Phylogenetic relationships among Staphylococcus species and refinement of cluster groups based on multilocus data.
Phylogenetic relationships among Staphylococcus species and refinement of cluster groups based on multilocus data.
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DOI：
10.1186/1471-2148-12-171
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发表时间：
2012-09-06
影响因子：
3.4
通讯作者：
Parkinson CL
中科院分区：
文献类型：
--
作者：
Lamers RP;Muthukrishnan G;Castoe TA;Tafur S;Cole AM;Parkinson CL
葡萄球菌物种间关系的估计一直受到系统发育的糟糕和不一致的解决的阻碍，这些系统发育主要是基于只包含有限的分类样本的单基因分析。因此，物种之间的进化关系和等级分类方案还没有确定下来。在这里，我们通过分析来自多个基因座(16S rRNA基因、dna J、rpoB和TUF基因片段)的DNA序列数据来解决这些问题，使用包括几乎所有已识别的葡萄球菌分类群的多种贝叶斯和最大似然系统发育方法。我们使用分区模型贝叶斯和最大似然分析以及贝叶斯基因树物种树方法来估计57个葡萄球菌分类群的系统发育。不管方法论如何，我们发现，尽管方法之间在解决更高阶关系方面存在一些分歧，但目前的聚类组需要修订的方法之间存在广泛的一致。基于我们的系统发育评估，我们提出了葡萄球菌的精细分类，将物种划分为15个聚类组(基于分子数据)，这些聚类组依附于6个物种组(基于表型属性)。我们的发现与葡萄球菌系统发育的基于基因树的报告基本一致，尽管我们在物种之间发现了多个以前未报道的关系。我们的结果支持这样的多位点评估作为微生物研究的标准的普遍重要性，以更有力地推断公认的和新发现的谱系之间的关系。
Estimates of relationships among Staphylococcus species have been hampered by poor and inconsistent resolution of phylogenies based largely on single gene analyses incorporating only a limited taxon sample. As such, the evolutionary relationships and hierarchical classification schemes among species have not been confidently established. Here, we address these points through analyses of DNA sequence data from multiple loci (16S rRNA gene, dnaJ, rpoB, and tuf gene fragments) using multiple Bayesian and maximum likelihood phylogenetic approaches that incorporate nearly all recognized Staphylococcus taxa. We estimated the phylogeny of fifty-seven Staphylococcus taxa using partitioned-model Bayesian and maximum likelihood analysis, as well as Bayesian gene-tree species-tree methods. Regardless of methodology, we found broad agreement among methods that the current cluster groups require revision, although there was some disagreement among methods in resolution of higher order relationships. Based on our phylogenetic estimates, we propose a refined classification for Staphylococcus with species being classified into 15 cluster groups (based on molecular data) that adhere to six species groups (based on phenotypic properties). Our findings are in general agreement with gene tree-based reports of the staphylococcal phylogeny, although we identify multiple previously unreported relationships among species. Our results support the general importance of such multilocus assessments as a standard in microbial studies to more robustly infer relationships among recognized and newly discovered lineages.
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影响因子：
3.2
作者：
Chan, Cheong Xin;Beiko, Robert G.;Ragan, Mark A.
通讯作者：
Ragan, Mark A.
DOI：
10.1111/j.1096-0031.1996.tb00196.x
发表时间：
1994-09-01
期刊：
CLADISTICS-THE INTERNATIONAL JOURNAL OF THE WILLI HENNIG SOCIETY
影响因子：
--
作者：
FARRIS, JS;KALLERSJO, M;BULT, C
通讯作者：
BULT, C
影响因子：
4.1
作者：
Castoe, TA;Parkinson, CL
通讯作者：
Parkinson, CL
影响因子：
9.4
作者：
Drancourt, M;Raoult, D
通讯作者：
Raoult, D
DOI：
10.1099/00207713-49-2-489
发表时间：
1999-04-01
期刊：
INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY
影响因子：
--
作者：
Freney, J;Kloos, WE;Vernozy-Rozand, C
通讯作者：
Vernozy-Rozand, C