The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences.
The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences.
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DOI：
10.1186/1741-7007-9-55
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发表时间：
2011-08-18
期刊：
影响因子：
5.4
通讯作者：
Misof B
中科院分区：
文献类型：
--
作者：
Peters RS;Meyer B;Krogmann L;Borner J;Meusemann K;Schütte K;Niehuis O;Misof B
在过去的几年中，巨大的分子序列数据已经积累了，并且随着使用更快，更便宜的测序技术的使用而成倍增长。对于使用这些数据进行系统发育分析，人们兴趣很高。但是，如果没有使流程自动化的专用软件，几乎不可能驯服一个人可以从公共序列存储库中检索的数据量。在这里，我们提出了一种新颖的生物信息学管道，用于下载，格式化，过滤和分析存放在Genbank中的公共序列数据。它结合了一些公认的程序与许多新开发的软件工具（可在http://software.zfmk.de/上找到）。
我们使用生物信息学管道来研究Megiverse昆虫秩序膜翅目（锯蝇，蜜蜂，黄蜂和蚂蚁）的系统发育，通过检索和处理超过120,000个序列，并在组成均匀性和定义的密度和重点的标准下选择子集。树木的重建是通过从超过80,000个地点和1,100多种物种的Supermatrix分配的最大似然分析进行的。在推断的树中，与以前的研究一致，“交响乐”是销育的。在Apocrita中，我们的分析提出了Stephanoidea +（Ichneumonoidea +（Proctotrupomorpha +（evanioidea + aculeata）））的拓扑结构。尽管有大量数据，但我们发现了膜翅目树中的几个持续问题。数据覆盖范围仍然非常低，必须收集其他数据以可靠地推断膜翅目的系统发育。
当我们将生物信息学管道应用于膜翅目，我们设计了尽可能一般的方法。使用此管道，可以为任何分类组生产系统发育树，并监视感兴趣的分类单元中的新数据和树木的鲁棒性。因此，它具有巨大的潜力，可以满足系统生物时代的挑战，并加深我们对生命树的理解。
Enormous molecular sequence data have been accumulated over the past several years and are still exponentially growing with the use of faster and cheaper sequencing techniques. There is high and widespread interest in using these data for phylogenetic analyses. However, the amount of data that one can retrieve from public sequence repositories is virtually impossible to tame without dedicated software that automates processes. Here we present a novel bioinformatics pipeline for downloading, formatting, filtering and analyzing public sequence data deposited in GenBank. It combines some well-established programs with numerous newly developed software tools (available at http://software.zfmk.de/). We used the bioinformatics pipeline to investigate the phylogeny of the megadiverse insect order Hymenoptera (sawflies, bees, wasps and ants) by retrieving and processing more than 120,000 sequences and by selecting subsets under the criteria of compositional homogeneity and defined levels of density and overlap. Tree reconstruction was done with a partitioned maximum likelihood analysis from a supermatrix with more than 80,000 sites and more than 1,100 species. In the inferred tree, consistent with previous studies, "Symphyta" is paraphyletic. Within Apocrita, our analysis suggests a topology of Stephanoidea + (Ichneumonoidea + (Proctotrupomorpha + (Evanioidea + Aculeata))). Despite the huge amount of data, we identified several persistent problems in the Hymenoptera tree. Data coverage is still extremely low, and additional data have to be collected to reliably infer the phylogeny of Hymenoptera. While we applied our bioinformatics pipeline to Hymenoptera, we designed the approach to be as general as possible. With this pipeline, it is possible to produce phylogenetic trees for any taxonomic group and to monitor new data and tree robustness in a taxon of interest. It therefore has great potential to meet the challenges of the phylogenomic era and to deepen our understanding of the tree of life.
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影响因子：
14.9
作者：
Benson DA;Cavanaugh M;Clark K;Karsch-Mizrachi I;Ostell J;Pruitt KD;Sayers EW
通讯作者：
Sayers EW
影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
DOI：
10.1073/pnas.91.21.9911
发表时间：
1994-10-11
影响因子：
11.1
作者：
DOWTON, M;AUSTIN, AD
通讯作者：
AUSTIN, AD
树突镜：大型系统发育树的互动观众。
影响因子：
3
作者：
Huson, Daniel H.;Richter, Daniel C.;Rausch, Christian;Dezulian, Tobias;Franz, Markus;Rupp, Regula
通讯作者：
Rupp, Regula
影响因子：
2.5
作者：
Carpenter, JM;Wheeler, WC
通讯作者：
Wheeler, WC