Phylogenetic conservatism of functional traits in microorganisms
Phylogenetic conservatism of functional traits in microorganisms
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DOI：
10.1038/ismej.2012.160
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发表时间：
2013-04-01
期刊：
影响因子：
11
通讯作者：
Pusch, Gordon
中科院分区：
文献类型：
--
作者：
Martiny, Adam C.;Treseder, Kathleen;Pusch, Gordon
生物学的一个核心问题是生物多样性如何影响生态系统的功能。这背后是生物体发育和特定功能性状的存在之间的关系。基因丢失和趋同进化使这种关系变得复杂，导致许多性状的多系分布。在微生物中，横向基因转移可以进一步扭曲遗传和特定功能性状之间的联系。为了确定微生物中特定性状的系统发育保守性，我们开发了一种新的系统发育度量-consenTRAIT-来估计生物体共享性状的分支深度。然后，我们使用基因型和表型数据分析了89个功能性状在广泛的细菌和真菌中的分布。93%的性状呈显著的非随机分布，表明垂直遗传对微生物功能性状的系统发育分散具有重要意义。此外，微生物中的性状与性状深度（tau（D））的连续体相关，范围从几个深的分支到许多浅的分支（平均tau（D）：0.101-0.0011 rRNA序列差异）。接下来，我们证明了包含性状的分支的分散度和深度与性状的复杂性相关。具体来说，在一些深簇中发现了由许多基因编码的复杂性状，如光合作用和甲烷生成，而使用简单碳底物的能力是高度遗传分散的。在这些结果的基础上，我们提出了一个框架来预测功能性状的系统发育保守性取决于性状的复杂性。该框架能够预测微生物组成的变化如何影响微生物介导的生态系统过程，以及将系统发育和基于特征的模式联系起来。The ISME Journal（2013）7，830-838; doi：10.1038/ismej.2012.160; 2012年12月13日在线发表
A central question in biology is how biodiversity influences ecosystem functioning. Underlying this is the relationship between organismal phylogeny and the presence of specific functional traits. The relationship is complicated by gene loss and convergent evolution, resulting in the polyphyletic distribution of many traits. In microorganisms, lateral gene transfer can further distort the linkage between phylogeny and the presence of specific functional traits. To identify the phylogenetic conservation of specific traits in microorganisms, we developed a new phylogenetic metric-consenTRAIT-to estimate the clade depth where organisms share a trait. We then analyzed the distribution of 89 functional traits across a broad range of Bacteria and Archaea using genotypic and phenotypic data. A total of 93% of the traits were significantly non-randomly distributed, which suggested that vertical inheritance was generally important for the phylogenetic dispersion of functional traits in microorganisms. Further, traits in microbes were associated with a continuum of trait depths (tau(D)), ranging from a few deep to many shallow clades (average tau(D): 0.101-0.0011 rRNA sequence dissimilarity). Next, we demonstrated that the dispersion and the depth of clades that contain a trait is correlated with the trait's complexity. Specifically, complex traits encoded by many genes like photosynthesis and methanogenesis were found in a few deep clusters, whereas the ability to use simple carbon substrates was highly phylogenetically dispersed. On the basis of these results, we propose a framework for predicting the phylogenetic conservatism of functional traits depending on the complexity of the trait. This framework enables predicting how variation in microbial composition may affect microbially-mediated ecosystem processes as well as linking phylogenetic and trait-based patterns of biogeography. The ISME Journal (2013) 7, 830-838; doi:10.1038/ismej.2012.160; published online 13 December 2012