Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample.
Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample.
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DOI：
10.1093/molbev/msv111
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发表时间：
2015-09
影响因子：
10.7
通讯作者：
Vogler AP
中科院分区：
文献类型：
--
作者：
Crampton-Platt A;Timmermans MJ;Gimmel ML;Kutty SN;Cockerill TD;Vun Khen C;Vogler AP
尽管分子生态学、系统学和下一代测序技术不断发展，但多样性的发现和分析目前还没有与构建生命之树相结合。如果通过大量诱捕获得的所有标本（其中许多将是新物种）都可以常规地纳入系统发育重建中，热带节肢动物生态学家就可以很好地加速这一进程。在这里，我们测试鸟枪测序的方法，即线粒体基因组组装从复杂的生态混合物通过线粒体宏基因组学，并展示了该方法如何克服许多生物多样性研究的分类障碍。从大约500甲虫标本的DNA，来自一个单一的雨林冠层雾化样品从婆罗洲，汇集和鸟枪测序，然后从头组装的完整和部分有丝分裂基因组的175个物种。从这个地方的样品中获得的系统发育树是高度相似的，从现有的有丝分裂基因组选择的主要谱系的鞘翅目全球覆盖。当所有的序列相结合，只有轻微的拓扑结构的变化，诱导对这个参考集，表明一个越来越稳定的估计鞘翅目昆虫的遗传，而生态样本扩大了几个谱系的尖端水平的代表性。从生态样本生成的健壮的树现在使生态学的进化框架成为可能。与此同时，将未表征的样本纳入生命树中，在无需形态学鉴定的情况下迅速扩展了谱系的分类群和生物地理学表示。未分类的环境样品的鸟枪测序的有丝分裂基因组及其相关的元数据，放置到系统发育树中，构成了新的DNA“超级条形码”，用于测试关于全球多样性模式的假设。
In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA “superbarcodes” for testing hypotheses regarding global patterns of diversity.