Do orthologous gene phylogenies really support tree-thinking?
Do orthologous gene phylogenies really support tree-thinking?
复制标题
DOI：
10.1186/1471-2148-5-33
复制
发表时间：
2005-05-24
影响因子：
3.4
通讯作者：
Doolittle WF
中科院分区：
文献类型：
--
作者：
Bapteste E;Susko E;Leigh J;MacLeod D;Charlebois RL;Doolittle WF
自达尔文的《物种起源》以来，重建生命之树一直是进化论者的目标，树思维也成为进化生物学的一个重要概念。实际上，建造生命之树已经被证明是乏味的。太少的形态特征是有用的进行结论性的系统发育分析在最高的分类水平。因此，分子序列（基因、蛋白质和基因组）很可能构成了构建所有生命进化史的唯一有用特征。出于这个原因，树木制造者对基因比较期望很高。同时研究尽可能多的分子标记有时被认为是重建生物谱系的最佳解决方案之一。这一结论是树形思维的直接结果：如果基因遗传符合树状进化模型，那么从这些分子中抽取更多的样本将提供足够的系统发育信号来构建生命之树。因此，选择一致的标记是同时分析许多基因的基本步骤。热图分析被用来调查同源物的一致性在四个数据集（古细菌，细菌，真核生物和α-变形菌）。我们的结论是，我们根本无法确定大部分基因是否具有共同的历史。此外，这些数据集都不能被认为是没有横向基因转移的。我们的系统发育分析不支持树思维。这些结果具有重要的概念和实际意义。我们认为，在这种情况下，表示以外的树应该进行调查，因为一个非关键的串联标记可能是高度误导。
Since Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes. Heat map analyses were used to investigate the congruence of orthologues in four datasets (archaeal, bacterial, eukaryotic and alpha-proteobacterial). We conclude that we simply cannot determine if a large portion of the genes have a common history. In addition, none of these datasets can be considered free of lateral gene transfer. Our phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.
登录
查看更多内容
影响因子：
3.4
作者：
Andersson JO;Roger AJ
通讯作者：
Roger AJ
影响因子：
7
作者：
Kunin, V;Ouzounis, CA
通讯作者：
Ouzounis, CA
影响因子：
12.3
作者：
Brochier C;Forterre P;Gribaldo S
通讯作者：
Gribaldo S
通过递归合并和重排来比较系统发育树，从而扣除了横向基因转移的可能事件。
影响因子：
3.4
作者：
MacLeod D;Charlebois RL;Doolittle F;Bapteste E
通讯作者：
Bapteste E
影响因子：
3.2
作者：
Gophna, U;Doolittle, WF;Charlebois, RL
通讯作者：
Charlebois, RL