几年中，使用分子技术来检测培养无关的真核生物多样性已被证明是一种强大的方法。基于小亚基核糖体RNA（SSU rRNA）基因分析，这些研究揭示了一种意想不到的新的核糖体类型的存在。它们中的一些代表了已知真核生物群中的新多样性，主要是层状体和肺泡。其他的似乎与任何分子描述的谱系无关，并被提出代表新的真核生物界。为了审查这一新的高层次的真核生物多样性的进化重要性，并测试潜在的技术和分析的陷阱和真核生物环境DNA调查（EES）的局限性，我们分析了484环境SSU rRNA基因序列，包括81个新的序列从沉积物的小河，塞马兹（日内瓦，瑞士）。基于一个详尽的真核SSU rRNA基因序列的比对和系统发育的重新分析，以前发表的环境序列使用贝叶斯方法的详细筛选，我们的研究结果表明，新的更高层次的类群的数量被高估了先前发表的EES。造成这种情况的三个主要错误来源是：（1）未检测到的嵌合序列的存在;（2）几个快速进化序列的错位;（3）描述的但尚未测序的真核生物的不完整采样。此外，由于某些分类群中SSU rRNA基因的扩增困难，EES对给定生境中存在的多样性给出了有偏见的观点。环境DNA调查无疑有助于揭示许多新的真核生物谱系，但没有明确的证据表明在王国水平上的多样性显著增加。在重新分析先前发表的数据后，我们发现只有五个候选谱系可能是新的高水平真核生物分类群，其中两个包括几个在不同研究中独立发现的新类型。然而，为了确定它们的分类地位，现在必须对生物体本身进行鉴定。
Over the past few years, the use of molecular techniques to detect cultivation-independent, eukaryotic diversity has proven to be a powerful approach. Based on small-subunit ribosomal RNA (SSU rRNA) gene analyses, these studies have revealed the existence of an unexpected variety of new phylotypes. Some of them represent novel diversity in known eukaryotic groups, mainly stramenopiles and alveolates. Others do not seem to be related to any molecularly described lineage, and have been proposed to represent novel eukaryotic kingdoms. In order to review the evolutionary importance of this novel high-level eukaryotic diversity critically, and to test the potential technical and analytical pitfalls and limitations of eukaryotic environmental DNA surveys (EES), we analysed 484 environmental SSU rRNA gene sequences, including 81 new sequences from sediments of the small river, the Seymaz (Geneva, Switzerland). Based on a detailed screening of an exhaustive alignment of eukaryotic SSU rRNA gene sequences and the phylogenetic re-analysis of previously published environmental sequences using Bayesian methods, our results suggest that the number of novel higher-level taxa revealed by previously published EES was overestimated. Three main sources of errors are responsible for this situation: (1) the presence of undetected chimeric sequences; (2) the misplacement of several fast-evolving sequences; and (3) the incomplete sampling of described, but yet unsequenced eukaryotes. Additionally, EES give a biased view of the diversity present in a given biotope because of the difficult amplification of SSU rRNA genes in some taxonomic groups. Environmental DNA surveys undoubtedly contribute to reveal many novel eukaryotic lineages, but there is no clear evidence for a spectacular increase of the diversity at the kingdom level. After re-analysis of previously published data, we found only five candidate lineages of possible novel high-level eukaryotic taxa, two of which comprise several phylotypes that were found independently in different studies. To ascertain their taxonomic status, however, the organisms themselves have now to be identified.
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影响因子：
2.2
作者：
Leander, BS;Kuvardina, ON;Keeling, PJ
通讯作者：
Keeling, PJ
影响因子：
10.7
作者：
Fahrni, JF;Bolivar, I;Pawlowski, J
通讯作者：
Pawlowski, J
DOI：
10.1099/00207713-52-2-297
发表时间：
2002-03-01
影响因子：
2.8
作者：
Cavalier-Smith, T
通讯作者：
Cavalier-Smith, T
DOI：
10.1073/pnas.062169599
发表时间：
2002-06-11
影响因子：
11.1
作者：
Dawson, SC;Pace, NR
通讯作者：
Pace, NR
影响因子：
3.6
作者：
LIESACK, W;WEYLAND, H;STACKEBRANDT, E
通讯作者：
STACKEBRANDT, E